METHODS AND SYSTEMS FOR DETERMINING A PREGNANCY-RELATED STATE OF A SUBJECT

Abstract

The present disclosure provides methods and systems directed to cell-free identification and/or monitoring of pregnancy-related states. A method for identifying or monitoring a presence or susceptibility of a pregnancy-related state of a subject may comprise assaying a cell-free biological sample derived from said subject to detect a set of biomarkers, and analyzing the set of biomarkers with a trained algorithm to determine the presence or susceptibility of the pregnancy-related state.

Description

BACKGROUND

Every year, about 15 million pre-term births are reported globally, and over 300,000 women die of pregnancy related complications such as hemorrhage and hypertensive disorders like preeclampsia. Pre-term birth may affect as many as about 10% of pregnancies, of which the majority are spontaneous pre-term births. Pregnancy-related complications such as pre-term birth are a leading cause of neonatal death and of complications later in life. Further, such pregnancy-related complications can cause negative health effects on maternal health.

SUMMARY

Currently, there may be a lack of meaningful, clinically actionable diagnostic screenings or tests available for many pregnancy-related complications such as pre-term birth. Thus, to make pregnancy as safe as possible, there exists a need for rapid, accurate methods for identifying and monitoring pregnancy-related states that are non-invasive and cost-effective, toward improving maternal and fetal health.

The present disclosure provides methods, systems, and kits for identifying or monitoring pregnancy-related states by processing cell-free biological samples obtained from or derived from subjects. Cell-free biological samples (e.g., plasma samples) obtained from subjects may be analyzed to identify the pregnancy-related state (which may include, e.g., measuring a presence, absence, or relative assessment of the pregnancy-related state). Such subjects may include subjects with one or more pregnancy-related states and subjects without pregnancy-related states. Pregnancy-related states may include, for example, pre-term birth, full-term birth, gestational age, due date (e.g., due date for an unborn baby or fetus of a subject), onset of labor, pregnancy-related hypertensive disorders (e.g., preeclampsia), eclampsia, gestational diabetes, a congenital disorder of a fetus of the subject, ectopic pregnancy, spontaneous abortion, stillbirth, post-partum complications (e.g., post-partum depression, hemorrhage or excessive bleeding, pulmonary embolism, cardiomyopathy, diabetes, anemia, and hypertensive disorders), hyperemesis gravidarum (morning sickness), hemorrhage or excessive bleeding during delivery, premature rupture of membrane, premature rupture of membrane in pre-term birth, placenta previa (placenta covering the cervix), intrauterine/fetal growth restriction, macrosomia (large fetus for gestational age), neonatal conditions (e.g., anemia, apnea, bradycardia and other heart defects, bronchopulmonary dysplasia or chronic lung disease, diabetes, gastroschisis, hydrocephaly, hyperbilirubinemia, hypocalcemia, hypoglycemia, intraventricular hemorrhage, jaundice, necrotizing enterocolitis, patent ductus arteriosis, periventricular leukomalacia, persistent pulmonary hypertension, polycythemia, respiratory distress syndrome, retinopathy of prematurity, and transient tachypnea), and fetal development stages or states (e.g., normal fetal organ function or development, and abnormal fetal organ function or development). For example, the fetal development stages or states may be related to normal fetal organ function or development and/or abnormal fetal organ function or development for a fetal organ selected from the group consisting of heart, large intestine, small intestine, retina, prefrontal cortex, midbrain, kidney, and esophagus.

In an aspect, the present disclosure provides a method for identifying a presence or susceptibility of a pregnancy-related state of a subject, comprising assaying transcripts and/or metabolites in a cell-free biological sample derived from the subject to detect a set of biomarkers, and analyzing the set of biomarkers with a trained algorithm to determine the presence or susceptibility of the pregnancy-related state. In some embodiments, the method comprises assaying the transcripts in the cell-free biological sample derived from the subject to detect the set of biomarkers. In some embodiments, the transcripts are assayed with nucleic acid sequencing. In some embodiments, the method comprises assaying the metabolites in the cell-free biological sample derived from the subject to detect the set of biomarkers. In some embodiments, the metabolites are assayed with a metabolomics assay.

In another aspect, the present disclosure provides a method for identifying a presence or susceptibility of a pregnancy-related state of a subject, comprising assaying a cell-free biological sample derived from the subject to detect a set of biomarkers, and analyzing the set of biomarkers with a trained algorithm to determine the presence or susceptibility of the pregnancy-related state among a set of at least three distinct pregnancy-related states at an accuracy of at least about 80%.

In some embodiments, the pregnancy-related state is selected from the group consisting of pre-term birth, full-term birth, gestational age, due date, onset of labor, pregnancy-related hypertensive disorders (e.g., preeclampsia), eclampsia, gestational diabetes, a congenital disorder of a fetus of the subject, ectopic pregnancy, spontaneous abortion, stillbirth, post-partum complications (e.g., post-partum depression, hemorrhage or excessive bleeding, pulmonary embolism, cardiomyopathy, diabetes, anemia, and hypertensive disorders), hyperemesis gravidarum (morning sickness), hemorrhage or excessive bleeding during delivery, premature rupture of membrane, premature rupture of membrane in pre-term birth, placenta previa (placenta covering the cervix), intrauterine/fetal growth restriction, macrosomia (large fetus for gestational age), neonatal conditions (e.g., anemia, apnea, bradycardia and other heart defects, bronchopulmonary dysplasia or chronic lung disease, diabetes, gastroschisis, hydrocephaly, hyperbilirubinemia, hypocalcemia, hypoglycemia, intraventricular hemorrhage, jaundice, necrotizing enterocolitis, patent ductus arteriosis, periventricular leukomalacia, persistent pulmonary hypertension, polycythemia, respiratory distress syndrome, retinopathy of prematurity, and transient tachypnea), and fetal development stages or states (e.g., normal fetal organ function or development, and abnormal fetal organ function or development). For example, the fetal development stages or states may be related to normal fetal organ function or development and/or abnormal fetal organ function or development for a fetal organ selected from the group consisting of heart, large intestine, small intestine, retina, prefrontal cortex, midbrain, kidney, and esophagus.

In some embodiments, the pregnancy-related state is a sub-type of pre-term birth, and the at least three distinct pregnancy-related states include at least two distinct sub-types of pre-term birth. In some embodiments, the sub-type of pre-term birth is a molecular sub-type of pre-term birth, and the at least two distinct sub-types of pre-term birth include at least two distinct molecular sub-types of pre-term birth. In some embodiments, the distinct molecular subtypes of pre-term birth comprise a molecular subtype of pre-term birth selected from the group consisting of presence or history of prior pre-term birth, presence or history of spontaneous pre-term birth, presence or history of late miscarriage, presence or history of receiving cervical surgery, presence or history of a uterine anomaly, presence or history of ethnicity specific pre-term birth risk (e.g., among an African-American population), and presence or history of pre-term premature rupture of membrane (PPROM).

In some embodiments, the pregnancy-related state is a sub-type of preeclampsia, and the at least three distinct pregnancy-related states include at least two distinct sub-types of preeclampsia. In some embodiments, the distinct molecular subtypes of preeclampsia comprise a molecular subtype of preeclampsia selected from the group consisting of: presence or history of chronic or pre-existing hypertension, presence or history of gestational hypertension, presence or history of mild preeclampsia (e.g., with delivery greater than 34 weeks gestational age), presence or history of severe preeclampsia (with delivery less than 34 weeks gestational age), presence or history of eclampsia, and presence or history of HELLP syndrome.

In some embodiments, the method further comprises identifying a clinical intervention for the subject based at least in part on the presence or susceptibility of the pregnancy-related state. In some embodiments, the clinical intervention is selected from a plurality of clinical interventions. In some embodiments, the method further comprises determining a likelihood of said determination of said susceptibility of said pregnancy-related state of said subject, after which subject can be provided with the clinical intervention. In some embodiments, the clinical intervention comprises a pharmacological, surgical, or procedural treatment to reduce severity, delay, or eliminate said future susceptibility pregnancy-related state of said subject (e.g., aspirin for preeclampsia and steroids for pre-term birth).

In some embodiments, the set of biomarkers comprises a genomic locus associated with due date, wherein the genomic locus is selected from the group consisting of genes listed in Table 1, Table 7, and Table 10. In some embodiments, the set of biomarkers comprises a genomic locus associated with gestational age, wherein the genomic locus is selected from the group consisting of genes listed in Table 2, genes listed in Table 3, genes listed in Table 4, genes listed in Table 23, genes listed in Table 24, genes listed in Table 25, and genes listed in Table 26. In some embodiments, the set of biomarkers comprises a genomic locus associated with pre-term birth, wherein the genomic locus is selected from the group consisting of genes listed in Table 5, genes listed in Table 6, genes listed in Table 8, RAB27B, RGS18, CLCN3, B3GNT2, COL24A1, CXCL8, and PTGS2. In some embodiments, the set of biomarkers comprises a genomic locus associated with pre-term birth, wherein the genomic locus is selected from the group consisting of genes listed in Table 12, genes listed in Table 14, genes listed in Table 20, genes listed in Table 21, genes listed in Table 34, genes listed in Table 40, genes listed in Table 41, genes listed in Table 42, genes listed in Table 43, genes listed in Table 44, genes listed in Table 45, genes listed in Table 46, and genes listed in Table 47. In some embodiments, the panel of said one or more genomic loci comprises a genomic locus associated with preeclampsia, wherein the genomic locus is selected from the group consisting of genes listed in Table 15, genes listed in Table 17, genes listed in Table 18, genes listed in Table 19, genes listed in Table 27, genes listed in Table 33, CLDN7, PAPPA2, SNORD14A, PLEKHH1, MAGEA10, TLE6, and FABP1. In some embodiments, the panel of said one or more genomic loci comprises a genomic locus associated with fetal organ development, wherein the genomic locus is selected from the group of genes listed in Table 29. In some embodiments, the set of biomarkers comprises a genomic locus associated with gestational diabetes mellitus, wherein the genomic locus is selected from the group consisting of genes listed in Table 36, genes listed in Table 37, genes listed in Table 38, and genes listed in Table 39.

In some embodiments, the set of biomarkers comprises at least 5 distinct genomic loci. In some embodiments, the set of biomarkers comprises at least 10 distinct genomic loci. In some embodiments, the set of biomarkers comprises at least 25 distinct genomic loci. In some embodiments, the set of biomarkers comprises at least 50 distinct genomic loci. In some embodiments, the set of biomarkers comprises at least 100 distinct genomic loci. In some embodiments, the set of biomarkers comprises at least 150 distinct genomic loci.

In another aspect, the present disclosure provides a method comprising assaying a cell-free biological sample derived from a subject; identifying said subject as having or at risk of having preeclampsia; and upon identifying said subject as having or at risk of having preeclampsia, administering an anti-hypertensive drug to said subject.

In another aspect, the present disclosure provides a method for identifying or monitoring a presence or susceptibility of a pregnancy-related state of a subject, comprising: (a) using a first assay to process a cell-free biological sample derived from said subject to generate a first dataset; (b) using a second assay to process a vaginal or cervical biological sample derived from said subject to generate a second dataset comprising a microbiome profile of said vaginal or cervical biological sample; (c) using an algorithm (e.g., a trained algorithm) to process at least said first dataset and said second dataset to determine said presence or susceptibility of said pregnancy-related state, which trained algorithm has an accuracy of at least about 80% over 50 independent samples; and (d) electronically outputting a report indicative of said presence or susceptibility of the pregnancy-related state of said subject.

In another aspect, the present disclosure provides a method for identifying or monitoring a presence or susceptibility of a pregnancy-related state of a subject, comprising: (a) using a first assay to process a cell-free biological sample derived from said subject to generate a first dataset; (b) using a second assay to process a second biological sample derived from said subject to generate a second dataset comprising a biomarker profile (e.g., DNA genetic profile, methylation profile, RNA transcriptomic profile, transcription product profile, proteomic profile, metabolome profile, and/or microbiome profile) of said second biological sample; (c) using an algorithm (e.g., a trained algorithm) to process at least said first dataset and said second dataset to determine said presence or susceptibility of said pregnancy-related state, which trained algorithm has an accuracy of at least about 80% over 50 independent samples; and (d) electronically outputting a report indicative of said presence or susceptibility of the pregnancy-related state of said subject.

In another aspect, the present disclosure provides a method for identifying or monitoring a presence or susceptibility of a pregnancy-related state of a subject, comprising: (a) using a first assay to process a cell-free biological sample derived from said subject to generate a first dataset; (b) using a second dataset comprising clinical data from a medical record of the subject; (c) using an algorithm (e.g., a trained algorithm) to process at least said first dataset and said second dataset to determine said presence or susceptibility of said pregnancy-related state, which trained algorithm has an accuracy of at least about 80% over 50 independent samples; and (d) electronically outputting a report indicative of said presence or susceptibility of the pregnancy-related state of said subject.

In some embodiments, said first assay comprises using cell-free ribonucleic acid (cfRNA) molecules derived from said cell-free biological sample to generate transcriptomic data, using transcription products (e.g., messenger RNA, transfer RNA, or ribosomal RNA) derived from said cell-free biological sample to generate transcription product data, using cell-free deoxyribonucleic acid (cfDNA) molecules derived from said cell-free biological sample to generate genomic data and/or methylation data, using proteins (e.g., pregnancy-associated proteins corresponding to pregnancy-associated genomic loci or genes) derived from said cell-free biological sample to generate proteomic data, or using metabolites derived from said cell-free biological sample to generate metabolomic data. In some embodiments, said cell-free biological sample is from a blood of said subject. In some embodiments, said cell-free biological sample is from a urine of said subject. In some embodiments, said first assay comprises using cell-free ribonucleic acid (cfRNA) molecules derived from said cell-free biological sample to generate transcriptomic data, and said second assay comprises using proteins (e.g., pregnancy-associated proteins corresponding to pregnancy-associated genomic loci or genes) derived from said cell-free biological sample to generate proteomic data. In some embodiments, said first assay comprises using cell-free deoxyribonucleic acid (cfDNA) molecules derived from said cell-free biological sample to generate genomic data and/or methylation data, and said second assay comprises using proteins (e.g., pregnancy-associated proteins corresponding to pregnancy-associated genomic loci or genes) derived from said cell-free biological sample to generate proteomic data.

In some embodiments, said first dataset comprises a first set of biomarkers associated with said pregnancy-related state. In some embodiments, said second dataset comprises a second set of biomarkers associated with said pregnancy-related state. In some embodiments, said second set of biomarkers is different from said first set of biomarkers.

In some embodiments, said pregnancy-related state is selected from the group consisting of pre-term birth, full-term birth, gestational age, due date, onset of labor, pregnancy-related hypertensive disorders, preeclampsia, eclampsia, gestational diabetes, a congenital disorder of a fetus of the subject, ectopic pregnancy, spontaneous abortion, stillbirth, post-partum complications, hyperemesis gravidarum (morning sickness), hemorrhage or excessive bleeding during delivery, premature rupture of membrane, premature rupture of membrane in pre-term birth, placenta previa (placenta covering the cervix), intrauterine/fetal growth restriction, macrosomia (large fetus for gestational age), neonatal conditions, and fetal development stages or states.

In some embodiments, said pregnancy-related state comprises pre-term birth. In some embodiments, said pregnancy-related state comprises gestational age. In some embodiments, said pregnancy-related state comprises preeclampsia.

In some embodiments, said cell-free biological sample is selected from the group consisting of cell-free ribonucleic acid (cfRNA), cell-free deoxyribonucleic acid (cfDNA), cell-free fetal DNA (cffDNA), plasma, serum, urine, saliva, amniotic fluid, and derivatives thereof. In some embodiments, said cell-free biological sample is obtained or derived from said subject using an ethylenediaminetetraacetic acid (EDTA) collection tube, a cell-free RNA collection tube, or a cell-free DNA collection tube. In some embodiments, the method further comprises fractionating a whole blood sample of said subject to obtain said cell-free biological sample.

In some embodiments, said first assay comprises a cfRNA assay or a metabolomics assay. In some embodiments, said metabolomics assay comprises targeted mass spectroscopy (MS) or an immune assay. In some embodiments, said cell-free biological sample comprises cfRNA or urine. In some embodiments, said first assay or said second assay comprises quantitative polymerase chain reaction (qPCR). In some embodiments, said first assay or said second assay comprises a home use test configured to be performed in a home setting.

In some embodiments, said trained algorithm determines said presence or susceptibility of said pregnancy-related state of said subject at a sensitivity of at least about 80%. In some embodiments, said trained algorithm determines said presence or susceptibility of said pregnancy-related state of said subject at a sensitivity of at least about 90%. In some embodiments, said trained algorithm determines said presence or susceptibility of said pregnancy-related state of said subject at a sensitivity of at least about 95%.

In some embodiments, said trained algorithm determines said presence or susceptibility of said pregnancy-related state of said subject at a positive predictive value (PPV) of at least about 70%. In some embodiments, said trained algorithm determines said presence or susceptibility of said pregnancy-related state of said subject at a positive predictive value (PPV) of at least about 80%. In some embodiments, said trained algorithm determines said presence or susceptibility of said pregnancy-related state thereof of said subject at a positive predictive value (PPV) of at least about 90%.

In some embodiments, said trained algorithm determines said presence or susceptibility of said pregnancy-related state of said subject with an Area Under Curve (AUC) of at least about 0.90. In some embodiments, said trained algorithm determines said presence or susceptibility of said pregnancy-related state of said subject with an Area Under Curve (AUC) of at least about 0.95. In some embodiments, said trained algorithm determines said presence or susceptibility of said pregnancy-related state of said subject with an Area Under Curve (AUC) of at least about 0.99.

In some embodiments, said subject is asymptomatic for one or more of: pre-term birth, onset of labor, pregnancy-related hypertensive disorders, preeclampsia, eclampsia, gestational diabetes, a congenital disorder of a fetus of the subject, ectopic pregnancy, spontaneous abortion, stillbirth, post-partum complications, hyperemesis gravidarum (morning sickness), hemorrhage or excessive bleeding during delivery, premature rupture of membrane, premature rupture of membrane in pre-term birth, placenta previa (placenta covering the cervix), intrauterine/fetal growth restriction, macrosomia (large fetus for gestational age), neonatal conditions, and abnormal fetal development stages or states. For example, the fetal development stages or states may be related to normal fetal organ function or development and/or abnormal fetal organ function or development for a fetal organ selected from the group consisting of heart, large intestine, small intestine, retina, prefrontal cortex, midbrain, kidney, and esophagus.

In some embodiments, said cell-free biological sample is collected from said subject within a given gestational age interval for detection of a pregnancy-related state. In some embodiments, said given gestational age interval is within about 1 day, about 2 days, about 3 days, about 4 days, about 5 days, about 6 days about 7 days, about 8 days, about 9 days, about 10 days, about 11 days, about 12 days, about 13 days, about 14 days, about 3 weeks, or about 4 weeks from a given gestational age. In some embodiments, said given gestational age is about 0 weeks, about 1 week, about 2 weeks, about 3 weeks, about 4 weeks, about 5 weeks, about 6 weeks, about 7 weeks, about 8 weeks, about 9 weeks, about 10 weeks, about 11 week, about 12 weeks, about 13 weeks, about 14 weeks, about 15 weeks, about 16 weeks, about 17 weeks, about 18 weeks, about 19 weeks, about 20 weeks, about 21 week, about 22 weeks, about 23 weeks, about 24 weeks, about 25 weeks, about 26 weeks, about 27 weeks, about 28 weeks, about 29 weeks, about 30 weeks, about 31 week, about 32 weeks, about 33 weeks, about 34 weeks, about 35 weeks, about 36 weeks, about 37 weeks, about 38 weeks, about 39 weeks, about 40 weeks, about 41 weeks, about 42 weeks, about 43 weeks, about 44 weeks, or about 45 weeks. In some embodiments, said pregnancy-related state comprises one or more of: pre-term birth, onset of labor, pregnancy-related hypertensive disorders, preeclampsia, eclampsia, gestational diabetes, a congenital disorder of a fetus of the subject, ectopic pregnancy, spontaneous abortion, stillbirth, post-partum complications, hyperemesis gravidarum (morning sickness), hemorrhage or excessive bleeding during delivery, premature rupture of membrane, premature rupture of membrane in pre-term birth, placenta previa (placenta covering the cervix), intrauterine/fetal growth restriction, macrosomia (large fetus for gestational age), neonatal conditions, and abnormal fetal development stages or states. For example, the fetal development stages or states may be related to normal fetal organ function or development and/or abnormal fetal organ function or development for a fetal organ selected from the group consisting of heart, large intestine, small intestine, retina, prefrontal cortex, midbrain, kidney, and esophagus.

In some embodiments, said trained algorithm is trained using at least about 10 independent training samples associated with said presence or susceptibility of said pregnancy-related state. In some embodiments, said trained algorithm is trained using no more than about 100 independent training samples associated with said presence or susceptibility of said pregnancy-related state. In some embodiments, said trained algorithm is trained using a first set of independent training samples associated with a presence or susceptibility of said pregnancy-related state and a second set of independent training samples associated with an absence or no susceptibility of said pregnancy-related state. In some embodiments, the method further comprises using said trained algorithm to process a set of clinical health data of said subject to determine said presence or susceptibility of said pregnancy-related state.

In some embodiments, (a) comprises (i) subjecting said cell-free biological sample to conditions that are sufficient to isolate, enrich, or extract a set of ribonucleic (RNA) molecules, deoxyribonucleic acid (DNA) molecules, transcription products (e.g., messenger RNA, transfer RNA, or ribosomal RNA), proteins (e.g., pregnancy-associated proteins corresponding to pregnancy-associated genomic loci or genes), or metabolites, and (ii) analyzing said set of RNA molecules, DNA molecules, proteins, or metabolites using said first assay to generate said first dataset. In some embodiments, the method further comprises extracting a set of nucleic acid molecules from said cell-free biological sample, and subjecting said set of nucleic acid molecules to sequencing to generate a set of sequencing reads, wherein said first dataset comprises said set of sequencing reads. In some embodiments, (b) comprises (i) subjecting said vaginal or cervical biological sample to conditions that are sufficient to isolate, enrich, or extract a population of microbes, and (ii) analyzing said population of microbes using said second assay to generate said second dataset.

In some embodiments, said sequencing is massively parallel sequencing. In some embodiments, said sequencing comprises nucleic acid amplification. In some embodiments, said nucleic acid amplification comprises polymerase chain reaction (PCR). In some embodiments, said sequencing comprises use of simultaneous reverse transcription (RT) and polymerase chain reaction (PCR). In some embodiments, the method further comprises using probes configured to selectively enrich said set of nucleic acid molecules corresponding to a panel of one or more genomic loci. In some embodiments, said probes are nucleic acid primers. In some embodiments, said probes have sequence complementarity with nucleic acid sequences of said panel of said one or more genomic loci.

In some embodiments, said panel of said one or more genomic loci comprises at least one genomic locus selected from the group consisting of ACTB, ADAM12, ALPP, ANXA3, APLF, ARG1, AVPR1A, CAMP, CAPN6, CD180, CGA, CGB, CLCN3, CPVL, CSH1, CSH2, CSHL1, CYP3A7, DAPP1, DCX, DEFA4, DGCR14, ELANE, ENAH, EPB42, FABP1, FAM212B-AS1, FGA, FGB, FRMD4B, FRZB, FSTL3, GH2, GNAZ, HAL, HSD17B1, HSD3B1, HSPB8, Immune, ITIH2, KLF9, KNG1, KRT8, LGALS14, LTF, LYPLAL1, MAP3K7CL, MEF2C, MMD, MMP8, MOB1B, NFATC2, OTC, P2RY12, PAPPA, PGLYRP1, PKHD1L1, PKHD1L1, PLAC1, PLAC4, POLE2, PPBP, PSG1, PSG4, PSG7, PTGER3, RAB11A, RAB27B, RAP1GAP, RGS18, RPL23AP7, S100A8, S100A9, S100P, SERPINA7, SLC2A2, SLC38A4, SLC4A1, TBC1D15, VCAN, VGLL1, B3GNT2, COL24A1, CXCL8, and PTGS2.

In some embodiments, said panel of said one or more genomic loci comprises at least 5 distinct genomic loci. In some embodiments, said panel of said one or more genomic loci comprises at least 10 distinct genomic loci.

In some embodiments, said panel of said one or more genomic loci comprises a genomic locus associated with pre-term birth, wherein said genomic locus is selected from the group consisting of ADAM12, ANXA3, APLF, AVPR1A, CAMP, CAPN6, CD180, CGA, CGB, CLCN3, CPVL, CSH2, CSHL1, CYP3A7, DAPP1, DGCR14, ELANE, ENAH, FAM212B-AS1, FRMD4B, GH2, HSPB8, Immune, KLF9, KRT8, LGALS14, LTF, LYPLAL1, MAP3K7CL, MMD, MOB1B, NFATC2, P2RY12, PAPPA, PGLYRP1, PKHD1L1, PKHD1L1, PLAC1, PLAC4, POLE2, PPBP, PSG1, PSG4, PSG7, RAB11A, RAB27B, RAP1GAP, RGS18, RPL23AP7, TBC1D15, VCAN, VGLL1, B3GNT2, COL24A1, CXCL8, and PTGS2.

In some embodiments, said panel of said one or more genomic loci comprises a genomic locus associated with gestational age, wherein said genomic locus is selected from the group consisting of ACTB, ADAM12, ALPP, ANXA3, ARG1, CAMP, CAPN6, CGA, CGB, CSH1, CSH2, CSHL1, CYP3A7, DCX, DEFA4, EPB42, FABP1, FGA, FGB, FRZB, FSTL3, GH2, GNAZ, HAL, HSD17B1, HSD3B1, HSPB8, ITIH2, KNG1, LGALS14, LTF, MEF2C, MMP8, OTC, PAPPA, PGLYRP1, PLAC1, PLAC4, PSG1, PSG4, PSG7, PTGER3, S100A8, S100A9, S100P, SERPINA7, SLC2A2, SLC38A4, SLC4A1, VGLL1, RAB27B, RGS18, CLCN3, B3GNT2, COL24A1, CXCL8, and PTGS2.

In some embodiments, the panel of said one or more genomic loci comprises a genomic locus associated with due date, wherein the genomic locus is selected from the group consisting of genes listed in Table 1, Table 7, and Table 10. In some embodiments, the panel of said one or more genomic loci comprises a genomic locus associated with gestational age, wherein the genomic locus is selected from the group of genes listed in Table 2, genes listed in Table 3, genes listed in Table 4, genes listed in Table 23, genes listed in Table 24, genes listed in Table 25, and genes listed in Table 26 In some embodiments, the panel of said one or more genomic loci comprises a genomic locus associated with pre-term birth, wherein the genomic locus is selected from the group consisting of genes listed in Table 5, genes listed in Table 6, genes listed in Table 8, genes listed in Table 12, genes listed in Table 14, genes listed in Table 20, genes listed in Table 21, genes listed in Table 34, genes listed in Table 40, genes listed in Table 41, genes listed in Table 42, genes listed in Table 43, genes listed in Table 44, genes listed in Table 45, genes listed in Table 46, genes listed in Table 47, RAB27B, RGS18, CLCN3, B3GNT2, COL24A1, CXCL8, and PTGS2. In some embodiments, the panel of said one or more genomic loci comprises a genomic locus associated with preeclampsia, wherein the genomic locus is selected from the group consisting of genes listed in Table 15, genes listed in Table 17, genes listed in Table 18, genes listed in Table 19, genes listed in Table 27, genes listed in Table 33, CLDN7, PAPPA2, SNORD14A, PLEKHH1, MAGEA10, TLE6, and FABP1. In some embodiments, the panel of said one or more genomic loci comprises a genomic locus associated with fetal organ development, wherein the genomic locus is selected from the group of genes listed in Table 29. In some embodiments, the set of biomarkers comprises a genomic locus associated with gestational diabetes mellitus, wherein the genomic locus is selected from the group consisting of genes listed in Table 36, genes listed in Table 37, genes listed in Table 38, and genes listed in Table 39. In some embodiments, the panel of the one or more genomic loci comprises at least 5 distinct genomic loci. In some embodiments, the panel of the one or more genomic loci comprises at least 10 distinct genomic loci. In some embodiments, the panel of the one or more genomic loci comprises at least 25 distinct genomic loci. In some embodiments, the panel of the one or more genomic loci comprises at least 50 distinct genomic loci. In some embodiments, the panel of the one or more genomic loci comprises at least 100 distinct genomic loci. In some embodiments, the panel of the one or more genomic loci comprises at least 150 distinct genomic loci.

In some embodiments, said cell-free biological sample is processed without nucleic acid isolation, enrichment, or extraction.

In some embodiments, said report is presented on a graphical user interface of an electronic device of a user. In some embodiments, said user is said subject.

In some embodiments, the method further comprises determining a likelihood of said determination of said presence or susceptibility of said pregnancy-related state of said subject.

In some embodiments, said trained algorithm comprises a supervised machine learning algorithm. In some embodiments, said supervised machine learning algorithm comprises a deep learning algorithm, a support vector machine (SVM), a neural network, or a Random Forest. In some embodiments, said trained algorithm comprises a differential expression algorithm. In some embodiments, said differential expression algorithm comprises a use comparison of stochastic models, generalized Poisson (GPseq), mixed Poisson (TSPM), Poisson log-linear (PoissonSeq), negative binomial (edgeR, DESeq, baySeq, NBPSeq), linear model fit by MAANOVA, or a combination thereof.

In some embodiments, the method further comprises providing said subject with a therapeutic intervention for said presence or susceptibility of said pregnancy-related state. In some embodiments, said therapeutic intervention comprises hydroxyprogesterone caproate, a vaginal progesterone, a natural progesterone IVR product, an prostaglandin F2 alpha receptor antagonist, or a beta2-adrenergic receptor agonist.

In some embodiments, the method further comprises monitoring said presence or susceptibility of said pregnancy-related state, wherein said monitoring comprises assessing said presence or susceptibility of said pregnancy-related state of said subject at a plurality of time points, wherein said assessing is based at least on said presence or susceptibility of said pregnancy-related state determined in (d) at each of said plurality of time points.

In some embodiments, a difference in said assessment of said presence or susceptibility of said pregnancy-related state of said subject among said plurality of time points is indicative of one or more clinical indications selected from the group consisting of: (i) a diagnosis of said presence or susceptibility of said pregnancy-related state of said subject, (ii) a prognosis of said presence or susceptibility of said pregnancy-related state of said subject, and (iii) an efficacy or non-efficacy of a course of treatment for treating said presence or susceptibility of said pregnancy-related state of said subject.

In some embodiments, the method further comprises stratifying said pre-term birth by using said trained algorithm to determine a molecular sub-type of said pre-term birth from among a plurality of distinct molecular subtypes of pre-term birth. In some embodiments, the plurality of distinct molecular subtypes of pre-term birth comprises a molecular subtype of pre-term birth selected from the group consisting of presence or history of prior pre-term birth, presence or history of spontaneous pre-term birth, presence or history of late miscarriage, presence or history of receiving cervical surgery, presence or history of a uterine anomaly, presence or history of ethnicity specific pre-term birth risk (e.g., among an African-American population), and presence or history of pre-term premature rupture of membrane (PPROM).

In some embodiments, the method further comprises stratifying said preeclampsia by using said trained algorithm to determine a molecular sub-type of said preeclampsia from among a plurality of distinct molecular subtypes of preeclampsia comprise a molecular subtype of preeclampsia selected from the group consisting of history of chronic/pre-existing hypertension, gestational hypertension, mild preeclampsia (with delivery >34 weeks), severe preeclampsia (with delivery <34 weeks), eclampsia, HELLP syndrome.

In another aspect, the present disclosure provides a computer-implemented method for predicting a risk of pre-term birth of a subject, comprising: (a) receiving clinical health data of said subject, wherein said clinical health data comprises a plurality of quantitative or categorical measures of said subject; (b) using an algorithm (e.g., a trained algorithm) to process said clinical health data of said subject to determine a risk score indicative of said risk of pre-term birth of said subject; and (c) electronically outputting a report indicative of said risk score indicative of said risk of pre-term birth of said subject.

In another aspect, the present disclosure provides a computer-implemented method for predicting a risk of preeclampsia of a subject, comprising: (a) receiving clinical health data of said subject, wherein said clinical health data comprises a plurality of quantitative or categorical measures of said subject; (b) using an algorithm (e.g., a trained algorithm) to process said clinical health data of said subject to determine a risk score indicative of said risk of preeclampsia of said subject; and (c) electronically outputting a report indicative of said risk score indicative of said risk of preeclampsia of said subject.

In some embodiments, said clinical health data comprises one or more quantitative measures selected from the group consisting of age, weight, height, body mass index (BMI), blood pressure, heart rate, glucose levels, number of previous pregnancies, and number of previous births. In some embodiments, said clinical health data comprises one or more categorical measures selected from the group consisting of race, ethnicity, history of medication or other clinical treatment, history of tobacco use, history of alcohol consumption, daily activity or fitness level, genetic test results, blood test results, imaging results, and fetal screening results.

In some embodiments, said trained algorithm determines said risk of pre-term birth of said subject at a sensitivity of at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99%. In some embodiments, said trained algorithm determines said risk of pre-term birth of said subject at a specificity of at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99%. In some embodiments, said trained algorithm determines said risk of pre-term birth of said subject at a positive predictive value (PPV) of at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99%. In some embodiments, said trained algorithm determines said risk of pre-term birth of said subject at a negative predictive value (NPV) of at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99%. In some embodiments, said trained algorithm determines said risk of pre-term birth of said subject with an Area Under Curve (AUC) of at least about 0.50, at least about 0.55, at least about 0.60, at least about 0.65, at least about 0.70, at least about 0.75, at least about 0.80, at least about 0.81, at least about 0.82, at least about 0.83, at least about 0.84, at least about 0.85, at least about 0.86, at least about 0.87, at least about 0.88, at least about 0.89, at least about 0.90, at least about 0.91, at least about 0.92, at least about 0.93, at least about 0.94, at least about 0.95, at least about 0.96, at least about 0.97, at least about 0.98, or at least about 0.99.

In some embodiments, said trained algorithm determines said risk of preeclampsia of said subject at a sensitivity of at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99%. In some embodiments, said trained algorithm determines said risk of preeclampsia of said subject at a specificity of at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99%. In some embodiments, said trained algorithm determines said risk of preeclampsia of said subject at a positive predictive value (PPV) of at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99%. In some embodiments, said trained algorithm determines said risk of preeclampsia of said subject at a negative predictive value (NPV) of at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99%. In some embodiments, said trained algorithm determines said risk of preeclampsia of said subject with an Area Under Curve (AUC) of at least about 0.50, at least about 0.55, at least about 0.60, at least about 0.65, at least about 0.70, at least about 0.75, at least about 0.80, at least about 0.81, at least about 0.82, at least about 0.83, at least about 0.84, at least about 0.85, at least about 0.86, at least about 0.87, at least about 0.88, at least about 0.89, at least about 0.90, at least about 0.91, at least about 0.92, at least about 0.93, at least about 0.94, at least about 0.95, at least about 0.96, at least about 0.97, at least about 0.98, or at least about 0.99.

In some embodiments, said subject is asymptomatic for one or more of: pre-term birth, onset of labor, pregnancy-related hypertensive disorders, preeclampsia, eclampsia, gestational diabetes, a congenital disorder of a fetus of said subject, ectopic pregnancy, spontaneous abortion, stillbirth, post-partum complications, hyperemesis gravidarum (morning sickness), hemorrhage or excessive bleeding during delivery, premature rupture of membrane, premature rupture of membrane in pre-term birth, placenta previa (placenta covering the cervix), intrauterine/fetal growth restriction, macrosomia (large fetus for gestational age), neonatal conditions, and abnormal fetal development stages or states. For example, the fetal development stages or states may be related to normal fetal organ function or development and/or abnormal fetal organ function or development for a fetal organ selected from the group consisting of heart, large intestine, small intestine, retina, prefrontal cortex, midbrain, kidney, and esophagus.

In some embodiments, said trained algorithm is trained using at least about 10 independent training samples associated with pre-term birth. In some embodiments, said trained algorithm is trained using no more than about 100 independent training samples associated with pre-term birth. In some embodiments, said trained algorithm is trained using a first set of independent training samples associated with a presence of pre-term birth and a second set of independent training samples associated with an absence of pre-term birth.

In some embodiments, said trained algorithm is trained using at least about 10 independent training samples associated with preeclampsia. In some embodiments, said trained algorithm is trained using no more than about 100 independent training samples associated with preeclampsia In some embodiments, said trained algorithm is trained using a first set of independent training samples associated with a presence of preeclampsia and a second set of independent training samples associated with an absence of preeclampsia.

In some embodiments, said report is presented on a graphical user interface of an electronic device of a user. In some embodiments, said user is said subject.

In some embodiments, said trained algorithm comprises a supervised machine learning algorithm. In some embodiments, said supervised machine learning algorithm comprises a deep learning algorithm, a support vector machine (SVM), a neural network, or a Random Forest. In some embodiments, said trained algorithm comprises a differential expression algorithm. In some embodiments, said differential expression algorithm comprises a use comparison of stochastic models, generalized Poisson (GPseq), mixed Poisson (TSPM), Poisson log-linear (PoissonSeq), negative binomial (edgeR, DESeq, baySeq, NBPSeq), linear model fit by MAANOVA, or a combination thereof.

In some embodiments, the method further comprises providing said subject with a therapeutic intervention based at least in part on said risk score indicative of said risk of pre-term birth. In some embodiments, said therapeutic intervention comprises hydroxyprogesterone caproate, a vaginal progesterone, a natural progesterone IVR product, an prostaglandin F2 alpha receptor antagonist, or a beta2-adrenergic receptor agonist.

In some embodiments, the method further comprises providing said subject with a therapeutic intervention based at least in part on said risk score indicative of said risk of preeclampsia. In some embodiments, said therapeutic intervention comprises antihypertensive drug therapy (such as but not limited to hydralazine, labetalol, nifedipine, and sodium nitroprusside), management or prevention of seizures (such as but not limited to magnesium sulfate, phenytoin, and diazepam), or prevention by low-dose aspirin therapy (e.g., 100 mg per day or less) to reduce the incidence of preeclampsia

In some embodiments, the method further comprises monitoring said risk of pre-term birth, wherein said monitoring comprises assessing said risk of pre-term birth of said subject at a plurality of time points, wherein said assessing is based at least on said risk score indicative of said risk of pre-term birth determined in (b) at each of said plurality of time points.

In some embodiments, the method further comprises monitoring said risk of preeclampsia, wherein said monitoring comprises assessing said risk of preeclampsia of said subject at a plurality of time points, wherein said assessing is based at least on said risk score indicative of said risk of preeclampsia determined in (b) at each of said plurality of time points.

In some embodiments, the method further comprises refining said risk score indicative of said risk of pre-term birth of said subject by performing one or more subsequent clinical tests for said subject, and processing results from said one or more subsequent clinical tests using a trained algorithm to determine an updated risk score indicative of said risk of pre-term birth of said subject. In some embodiments, said one or more subsequent clinical tests comprise an ultrasound imaging or a blood test. In some embodiments, said risk score comprises a likelihood of said subject having a pre-term birth within a pre-determined duration of time.

In some embodiments, the method further comprises refining said risk score indicative of said risk of preeclampsia of said subject by performing one or more subsequent clinical tests for said subject, and processing results from said one or more subsequent clinical tests using a trained algorithm to determine an updated risk score indicative of said risk of preeclampsia of said subject. In some embodiments, said one or more subsequent clinical tests comprise an ultrasound imaging or a blood test. In some embodiments, said risk score comprises a likelihood of said subject having a preeclampsia within a pre-determined duration of time.

In some embodiments, said pre-determined duration of time is about 1 hour, about 2 hours, about 4 hours, about 6 hours, about 8 hours, about 10 hours, about 12 hours, about 14 hours, about 16 hours, about 18 hours, about 20 hours, about 22 hours, about 24 hours, about 1.5 days, about 2 days, about 2.5 days, about 3 days, about 3.5 days, about 4 days, about 4.5 days, about 5 days, about 5.5 days, about 6 days, about 6.5 days, about 7 days, about 8 days, about 9 days, about 10 days, about 12 days, about 14 days, about 3 weeks, about 4 weeks, about 5 weeks, about 6 weeks, about 7 weeks, about 8 weeks, about 9 weeks, about 10 weeks, about 11 weeks, about 12 weeks, about 13 weeks, or more than about 13 weeks.

In another aspect, the present disclosure provides a computer system for predicting a risk of pre-term birth of a subject, comprising: a database that is configured to store clinical health data of said subject, wherein said clinical health data comprises a plurality of quantitative or categorical measures of said subject; and one or more computer processors operatively coupled to said database, wherein said one or more computer processors are individually or collectively programmed to: (i) use an algorithm (e.g., a trained algorithm) to process said clinical health data of said subject to determine a risk score indicative of said risk of pre-term birth of said subject; and (ii) electronically output a report indicative of said risk score indicative of said risk of pre-term birth of said subject.

In another aspect, the present disclosure provides a computer system for predicting a risk of preeclampsia of a subject, comprising: a database that is configured to store clinical health data of said subject, wherein said clinical health data comprises a plurality of quantitative or categorical measures of said subject; and one or more computer processors operatively coupled to said database, wherein said one or more computer processors are individually or collectively programmed to: (i) use an algorithm (e.g., a trained algorithm) to process said clinical health data of said subject to determine a risk score indicative of said risk of preeclampsia of said subject; and (ii) electronically output a report indicative of said risk score indicative of said risk of preeclampsia of said subject.

In some embodiments, the computer system further comprises an electronic display operatively coupled to said one or more computer processors, wherein said electronic display comprises a graphical user interface that is configured to display said report.

In another aspect, the present disclosure provides a non-transitory computer readable medium comprising machine-executable code that, upon execution by one or more computer processors, implements a method for predicting a risk of pre-term birth of a subject, said method comprising: (a) receiving clinical health data of said subject, wherein said clinical health data comprises a plurality of quantitative or categorical measures of said subject; (b) using an algorithm (e.g., a trained algorithm) to process said clinical health data of said subject to determine a risk score indicative of said risk of pre-term birth of said subject; and (c) electronically outputting a report indicative of said risk score indicative of said risk of pre-term birth of said subject.

In another aspect, the present disclosure provides a non-transitory computer readable medium comprising machine-executable code that, upon execution by one or more computer processors, implements a method for predicting a risk of preeclampsia of a subject, said method comprising: (a) receiving clinical health data of said subject, wherein said clinical health data comprises a plurality of quantitative or categorical measures of said subject; (b) using an algorithm (e.g., a trained algorithm) to process said clinical health data of said subject to determine a risk score indicative of said risk of preeclampsia of said subject; and (c) electronically outputting a report indicative of said risk score indicative of said risk of preeclampsia of said subject.

In another aspect, the present disclosure provides a method for determining a due date, due date range, or gestational age of a fetus of a pregnant subject, comprising assaying a cell-free biological sample derived from said pregnant subject to detect a set of biomarkers, and analyzing said set of biomarkers with a trained algorithm to determine said due date, due date range, or gestational age of said fetus.

In some embodiments, the method further comprises analyzing an estimated due date of said fetus of said pregnant subject using said trained algorithm, wherein said estimated due date is generated from ultrasound measurements of said fetus. In some embodiments, said set of biomarkers comprises a genomic locus associated with due date, wherein said genomic locus is selected from the group of genes listed in Table 1, Table 7, and Table 10.

In some embodiments, said set of biomarkers comprises at least 5 distinct genomic loci. In some embodiments, said set of biomarkers comprises at least 10 distinct genomic loci. In some embodiments, said set of biomarkers comprises at least 25 distinct genomic loci. In some embodiments, said set of biomarkers comprises at least 50 distinct genomic loci. In some embodiments, said set of biomarkers comprises at least 100 distinct genomic loci. In some embodiments, said set of biomarkers comprises at least 150 distinct genomic loci.

In some embodiments, the method further comprises identifying a clinical intervention for said pregnant subject based at least in part on said determined due date. In some embodiments, said clinical intervention is selected from a plurality of clinical interventions. In some embodiments, the method further comprises determining a likelihood of said determination of said susceptibility of said pregnancy-related state of said subject, after which subject can be provided with the clinical intervention. In some embodiments, the clinical intervention comprises a pharmacological, surgical, or procedural treatment to reduce severity, delay, or eliminate said future susceptibility pregnancy-related state of said subject (e.g., aspirin for PE and steroids for PTB).

In some embodiments, said time-to-delivery is less than 7.5 weeks. In some embodiments, said genomic locus is selected from ACKR2, AKAP3, ANO5, Clorf21, C2orf42, CARNS1, CASC15, CCDC102B, CDC45, CDIPT, CMTM1, COPS8, CTD-2267D19.3, CTD-2349P21.9, CXorf65, DDX11L1, DGUOK, DPAGT1, EIF4A1P2, FANK1, FERMT1, FKRP, GAMT, GOLGA6L4, KLLN, LINC01347, LTA, MAPK12, METRN, MKRN4P, MPC2, MYL12BP1, NME4, NPM1P30, PCLO, PIF1, PTP4A3, RIMKLB, RP13-88F20.1, S100B, SIGLEC14, SLAIN1, SPATA33, TFAP2C, TMSB4XP8, TRGV10, and ZNF124.

In some embodiments, said time-to-delivery is less than 5 weeks. In some embodiments, said genomic locus is selected from C2orf68, CACNB3, CD40, CDKL5, CTBS, CTD-2272G21.2, CXCL8, DHRS7B, EIF5A2, IFITM3, MIR24-2, MTSS1, MYSM1, NCK1-AS1, NR1H4, PDE1C, PEMT, PEX7, PIF1, PPP2R3A, RABIF, SIGLEC14, SLC25A53, SPANXN4, SUPT3H, ZC2HC1C, ZMYM1, and ZNF124.

In some embodiments, said time-to-delivery is less than 7.5 weeks. In some embodiments, said genomic locus is selected from ACKR2, AKAP3, ANO5, Clorf21, C2orf42, CARNS1, CASC15, CCDC102B, CDC45, CDIPT, CMTM1, collectionga, COPS8, CTD-2267D19.3, CTD-2349P21.9, DDX11L1, DGUOK, DPAGT1, EIF4A1P2, FANK1, FERMT1, FKRP, GAMT, GOLGA6L4, KLLN, LINC01347, LTA, MAPK12, METRN, MPC2, MYL12BP1, NME4, NPM1P30, PCLO, PIF1, PTP4A3, RIMKLB, RP13-88F20.1, S100B, SIGLEC14, SLAIN1, SPATA33, STAT1, TFAP2C, TMEM94, TMSB4XP8, TRGV10, ZNF124, and ZNF713.

In some embodiments, said time-to-delivery is less than 5 weeks. In some embodiments, said genomic locus is selected from ATP6V1E1P1, ATP8A2, C2orf68, CACNB3, CD40, CDKL4, CDKL5, CEP152, CLEC4D, COL18A1, collectionga, COX16, CTBS, CTD-2272G21.2, CXCL2, CXCL8, DHRS7B, DPPA4, EIF5A2, FERMT1, GNB1L, IFITM3, KATNAL1, LRCH4, MBD6, MIR24-2, MTSS1, MYSM1, NCK1-AS1, NPIPB4, NR1H4, PDE1C, PEMT, PEX7, PIF1, PPP2R3A, PXDN, RABIF, SERTAD3, SIGLEC14, SLC25A53, SPANXN4, SSH3, SUPT3H, TMEM150C, TNFAIP6, UPP1, XKR8, ZC2HC1C, ZMYM1, and ZNF124.

In some embodiments, said time-to-delivery is within about 1 hour, about 2 hours, about 3 hours, about 4 hours, about 5 hours, about 6 hours, about 7 hours, about 8 hours, about 9 hours, about 10 hours, about 11 hours, about 12 hours, about 13 hours, about 14 hours, about 15 hours, about 16 hours, about 17 hours, about 18 hours, about 19 hours, about 20 hours, about 21 hours, about 22 hours, about 23 hours, about 24 hours, about 2 days, about 3 days, about 4 days, about 5 days, about 6 days about 7 days, about 8 days, about 9 days, about 10 days, about 11 days, about 12 days, about 13 days, about 14 days, or about 3 weeks.

In some embodiments, said trained algorithm comprises a linear regression model or an ANOVA model. In some embodiments, said ANOVA model determines a maximum-likelihood time window corresponding to said due date from among a plurality of time windows. In some embodiments, said maximum-likelihood time window corresponds to a time-to-delivery of 1 week, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks, 8 weeks, 9 weeks, 10 weeks, 11 weeks, 12 weeks, 13 weeks, 14 weeks, 15 weeks, 16 weeks, 17 weeks, 18 weeks, 19 weeks, or 20 weeks. In some embodiments, said ANOVA model determines a probability or likelihood of a time window corresponding to said due date from among a plurality of time windows. In some embodiments, said ANOVA model calculates a probability-weighted average across said plurality of time windows to determine an average or expected time window distance.

In another aspect, the present disclosure provides a method for identifying or monitoring a presence or susceptibility of a pregnancy-related state of a subject, comprising: (a) using a first assay to process a first cell-free biological sample derived from the subject to generate a first dataset; (b) based at least in part on the first dataset generated in (a), using a second assay different from the first assay to process a second cell-free biological sample derived from the subject to generate a second dataset indicative of the presence or susceptibility of the pregnancy-related state at a specificity greater than the first dataset; (c) using a trained algorithm to process at least the second dataset to determine the presence or susceptibility of the pregnancy-related state, which trained algorithm has an accuracy of at least about 80% over 50 independent samples; and (d) electronically outputting a report indicative of the presence or susceptibility of the pregnancy-related state of the subject.

In some embodiments, the first assay comprises using cell-free ribonucleic acid (cfRNA) molecules derived from the first cell-free biological sample to generate transcriptomic data, using transcription products (e.g., messenger RNA, transfer RNA, or ribosomal RNA) derived from said cell-free biological sample to generate transcription product data, using cell-free deoxyribonucleic acid (cfDNA) molecules derived from the first cell-free biological sample to generate genomic data and/or methylation data, using proteins (e.g., pregnancy-associated proteins corresponding to pregnancy-associated genomic loci or genes) derived from the first cell-free biological sample to generate proteomic data, or using metabolites derived from the first cell-free biological sample to generate metabolomic data. In some embodiments, the first cell-free biological sample is from a blood of the subject. In some embodiments, the first cell-free biological sample is from a urine of the subject. In some embodiments, the first dataset comprises a first set of biomarkers associated with the pregnancy-related state. In some embodiments, the second dataset comprises a second set of biomarkers associated with the pregnancy-related state. In some embodiments, the second set of biomarkers is different from the first set of biomarkers.

In some embodiments, the pregnancy-related state is selected from the group consisting of pre-term birth, full-term birth, gestational age, due date, onset of labor, pregnancy-related hypertensive disorders (e.g., preeclampsia), eclampsia, gestational diabetes, a congenital disorder of a fetus of the subject, ectopic pregnancy, spontaneous abortion, stillbirth, post-partum complications (e.g., post-partum depression, hemorrhage or excessive bleeding, pulmonary embolism, cardiomyopathy, diabetes, anemia, and hypertensive disorders), hyperemesis gravidarum (morning sickness), hemorrhage or excessive bleeding during delivery, premature rupture of membrane, premature rupture of membrane in pre-term birth, placenta previa (placenta covering the cervix), intrauterine/fetal growth restriction, macrosomia (large fetus for gestational age), neonatal conditions (e.g., anemia, apnea, bradycardia and other heart defects, bronchopulmonary dysplasia or chronic lung disease, diabetes, gastroschisis, hydrocephaly, hyperbilirubinemia, hypocalcemia, hypoglycemia, intraventricular hemorrhage, jaundice, necrotizing enterocolitis, patent ductus arteriosis, periventricular leukomalacia, persistent pulmonary hypertension, polycythemia, respiratory distress syndrome, retinopathy of prematurity, and transient tachypnea), and fetal development stages or states (e.g., normal fetal organ function or development, and abnormal fetal organ function or development). For example, the fetal development stages or states may be related to normal fetal organ function or development and/or abnormal fetal organ function or development for a fetal organ selected from the group consisting of heart, large intestine, small intestine, retina, prefrontal cortex, midbrain, kidney, and esophagus. In some embodiments, the pregnancy-related state comprises pre-term birth. In some embodiments, the pregnancy-related state comprises gestational age.

In some embodiments, the cell-free biological sample is selected from the group consisting of cell-free ribonucleic acid (cfRNA), cell-free deoxyribonucleic acid (cfDNA), cell-free fetal DNA (cffDNA), plasma, serum, urine, saliva, amniotic fluid, and derivatives thereof. In some embodiments, the first cell-free biological sample or the second cell-free biological sample is obtained or derived from the subject using an ethylenediaminetetraacetic acid (EDTA) collection tube, a cell-free RNA collection tube, or a cell-free DNA collection tube. In some embodiments, the method further comprises fractionating a whole blood sample of the subject to obtain the first cell-free biological sample or the second cell-free biological sample. In some embodiments, (i) the first assay comprises a cfRNA assay and the second assay comprises a metabolomics assay, or (ii) the first assay comprises a metabolomics assay and the second assay comprises a cfRNA assay. In some embodiments, (i) the first cell-free biological sample comprises cfRNA and the second cell-free biological sample comprises urine, or (ii) the first cell-free biological sample comprises urine and the second cell-free biological sample comprises cfRNA. In some embodiments, the first assay or the second assay comprises quantitative polymerase chain reaction (qPCR). In some embodiments, the first assay or the second assay comprises a home use test configured to be performed in a home setting. In some embodiments, the first assay or the second assay comprises a metabolomics assay. In some embodiments, the metabolomics assay comprises targeted mass spectroscopy (MS) or an immune assay.

In some embodiments, the first dataset is indicative of the presence or susceptibility of the pregnancy-related state at a sensitivity of at least about 80%. In some embodiments, the first dataset is indicative of the presence or susceptibility of the pregnancy-related state at a sensitivity of at least about 90%. In some embodiments, the first dataset is indicative of the presence or susceptibility of the pregnancy-related state at a sensitivity of at least about 95%. In some embodiments, the first dataset is indicative of the presence or susceptibility of the pregnancy-related state at a positive predictive value (PPV) of at least about 70%. In some embodiments, the first dataset is indicative of the presence or susceptibility of the pregnancy-related state at a positive predictive value (PPV) of at least about 80%. In some embodiments, the first dataset is indicative of the presence or susceptibility of the pregnancy-related state at a positive predictive value (PPV) of at least about 90%. In some embodiments, the second dataset is indicative of the presence or susceptibility of the pregnancy-related state at a specificity of at least about 90%. In some embodiments, the second dataset is indicative of the presence or susceptibility of the pregnancy-related state at a specificity of at least about 95%. In some embodiments, the second dataset is indicative of the presence or susceptibility of the pregnancy-related state at a specificity of at least about 99%. In some embodiments, the second dataset is indicative of the presence or susceptibility of the pregnancy-related state at a negative predictive value (NPV) of at least about 90%. In some embodiments, the second dataset is indicative of the presence or susceptibility of the pregnancy-related state at a negative predictive value (NPV) of at least about 95%. In some embodiments, the second dataset is indicative of the presence or susceptibility of the pregnancy-related state at a negative predictive value (NPV) of at least about 99%. In some embodiments, the trained algorithm determines the presence or susceptibility of the pregnancy-related state of the subject with an Area Under Curve (AUC) of at least about 0.90. In some embodiments, the trained algorithm determines the presence or susceptibility of the pregnancy-related state of the subject with an Area Under Curve (AUC) of at least about 0.95. In some embodiments, the trained algorithm determines the presence or susceptibility of the pregnancy-related state of the subject with an Area Under Curve (AUC) of at least about 0.99.

In some embodiments, the subject is asymptomatic for one or more of: pre-term birth, onset of labor, pregnancy-related hypertensive disorders (e.g., preeclampsia), eclampsia, gestational diabetes, a congenital disorder of a fetus of the subject, ectopic pregnancy, spontaneous abortion, stillbirth, post-partum complications (e.g., post-partum depression, hemorrhage or excessive bleeding, pulmonary embolism, cardiomyopathy, diabetes, anemia, and hypertensive disorders), hyperemesis gravidarum (morning sickness), hemorrhage or excessive bleeding during delivery, premature rupture of membrane, premature rupture of membrane in pre-term birth, placenta previa (placenta covering the cervix), intrauterine/fetal growth restriction, macrosomia (large fetus for gestational age), neonatal conditions (e.g., anemia, apnea, bradycardia and other heart defects, bronchopulmonary dysplasia or chronic lung disease, diabetes, gastroschisis, hydrocephaly, hyperbilirubinemia, hypocalcemia, hypoglycemia, intraventricular hemorrhage, jaundice, necrotizing enterocolitis, patent ductus arteriosis, periventricular leukomalacia, persistent pulmonary hypertension, polycythemia, respiratory distress syndrome, retinopathy of prematurity, and transient tachypnea), and abnormal fetal development stages or states (e.g., abnormal fetal organ function or development). For example, the fetal development stages or states may be related to normal fetal organ function or development and/or abnormal fetal organ function or development for a fetal organ selected from the group consisting of heart, large intestine, small intestine, retina, prefrontal cortex, midbrain, kidney, and esophagus.

In some embodiments, the trained algorithm is trained using at least about 10 independent training samples associated with the pregnancy-related state. In some embodiments, the trained algorithm is trained using no more than about 100 independent training samples associated with the pregnancy-related state. In some embodiments, the trained algorithm is trained using a first set of independent training samples associated with a presence of the pregnancy-related state and a second set of independent training samples associated with an absence of the pregnancy-related state. In some embodiments, the method further comprises using the trained algorithm to process the first dataset to determine the presence or susceptibility of the pregnancy-related state. In some embodiments, the method further comprises using the trained algorithm to process a set of clinical health data of the subject to determine the presence or susceptibility of the pregnancy-related state.

In some embodiments, (a) comprises (i) subjecting the first cell-free biological sample to conditions that are sufficient to isolate, enrich, or extract a first set of ribonucleic acid (RNA) molecules, deoxyribonucleic acid (DNA) molecules, proteins (e.g., pregnancy-associated proteins corresponding to pregnancy-associated genomic loci or genes), or metabolites, and (ii) analyzing the first set of RNA molecules, DNA molecules, proteins, or metabolites using the first assay to generate the first dataset. In some embodiments, the method further comprises extracting a first set of nucleic acid molecules from the first cell-free biological sample, and subjecting the first set of nucleic acid molecules to sequencing to generate a first set of sequencing reads, wherein the first dataset comprises the first set of sequencing reads. In some embodiments, the method further comprises extracting a first set of metabolites from the first cell-free biological sample, and assaying the first set of metabolites to generate the first dataset In some embodiments, (b) comprises (i) subjecting the second cell-free biological sample to conditions that are sufficient to isolate, enrich, or extract a second set of ribonucleic acid (RNA) molecules, deoxyribonucleic acid (DNA) molecules, proteins (e.g., pregnancy-associated proteins corresponding to pregnancy-associated genomic loci or genes), or metabolites, and (ii) analyzing the second set of RNA molecules, DNA molecules, proteins, or metabolites using the second assay to generate the second dataset. In some embodiments, the method further comprises extracting a second set of nucleic acid molecules from the second cell-free biological sample, and subjecting the second set of nucleic acid molecules to sequencing to generate a second set of sequencing reads, wherein the second dataset comprises the second set of sequencing reads. In some embodiments, the method further comprises extracting a second set of metabolites from the second cell-free biological sample, and assaying the second set of metabolites to generate the second dataset. In some embodiments, the sequencing is massively parallel sequencing. In some embodiments, the sequencing comprises nucleic acid amplification. In some embodiments, the nucleic acid amplification comprises polymerase chain reaction (PCR). In some embodiments, the sequencing comprises use of simultaneous reverse transcription (RT) and polymerase chain reaction (PCR).

In some embodiments, the method further comprises using probes configured to selectively enrich the first set of nucleic acid molecules or the second set of nucleic acid molecules corresponding to a panel of one or more genomic loci. In some embodiments, the probes are nucleic acid primers. In some embodiments, the probes have sequence complementarity with nucleic acid sequences of the panel of the one or more genomic loci. In some embodiments, the panel of the one or more genomic loci comprises at least one genomic locus selected from the group consisting of ACTB, ADAM12, ALPP, ANXA3, APLF, ARG1, AVPR1A, CAMP, CAPN6, CD180, CGA, CGB, CLCN3, CPVL, CSH1, CSH2, CSHL1, CYP3A7, DAPP1, DCX, DEFA4, DGCR14, ELANE, ENAH, EPB42, FABP1, FAM212B-AS1, FGA, FGB, FRMD4B, FRZB, FSTL3, GH2, GNAZ, HAL, HSD17B1, HSD3B1, HSPB8, Immune, ITIH2, KLF9, KNG1, KRT8, LGALS14, LTF, LYPLAL1, MAP3K7CL, MEF2C, MMD, MMP8, MOB1B, NFATC2, OTC, P2RY12, PAPPA, PGLYRP1, PKHD1L1, PKHD1L1, PLAC1, PLAC4, POLE2, PPBP, PSG1, PSG4, PSG7, PTGER3, RAB11A, RAB27B, RAP1GAP, RGS18, RPL23AP7, S100A8, S100A9, S100P, SERPINA7, SLC2A2, SLC38A4, SLC4A1, TBC1D15, VCAN, VGLL1, B3GNT2, COL24A1, CXCL8, and PTGS2.

In some embodiments, the panel of the one or more genomic loci comprises at least 5 distinct genomic loci. In some embodiments, the panel of the one or more genomic loci comprises at least 10 distinct genomic loci. In some embodiments, the panel of the one or more genomic loci comprises a genomic locus associated with pre-term birth, wherein said genomic locus is selected from the group consisting of ADAM12, ANXA3, APLF, AVPR1A, CAMP, CAPN6, CD180, CGA, CGB, CLCN3, CPVL, CSH2, CSHL1, CYP3A7, DAPP1, DGCR14, ELANE, ENAH, FAM212B-AS1, FRMD4B, GH2, HSPB8, Immune, KLF9, KRT8, LGALS14, LTF, LYPLAL1, MAP3K7CL, MMD, MOB1B, NFATC2, P2RY12, PAPPA, PGLYRP1, PKHD1L1, PKHD1L1, PLAC1, PLAC4, POLE2, PPBP, PSG1, PSG4, PSG7, RAB11A, RAB27B, RAP1GAP, RGS18, RPL23AP7, TBC1D15, VCAN, VGLL1, B3GNT2, COL24A1, CXCL8, and PTGS2. In some embodiments, the panel of the one or more genomic loci comprises a genomic locus associated with gestational age, wherein said genomic locus is selected from the group consisting of ACTB, ADAM12, ALPP, ANXA3, ARG1, CAMP, CAPN6, CGA, CGB, CSH1, CSH2, CSHL1, CYP3A7, DCX, DEFA4, EPB42, FABP1, FGA, FGB, FRZB, FSTL3, GH2, GNAZ, HAL, HSD17B1, HSD3B1, HSPB8, ITIH2, KNG1, LGALS14, LTF, MEF2C, MMP8, OTC, PAPPA, PGLYRP1, PLAC1, PLAC4, PSG1, PSG4, PSG7, PTGER3, S100A8, S100A9, S100P, SERPINA7, SLC2A2, SLC38A4, SLC4A1, VGLL1, B3GNT2, COL24A1, CXCL8, and PTGS2. In some embodiments, the panel of said one or more genomic loci comprises a genomic locus associated with due date, wherein the genomic locus is selected from the group of genes listed in Table 1, Table 7, and Table 10. In some embodiments, the panel of said one or more genomic loci comprises a genomic locus associated with gestational age, wherein the genomic locus is selected from the group of genes listed in Table 2, genes listed in Table 3, genes listed in Table 4, genes listed in Table 23, genes listed in Table 24, gene listed in Table 25, and genes listed in Table 26 In some embodiments, the panel of said one or more genomic loci comprises a genomic locus associated with pre-term birth, wherein the genomic locus is selected from the group of genes listed in Table 5, genes listed in Table 6, genes listed in Table 8, genes listed in Table 12, genes listed in Table 14, genes listed in Table 20, genes listed in Table 21, genes listed in Table 34, genes listed in Table 40, genes listed in Table 41, genes listed in Table 42, genes listed in Table 43, genes listed in Table 44, genes listed in Table 45, genes listed in Table 46, genes listed in Table 47, RAB27B, RGS18, CLCN3, B3GNT2, COL24A1, CXCL8, and PTGS2. In some embodiments, the panel of said one or more genomic loci comprises a genomic locus associated with preeclampsia, wherein the genomic locus is selected from the group consisting of genes listed in Table 15, genes listed in Table 17, genes listed in Table 18, genes listed in Table 19, genes listed in Table 27, genes listed in Table 33, CLDN7, PAPPA2, SNORD14A, PLEKHH1, MAGEA10, TLE6, and FABP1. In some embodiments, the panel of said one or more genomic loci comprises a genomic locus associated with fetal organ development, wherein the genomic locus is selected from the group of genes listed in Table 29. In some embodiments, the set of biomarkers comprises a genomic locus associated with gestational diabetes mellitus, wherein the genomic locus is selected from the group consisting of genes listed in Table 36, genes listed in Table 37, genes listed in Table 38, and genes listed in Table 39.

In some embodiments, the panel of the one or more genomic loci comprises at least 5 distinct genomic loci. In some embodiments, the panel of the one or more genomic loci comprises at least 10 distinct genomic loci. In some embodiments, the panel of the one or more genomic loci comprises at least 25 distinct genomic loci. In some embodiments, the panel of the one or more genomic loci comprises at least 50 distinct genomic loci. In some embodiments, the panel of the one or more genomic loci comprises at least 100 distinct genomic loci. In some embodiments, the panel of the one or more genomic loci comprises at least 150 distinct genomic loci. In some embodiments, the first cell-free biological sample or the second cell-free biological sample is processed without nucleic acid isolation, enrichment, or extraction. In some embodiments, the report is presented on a graphical user interface of an electronic device of a user. In some embodiments, the user is the subject.

In some embodiments, the method further comprises determining a likelihood of the determination of the presence or susceptibility of the pregnancy-related state of the subject. In some embodiments, the trained algorithm comprises a supervised machine learning algorithm. In some embodiments, the supervised machine learning algorithm comprises a deep learning algorithm, a support vector machine (SVM), a neural network, or a Random Forest. In some embodiments, said trained algorithm comprises a differential expression algorithm. In some embodiments, said differential expression algorithm comprises a use comparison of stochastic models, generalized Poisson (GPseq), mixed Poisson (TSPM), Poisson log-linear (PoissonSeq), negative binomial (edgeR, DESeq, baySeq, NBPSeq), linear model fit by MAANOVA, or a combination thereof. In some embodiments, the method further comprises providing the subject with a therapeutic intervention for the presence or susceptibility of the pregnancy-related state. In some embodiments, therapeutic intervention comprises a progesterone treatment such as hydroxyprogesterone caproate (e.g., 17-alpha hydroxyprogesterone caproate (17-P), LPCN 1107 from Lipocine, Makena from AMAG Pharma), a vaginal progesterone, or a natural progesterone IVR product (e.g., DARE-FRT1 (JNP-0301) from Juniper Pharma); a prostaglandin F2 alpha receptor antagonist (e.g., OBE022 from ObsEva); or a beta2-adrenergic receptor agonist (e.g., bedoradrine sulfate (MN-221) from MediciNova). Therapeutic interventions may be described by, for example, “WHO Recommendations on Interventions to Improve Preterm Birth Outcomes,” ISBN 9789241508988, World Health Organization, 2015, which is hereby incorporated by reference in its entirety. In some embodiments, the method further comprises monitoring the presence or susceptibility of the pregnancy-related state, wherein the monitoring comprises assessing the presence or susceptibility of the pregnancy-related state of the subject at a plurality of time points, wherein the assessing is based at least on the presence or susceptibility of the pregnancy-related state determined in (d) at each of the plurality of time points. In some embodiments, a difference in the assessment of the presence or susceptibility of the pregnancy-related state of the subject among the plurality of time points is indicative of one or more clinical indications selected from the group consisting of: (i) a diagnosis of the presence or susceptibility of the pregnancy-related state of the subject, (ii) a prognosis of the presence or susceptibility of the pregnancy-related state of the subject, and (iii) an efficacy or non-efficacy of a course of treatment for treating the presence or susceptibility of the pregnancy-related state of the subject.

In some embodiments, the method further comprises stratifying the pre-term birth by using the trained algorithm to determine a molecular sub-type of the pre-term birth from among a plurality of distinct molecular subtypes of pre-term birth. In some embodiments, the plurality of distinct molecular subtypes of pre-term birth comprises a molecular subtype of pre-term birth selected from the group consisting of presence or history of prior pre-term birth, presence or history of spontaneous pre-term birth, presence or history of late miscarriage, presence or history of receiving cervical surgery, presence or history of a uterine anomaly, presence or history of ethnicity specific pre-term birth risk (e.g., among an African-American population), and presence or history of pre-term premature rupture of membrane (PPROM).

In some embodiments, the method further comprises stratifying the preeclampsia by using said trained algorithm to determine a molecular sub-type of said preeclampsia from among a plurality of distinct molecular subtypes of preeclampsia. In some embodiments, the plurality of distinct molecular subtypes of preeclampsia comprises a molecular subtype of preeclampsia selected from the group consisting of: presence or history of chronic or pre-existing hypertension, presence or history of gestational hypertension, presence or history of mild preeclampsia (e.g., with delivery greater than 34 weeks gestational age), presence or history of severe preeclampsia (with delivery less than 34 weeks gestational age), presence or history of eclampsia, and presence or history of HELLP syndrome.

In another aspect, the present disclosure provides a computer system for identifying or monitoring a presence or susceptibility of the pregnancy-related state of a subject, comprising: a database that is configured to store a first dataset and a second dataset, wherein the second dataset is indicative of the presence or susceptibility of the pregnancy-related state at a specificity greater than the first dataset; and one or more computer processors operatively coupled to the database, wherein the one or more computer processors are individually or collectively programmed to: (i) use a trained algorithm to process at least the second dataset to determine the presence or susceptibility of the pregnancy-related state, which trained algorithm has an accuracy of at least about 80% over 50 independent samples; and (ii) electronically output a report indicative of the presence or susceptibility of the pregnancy-related state of the subject.

In some embodiments, the computer system further comprises an electronic display operatively coupled to the one or more computer processors, wherein the electronic display comprises a graphical user interface that is configured to display the report.

In another aspect, the present disclosure provides a non-transitory computer readable medium comprising machine-executable code that, upon execution by one or more computer processors, implements a method for identifying or monitoring a presence or susceptibility of the pregnancy-related state of a subject, the method comprising: (a) obtaining a first dataset, and a second dataset, wherein the second dataset is indicative of the presence or susceptibility of the pregnancy-related state at a specificity greater than the first dataset; (b) using a trained algorithm to process at least the second dataset to determine the pregnancy-related state, which trained algorithm has an accuracy of at least about 80% over 50 independent samples; and (c) electronically outputting a report indicative of the presence or susceptibility of the pregnancy-related state of the subject.

In another aspect, the present disclosure provides a method for identifying a presence or susceptibility of pregnancy-related state of a subject, comprising (i) assaying a first cell-free biological sample derived from the subject with a first assay to generate a first dataset, (ii) assaying a second cell-free biological sample derived from the subject with a second assay to generate a second dataset that is indicative of the presence or susceptibility of the pregnancy-related state at a specificity greater than the first dataset, and (iii) using a trained algorithm to process at least the second dataset to determine the presence or susceptibility of the pregnancy-related state at an accuracy of at least about 80%. In some embodiments, the accuracy is at least about 90%. In some embodiments, the pregnancy-related state is selected from the group consisting of pre-term birth, full-term birth, gestational age, due date, onset of labor, pregnancy-related hypertensive disorders (e.g., preeclampsia), eclampsia, gestational diabetes, a congenital disorder of a fetus of the subject, ectopic pregnancy, spontaneous abortion, stillbirth, post-partum complications (e.g., post-partum depression, hemorrhage or excessive bleeding, pulmonary embolism, cardiomyopathy, diabetes, anemia, and hypertensive disorders), hyperemesis gravidarum (morning sickness), hemorrhage or excessive bleeding during delivery, premature rupture of membrane, premature rupture of membrane in pre-term birth, placenta previa (placenta covering the cervix), intrauterine/fetal growth restriction, macrosomia (large fetus for gestational age), neonatal conditions (e.g., anemia, apnea, bradycardia and other heart defects, bronchopulmonary dysplasia or chronic lung disease, diabetes, gastroschisis, hydrocephaly, hyperbilirubinemia, hypocalcemia, hypoglycemia, intraventricular hemorrhage, jaundice, necrotizing enterocolitis, patent ductus arteriosis, periventricular leukomalacia, persistent pulmonary hypertension, polycythemia, respiratory distress syndrome, retinopathy of prematurity, and transient tachypnea), and fetal development stages or states (e.g., normal fetal organ function or development, and abnormal fetal organ function or development). For example, the fetal development stages or states may be related to normal fetal organ function or development and/or abnormal fetal organ function or development for a fetal organ selected from the group consisting of heart, large intestine, small intestine, retina, prefrontal cortex, midbrain, kidney, and esophagus.

In another aspect, the present disclosure provides a method for determining that a subject is at risk of pre-term birth, comprising assaying a cell-free biological sample derived from the subject to generate a dataset that is indicative of the pre-term birth risk at a specificity of at least 80%, and using a trained algorithm that is trained on samples independent of the cell-free biological sample to determine that the subject is at risk of pre-term birth at an accuracy of at least about 80%. In some embodiments, the accuracy is at least about 90%.

In another aspect, the present disclosure provides a method for determining that a subject is at risk of preeclampsia, comprising assaying a cell-free biological sample derived from the subject to generate a dataset that is indicative of the preeclampsia risk at a specificity of at least 80%, and using a trained algorithm that is trained on samples independent of the cell-free biological sample to determine that the subject is at risk of preeclampsia at an accuracy of at least about 80%. In some embodiments, the accuracy is at least about 90%.

In another aspect, the present disclosure provides a method for detecting a presence or risk of a prenatal metabolic genetic disease of a fetus of a pregnant subject, comprising: assaying ribonucleic acid (RNA) in a cell-free biological sample derived from said pregnant subject to detect a set of biomarkers; and analyzing said set of biomarkers with an algorithm (e.g., a trained algorithm) to detect said presence or risk of said prenatal metabolic genetic disease.

In another aspect, the present disclosure provides a method for detecting at least two health or physiological conditions of a fetus of a pregnant subject or of said pregnant subject, comprising: assaying a first cell-free biological sample obtained or derived from said pregnant subject at a first time point and a second cell-free biological sample obtained or derived from said pregnant subject at a second time point, to detect a first set of biomarkers at said first time point and a second set of biomarkers at said second time point, and analyzing said first set of biomarkers or said second set of biomarkers with a trained algorithm to detect said at least two health or physiological conditions.

In some embodiments, said at least two health or physiological conditions are selected from the group consisting of pre-term birth, full-term birth, gestational age, due date, onset of labor, a pregnancy-related hypertensive disorder, eclampsia, gestational diabetes, a congenital disorder of a fetus of said subject, ectopic pregnancy, spontaneous abortion, stillbirth, a post-partum complication, hyperemesis gravidarum, hemorrhage or excessive bleeding during delivery, premature rupture of membrane, premature rupture of membrane in pre-term birth, placenta previa, intrauterine/fetal growth restriction, macrosomia, a neonatal condition, and a fetal development stage or state. In some embodiments, said set of biomarkers comprises a genomic locus associated with due date, wherein said genomic locus is selected from the group consisting of genes listed in Table 1, Table 7, and Table 10. In some embodiments, said set of biomarkers comprises a genomic locus associated with gestational age, wherein said genomic locus is selected from the group consisting of genes listed in Table 2, genes listed in Table 3, genes listed in Table 4, genes listed in Table 23, genes listed in Table 24, genes listed in Table 25, and genes listed in Table 26. In some embodiments, said set of biomarkers comprises a genomic locus associated with pre-term birth, wherein said genomic locus is selected from the group consisting of genes listed in Table 5, genes listed in Table 6, genes listed in Table 8, genes listed in Table 12, genes listed in Table 14, genes listed in Table 20, genes listed in Table 21, genes listed in Table 34, genes listed in Table 40, genes listed in Table 41, genes listed in Table 42, genes listed in Table 43, genes listed in Table 44, genes listed in Table 45, genes listed in Table 46, genes listed in Table 47, RAB27B, RGS18, CLCN3, B3GNT2, COL24A1, CXCL8, and PTGS2. In some embodiments, said set of biomarkers comprises at least 5 distinct genomic loci. In some embodiments, the panel of said one or more genomic loci comprises a genomic locus associated with preeclampsia, wherein the genomic locus is selected from the group consisting of genes listed in Table 15, genes listed in Table 17, genes listed in Table 18, genes listed in Table 19, genes listed in Table 27, genes listed in Table 33, CLDN7, PAPPA2, SNORD14A, PLEKHH1, MAGEA10, TLE6, and FABP1. In some embodiments, the panel of said one or more genomic loci comprises a genomic locus associated with fetal organ development, wherein the genomic locus is selected from the group of genes listed in Table 29. In some embodiments, the set of biomarkers comprises a genomic locus associated with gestational diabetes mellitus, wherein the genomic locus is selected from the group consisting of genes listed in Table 36, genes listed in Table 37, genes listed in Table 38, and genes listed in Table 39.

In another aspect, the present disclosure provides a method comprising: assaying one or more cell-free biological samples obtained or derived from a pregnant subject to detect a set of biomarkers; and analyzing said set of biomarkers to identify (1) a due date or a range thereof of a fetus of said pregnant subject and (2) a health or physiological condition of said fetus of said pregnant subject or of said pregnant subject.

In some embodiments, the method further comprises analyzing said set of biomarkers with a trained algorithm. In some embodiments, said health or physiological condition is selected from the group consisting of pre-term birth, full-term birth, gestational age, due date, onset of labor, a pregnancy-related hypertensive disorder, eclampsia, gestational diabetes, a congenital disorder of a fetus of said subject, ectopic pregnancy, spontaneous abortion, stillbirth, a post-partum complication, hyperemesis gravidarum, hemorrhage or excessive bleeding during delivery, premature rupture of membrane, premature rupture of membrane in pre-term birth, placenta previa, intrauterine/fetal growth restriction, macrosomia, a neonatal condition, and a fetal development stage or state. In some embodiments, said set of biomarkers comprises a genomic locus associated with due date, wherein said genomic locus is selected from the group consisting of genes listed in Table 1, Table 7, and Table 10. In some embodiments, said set of biomarkers comprises a genomic locus associated with gestational age, wherein said genomic locus is selected from the group consisting of genes listed in Table 2, genes listed in Table 3, genes listed in Table 4, genes listed in Table 23, genes listed in Table 24, genes listed in Table 25, and genes listed in Table 26. In some embodiments, said set of biomarkers comprises a genomic locus associated with pre-term birth, wherein said genomic locus is selected from the group consisting of genes listed in Table 5, genes listed in Table 6, genes listed in Table 8, genes listed in Table 12, genes listed in Table 14, genes listed in Table 20, genes listed in Table 21, genes listed in Table 34, genes listed in Table 40, genes listed in Table 41, genes listed in Table 42, genes, listed in Table 43, genes listed in Table 44, genes listed in Table 45, genes listed in Table 46, genes listed in Table 47, RAB27B, RGS18, CLCN3, B3GNT2, COL24A1, CXCL8, and PTGS2. In some embodiments, said set of biomarkers comprises at least 5 distinct genomic loci. In some embodiments, the panel of said one or more genomic loci comprises a genomic locus associated with preeclampsia, wherein the genomic locus is selected from the group consisting of genes listed in Table 15, genes listed in Table 17, genes listed in Table 18, genes listed in Table 19, genes listed in Table 27, genes listed in Table 33, CLDN7, PAPPA2, SNORD14A, PLEKHH1, MAGEA10, TLE6, and FABP1. In some embodiments, the panel of said one or more genomic loci comprises a genomic locus associated with fetal organ development, wherein the genomic locus is selected from the group of genes listed in Table 29. In some embodiments, the set of biomarkers comprises a genomic locus associated with gestational diabetes mellitus, wherein the genomic locus is selected from the group consisting of genes listed in Table 36, genes listed in Table 37, genes listed in Table 38, and genes listed in Table 39.

In some embodiments, the method further comprises selecting a therapeutic intervention for said health or physiological condition of said fetus of said pregnant subject or of said pregnant subject, based at least in part on said set of biomarkers. In some embodiments, said therapeutic intervention is selected from among a plurality of therapeutic interventions. In some embodiments, said therapeutic intervention is selected based at least in part on a molecular subtype of said health or physiological condition determined based at least in part on said set of biomarkers.

In some embodiments, said health or physiological condition comprises preeclampsia. In some embodiments, said therapeutic intervention for said preeclampsia comprises a drug, a supplement, or a lifestyle recommendation. In some embodiments, said drug is selected from the group consisting of aspirin, progesterone, magnesium sulfate, a cholesterol medication (such as pravastatin), a heartburn medication (such as esomeprazole), an angiotensin II receptor antagonist (such as losartan), a calcium channel blocker (such as nifedipine), a diabetes medication (such as myo-inositol, metformin, glucovance, and liraglutide), and an erectile dysfunction medication (such as sildenafil citrate). In some embodiments, said supplement is selected from the group consisting of calcium, vitamin D, vitamin B3, and DHA. In some embodiments, said lifestyle recommendation is selected from the group consisting of exercise, nutrition counseling, meditation, stress relief, weight loss or maintenance, and improving sleep quality. In some embodiments, said therapeutic intervention for said preeclampsia is selected from a therapeutic intervention (e.g., treatment or prophylaxis) as disclosed in “WHO recommendations: Prevention and treatment of pre-eclampsia and eclampsia,” World Health Organization, ISBN 9789241548335, World Health Organization, 2011, which is incorporated by reference herein in its entirety. In some embodiments, said therapeutic intervention for said preeclampsia is selected from a therapeutic intervention (e.g., treatment or prophylaxis) as disclosed in “Summary of recommendations: Prevention and treatment of pre-eclampsia and eclampsia,” World Health Organization, WHO reference number WHO/RHR/11.30, World Health Organization, 2011, which is incorporated by reference herein in its entirety. In some embodiments, said therapeutic intervention for said preeclampsia is selected from a therapeutic intervention (e.g., treatment or prophylaxis) as disclosed in “WHO recommendations: Drug treatment for severe hypertension in pregnancy,” World Health Organization, ISBN 9789241550437, World Health Organization, 2018, which is incorporated by reference herein in its entirety.

In some embodiments, said health or physiological condition comprises pre-term birth. In some embodiments, said therapeutic intervention for said pre-term birth comprises a drug, a supplement, a lifestyle recommendation, a cervical cerclage, a cervical pessary, or electrical contraction inhibition. In some embodiments, said drug is selected from the group consisting of progesterone, erythromycin, a tocolytic medication (such as indomethacin), a corticosteroid, a vaginal flora (such as clindamycin and metronidazole), and an antioxidant (such as N-acetylcysteine). In some embodiments, said supplement is selected from the group consisting of calcium, vitamin D, and a probiotic (such as lactobacillus). In some embodiments, said lifestyle recommendation is selected from the group consisting of exercise, nutrition counseling, meditation, stress relief, weight loss or maintenance, and improving sleep quality. In some embodiments, said therapeutic intervention for said pre-term birth is selected from a therapeutic intervention (e.g., treatment or prophylaxis) as disclosed “WHO Recommendations on Interventions to Improve Preterm Birth Outcomes,” ISBN 9789241508988, World Health Organization, 2015, which is incorporated by reference herein in its entirety.

In some embodiments, said health or physiological condition comprises gestational diabetes mellitus (GDM). In some embodiments, said therapeutic intervention for said GDM comprises a drug, a supplement, or a lifestyle recommendation. In some embodiments, said drug is selected from the group consisting of insulin and a diabetes medication (such as myo-inositol, metformin, glucovance, and liraglutide). In some embodiments, said supplement is selected from the group consisting of vitamin D, choline, probiotics, and DHA. In some embodiments, said lifestyle recommendation is selected from the group consisting of exercise, nutrition counseling, meditation, stress relief, weight loss or maintenance, and improving sleep quality. In some embodiments, said therapeutic intervention for said gestational diabetes mellitus (GDM) is selected from a therapeutic intervention (e.g., treatment or prophylaxis) as disclosed “Diagnostic criteria and classification of hyperglycaemia first detected in pregnancy,” WHO reference number WHO/NMH/MND/13.2, World Health Organization, 2013, which is incorporated by reference herein in its entirety.

In another aspect, the present disclosure provides a method comprising: assaying one or more cell-free biological samples obtained or derived from a pregnant subject to detect a set of nucleic acids of non-human origin; and analyzing said set of nucleic acids of non-human origin to detect a health or physiological condition of a fetus of said pregnant subject or of said pregnant subject. In some embodiments, the nucleic acids of non-human origin comprise DNA or RNA of a non-human organism. In some embodiments, the non-human organism is a bacteria, a virus, or a parasite. In some embodiments, the method further comprises analyzing said set of nucleic acids of non-human origin using a trained algorithm.

Another aspect of the present disclosure provides a non-transitory computer readable medium comprising machine executable code that, upon execution by one or more computer processors, implements any of the methods above or elsewhere herein.

Another aspect of the present disclosure provides a system comprising one or more computer processors and computer memory coupled thereto. The computer memory comprises machine executable code that, upon execution by the one or more computer processors, implements any of the methods above or elsewhere herein.

Additional aspects and advantages of the present disclosure will become readily apparent to those skilled in this art from the following detailed description, wherein only illustrative embodiments of the present disclosure are shown and described. As will be realized, the present disclosure is capable of other and different embodiments, and its several details are capable of modifications in various obvious respects, all without departing from the disclosure. Accordingly, the drawings and description are to be regarded as illustrative in nature, and not as restrictive.

INCORPORATION BY REFERENCE

All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference. To the extent publications and patents or patent applications incorporated by reference contradict the disclosure contained in the specification, the specification is intended to supersede and/or take precedence over any such contradictory material.

BRIEF DESCRIPTION OF THE DRAWINGS

The novel features of the invention are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present invention will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the invention are utilized, and the accompanying drawings (also “Figure” and “FIG.” herein), of which:

FIG. 1 illustrates an example workflow of a method for identifying or monitoring a pregnancy-related state of a subject, in accordance with disclosed embodiments.

FIG. 2 illustrates a computer system that is programmed or otherwise configured to implement methods provided herein.

FIG. 3A shows a first cohort of subjects (e.g., pregnant women) that was established (with patient identification numbers shown on the x-axis), from which one or more biological samples (e.g., 2 or 3 each) were collected and assayed at different time points corresponding to an estimated gestational age (shown on the y-axis, in increasing order of estimated gestational age at delivery) of a fetus of each subject, in accordance with disclosed embodiments.

FIG. 3B shows a distribution of participants in the first cohort based on each participant's age at the time of medical record abstraction, in accordance with disclosed embodiments.

FIG. 3C shows a distribution of 100 participants in the first cohort based on each participant's race, in accordance with disclosed embodiments.

FIG. 3D shows a distribution of collected samples in the gestational age cohort based on each participant's estimated gestational age and trimester at the time of collection of each sample, in accordance with disclosed embodiments.

FIG. 3E shows a distribution of 225 collected samples in the first cohort based on the study sample type of the collected samples, in accordance with disclosed embodiments.

FIG. 4A shows a second cohort of subjects (e.g., pregnant women) that was established (with patient identification numbers shown on the x-axis), from which one or more biological samples (e.g., 1, 2, or 3 each) were collected and assayed at different time points corresponding to an estimated gestational age (shown on the y-axis, in increasing order of estimated gestational age at delivery) of a fetus of each subject, in accordance with disclosed embodiments.

FIG. 4B shows a distribution of participants in the second cohort based on each participant's age at the time of medical record abstraction, in accordance with disclosed embodiments.

FIG. 4C shows a distribution of 128 participants in the second cohort based on each participant's race, in accordance with disclosed embodiments.

FIG. 4D shows a distribution of collected samples in the second cohort based on each participant's estimated gestational age and trimester at the time of collection of each sample, in accordance with disclosed embodiments.

FIG. 4E shows a distribution of 160 collected samples in the second cohort based on the study sample type of the collected samples, in accordance with disclosed embodiments.

FIG. 5A shows a due date cohort of subjects (e.g., pregnant women) that was established (with patient identification numbers shown on the x-axis), from which one or more biological samples (e.g., 1 or 2 each) were collected and assayed at different time points corresponding to an estimated gestational age (shown on the y-axis, in increasing order of estimated gestational age at delivery) of a fetus of each subject, in accordance with disclosed embodiments.

FIG. 5B shows a distribution of collected samples in the due date cohort based on the time between the date of sample collection and the date of delivery (time to delivery), in accordance with disclosed embodiments.

FIG. 5C is a Venn diagram showing the overlap of genes used in the first and second predictive models of due date, in accordance with disclosed embodiments. The first predictive model had a total of 51 most predictive genes, and the second predictive model had a total of 49 most predictive genes; further, only 5 genes overlapped between the two predictive models.

FIG. 5D is a plot showing the concordance between a predicted time to delivery (in weeks) and the observed (actual) time to delivery (in weeks) for the subjects in the due date cohort, in accordance with disclosed embodiments.

FIG. 5E shows a summary of the predictive models for predicting due date, including a predictive model using samples with a time-to-delivery of less than 5 weeks and predictive model using samples with a time-to-delivery of less than 7.5 weeks; different predictive models were generated with estimated due date information (e.g., determined using estimated gestational age from ultrasound measurements) and without the estimated due date information.

FIG. 6A shows a gestational age cohort of subjects (e.g., pregnant women) that was established (with patient identification numbers shown on the x-axis), from which one or more biological samples (e.g., 1 or 2 each) were collected and assayed at different time points corresponding to an estimated gestational age (shown on the y-axis, in increasing order of estimated gestational age at delivery) of a fetus of each subject, in accordance with disclosed embodiments.

FIG. 6B is a visual model showing mutual information of the whole transcriptome, where expression of a plurality of gestational age-associated genes varies with gestational age throughout the course of a pregnancy, in accordance with disclosed embodiments.

FIG. 6C is a plot showing the concordance between a predicted gestational age (in weeks) and the measured gestational age (in weeks) for the subjects in the gestational age cohort, in accordance with disclosed embodiments. The subjects are stratified in the plot by major race (e.g., white, non-black Hispanic, Asian, Afro-American, Native American, mixed race (e.g., two or more races), or unknown).

FIGS. 7A-7B show results for a pre-term birth (PTB) cohort of subjects (e.g., pregnant women), which included a set of pre-term case samples (e.g., from women having pre-term births) and a set of pre-term control samples (e.g., from women having full-term births), in accordance with disclosed embodiments. Across the pre-term case samples and pre-term control samples, the distributions of gestational age at time of collection were similar (FIG. 7A), while the distributions of gestational age at delivery were clearly distinguishable to a statistically significant extent (FIG. 7B).

FIGS. 7C-7E show differential gene expression of the B3GNT2, BPI, and ELANE genes, respectively, between the pre-term case samples (left) and pre-term control samples (right), in accordance with disclosed embodiments.

FIG. 7F shows a legend for the results from pre-term case samples and pre-term control samples shown in FIGS. 7C-7E, in accordance with disclosed embodiments.

FIG. 7G shows a receiver-operating characteristic (ROC) curve showing the performance of the predictive model for pre-term delivery across the 10-fold cross-validation, in accordance with disclosed embodiments.

FIG. 8 shows an example of a distribution of vaginal singleton births by obstetrician-estimated gestational age in the U.S.

FIG. 9A-9E show different methods of predicting due date for a fetus of a pregnant subject, including predicting an actual day (with error) (FIG. 9A), predicting a week (or other window) of delivery (FIG. 9B), predicting whether a delivery is expected to occur before or after a certain time boundary (FIG. 9C), predicting in which bin among a plurality of bins (e.g., 6 bins) a delivery is expected to occur (FIG. 9D), and predicting a relative risk or relative likelihood of an early delivery or a late delivery (FIG. 9E).

FIG. 10 shows a data workflow that is performed to develop a due date prediction model (e.g., classifier).

FIGS. 11A-11B show prediction error of a due date prediction model that is trained on 270 and 310 patients, respectively.

FIG. 12 shows a receiver-operator characteristic ROC) curve for a pre-term birth prediction model, using a set of 22 genes for a set of 79 samples obtained from a cohort of Caucasian subjects. The mean area-under-the-curve (AUC) for the ROC curve was 0.91±0.10.

FIG. 13A shows a receiver-operator characteristic ROC) curve for a pre-term birth prediction model, using a set of genes for a set of 45 samples obtained from a cohort of subjects having African or African-American ancestries (AA cohort). The mean area-under-the-curve (AUC) for the ROC curve was 0.82±0.08.

FIG. 13B shows a gene panel for a pre-term birth prediction model for three different AA cohorts (cohort 1, cohort 2, and cohort 3), including RAB27B, RGS18, CLCN3, B3GNT2, COL24A1, CXCL8, and PTGS2.

FIG. 14A shows a workflow for performing multiple assays for assessment of a plurality of pregnancy-related conditions using a single bodily sample (e.g., a single blood draw) obtained from a pregnant subject.

FIG. 14B shows a combination of conditions which can be tested from a single blood draw along a pregnancy progression of a pregnant subject.

FIG. 15A shows a Discovery 1 cohort of 310 mixed race subjects (e.g., pregnant women) that was established (with patient identification numbers shown on the x-axis), from which biological samples were collected and assayed at different time points corresponding to an estimated gestational age (shown on the y-axis, in increasing order of estimated gestational age at delivery) of a fetus of each subject, in accordance with disclosed embodiments.

FIG. 15B shows a Discovery 2 cohort of 86 Caucasian subjects, respectively, that was established (with patient identification numbers shown on the x-axis), from which biological samples were collected and assayed at different time points corresponding to an estimated gestational age (shown on the y-axis, in increasing order of estimated gestational age at delivery) of a fetus of each subject, in accordance with disclosed embodiments.

FIG. 15C shows a distribution of participants in the Discovery 1 mixed race cohort based on blood sample collection gestation.

FIG. 15D shows a distribution of participants in the Discovery 2 Caucasian cohort, respectively, based on blood sample collection gestation.

FIG. 15E shows a distribution of samples collected in the Discovery 1 mixed race cohort by weeks before birth.

FIG. 15F shows a distribution of participants in the Discovery 2 Caucasian cohort by weeks before birth.

FIG. 16A shows expression trends and significant abundance level separation for a set of top 4 genes (EFHD1, ADCY6, HTR1, and PAPPA2) between samples collected at 1 week before birth.

FIG. 16B shows correlation p-value significance of log₁₀(p-value) exceeds a threshold of 1 for 3 genes (HTRA1, PAPPA2, and EFHD1) in several discovery and validation cohorts.

FIG. 17A shows a first cohort of 192 subjects (e.g., pregnant women) that was established (with patient identification numbers shown on the x-axis), from which biological samples were collected and assayed at different time points corresponding to an estimated gestational age (shown on the y-axis, in increasing order of estimated gestational age at delivery) of a fetus of each subject, in accordance with disclosed embodiments.

FIG. 17B shows a first cohort distribution of participants in case (upper graph) and control (lower graph) group based on each participant's age at the time of medical record abstraction, in accordance with disclosed embodiments.

FIG. 17C shows a first cohort distribution of participants in case (left graph) and control (right graph) group based on each participant's race, in accordance with disclosed embodiments.

FIG. 17D shows a distribution of 192 collected samples in the first cohort based on the study sample type of the collected samples.

FIG. 18A shows a second cohort of 76 subjects (e.g., pregnant women) that was established (with patient identification numbers shown on the x-axis), from which biological samples were collected and assayed at different time points corresponding to an estimated gestational age (shown on the y-axis, in increasing order of estimated gestational age at delivery) of a fetus of each subject, in accordance with disclosed embodiments.

FIG. 18B shows a second cohort distribution of participants in case (left graph) and control (right graph) group based on each participant's race, in accordance with disclosed embodiments.

FIG. 18C shows a distribution of 76 collected samples (25 pre-term samples and 51 full-term controls) in the second cohort based on the study sample type of the collected samples.

FIG. 19A shows a quantile-quantile (QQ) plot for a signal in pre-term birth-associated genes in the first cohort.

FIG. 19B shows a receiver-operator characteristic (ROC) curve for the high pre-term birth prediction model, using all differentially expressed genes in the first cohort. The mean area-under-the-curve (AUC) for the ROC curve was 0.75±0.08.

FIG. 19C shows a receiver-operator characteristic (ROC) curve for a set of top 9 genes (EFHD1, ABI3BP, NEAT1, HSD17B1, CDR1-AS, GCM1, DAPK2, ZCCHC7, COL3A1, and AKR7A2) in the first cohort. The mean area-under-the-curve (AUC) for the ROC curve was 0.80±0.07, with relative contributions from each gene.

FIG. 20A shows a distribution of demographic statistics for this subset of early PTB samples and controls in the second cohort that were included in the analysis.

FIG. 20B shows a quantile-quantile (QQ) plot for a differential expression signal in pre-term birth-associated genes in the second cohort.

FIG. 20C shows boxplots and significant abundance level separation for the top 12 differentially expressed genes (ANGPTL3, NPM1P26, HIST1H4F, CRY1, BHMT, C2orf49, OASL, SELE, CHD4, IFIT1, DHX38, and DNASE1) for early PTB in the second cohort.

FIG. 21 shows a first cohort of 18 subjects (e.g., pregnant women) that was established (with patient identification numbers shown on the x-axis), from which biological samples were collected and assayed at different time points corresponding to an estimated gestational age (shown on the y-axis, in increasing order of estimated gestational age at delivery) of a fetus of each subject, in accordance with disclosed embodiments.

FIG. 22A shows a second cohort of 130 subjects (pregnant women) that was established (with patient identification numbers shown on the x-axis), from which 144 biological samples were collected and assayed at different time points corresponding to an estimated gestational age (shown on the y-axis, in increasing order of estimated gestational age at delivery) of a fetus of each subject, in accordance with disclosed embodiments.

FIG. 22B shows a second cohort distribution of 130 participants in case (left graph) and control (right graph) group based on each participant's race, in accordance with disclosed embodiments.

FIG. 22C shows a distribution of 144 collected samples in the second cohort based on the study sample type of the collected samples.

FIG. 23 shows a significant abundance level separation between cases and healthy controls for the top 20 differentially expressed genes for preeclampsia (PE) in the first cohort.

FIG. 24A shows a distribution of demographic statistics for the subset of PE samples and controls in the second cohort.

FIG. 24B shows a quantile-quantile (QQ) plot for a differential expression signal in preeclampsia-associated genes in the second cohort.

FIG. 24C show boxplots and significant abundance level separation in a set of top 12 genes for preeclampsia in the second cohort (AGAP9, ANKRD1, CIS, CCDC181, CIAPIN1, EPS8L1, FBLN1, FUNDC2P2, KISS1, MLF1, PAPPA2, and TFPI2).

FIG. 25A shows a cohort of 351 subjects (pregnant women) that was established (with patient identification numbers shown on the x-axis), from which 351 biological samples were collected and assayed at different time points corresponding to an estimated gestational age (shown on the y-axis, in increasing order of estimated gestational age at delivery) of a fetus of each subject, in accordance with disclosed embodiments.

FIG. 25B shows quantile-quantile (QQ) plots for a differential expression signal in preeclampsia-associated genes in the analyses with and without chronic hypertension control subjects.

FIG. 25C shows a receiver-operator characteristic (ROC) curve for a training cohort (Example 9) and a test (Example 10) cohort for a preeclampsia prediction model, using all differentially expressed genes in the Example 9 cohort. The mean area-under-the-curve (AUC) for the ROC curve was 0.75 and 0.66 for the training cohort and the test cohort, respectively.

FIG. 25D shows a receiver-operator characteristic (ROC) curve for combined cohorts. The mean area-under-the-curve (AUC) for the ROC curve was 0.76.

FIG. 26A shows a combined data set for pre-term birth cohorts from Example 4 and Example 8, and an additional cohort based on blood collection and delivery gestational age.

FIG. 26B shows a cohort of 281 subjects (pregnant women) that was established (with patient identification numbers shown on the x-axis), from which 281 biological samples were collected and assayed at different time points corresponding to an estimated gestational age (shown on the y-axis, in increasing order of estimated gestational age at delivery) of a fetus of each subject, in accordance with disclosed embodiments.

FIG. 26C shows a quantile-quantile (QQ) plot for a differential expression signal in pre-term birth cases with delivery between 28 to 35 weeks for blood samples collected from subjects at between 20 to 28 weeks of gestation age.

FIG. 27A shows a combined data set for combined cohorts based on blood collection and delivery gestational age, which comprises different races of maternal donors.

FIG. 27B is a plot showing the relationship between a predicted gestational age (in weeks) and the measured gestational age (in weeks) for the subjects in the gestational age cohort in held-out test data. Gray bands represent one and two standard deviations. 494 genes were used for Lasso modeling.

FIG. 27C is a plot showing the concordance between a predicted gestational age (in weeks) and the measured gestational age (in weeks) for the subjects in the gestational age cohort in held-out test data. 57 transcriptomic features were used for Lasso modeling.

FIG. 27D is a plot showing the concordance between a predicted gestational age (in weeks) and the measured gestational age (in weeks) for the subjects in the gestational age cohort in the held-out testing data. 70 genes were used for the RFE method.

FIG. 27E is a plot showing the concordance between a predicted gestational age (in weeks) and the measured gestational age (in weeks) for the subjects in the gestational age cohort in held-out test data in first trimester modeling.

FIG. 28A shows a quantile-quantile (QQ) plot for differential expression between preeclampsia and control for genes across the whole transcriptome in one of the outer training sets. FABP1 is labeled to highlight its relative ranking among the differentially expressed genes.

FIG. 28B shows the distribution of the area-under-the-curve (AUC) across the one hundred held-out outer testing sets for a preeclampsia prediction linear model based on FABP1. The mean AUC across the outer testing sets is 0.67.

FIG. 28C shows the distribution of the area-under-the-curve (AUC) across the one hundred held-out outer testing sets for a preeclampsia prediction linear model based on PAPPA2 in combination with the nine abundant genes with significant differential expression (adjusted p-value<0.05) between preeclampsia cases and controls. The nine abundant genes include FABP1, CDCA2, HMGB3, ELANE, CDC20, SHCBP1, OLFM4, S100A9, S100A12. The mean AUC across the outer testing sets is 0.73.

FIG. 29A shows upward temporal profiles of fetal organ developmental signatures of fetal small intestine, developing hearts, and fetal retina gene sets in training cohort. Plasma transcriptome fractions for 3 top upregulated embryonic gene sets were averaged across all samples in a given collection window with error bars corresponding to 95% confidence interval around the mean.

FIG. 29B shows upward trends for fetal organ developmental signatures of fetal small intestine, developing hearts, and fetal retina gene sets in the training and holdout cohorts as a linear function of gestational age.

FIG. 29C shows the verification modeling of the top three downward trending gene sets with gestation age (kidney nephron progenitor cells, esophagus C4 epithelial cells, and prefrontal cortex (PFC) brain C4 cells in training (H) and held out test cohorts (A, B, G).

FIG. 30 shows plasma sampling and cohort overview by gestational age. Different cohorts labeled are A-H. Circles represent plasma samples from liquid biopsies. Maternal donors are of different races.

FIGS. 31A-31C show gestational age modeling in full term pregnancies. FIG. 31A: Model predictions from held-out test cfRNA transcript data in Lasso linear model versus ultrasound predicted gestational age. Dark gray zone is 1 standard deviation, light gray zone is 2 standard deviations. FIG. 31B: Variance explained from ANOVA. FIG. 31C: Learning curve for gestational age modeling. Model for gestational age is trained with increasing sample size, error is plotted for both training set (Cross-validated) and held-out test set. Error bars are 1 standard deviation.

FIGS. 32A-32C show temporal profiles of developmental signatures from embryonic gene sets. Maternal plasma transcriptome fractions for gene set averaged across all samples in a given collection window. FIG. 32A: Fetal small intestine gene set. FIG. 32B: Developing heart gene set. FIG. 32C: Nephron progenitor gene set. Error bars correspond to 95% confidence interval around the mean. CPM, counts per million. N=91 for each timepoint and gene set.

FIGS. 33A-33B show features and model performance for prediction of preeclampsia. FIG. 33A: Quantile-quantile plot ranked Spearman p-values for preeclamptic women versus controls. p-values are calculated from Spearman correlations on cohort corrected data for each gene. Genes used in model are labeled. Black dotted line is expectation. FIG. 33B: Receiver operating characteristic curve (mean and 95% confidence intervals) for logistic regression model for preeclampsia without the intermediate risk group.

FIG. 34 shows principal components analysis of all samples used in the gestational age model.

FIGS. 35A-35B show temporal profiles of pregnancy-related endocrine signatures during pregnancy. Seven pregnancy-related gene ontology term signatures identified as highly significantly enriched (α=0.01) were profiled across collection times using cumulative CPM. Plasma transcriptome fractions for each gene set were averaged across all samples in a given collection window with error bars corresponding to 95% confidence interval around the mean. Panels correspond to different ranges of CPM, for the ease of comparison. CPM, counts per million. N=91 for each timepoint and gene set.

FIG. 36 shows validation of gene set signature across all cohorts with longitudinal samples. Linear fits of transcriptome fractions for all samples across corresponding gestational ages recorded at the collection times. The band around the solid line corresponds to the 95% CI. a, Fetal small intestine gene set. b, Developing heart gene set. c, Nephron progenitor gene set. All slopes for the gestational age coefficient are distinct from 0 at a confidence level of 0.05, except for the “Nephron progenitor” set in cohort G.

FIG. 37 shows temporal structure in the data determines the trends. For each of the significantly enriched gene sets, the trends were evaluated by bootstrapping (B=1,000) the original data (blue lines) and the time-scrambled data obtained by reshuffling collection times (grey lines). a, Fetal small intestine gene set. b, Developing heart gene set. c, Nephron progenitor gene set.

FIGS. 38A-38B show gene set enrichment analysis for gene ontology sets. a, Top-20 upregulated gene sets. b, Top-20 downregulated gene sets. ES, enrichment score. −ES, negative enrichment score. Color gradient for adjusted p-value.

FIG. 39 shows a quantile-quantile (QQ) plot for a differential expression signal in a QQ plot for differential expression in ePTB cases.

FIG. 40 shows a quantile-quantile (QQ) plot for a differential expression signal in a QQ plot for differential expression in gestational diabetes mellitus (GDM) cases, including the top 4 differentially expressed genes.

FIG. 41 shows a clinical intervention care plan algorithm to improve early pre-term birth outcomes following results of predictive tests administered in the second trimester.

FIG. 42 shows a clinical intervention care plan algorithm to improve preeclampsia outcomes following results of predictive tests administered in the second trimester.

FIG. 43 shows a clinical intervention care plan algorithm to improve gestational diabetes mellitus (GDM) outcomes based on prediction test administered in the second trimester.

FIG. 44A shows a combined data set for pre-term birth cohorts from Examples 4, 8, and 11, and an additional cohort based on blood collection and delivery gestational age.

FIG. 44B shows a cohort of 150 subjects (pregnant women) that was established (with patient identification numbers shown on the x-axis), from which 150 biological samples were collected and assayed at different time points corresponding to an estimated gestational age (shown on the y-axis, in increasing order of estimated gestational age at delivery) of a fetus of each subject.

FIG. 44C shows a quantile-quantile (QQ) plot for a differential expression signal in a QQ plot for differentially expressed genes in pre-term birth cases for samples collected between 17 and 28 weeks of gestation.

FIG. 44D shows a quantile-quantile (QQ) plot for a differential expression signal in a QQ plot for differentially expressed genes in pre-term birth cases for samples collected between 23 and 26 weeks of gestation.

FIG. 44E shows a quantile-quantile (QQ) plot for a differential expression signal in a QQ plot for differentially expressed genes in pre-term birth cases for samples collected between 17 and 23 weeks of gestation.

DETAILED DESCRIPTION

While various embodiments of the invention have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions may occur to those skilled in the art without departing from the invention. It should be understood that various alternatives to the embodiments of the invention described herein may be employed.

As used in the specification and claims, the singular form “a”, “an”, and “the” include plural references unless the context clearly dictates otherwise. For example, the term “a nucleic acid” includes a plurality of nucleic acids, including mixtures thereof.

As used herein, the term “subject,” generally refers to an entity or a medium that has testable or detectable genetic information. A subject can be a person, individual, or patient. A subject can be a vertebrate, such as, for example, a mammal. Non-limiting examples of mammals include humans, simians, farm animals, sport animals, rodents, and pets. A subject can be a pregnant female subject. The subject can be a woman having a fetus (or multiple fetuses) or suspected of having the fetus (or multiple fetuses). The subject can be a person that is pregnant or is suspected of being pregnant. The subject may be displaying a symptom(s) indicative of a health or physiological state or condition of the subject, such as a pregnancy-related health or physiological state or condition of the subject. As an alternative, the subject can be asymptomatic with respect to such health or physiological state or condition.

The term “pregnancy-related state,” as used herein, generally refers to any health, physiological, and/or biochemical state or condition of a subject that is pregnant or is suspected of being pregnant, or of a fetus (or multiple fetuses) of the subject. Examples of pregnancy-related states include, without limitation, pre-term birth, full-term birth, gestational age, due date, onset of labor, pregnancy-related hypertensive disorders (e.g., preeclampsia), eclampsia, gestational diabetes, a congenital disorder of a fetus of the subject, ectopic pregnancy, spontaneous abortion, stillbirth, post-partum complications (e.g., post-partum depression, hemorrhage or excessive bleeding, pulmonary embolism, cardiomyopathy, diabetes, anemia, and hypertensive disorders), hyperemesis gravidarum (morning sickness), hemorrhage or excessive bleeding during delivery, premature rupture of membrane, premature rupture of membrane in pre-term birth, placenta previa (placenta covering the cervix), intrauterine/fetal growth restriction, macrosomia (large fetus for gestational age), neonatal conditions (e.g., anemia, apnea, bradycardia and other heart defects, bronchopulmonary dysplasia or chronic lung disease, diabetes, gastroschisis, hydrocephaly, hyperbilirubinemia, hypocalcemia, hypoglycemia, intraventricular hemorrhage, jaundice, necrotizing enterocolitis, patent ductus arteriosis, periventricular leukomalacia, persistent pulmonary hypertension, polycythemia, respiratory distress syndrome, retinopathy of prematurity, and transient tachypnea), and fetal development stages or states (e.g., normal fetal organ function or development, and abnormal fetal organ function or development). For example, the fetal development stages or states may be related to normal fetal organ function or development and/or abnormal fetal organ function or development for a fetal organ selected from the group consisting of heart, large intestine, small intestine, retina, prefrontal cortex, midbrain, kidney, and esophagus. In some situations, the pregnancy-related state is not associated with the health or physiological state or condition of a fetus (or multiple fetuses) of the subject.

As used herein, the term “sample,” generally refers to a biological sample obtained from or derived from one or more subjects. Biological samples may be cell-free biological samples or substantially cell-free biological samples, or may be processed or fractionated to produce cell-free biological samples. For example, cell-free biological samples may include cell-free ribonucleic acid (cfRNA), cell-free deoxyribonucleic acid (cfDNA), cell-free fetal DNA (cffDNA), plasma, serum, urine, saliva, amniotic fluid, and derivatives thereof. Cell-free biological samples may be obtained or derived from subjects using an ethylenediaminetetraacetic acid (EDTA) collection tube, a cell-free RNA collection tube (e.g., Streck), or a cell-free DNA collection tube (e.g., Streck). Cell-free biological samples may be derived from whole blood samples by fractionation. Biological samples or derivatives thereof may contain cells. For example, a biological sample may be a blood sample or a derivative thereof (e.g., blood collected by a collection tube or blood drops), a vaginal sample (e.g., a vaginal swab), or a cervical sample (e.g., a cervical swab).

As used herein, the term “nucleic acid” generally refers to a polymeric form of nucleotides of any length, either deoxyribonucleotides (dNTPs) or ribonucleotides (rNTPs), or analogs thereof. Nucleic acids may have any three-dimensional structure, and may perform any function, known or unknown. Non-limiting examples of nucleic acids include deoxyribonucleic (DNA), ribonucleic acid (RNA), coding or non-coding regions of a gene or gene fragment, loci (locus) defined from linkage analysis, exons, introns, messenger RNA (mRNA), transfer RNA, ribosomal RNA, short interfering RNA (siRNA), short-hairpin RNA (shRNA), micro-RNA (miRNA), ribozymes, cDNA, recombinant nucleic acids, branched nucleic acids, plasmids, vectors, isolated DNA of any sequence, isolated RNA of any sequence, nucleic acid probes, and primers. A nucleic acid may comprise one or more modified nucleotides, such as methylated nucleotides and nucleotide analogs. If present, modifications to the nucleotide structure may be made before or after assembly of the nucleic acid. The sequence of nucleotides of a nucleic acid may be interrupted by non-nucleotide components. A nucleic acid may be further modified after polymerization, such as by conjugation or binding with a reporter agent.

As used herein, the term “target nucleic acid” generally refers to a nucleic acid molecule in a starting population of nucleic acid molecules having a nucleotide sequence whose presence, amount, and/or sequence, or changes in one or more of these, are desired to be determined. A target nucleic acid may be any type of nucleic acid, including DNA, RNA, and analogs thereof. As used herein, a “target ribonucleic acid (RNA)” generally refers to a target nucleic acid that is RNA. As used herein, a “target deoxyribonucleic acid (DNA)” generally refers to a target nucleic acid that is DNA.

As used herein, the terms “amplifying” and “amplification” generally refer to increasing the size or quantity of a nucleic acid molecule. The nucleic acid molecule may be single-stranded or double-stranded. Amplification may include generating one or more copies or “amplified product” of the nucleic acid molecule. Amplification may be performed, for example, by extension (e.g., primer extension) or ligation. Amplification may include performing a primer extension reaction to generate a strand complementary to a single-stranded nucleic acid molecule, and in some cases generate one or more copies of the strand and/or the single-stranded nucleic acid molecule. The term “DNA amplification” generally refers to generating one or more copies of a DNA molecule or “amplified DNA product.” The term “reverse transcription amplification” generally refers to the generation of deoxyribonucleic acid (DNA) from a ribonucleic acid (RNA) template via the action of a reverse transcriptase.

Every year, about 15 million pre-term births are reported globally. Pre-term birth may affect as many as about 10% of pregnancies, of which the majority are spontaneous pre-term births. Currently, there may be no meaningful, clinically actionable diagnostic screenings or tests available for many pregnancy-related complications such as pre-term birth. However, pregnancy-related complications such as pre-term birth are a leading cause of neonatal death and of complications later in life. Further, such pregnancy-related complications can cause negative health effects on maternal health. Thus, to make pregnancy as safe as possible, there exists a need for rapid, accurate methods for identifying and monitoring pregnancy-related states that are non-invasive and cost-effective, toward improving maternal and fetal health.

Current tests for prenatal care may be in inaccessible and incomplete. For cases in which pregnancies progress without pregnancy-related complications, limited methods of pregnancy monitoring may be available for a pregnancy subject, such as molecular tests, ultrasound imaging, and estimation of gestational age and/or due date using the last menstrual period. However, such monitoring methods may be complex, expensive, and unreliable. For example, molecular tests cannot predict gestational age, ultrasound imaging is expensive and best performed during the first trimester of pregnancy, and estimation of gestational age and/or due date using the last menstrual period can be unreliable. Further, for cases in which pregnancies progress with pregnancy-related complications such as risk of spontaneous pre-term delivery, the clinical utility of molecular tests, ultrasound imaging, and demographic factors may be limited. For example, molecular tests may have a limited BMI (body mass index) range, a limited gestational age and/or due date range (about 2 weeks), and a low positive predictive value (PPV); ultrasound imaging may be expensive and have low PPV and specificity; and the use of demographic factors to predict risk of pregnancy-related complications may be unreliable. Therefore, there exists an urgent clinical need for accurate and affordable non-invasive diagnostic methods for detection and monitoring of pregnancy-related states (e.g., estimation of gestational age, due date, and/or onset of labor, and prediction of pregnancy-related complications such as pre-term birth) toward clinically actionable outcomes.

The present disclosure provides methods, systems, and kits for identifying or monitoring pregnancy-related states by processing cell-free biological samples obtained from or derived from subjects (e.g., pregnancy female subjects). Cell-free biological samples (e.g., plasma samples) obtained from subjects may be analyzed to identify the pregnancy-related state (which may include, e.g., measuring a presence, absence, or quantitative assessment (e.g., risk) of the pregnancy-related state). Such subjects may include subjects with one or more pregnancy-related states and subjects without pregnancy-related states. Pregnancy-related states may include, for example, pre-term birth, full-term birth, gestational age, due date, onset of labor, pregnancy-related hypertensive disorders (e.g., preeclampsia), eclampsia, gestational diabetes, a congenital disorder of a fetus of the subject, ectopic pregnancy, spontaneous abortion, stillbirth, post-partum complications (e.g., post-partum depression, hemorrhage or excessive bleeding, pulmonary embolism, cardiomyopathy, diabetes, anemia, and hypertensive disorders), hyperemesis gravidarum (morning sickness), hemorrhage or excessive bleeding during delivery, premature rupture of membrane, premature rupture of membrane in pre-term birth, placenta previa (placenta covering the cervix), intrauterine/fetal growth restriction, and macrosomia (large fetus for gestational age). In some embodiments, pregnancy-related states are not associated with the health of a fetus. In some embodiments, pregnancy-related states include neonatal conditions (e.g., anemia, apnea, bradycardia and other heart defects, bronchopulmonary dysplasia or chronic lung disease, diabetes, gastroschisis, hydrocephaly, hyperbilirubinemia, hypocalcemia, hypoglycemia, intraventricular hemorrhage, jaundice, necrotizing enterocolitis, patent ductus arteriosis, periventricular leukomalacia, persistent pulmonary hypertension, polycythemia, respiratory distress syndrome, retinopathy of prematurity, and transient tachypnea) and fetal development stages or states (e.g., normal fetal organ function or development, and abnormal fetal organ function or development). For example, the fetal development stages or states may be related to normal fetal organ function or development and/or abnormal fetal organ function or development for a fetal organ selected from the group consisting of heart, large intestine, small intestine, retina, prefrontal cortex, midbrain, kidney, and esophagus.

FIG. 1 illustrates an example workflow of a method for identifying or monitoring a pregnancy-related state of a subject, in accordance with disclosed embodiments. In an aspect, the present disclosure provides a method 100 for identifying or monitoring a pregnancy-related state of a subject. The method 100 may comprise using a first assay to process a first cell-free biological sample derived from said subject to generate a first dataset (as in operation 102). Next, based at least in part on the first dataset generated, the method 100 may optionally comprise using a second assay (e.g., different from the first assay) to process a second cell-free biological sample derived from the subject to generate a second dataset indicative of the pregnancy-related state at a specificity greater than the first dataset. For example, ribonucleic acid (RNA) molecules extracted from a second cell-free plasma sample may be sequenced to generate a set of sequence reads indicative of a pregnancy-related state of the subject (as in operation 104). In some embodiments, a first cell-free biological sample can be obtained from a subject at a first time point for processing with a first assay. Then, optionally a second cell-free biological sample can be obtained from the same subject at a second time point for processing with a second assay. In some embodiments, a cell-free biological sample can be obtained from a subject and then aliquoted to produce a first cell-free biological sample and a second cell-free biological sample, which are then processed with a first assay and a second assay, respectively. Next, a trained algorithm may be used to process the first dataset and/or the second dataset to determine the pregnancy-related state of the subject (as in operation 106). The trained algorithm may be configured to identify the pregnancy-related state at an accuracy of at least about 80% over 50 independent samples. A report may then be electronically outputted that is indicative of (e.g., identifies or provides an indication of) presence or susceptibility of the pregnancy-related state of the subject (as in operation 108).

Assaying Cell-Free Biological Samples

The cell-free biological samples may be obtained or derived from a human subject (e.g., a pregnant female subject). The cell-free biological samples may be stored in a variety of storage conditions before processing, such as different temperatures (e.g., at room temperature, under refrigeration or freezer conditions, at 25° C., at 4° C., at −18° C., −20° C., or at −80° C.) or different suspensions (e.g., EDTA collection tubes, cell-free RNA collection tubes, or cell-free DNA collection tubes).

The cell-free biological sample may be obtained from a subject with a pregnancy-related state (e.g., a pregnancy-related complication), from a subject that is suspected of having a pregnancy-related state (e.g., a pregnancy-related complication), or from a subject that does not have or is not suspected of having the pregnancy-related state (e.g., a pregnancy-related complication). The pregnancy-related state may comprise a pregnancy-related complication, such as pre-term birth, pregnancy-related hypertensive disorders (e.g., preeclampsia), eclampsia, gestational diabetes, a congenital disorder of a fetus of the subject, ectopic pregnancy, spontaneous abortion, stillbirth, post-partum complications (e.g., post-partum depression, hemorrhage or excessive bleeding, pulmonary embolism, cardiomyopathy, diabetes, anemia, and hypertensive disorders), hyperemesis gravidarum (morning sickness), hemorrhage or excessive bleeding during delivery, premature rupture of membrane, premature rupture of membrane in pre-term birth, placenta previa (placenta covering the cervix), intrauterine/fetal growth restriction, macrosomia (large fetus for gestational age), neonatal conditions (e.g., anemia, apnea, bradycardia and other heart defects, bronchopulmonary dysplasia or chronic lung disease, diabetes, gastroschisis, hydrocephaly, hyperbilirubinemia, hypocalcemia, hypoglycemia, intraventricular hemorrhage, jaundice, necrotizing enterocolitis, patent ductus arteriosis, periventricular leukomalacia, persistent pulmonary hypertension, polycythemia, respiratory distress syndrome, retinopathy of prematurity, and transient tachypnea), and abnormal fetal development stages or states (e.g., abnormal fetal organ function or development). The pregnancy-related state may comprise a full-term birth, normal fetal development stages or states (e.g., normal fetal organ function or development), or absence of a pregnancy-related complication (e.g., pre-term birth, pregnancy-related hypertensive disorders (e.g., preeclampsia), eclampsia, gestational diabetes, a congenital disorder of a fetus of the subject, ectopic pregnancy, spontaneous abortion, stillbirth, post-partum complications (e.g., post-partum depression, hemorrhage or excessive bleeding, pulmonary embolism, cardiomyopathy, diabetes, anemia, and hypertensive disorders), hyperemesis gravidarum (morning sickness), hemorrhage or excessive bleeding during delivery, premature rupture of membrane, premature rupture of membrane in pre-term birth, placenta previa (placenta covering the cervix), intrauterine/fetal growth restriction, macrosomia (large fetus for gestational age), neonatal conditions (e.g., anemia, apnea, bradycardia and other heart defects, bronchopulmonary dysplasia or chronic lung disease, diabetes, gastroschisis, hydrocephaly, hyperbilirubinemia, hypocalcemia, hypoglycemia, intraventricular hemorrhage, jaundice, necrotizing enterocolitis, patent ductus arteriosis, periventricular leukomalacia, persistent pulmonary hypertension, polycythemia, respiratory distress syndrome, retinopathy of prematurity, and transient tachypnea), and abnormal fetal development stages or states (e.g., abnormal fetal organ function or development)). The pregnancy-related state may comprise a quantitative assessment of pregnancy such as gestational age (e.g., measured in days, weeks or months) or due date (e.g., expressed as a predicted or estimated calendar date or range of calendar dates). The pregnancy-related state may comprise a quantitative assessment of a pregnancy-related complication such as a likelihood, a susceptibility, or a risk (e.g., expressed as a probability, a relative probability, an odds ratio, or a risk score or risk index) of the pregnancy-related complication (e.g., pre-term birth, onset of labor, pregnancy-related hypertensive disorders (e.g., preeclampsia), eclampsia, gestational diabetes, a congenital disorder of a fetus of the subject, ectopic pregnancy, spontaneous abortion, stillbirth, post-partum complications (e.g., post-partum depression, hemorrhage or excessive bleeding, pulmonary embolism, cardiomyopathy, diabetes, anemia, and hypertensive disorders), hyperemesis gravidarum (morning sickness), hemorrhage or excessive bleeding during delivery, premature rupture of membrane, premature rupture of membrane in pre-term birth, placenta previa (placenta covering the cervix), intrauterine/fetal growth restriction, macrosomia (large fetus for gestational age), neonatal conditions (e.g., anemia, apnea, bradycardia and other heart defects, bronchopulmonary dysplasia or chronic lung disease, diabetes, gastroschisis, hydrocephaly, hyperbilirubinemia, hypocalcemia, hypoglycemia, intraventricular hemorrhage, jaundice, necrotizing enterocolitis, patent ductus arteriosis, periventricular leukomalacia, persistent pulmonary hypertension, polycythemia, respiratory distress syndrome, retinopathy of prematurity, and transient tachypnea), and abnormal fetal development stages or states (e.g., abnormal fetal organ function or development)). For example, the pregnancy-related state may comprise a likelihood or susceptibility of an onset of labor in the future (e.g., within about 1 hour, about 2 hours, about 4 hours, about 6 hours, about 8 hours, about 10 hours, about 12 hours, about 14 hours, about 16 hours, about 18 hours, about 20 hours, about 22 hours, about 24 hours, about 1.5 days, about 2 days, about 2.5 days, about 3 days, about 3.5 days, about 4 days, about 4.5 days, about 5 days, about 5.5 days, about 6 days, about 6.5 days, about 7 days, about 8 days, about 9 days, about 10 days, about 12 days, about 14 days, about 3 weeks, about 4 weeks, about 5 weeks, about 6 weeks, about 7 weeks, about 8 weeks, about 9 weeks, about 10 weeks, about 11 weeks, about 12 weeks, about 13 weeks, or more than about 13 weeks). For example, the fetal development stages or states may be related to normal fetal organ function or development and/or abnormal fetal organ function or development for a fetal organ selected from the group consisting of heart, large intestine, small intestine, retina, prefrontal cortex, midbrain, kidney, and esophagus.

The cell-free biological sample may be taken before and/or after treatment of a subject with the pregnancy-related complication. Cell-free biological samples may be obtained from a subject during a treatment or a treatment regime. Multiple cell-free biological samples may be obtained from a subject to monitor the effects of the treatment over time. The cell-free biological sample may be taken from a subject known or suspected of having a pregnancy-related state (e.g., pregnancy-related complication) for which a definitive positive or negative diagnosis is not available via clinical tests. The sample may be taken from a subject suspected of having a pregnancy-related complication. The cell-free biological sample may be taken from a subject experiencing unexplained symptoms, such as fatigue, nausea, weight loss, aches and pains, weakness, or bleeding. The cell-free biological sample may be taken from a subject having explained symptoms. The cell-free biological sample may be taken from a subject at risk of developing a pregnancy-related complication due to factors such as familial history, age, hypertension or pre-hypertension, diabetes or pre-diabetes, overweight or obesity, environmental exposure, lifestyle risk factors (e.g., smoking, alcohol consumption, or drug use), or presence of other risk factors.

The cell-free biological sample may contain one or more analytes capable of being assayed, such as cell-free ribonucleic acid (cfRNA) molecules suitable for assaying to generate transcriptomic data, using transcription products (e.g., messenger RNA, transfer RNA, or ribosomal RNA) derived from said cell-free biological sample to generate transcription product data, cell-free deoxyribonucleic acid (cfDNA) molecules suitable for assaying to generate genomic data and/or methylation data, proteins (e.g., pregnancy-associated proteins corresponding to pregnancy-associated genomic loci or genes) suitable for assaying to generate proteomic data, metabolites suitable for assaying to generate metabolomic data, or a mixture or combination thereof. One or more such analytes (e.g., cfRNA molecules, cfDNA molecules, proteins, or metabolites) may be isolated or extracted from one or more cell-free biological samples of a subject for downstream assaying using one or more suitable assays.

After obtaining a cell-free biological sample from the subject, the cell-free biological sample may be processed to generate datasets indicative of a pregnancy-related state of the subject. For example, a presence, absence, or quantitative assessment of nucleic acid molecules of the cell-free biological sample at a panel of pregnancy-related state-associated genomic loci (e.g., quantitative measures of RNA transcripts or DNA at the pregnancy-related state-associated genomic loci), proteomic data comprising quantitative measures of proteins of the dataset at a panel of pregnancy-related state-associated proteins (e.g., corresponding to pregnancy-associated genomic loci or genes), and/or metabolome data comprising quantitative measures of a panel of pregnancy-related state-associated metabolites may be indicative of a pregnancy-related state. Processing the cell-free biological sample obtained from the subject may comprise (i) subjecting the cell-free biological sample to conditions that are sufficient to isolate, enrich, or extract a plurality of nucleic acid molecules, proteins (e.g., pregnancy-associated proteins corresponding to pregnancy-associated genomic loci or genes), and/or metabolites, and (ii) assaying the plurality of nucleic acid molecules, proteins, and/or metabolites to generate the dataset.

In some embodiments, a plurality of nucleic acid molecules is extracted from the cell-free biological sample and subjected to sequencing to generate a plurality of sequencing reads. The nucleic acid molecules may comprise ribonucleic acid (RNA) or deoxyribonucleic acid (DNA). The nucleic acid molecules (e.g., RNA or DNA) may be extracted from the cell-free biological sample by a variety of methods, such as a FastDNA Kit protocol from MP Biomedicals, a QIAamp DNA cell-free biological mini kit from Qiagen, or a cell-free biological DNA isolation kit protocol from Norgen Biotek. The extraction method may extract all RNA or DNA molecules from a sample. Alternatively, the extract method may selectively extract a portion of RNA or DNA molecules from a sample. Extracted RNA molecules from a sample may be converted to DNA molecules by reverse transcription (RT).

The sequencing may be performed by any suitable sequencing methods, such as massively parallel sequencing (MPS), paired-end sequencing, high-throughput sequencing, next-generation sequencing (NGS), shotgun sequencing, single-molecule sequencing, nanopore sequencing, semiconductor sequencing, pyrosequencing, sequencing-by-synthesis (SBS), sequencing-by-ligation, sequencing-by-hybridization, and RNA-Seq (Illumina).

The sequencing may comprise nucleic acid amplification (e.g., of RNA or DNA molecules). In some embodiments, the nucleic acid amplification is polymerase chain reaction (PCR). A suitable number of rounds of PCR (e.g., PCR, qPCR, reverse-transcriptase PCR, digital PCR, etc.) may be performed to sufficiently amplify an initial amount of nucleic acid (e.g., RNA or DNA) to a desired input quantity for subsequent sequencing. In some cases, the PCR may be used for global amplification of target nucleic acids. This may comprise using adapter sequences that may be first ligated to different molecules followed by PCR amplification using universal primers. PCR may be performed using any of a number of commercial kits, e.g., provided by Life Technologies, Affymetrix, Promega, Qiagen, etc. In other cases, only certain target nucleic acids within a population of nucleic acids may be amplified. Specific primers, possibly in conjunction with adapter ligation, may be used to selectively amplify certain targets for downstream sequencing. The PCR may comprise targeted amplification of one or more genomic loci, such as genomic loci associated with pregnancy-related states. The sequencing may comprise use of simultaneous reverse transcription (RT) and polymerase chain reaction (PCR), such as a OneStep RT-PCR kit protocol by Qiagen, NEB, Thermo Fisher Scientific, or Bio-Rad.

RNA or DNA molecules isolated or extracted from a cell-free biological sample may be tagged, e.g., with identifiable tags, to allow for multiplexing of a plurality of samples. Any number of RNA or DNA samples may be multiplexed. For example a multiplexed reaction may contain RNA or DNA from at least about 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, or more than 100 initial cell-free biological samples. For example, a plurality of cell-free biological samples may be tagged with sample barcodes such that each DNA molecule may be traced back to the sample (and the subject) from which the DNA molecule originated. Such tags may be attached to RNA or DNA molecules by ligation or by PCR amplification with primers.

After subjecting the nucleic acid molecules to sequencing, suitable bioinformatics processes may be performed on the sequence reads to generate the data indicative of the presence, absence, or relative assessment of the pregnancy-related state. For example, the sequence reads may be aligned to one or more reference genomes (e.g., a genome of one or more species such as a human genome). The aligned sequence reads may be quantified at one or more genomic loci to generate the datasets indicative of the pregnancy-related state. For example, quantification of sequences corresponding to a plurality of genomic loci associated with pregnancy-related states may generate the datasets indicative of the pregnancy-related state.

The cell-free biological sample may be processed without any nucleic acid extraction. For example, the pregnancy-related state may be identified or monitored in the subject by using probes configured to selectively enrich nucleic acid (e.g., RNA or DNA) molecules corresponding to the plurality of pregnancy-related state-associated genomic loci. The probes may be nucleic acid primers. The probes may have sequence complementarity with nucleic acid sequences from one or more of the plurality of pregnancy-related state-associated genomic loci or genomic regions. The plurality of pregnancy-related state-associated genomic loci or genomic regions may comprise at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least about 25, at least about 30, at least about 35, at least about 40, at least about 45, at least about 50, at least about 55, at least about 60, at least about 65, at least about 70, at least about 75, at least about 80, at least about 85, at least about 90, at least about 95, at least about 100, or more distinct pregnancy-related state-associated genomic loci or genomic regions. The plurality of pregnancy-related state-associated genomic loci or genomic regions may comprise one or more members (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, about 25, about 30, about 35, about 40, about 45, about 50, about 55, about 60, about 65, about 70, about 75, about 80, or more) selected from the group consisting of ACTB, ADAM12, ALPP, ANXA3, APLF, ARG1, AVPR1A, CAMP, CAPN6, CD180, CGA, CGB, CLCN3, CPVL, CSH1, CSH2, CSHL1, CYP3A7, DAPP1, DCX, DEFA4, DGCR14, ELANE, ENAH, EPB42, FABP1, FAM212B-AS1, FGA, FGB, FRMD4B, FRZB, FSTL3, GH2, GNAZ, HAL, HSD17B1, HSD3B1, HSPB8, Immune, ITIH2, KLF9, KNG1, KRT8, LGALS14, LTF, LYPLAL1, MAP3K7CL, MEF2C, MMD, MMP8, MOB1B, NFATC2, OTC, P2RY12, PAPPA, PGLYRP1, PKHD1L1, PKHD1L1, PLAC1, PLAC4, POLE2, PPBP, PSG1, PSG4, PSG7, PTGER3, RAB11A, RAB27B, RAP1GAP, RGS18, RPL23AP7, S100A8, S100A9, S100P, SERPINA7, SLC2A2, SLC38A4, SLC4A1, TBC1D15, VCAN, VGLL1, B3GNT2, COL24A1, CXCL8, and PTGS2. The pregnancy-related state-associated genomic loci or genomic regions may be associated with gestational age, pre-term birth, due date, onset of labor, or other pregnancy-related states or complications, such as the genomic loci described by, for example, Ngo et al. (“Noninvasive blood tests for fetal development predict gestational age and preterm delivery,” Science, 360(6393), pp. 1133-1136, 8 Jun. 2018), which is hereby incorporated by reference in its entirety.

The probes may be nucleic acid molecules (e.g., RNA or DNA) having sequence complementarity with nucleic acid sequences (e.g., RNA or DNA) of the one or more genomic loci (e.g., pregnancy-related state-associated genomic loci). These nucleic acid molecules may be primers or enrichment sequences. The assaying of the cell-free biological sample using probes that are selective for the one or more genomic loci (e.g., pregnancy-related state-associated genomic loci) may comprise use of array hybridization (e.g., microarray-based), polymerase chain reaction (PCR), or nucleic acid sequencing (e.g., RNA sequencing or DNA sequencing). In some embodiments, DNA or RNA may be assayed by one or more of: isothermal DNA/RNA amplification methods (e.g., loop-mediated isothermal amplification (LAMP), helicase dependent amplification (HDA), rolling circle amplification (RCA), recombinase polymerase amplification (RPA)), immunoassays, electrochemical assays, surface-enhanced Raman spectroscopy (SERS), quantum dot (QD)-based assays, molecular inversion probes, droplet digital PCR (ddPCR), CRISPR/Cas-based detection (e.g., CRISPR-typing PCR (ctPCR), specific high-sensitivity enzymatic reporter un-locking (SHERLOCK), DNA endonuclease targeted CRISPR trans reporter (DETECTR), and CRISPR-mediated analog multi-event recording apparatus (CAMERA)), and laser transmission spectroscopy (LTS).

The assay readouts may be quantified at one or more genomic loci (e.g., pregnancy-related state-associated genomic loci) to generate the data indicative of the pregnancy-related state. For example, quantification of array hybridization or polymerase chain reaction (PCR) corresponding to a plurality of genomic loci (e.g., pregnancy-related state-associated genomic loci) may generate data indicative of the pregnancy-related state. Assay readouts may comprise quantitative PCR (qPCR) values, digital PCR (dPCR) values, digital droplet PCR (ddPCR) values, fluorescence values, etc., or normalized values thereof. The assay may be a home use test configured to be performed in a home setting.

In some embodiments, multiple assays are used to process cell-free biological samples of a subject. For example, a first assay may be used to process a first cell-free biological sample obtained or derived from the subject to generate a first dataset; and based at least in part on the first dataset, a second assay different from said first assay may be used to process a second cell-free biological sample obtained or derived from the subject to generate a second dataset indicative of said pregnancy-related state. The first assay may be used to screen or process cell-free biological samples of a set of subjects, while the second or subsequent assays may be used to screen or process cell-free biological samples of a smaller subset of the set of subjects. The first assay may have a low cost and/or a high sensitivity of detecting one or more pregnancy-related states (e.g., pregnancy-related complication), that is amenable to screening or processing cell-free biological samples of a relatively large set of subjects. The second assay may have a higher cost and/or a higher specificity of detecting one or more pregnancy-related states (e.g., pregnancy-related complication), that is amenable to screening or processing cell-free biological samples of a relatively small set of subjects (e.g., a subset of the subjects screened using the first assay). The second assay may generate a second dataset having a specificity (e.g., for one or more pregnancy-related states such as pregnancy-related complications) greater than the first dataset generated using the first assay. As an example, one or more cell-free biological samples may be processed using a cfRNA assay on a large set of subjects and subsequently a metabolomics assay on a smaller subset of subjects, or vice versa. The smaller subset of subjects may be selected based at least in part on the results of the first assay.

Alternatively, multiple assays may be used to simultaneously process cell-free biological samples of a subject. For example, a first assay may be used to process a first cell-free biological sample obtained or derived from the subject to generate a first dataset indicative of the pregnancy-related state; and a second assay different from the first assay may be used to process a second cell-free biological sample obtained or derived from the subject to generate a second dataset indicative of the pregnancy-related state. Any or all of the first dataset and the second dataset may then be analyzed to assess the pregnancy-related state of the subject. For example, a single diagnostic index or diagnosis score can be generated based on a combination of the first dataset and the second dataset. As another example, separate diagnostic indexes or diagnosis scores can be generated based on the first dataset and the second dataset.

The cell-free biological samples may be processed to identify a set of biomarker RNA transcripts that are indicative of a set of corresponding biomarker proteins (e.g., pregnancy-associated proteins corresponding to pregnancy-associated genomic loci or genes), pathways, and/or metabolites. For example, a given biomarker RNA transcript may be expected to be translated into a corresponding given biomarker protein or a gene regulator for a corresponding given biomarker protein. Therefore, identifying a presence or absence of the given biomarker RNA transcript in a biological sample may be indicative of a presence or absence of a corresponding biomarker protein. As another example, a given biomarker RNA transcript may be expected to correlate with a corresponding given pathway. Therefore, identifying a presence or absence of the given biomarker RNA transcript in a biological sample may be indicative of a presence or absence of the corresponding pathway activity. As another example, a given biomarker RNA transcript may be expected to correlate with a corresponding given biomarker metabolite. Therefore, identifying a presence or absence of the given biomarker RNA transcript in a biological sample may be indicative of a presence or absence of the corresponding biomarker metabolite. In some embodiments, the set of corresponding biomarker proteins, pathways, and/or metabolites comprises pregnancy-related state-associated proteins (e.g., corresponding to pregnancy-associated genomic loci or genes), pathways, and/or metabolites. In some embodiments, the set of corresponding biomarker proteins, pathways, and/or metabolites comprises placental proteins, pathways, and/or metabolites. For example, identifying a presence or absence of the PAPPA gene may be indicative of a presence or absence of the PAPPA protein analog.

The cell-free biological samples may be processed using a metabolomics assay. For example, a metabolomics assay can be used to identify a quantitative measure (e.g., indicative of a presence, absence, or relative amount) of each of a plurality of pregnancy-related state-associated metabolites in a cell-free biological sample of the subject. The metabolomics assay may be configured to process cell-free biological samples such as a blood sample or a urine sample (or derivatives thereof) of the subject. A quantitative measure (e.g., indicative of a presence, absence, or relative amount) of pregnancy-related state-associated metabolites in the cell-free biological sample may be indicative of one or more pregnancy-related states. The metabolites in the cell-free biological sample may be produced (e.g., as an end product or a byproduct) as a result of one or more metabolic pathways corresponding to pregnancy-related state-associated genes. Assaying one or more metabolites of the cell-free biological sample may comprise isolating or extracting the metabolites from the cell-free biological sample. The metabolomics assay may be used to generate datasets indicative of the quantitative measure (e.g., indicative of a presence, absence, or relative amount) of each of a plurality of pregnancy-related state-associated metabolites in the cell-free biological sample of the subject.

The metabolomics assay may analyze a variety of metabolites in the cell-free biological sample, such as small molecules, lipids, amino acids, peptides, nucleotides, hormones and other signaling molecules, cytokines, minerals and elements, polyphenols, fatty acids, dicarboxylic acids, alcohols and polyols, alkanes and alkenes, keto acids, glycolipids, carbohydrates, hydroxy acids, purines, prostanoids, catecholamines, acyl phosphates, phospholipids, cyclic amines, amino ketones, nucleosides, glycerolipids, aromatic acids, retinoids, amino alcohols, pterins, steroids, carnitines, leukotrienes, indoles, porphyrins, sugar phosphates, coenzyme A derivatives, glucuronides, ketones, sugar phosphates, inorganic ions and gases, sphingolipids, bile acids, alcohol phosphates, amino acid phosphates, aldehydes, quinones, pyrimidines, pyridoxals, tricarboxylic acids, acyl glycines, cobalamin derivatives, lipoamides, biotin, and polyamines.

The metabolomics assay may comprise, for example, one or more of: mass spectroscopy (MS), targeted MS, gas chromatography (GC), high performance liquid chromatography (HPLC), capillary electrophoresis (CE), nuclear magnetic resonance (NMR) spectroscopy, ion-mobility spectrometry, Raman spectroscopy, electrochemical assay, or immune assay.

The cell-free biological samples may be processed using a methylation-specific assay. For example, a methylation-specific assay can be used to identify a quantitative measure (e.g., indicative of a presence, absence, or relative amount) of methylation each of a plurality of pregnancy-related state-associated genomic loci in a cell-free biological sample of the subject. The methylation-specific assay may be configured to process cell-free biological samples such as a blood sample or a urine sample (or derivatives thereof) of the subject. A quantitative measure (e.g., indicative of a presence, absence, or relative amount) of methylation of pregnancy-related state-associated genomic loci in the cell-free biological sample may be indicative of one or more pregnancy-related states. The methylation-specific assay may be used to generate datasets indicative of the quantitative measure (e.g., indicative of a presence, absence, or relative amount) of methylation of each of a plurality of pregnancy-related state-associated genomic loci in the cell-free biological sample of the subject.

The methylation-specific assay may comprise, for example, one or more of: a methylation-aware sequencing (e.g., using bisulfite treatment), pyrosequencing, methylation-sensitive single-strand conformation analysis (MS-SSCA), high-resolution melting analysis (HRM), methylation-sensitive single-nucleotide primer extension (MS-SnuPE), base-specific cleavage/MALDI-TOF, microarray-based methylation assay, methylation-specific PCR, targeted bisulfite sequencing, oxidative bisulfite sequencing, mass spectroscopy-based bisulfite sequencing, or reduced representation bisulfite sequence (RRBS).

The cell-free biological samples may be processed using a proteomics assay. For example, a proteomics assay can be used to identify a quantitative measure (e.g., indicative of a presence, absence, or relative amount) of each of a plurality of pregnancy-related state-associated proteins (e.g., corresponding to pregnancy-associated genomic loci or genes) or polypeptides in a cell-free biological sample of the subject. The proteomics assay may be configured to process cell-free biological samples such as a blood sample or a urine sample (or derivatives thereof) of the subject. A quantitative measure (e.g., indicative of a presence, absence, or relative amount) of pregnancy-related state-associated proteins (e.g., corresponding to pregnancy-associated genomic loci or genes) or polypeptides in the cell-free biological sample may be indicative of one or more pregnancy-related states. The proteins or polypeptides in the cell-free biological sample may be produced (e.g., as an end product, an intermediate product, or a byproduct) as a result of one or more biochemical pathways corresponding to pregnancy-related state-associated genes. Assaying one or more proteins or polypeptides of the cell-free biological sample may comprise isolating or extracting the proteins or polypeptides from the cell-free biological sample. The proteomics assay may be used to generate datasets indicative of the quantitative measure (e.g., indicative of a presence, absence, or relative amount) of each of a plurality of pregnancy-related state-associated proteins or polypeptides in the cell-free biological sample of the subject.

The proteomics assay may analyze a variety of proteins (e.g., pregnancy-associated proteins corresponding to pregnancy-associated genomic loci or genes) or polypeptides in the cell-free biological sample, such as proteins made under different cellular conditions (e.g., development, cellular differentiation, or cell cycle). The proteomics assay may comprise, for example, one or more of: an antibody-based immunoassay, an Edman degradation assay, a mass spectrometry-based assay (e.g., matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI)), a top-down proteomics assay, a bottom-up proteomics assay, a mass spectrometric immunoassay (MSIA), a stable isotope standard capture with anti-peptide antibodies (SISCAPA) assay, a fluorescence two-dimensional differential gel electrophoresis (2-D DIGE) assay, a quantitative proteomics assay, a protein microarray assay, or a reverse-phased protein microarray assay. The proteomics assay may detect post-translational modifications of proteins or polypeptides (e.g., phosphorylation, ubiquitination, methylation, acetylation, glycosylation, oxidation, and nitrosylation). The proteomics assay may identify or quantify one or more proteins or polypeptides from a database (e.g., Human Protein Atlas, PeptideAtlas, and UniProt).

Kits

The present disclosure provides kits for identifying or monitoring a pregnancy-related state of a subject. A kit may comprise probes for identifying a quantitative measure (e.g., indicative of a presence, absence, or relative amount) of sequences at each of a plurality of pregnancy-related state-associated genomic loci in a cell-free biological sample of the subject. A quantitative measure (e.g., indicative of a presence, absence, or relative amount) of sequences at each of a plurality of pregnancy-related state-associated genomic loci in the cell-free biological sample may be indicative of one or more pregnancy-related states. The probes may be selective for the sequences at the plurality of pregnancy-related state-associated genomic loci in the cell-free biological sample. A kit may comprise instructions for using the probes to process the cell-free biological sample to generate datasets indicative of a quantitative measure (e.g., indicative of a presence, absence, or relative amount) of sequences at each of the plurality of pregnancy-related state-associated genomic loci in a cell-free biological sample of the subject.

The probes in the kit may be selective for the sequences at the plurality of pregnancy-related state-associated genomic loci in the cell-free biological sample. The probes in the kit may be configured to selectively enrich nucleic acid (e.g., RNA or DNA) molecules corresponding to the plurality of pregnancy-related state-associated genomic loci. The probes in the kit may be nucleic acid primers. The probes in the kit may have sequence complementarity with nucleic acid sequences from one or more of the plurality of pregnancy-related state-associated genomic loci or genomic regions. The plurality of pregnancy-related state-associated genomic loci or genomic regions may comprise at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or more distinct pregnancy-related state-associated genomic loci or genomic regions. The plurality of pregnancy-related state-associated genomic loci or genomic regions may comprise one or more members selected from the group consisting of ACTB, ADAM12, ALPP, ANXA3, APLF, ARG1, AVPR1A, CAMP, CAPN6, CD180, CGA, CGB, CLCN3, CPVL, CSH1, CSH2, CSHL1, CYP3A7, DAPP1, DCX, DEFA4, DGCR14, ELANE, ENAH, EPB42, FABP1, FAM212B-AS1, FGA, FGB, FRMD4B, FRZB, FSTL3, GH2, GNAZ, HAL, HSD17B1, HSD3B1, HSPB8, Immune, ITIH2, KLF9, KNG1, KRT8, LGALS14, LTF, LYPLAL1, MAP3K7CL, MEF2C, MMD, MMP8, MOB1B, NFATC2, OTC, P2RY12, PAPPA, PGLYRP1, PKHD1L1, PKHD1L1, PLAC1, PLAC4, POLE2, PPBP, PSG1, PSG4, PSG7, PTGER3, RAB11A, RAB27B, RAP1GAP, RGS18, RPL23AP7, S100A8, S100A9, S1OOP, SERPINA7, SLC2A2, SLC38A4, SLC4A1, TBC1D15, VCAN, VGLL1, B3GNT2, COL24A1, CXCL8, and PTGS2.

The instructions in the kit may comprise instructions to assay the cell-free biological sample using the probes that are selective for the sequences at the plurality of pregnancy-related state-associated genomic loci in the cell-free biological sample. These probes may be nucleic acid molecules (e.g., RNA or DNA) having sequence complementarity with nucleic acid sequences (e.g., RNA or DNA) from one or more of the plurality of pregnancy-related state-associated genomic loci. These nucleic acid molecules may be primers or enrichment sequences. The instructions to assay the cell-free biological sample may comprise introductions to perform array hybridization, polymerase chain reaction (PCR), or nucleic acid sequencing (e.g., DNA sequencing or RNA sequencing) to process the cell-free biological sample to generate datasets indicative of a quantitative measure (e.g., indicative of a presence, absence, or relative amount) of sequences at each of the plurality of pregnancy-related state-associated genomic loci in the cell-free biological sample. A quantitative measure (e.g., indicative of a presence, absence, or relative amount) of sequences at each of a plurality of pregnancy-related state-associated genomic loci in the cell-free biological sample may be indicative of one or more pregnancy-related states.

The instructions in the kit may comprise instructions to measure and interpret assay readouts, which may be quantified at one or more of the plurality of pregnancy-related state-associated genomic loci to generate the datasets indicative of a quantitative measure (e.g., indicative of a presence, absence, or relative amount) of sequences at each of the plurality of pregnancy-related state-associated genomic loci in the cell-free biological sample. For example, quantification of array hybridization or polymerase chain reaction (PCR) corresponding to the plurality of pregnancy-related state-associated genomic loci may generate the datasets indicative of a quantitative measure (e.g., indicative of a presence, absence, or relative amount) of sequences at each of the plurality of pregnancy-related state-associated genomic loci in the cell-free biological sample. Assay readouts may comprise quantitative PCR (qPCR) values, digital PCR (dPCR) values, digital droplet PCR (ddPCR) values, fluorescence values, etc., or normalized values thereof.

A kit may comprise a metabolomics assay for identifying a quantitative measure (e.g., indicative of a presence, absence, or relative amount) of each of a plurality of pregnancy-related state-associated metabolites in a cell-free biological sample of the subject. A quantitative measure (e.g., indicative of a presence, absence, or relative amount) of pregnancy-related state-associated metabolites in the cell-free biological sample may be indicative of one or more pregnancy-related states. The metabolites in the cell-free biological sample may be produced (e.g., as an end product or a byproduct) as a result of one or more metabolic pathways corresponding to pregnancy-related state-associated genes. A kit may comprise instructions for isolating or extracting the metabolites from the cell-free biological sample and/or for using the metabolomics assay to generate datasets indicative of the quantitative measure (e.g., indicative of a presence, absence, or relative amount) of each of a plurality of pregnancy-related state-associated metabolites in the cell-free biological sample of the subject.

Trained Algorithms

After using one or more assays to process one or more cell-free biological samples derived from the subject to generate one or more datasets indicative of the pregnancy-related state or pregnancy-related complication, a trained algorithm may be used to process one or more of the datasets (e.g., at each of a plurality of pregnancy-related state-associated genomic loci) to determine the pregnancy-related state. For example, the trained algorithm may be used to determine quantitative measures of sequences at each of the plurality of pregnancy-related state-associated genomic loci in the cell-free biological samples. The trained algorithm may be configured to identify the pregnancy-related state with an accuracy of at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more than 99% for at least about 25, at least about 50, at least about 100, at least about 150, at least about 200, at least about 250, at least about 300, at least about 350, at least about 400, at least about 450, at least about 500, or more than about 500 independent samples.

The trained algorithm may comprise a supervised machine learning algorithm. The trained algorithm may comprise a classification and regression tree (CART) algorithm. The supervised machine learning algorithm may comprise, for example, a Random Forest, a support vector machine (SVM), a neural network, or a deep learning algorithm. The trained algorithm may comprise a differential expression algorithm. The differential expression algorithm may comprise a use comparison of stochastic models, generalized Poisson (GPseq), mixed Poisson (TSPM), Poisson log-linear (PoissonSeq), negative binomial (edgeR, DESeq, baySeq, NBPSeq), linear model fit by MAANOVA, or a combination thereof. The trained algorithm may comprise an unsupervised machine learning algorithm.

The trained algorithm may be configured to accept a plurality of input variables and to produce one or more output values based on the plurality of input variables. The plurality of input variables may comprise one or more datasets indicative of a pregnancy-related state. For example, an input variable may comprise a number of sequences corresponding to or aligning to each of the plurality of pregnancy-related state-associated genomic loci. The plurality of input variables may also include clinical health data of a subject.

The trained algorithm may comprise a classifier, such that each of the one or more output values comprises one of a fixed number of possible values (e.g., a linear classifier, a logistic regression classifier, etc.) indicating a classification of the cell-free biological sample by the classifier. The trained algorithm may comprise a binary classifier, such that each of the one or more output values comprises one of two values (e.g., {0, 1}, {positive, negative}, or {high-risk, low-risk}) indicating a classification of the cell-free biological sample by the classifier. The trained algorithm may be another type of classifier, such that each of the one or more output values comprises one of more than two values (e.g., {0, 1, 2}, {positive, negative, or indeterminate}, or {high-risk, intermediate-risk, or low-risk}) indicating a classification of the cell-free biological sample by the classifier. The output values may comprise descriptive labels, numerical values, or a combination thereof. Some of the output values may comprise descriptive labels. Such descriptive labels may provide an identification or indication of the disease or disorder state of the subject, and may comprise, for example, positive, negative, high-risk, intermediate-risk, low-risk, or indeterminate. Such descriptive labels may provide an identification of a treatment for the subject's pregnancy-related state, and may comprise, for example, a therapeutic intervention, a duration of the therapeutic intervention, and/or a dosage of the therapeutic intervention suitable to treat a pregnancy-related condition. Such descriptive labels may provide an identification of secondary clinical tests that may be appropriate to perform on the subject, and may comprise, for example, an imaging test, a blood test, a computed tomography (CT) scan, a magnetic resonance imaging (MRI) scan, an ultrasound scan, a chest X-ray, a positron emission tomography (PET) scan, a PET-CT scan, a cell-free biological cytology, an amniocentesis, a non-invasive prenatal test (NIPT), or any combination thereof. For example, such descriptive labels may provide a prognosis of the pregnancy-related state of the subject. As another example, such descriptive labels may provide a relative assessment of the pregnancy-related state (e.g., an estimated gestational age in number of days, weeks, or months) of the subject. Some descriptive labels may be mapped to numerical values, for example, by mapping “positive” to 1 and “negative” to 0.

Some of the output values may comprise numerical values, such as binary, integer, or continuous values. Such binary output values may comprise, for example, {0, 1},{positive, negative}, or {high-risk, low-risk}. Such integer output values may comprise, for example, {0, 1, 2}. Such continuous output values may comprise, for example, a probability value of at least 0 and no more than 1. Such continuous output values may comprise, for example, an un-normalized probability value of at least 0. Such continuous output values may indicate a prognosis of the pregnancy-related state of the subject. Some numerical values may be mapped to descriptive labels, for example, by mapping 1 to “positive” and 0 to “negative.”

Some of the output values may be assigned based on one or more cutoff values. For example, a binary classification of samples may assign an output value of “positive” or 1 if the sample indicates that the subject has at least a 50% probability of having a pregnancy-related state (e.g., pregnancy-related complication). For example, a binary classification of samples may assign an output value of “negative” or 0 if the sample indicates that the subject has less than a 50% probability of having a pregnancy-related state (e.g., pregnancy-related complication). In this case, a single cutoff value of 50% is used to classify samples into one of the two possible binary output values. Examples of single cutoff values may include about 1%, about 2%, about 5%, about 10%, about 15%, about 20%, about 25%, about 30%, about 35%, about 40%, about 45%, about 50%, about 55%, about 60%, about 65%, about 70%, about 75%, about 80%, about 85%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, and about 99%.

As another example, a classification of samples may assign an output value of “positive” or 1 if the sample indicates that the subject has a probability of having a pregnancy-related state (e.g., pregnancy-related complication) of at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more. The classification of samples may assign an output value of “positive” or 1 if the sample indicates that the subject has a probability of having a pregnancy-related state (e.g., pregnancy-related complication) of more than about 50%, more than about 55%, more than about 60%, more than about 65%, more than about 70%, more than about 75%, more than about 80%, more than about 85%, more than about 90%, more than about 91%, more than about 92%, more than about 93%, more than about 94%, more than about 95%, more than about 96%, more than about 97%, more than about 98%, or more than about 99%.

The classification of samples may assign an output value of “negative” or 0 if the sample indicates that the subject has a probability of having a pregnancy-related state (e.g., pregnancy-related complication) of less than about 50%, less than about 45%, less than about 40%, less than about 35%, less than about 30%, less than about 25%, less than about 20%, less than about 15%, less than about 10%, less than about 9%, less than about 8%, less than about 7%, less than about 6%, less than about 5%, less than about 4%, less than about 3%, less than about 2%, or less than about 1%. The classification of samples may assign an output value of “negative” or 0 if the sample indicates that the subject has a probability of having a pregnancy-related state (e.g., pregnancy-related complication) of no more than about 50%, no more than about 45%, no more than about 40%, no more than about 35%, no more than about 30%, no more than about 25%, no more than about 20%, no more than about 15%, no more than about 10%, no more than about 9%, no more than about 8%, no more than about 7%, no more than about 6%, no more than about 5%, no more than about 4%, no more than about 3%, no more than about 2%, or no more than about 1%.

The classification of samples may assign an output value of “indeterminate” or 2 if the sample is not classified as “positive”, “negative”, 1, or 0. In this case, a set of two cutoff values is used to classify samples into one of the three possible output values. Examples of sets of cutoff values may include {1%, 99%}, {2%, 98%}, {5%, 95%}, {10%, 90%}, {15%, 85%}, {20%, 80%}, {25%, 75%}, {30%, 70%}, {35%, 65%}, {40%, 60%}, and {45%, 55%}. Similarly, sets of n cutoff values may be used to classify samples into one of n+1 possible output values, where n is any positive integer.

The trained algorithm may be trained with a plurality of independent training samples. Each of the independent training samples may comprise a cell-free biological sample from a subject, associated datasets obtained by assaying the cell-free biological sample (as described elsewhere herein), and one or more known output values corresponding to the cell-free biological sample (e.g., a clinical diagnosis, prognosis, absence, or treatment efficacy of a pregnancy-related state of the subject). Independent training samples may comprise cell-free biological samples and associated datasets and outputs obtained or derived from a plurality of different subjects. Independent training samples may comprise cell-free biological samples and associated datasets and outputs obtained at a plurality of different time points from the same subject (e.g., on a regular basis such as weekly, biweekly, or monthly). Independent training samples may be associated with presence of the pregnancy-related state (e.g., training samples comprising cell-free biological samples and associated datasets and outputs obtained or derived from a plurality of subjects known to have the pregnancy-related state). Independent training samples may be associated with absence of the pregnancy-related state (e.g., training samples comprising cell-free biological samples and associated datasets and outputs obtained or derived from a plurality of subjects who are known to not have a previous diagnosis of the pregnancy-related state or who have received a negative test result for the pregnancy-related state).

The trained algorithm may be trained with at least about 5, at least about 10, at least about 15, at least about 20, at least about 25, at least about 30, at least about 35, at least about 40, at least about 45, at least about 50, at least about 100, at least about 150, at least about 200, at least about 250, at least about 300, at least about 350, at least about 400, at least about 450, or at least about 500 independent training samples. The independent training samples may comprise cell-free biological samples associated with presence of the pregnancy-related state and/or cell-free biological samples associated with absence of the pregnancy-related state. The trained algorithm may be trained with no more than about 500, no more than about 450, no more than about 400, no more than about 350, no more than about 300, no more than about 250, no more than about 200, no more than about 150, no more than about 100, or no more than about 50 independent training samples associated with presence of the pregnancy-related state. In some embodiments, the cell-free biological sample is independent of samples used to train the trained algorithm.

The trained algorithm may be trained with a first number of independent training samples associated with presence of the pregnancy-related state and a second number of independent training samples associated with absence of the pregnancy-related state. The first number of independent training samples associated with presence of the pregnancy-related state may be no more than the second number of independent training samples associated with absence of the pregnancy-related state. The first number of independent training samples associated with presence of the pregnancy-related state may be equal to the second number of independent training samples associated with absence of the pregnancy-related state. The first number of independent training samples associated with presence of the pregnancy-related state may be greater than the second number of independent training samples associated with absence of the pregnancy-related state.

The trained algorithm may be configured to identify the pregnancy-related state at an accuracy of at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more; for at least about 5, at least about 10, at least about 15, at least about 20, at least about 25, at least about 30, at least about 35, at least about 40, at least about 45, at least about 50, at least about 100, at least about 150, at least about 200, at least about 250, at least about 300, at least about 350, at least about 400, at least about 450, or at least about 500 independent training samples. The accuracy of identifying the pregnancy-related state by the trained algorithm may be calculated as the percentage of independent test samples (e.g., subjects known to have the pregnancy-related state or subjects with negative clinical test results for the pregnancy-related state) that are correctly identified or classified as having or not having the pregnancy-related state.

The trained algorithm may be configured to identify the pregnancy-related state with a positive predictive value (PPV) of at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more. The PPV of identifying the pregnancy-related state using the trained algorithm may be calculated as the percentage of cell-free biological samples identified or classified as having the pregnancy-related state that correspond to subjects that truly have the pregnancy-related state.

The trained algorithm may be configured to identify the pregnancy-related state with a negative predictive value (NPV) of at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more. The NPV of identifying the pregnancy-related state using the trained algorithm may be calculated as the percentage of cell-free biological samples identified or classified as not having the pregnancy-related state that correspond to subjects that truly do not have the pregnancy-related state.

The trained algorithm may be configured to identify the pregnancy-related state with a clinical sensitivity at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.1%, at least about 99.2%, at least about 99.3%, at least about 99.4%, at least about 99.5%, at least about 99.6%, at least about 99.7%, at least about 99.8%, at least about 99.9%, at least about 99.99%, at least about 99.999%, or more. The clinical sensitivity of identifying the pregnancy-related state using the trained algorithm may be calculated as the percentage of independent test samples associated with presence of the pregnancy-related state (e.g., subjects known to have the pregnancy-related state) that are correctly identified or classified as having the pregnancy-related state.

The trained algorithm may be configured to identify the pregnancy-related state with a clinical specificity of at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.1%, at least about 99.2%, at least about 99.3%, at least about 99.4%, at least about 99.5%, at least about 99.6%, at least about 99.7%, at least about 99.8%, at least about 99.9%, at least about 99.99%, at least about 99.999%, or more. The clinical specificity of identifying the pregnancy-related state using the trained algorithm may be calculated as the percentage of independent test samples associated with absence of the pregnancy-related state (e.g., subjects with negative clinical test results for the pregnancy-related state) that are correctly identified or classified as not having the pregnancy-related state.

The trained algorithm may be configured to identify the pregnancy-related state with an Area-Under-Curve (AUC) of at least about 0.50, at least about 0.55, at least about 0.60, at least about 0.65, at least about 0.70, at least about 0.75, at least about 0.80, at least about 0.81, at least about 0.82, at least about 0.83, at least about 0.84, at least about 0.85, at least about 0.86, at least about 0.87, at least about 0.88, at least about 0.89, at least about 0.90, at least about 0.91, at least about 0.92, at least about 0.93, at least about 0.94, at least about 0.95, at least about 0.96, at least about 0.97, at least about 0.98, at least about 0.99, or more. The AUC may be calculated as an integral of the Receiver Operator Characteristic (ROC) curve (e.g., the area under the ROC curve) associated with the trained algorithm in classifying cell-free biological samples as having or not having the pregnancy-related state.

The trained algorithm may be adjusted or tuned to improve one or more of the performance, accuracy, PPV, NPV, clinical sensitivity, clinical specificity, or AUC of identifying the pregnancy-related state. The trained algorithm may be adjusted or tuned by adjusting parameters of the trained algorithm (e.g., a set of cutoff values used to classify a cell-free biological sample as described elsewhere herein, or weights of a neural network). The trained algorithm may be adjusted or tuned continuously during the training process or after the training process has completed.

After the trained algorithm is initially trained, a subset of the inputs may be identified as most influential or most important to be included for making high-quality classifications. For example, a subset of the plurality of pregnancy-related state-associated genomic loci may be identified as most influential or most important to be included for making high-quality classifications or identifications of pregnancy-related states (or sub-types of pregnancy-related states). The plurality of pregnancy-related state-associated genomic loci or a subset thereof may be ranked based on classification metrics indicative of each genomic locus's influence or importance toward making high-quality classifications or identifications of pregnancy-related states (or sub-types of pregnancy-related states). Such metrics may be used to reduce, in some cases significantly, the number of input variables (e.g., predictor variables) that may be used to train the trained algorithm to a desired performance level (e.g., based on a desired minimum accuracy, PPV, NPV, clinical sensitivity, clinical specificity, AUC, or a combination thereof). For example, if training the trained algorithm with a plurality comprising several dozen or hundreds of input variables in the trained algorithm results in an accuracy of classification of more than 99%, then training the trained algorithm instead with only a selected subset of no more than about 5, no more than about 10, no more than about 15, no more than about 20, no more than about 25, no more than about 30, no more than about 35, no more than about 40, no more than about 45, no more than about 50, or no more than about 100 such most influential or most important input variables among the plurality can yield decreased but still acceptable accuracy of classification (e.g., at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99%). The subset may be selected by rank-ordering the entire plurality of input variables and selecting a predetermined number (e.g., no more than about 5, no more than about 10, no more than about 15, no more than about 20, no more than about 25, no more than about 30, no more than about 35, no more than about 40, no more than about 45, no more than about 50, or no more than about 100) of input variables with the best classification metrics.

Identifying or Monitoring a Pregnancy-Related State

After using a trained algorithm to process the dataset, the pregnancy-related state or pregnancy-related complication may be identified or monitored in the subject. The identification may be based at least in part on quantitative measures of sequence reads of the dataset at a panel of pregnancy-related state-associated genomic loci (e.g., quantitative measures of RNA transcripts or DNA at the pregnancy-related state-associated genomic loci), proteomic data comprising quantitative measures of proteins of the dataset at a panel of pregnancy-related state-associated proteins, and/or metabolome data comprising quantitative measures of a panel of pregnancy-related state-associated metabolites.

The pregnancy-related state may be identified in the subject at an accuracy of at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more. The accuracy of identifying the pregnancy-related state by the trained algorithm may be calculated as the percentage of independent test samples (e.g., subjects known to have the pregnancy-related state or subjects with negative clinical test results for the pregnancy-related state) that are correctly identified or classified as having or not having the pregnancy-related state.

The pregnancy-related state may be identified in the subject with a positive predictive value (PPV) of at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more. The PPV of identifying the pregnancy-related state using the trained algorithm may be calculated as the percentage of cell-free biological samples identified or classified as having the pregnancy-related state that correspond to subjects that truly have the pregnancy-related state.

The pregnancy-related state may be identified in the subject with a negative predictive value (NPV) of at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more. The NPV of identifying the pregnancy-related state using the trained algorithm may be calculated as the percentage of cell-free biological samples identified or classified as not having the pregnancy-related state that correspond to subjects that truly do not have the pregnancy-related state.

The pregnancy-related state may be identified in the subject with a clinical sensitivity of at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.1%, at least about 99.2%, at least about 99.3%, at least about 99.4%, at least about 99.5%, at least about 99.6%, at least about 99.7%, at least about 99.8%, at least about 99.9%, at least about 99.99%, at least about 99.999%, or more. The clinical sensitivity of identifying the pregnancy-related state using the trained algorithm may be calculated as the percentage of independent test samples associated with presence of the pregnancy-related state (e.g., subjects known to have the pregnancy-related state) that are correctly identified or classified as having the pregnancy-related state.

The pregnancy-related state may be identified in the subject with a clinical specificity of at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.1%, at least about 99.2%, at least about 99.3%, at least about 99.4%, at least about 99.5%, at least about 99.6%, at least about 99.7%, at least about 99.8%, at least about 99.9%, at least about 99.99%, at least about 99.999%, or more. The clinical specificity of identifying the pregnancy-related state using the trained algorithm may be calculated as the percentage of independent test samples associated with absence of the pregnancy-related state (e.g., subjects with negative clinical test results for the pregnancy-related state) that are correctly identified or classified as not having the pregnancy-related state.

In an aspect, the present disclosure provides a method for determining that a subject is at risk of pre-term birth, comprising assaying a cell-free biological sample derived from the subject to generate a dataset that is indicative of said pre-term birth risk at a specificity of at least 80%, and using a trained algorithm that is trained on samples independent of the cell-free biological sample to determine that the subject is at risk of pre-term birth at an accuracy of at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more.

After the pregnancy-related state is identified in a subject, a sub-type of the pregnancy-related state (e.g., selected from among a plurality of sub-types of the pregnancy-related state) may further be identified. The sub-type of the pregnancy-related state may be determined based at least in part on the quantitative measures of sequence reads of the dataset at a panel of pregnancy-related state-associated genomic loci (e.g., quantitative measures of RNA transcripts or DNA at the pregnancy-related state-associated genomic loci), proteomic data comprising quantitative measures of proteins of the dataset at a panel of pregnancy-related state-associated proteins, and/or metabolome data comprising quantitative measures of a panel of pregnancy-related state-associated metabolites. For example, the subject may be identified as being at risk of a sub-type of pre-term birth (e.g., selected from among a plurality of sub-types of pre-term birth). After identifying the subject as being at risk of a sub-type of pre-term birth, a clinical intervention for the subject may be selected based at least in part on the sub-type of pre-term birth for which the subject is identified as being at risk. In some embodiments, the clinical intervention is selected from a plurality of clinical interventions (e.g., clinically indicated for different sub-types of pre-term birth).

In some embodiments, the trained algorithm may determine that the subject is at risk of pre-term birth of at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more.

The trained algorithm may determine that the subject is at risk of pre-term birth at an accuracy of at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.1%, at least about 99.2%, at least about 99.3%, at least about 99.4%, at least about 99.5%, at least about 99.6%, at least about 99.7%, at least about 99.8%, at least about 99.9%, at least about 99.99%, at least about 99.999%, or more.

Upon identifying the subject as having the pregnancy-related state, the subject may be optionally provided with a therapeutic intervention (e.g., prescribing an appropriate course of treatment to treat the pregnancy-related state of the subject). The therapeutic intervention may comprise a prescription of an effective dose of a drug, a further testing or evaluation of the pregnancy-related state, a further monitoring of the pregnancy-related state, an induction or inhibition of labor, or a combination thereof. If the subject is currently being treated for the pregnancy-related state with a course of treatment, the therapeutic intervention may comprise a subsequent different course of treatment (e.g., to increase treatment efficacy due to non-efficacy of the current course of treatment).

The therapeutic intervention may comprise recommending the subject for a secondary clinical test to confirm a diagnosis of the pregnancy-related state. This secondary clinical test may comprise an imaging test, a blood test, a computed tomography (CT) scan, a magnetic resonance imaging (MRI) scan, an ultrasound scan, a chest X-ray, a positron emission tomography (PET) scan, a PET-CT scan, a cell-free biological cytology, an amniocentesis, a non-invasive prenatal test (NIPT), or any combination thereof.

The quantitative measures of sequence reads of the dataset at the panel of pregnancy-related state-associated genomic loci (e.g., quantitative measures of RNA transcripts or DNA at the pregnancy-related state-associated genomic loci), proteomic data comprising quantitative measures of proteins of the dataset at a panel of pregnancy-related state-associated proteins, and/or metabolome data comprising quantitative measures of a panel of pregnancy-related state-associated metabolites may be assessed over a duration of time to monitor a patient (e.g., subject who has pregnancy-related state or who is being treated for pregnancy-related state). In such cases, the quantitative measures of the dataset of the patient may change during the course of treatment. For example, the quantitative measures of the dataset of a patient with decreasing risk of the pregnancy-related state due to an effective treatment may shift toward the profile or distribution of a healthy subject (e.g., a subject without a pregnancy-related complication). Conversely, for example, the quantitative measures of the dataset of a patient with increasing risk of the pregnancy-related state due to an ineffective treatment may shift toward the profile or distribution of a subject with higher risk of the pregnancy-related state or a more advanced pregnancy-related state.

The pregnancy-related state of the subject may be monitored by monitoring a course of treatment for treating the pregnancy-related state of the subject. The monitoring may comprise assessing the pregnancy-related state of the subject at two or more time points. The assessing may be based at least on the quantitative measures of sequence reads of the dataset at a panel of pregnancy-related state-associated genomic loci (e.g., quantitative measures of RNA transcripts or DNA at the pregnancy-related state-associated genomic loci), proteomic data comprising quantitative measures of proteins of the dataset at a panel of pregnancy-related state-associated proteins, and/or metabolome data comprising quantitative measures of a panel of pregnancy-related state-associated metabolites determined at each of the two or more time points.

In some embodiments, a difference in the quantitative measures of sequence reads of the dataset at a panel of pregnancy-related state-associated genomic loci (e.g., quantitative measures of RNA transcripts or DNA at the pregnancy-related state-associated genomic loci), proteomic data comprising quantitative measures of proteins of the dataset at a panel of pregnancy-related state-associated proteins, and/or metabolome data comprising quantitative measures of a panel of pregnancy-related state-associated metabolites determined between the two or more time points may be indicative of one or more clinical indications, such as (i) a diagnosis of the pregnancy-related state of the subject, (ii) a prognosis of the pregnancy-related state of the subject, (iii) an increased risk of the pregnancy-related state of the subject, (iv) a decreased risk of the pregnancy-related state of the subject, (v) an efficacy of the course of treatment for treating the pregnancy-related state of the subject, and (vi) a non-efficacy of the course of treatment for treating the pregnancy-related state of the subject.

In some embodiments, a difference in the quantitative measures of sequence reads of the dataset at a panel of pregnancy-related state-associated genomic loci (e.g., quantitative measures of RNA transcripts or DNA at the pregnancy-related state-associated genomic loci), proteomic data comprising quantitative measures of proteins of the dataset at a panel of pregnancy-related state-associated proteins, and/or metabolome data comprising quantitative measures of a panel of pregnancy-related state-associated metabolites determined between the two or more time points may be indicative of a diagnosis of the pregnancy-related state of the subject. For example, if the pregnancy-related state was not detected in the subject at an earlier time point but was detected in the subject at a later time point, then the difference is indicative of a diagnosis of the pregnancy-related state of the subject. A clinical action or decision may be made based on this indication of diagnosis of the pregnancy-related state of the subject, such as, for example, prescribing a new therapeutic intervention for the subject. The clinical action or decision may comprise recommending the subject for a secondary clinical test to confirm the diagnosis of the pregnancy-related state. This secondary clinical test may comprise an imaging test, a blood test, a computed tomography (CT) scan, a magnetic resonance imaging (MRI) scan, an ultrasound scan, a chest X-ray, a positron emission tomography (PET) scan, a PET-CT scan, a cell-free biological cytology, an amniocentesis, a non-invasive prenatal test (NIPT), or any combination thereof.

In some embodiments, a difference in the quantitative measures of sequence reads of the dataset at a panel of pregnancy-related state-associated genomic loci (e.g., quantitative measures of RNA transcripts or DNA at the pregnancy-related state-associated genomic loci), proteomic data comprising quantitative measures of proteins of the dataset at a panel of pregnancy-related state-associated proteins, and/or metabolome data comprising quantitative measures of a panel of pregnancy-related state-associated metabolites determined between the two or more time points may be indicative of a prognosis of the pregnancy-related state of the subject.

In some embodiments, a difference in the quantitative measures of sequence reads of the dataset at a panel of pregnancy-related state-associated genomic loci (e.g., quantitative measures of RNA transcripts or DNA at the pregnancy-related state-associated genomic loci), proteomic data comprising quantitative measures of proteins of the dataset at a panel of pregnancy-related state-associated proteins, and/or metabolome data comprising quantitative measures of a panel of pregnancy-related state-associated metabolites determined between the two or more time points may be indicative of the subject having an increased risk of the pregnancy-related state. For example, if the pregnancy-related state was detected in the subject both at an earlier time point and at a later time point, and if the difference is a negative difference (e.g., the quantitative measures of sequence reads of the dataset at a panel of pregnancy-related state-associated genomic loci (e.g., quantitative measures of RNA transcripts or DNA at the pregnancy-related state-associated genomic loci), proteomic data comprising quantitative measures of proteins of the dataset at a panel of pregnancy-related state-associated proteins, and/or metabolome data comprising quantitative measures of a panel of pregnancy-related state-associated metabolites increased from the earlier time point to the later time point), then the difference may be indicative of the subject having an increased risk of the pregnancy-related state. A clinical action or decision may be made based on this indication of the increased risk of the pregnancy-related state, e.g., prescribing a new therapeutic intervention or switching therapeutic interventions (e.g., ending a current treatment and prescribing a new treatment) for the subject. The clinical action or decision may comprise recommending the subject for a secondary clinical test to confirm the increased risk of the pregnancy-related state. This secondary clinical test may comprise an imaging test, a blood test, a computed tomography (CT) scan, a magnetic resonance imaging (MRI) scan, an ultrasound scan, a chest X-ray, a positron emission tomography (PET) scan, a PET-CT scan, a cell-free biological cytology, an amniocentesis, a non-invasive prenatal test (NIPT), or any combination thereof.

In some embodiments, a difference in the quantitative measures of sequence reads of the dataset at a panel of pregnancy-related state-associated genomic loci (e.g., quantitative measures of RNA transcripts or DNA at the pregnancy-related state-associated genomic loci), proteomic data comprising quantitative measures of proteins of the dataset at a panel of pregnancy-related state-associated proteins, and/or metabolome data comprising quantitative measures of a panel of pregnancy-related state-associated metabolites determined between the two or more time points may be indicative of the subject having a decreased risk of the pregnancy-related state. For example, if the pregnancy-related state was detected in the subject both at an earlier time point and at a later time point, and if the difference is a positive difference (e.g., the quantitative measures of sequence reads of the dataset at a panel of pregnancy-related state-associated genomic loci (e.g., quantitative measures of RNA transcripts or DNA at the pregnancy-related state-associated genomic loci), proteomic data comprising quantitative measures of proteins of the dataset at a panel of pregnancy-related state-associated proteins, and/or metabolome data comprising quantitative measures of a panel of pregnancy-related state-associated metabolites decreased from the earlier time point to the later time point), then the difference may be indicative of the subject having a decreased risk of the pregnancy-related state. A clinical action or decision may be made based on this indication of the decreased risk of the pregnancy-related state (e.g., continuing or ending a current therapeutic intervention) for the subject. The clinical action or decision may comprise recommending the subject for a secondary clinical test to confirm the decreased risk of the pregnancy-related state. This secondary clinical test may comprise an imaging test, a blood test, a computed tomography (CT) scan, a magnetic resonance imaging (MRI) scan, an ultrasound scan, a chest X-ray, a positron emission tomography (PET) scan, a PET-CT scan, a cell-free biological cytology, an amniocentesis, a non-invasive prenatal test (NIPT), or any combination thereof.

In some embodiments, a difference in the quantitative measures of sequence reads of the dataset at a panel of pregnancy-related state-associated genomic loci (e.g., quantitative measures of RNA transcripts or DNA at the pregnancy-related state-associated genomic loci), proteomic data comprising quantitative measures of proteins of the dataset at a panel of pregnancy-related state-associated proteins, and/or metabolome data comprising quantitative measures of a panel of pregnancy-related state-associated metabolites determined between the two or more time points may be indicative of an efficacy of the course of treatment for treating the pregnancy-related state of the subject. For example, if the pregnancy-related state was detected in the subject at an earlier time point but was not detected in the subject at a later time point, then the difference may be indicative of an efficacy of the course of treatment for treating the pregnancy-related state of the subject. A clinical action or decision may be made based on this indication of the efficacy of the course of treatment for treating the pregnancy-related state of the subject, e.g., continuing or ending a current therapeutic intervention for the subject. The clinical action or decision may comprise recommending the subject for a secondary clinical test to confirm the efficacy of the course of treatment for treating the pregnancy-related state. This secondary clinical test may comprise an imaging test, a blood test, a computed tomography (CT) scan, a magnetic resonance imaging (MRI) scan, an ultrasound scan, a chest X-ray, a positron emission tomography (PET) scan, a PET-CT scan, a cell-free biological cytology, an amniocentesis, a non-invasive prenatal test (NIPT), or any combination thereof.

In some embodiments, a difference in the quantitative measures of sequence reads of the dataset at a panel of pregnancy-related state-associated genomic loci (e.g., quantitative measures of RNA transcripts or DNA at the pregnancy-related state-associated genomic loci), proteomic data comprising quantitative measures of proteins of the dataset at a panel of pregnancy-related state-associated proteins, and/or metabolome data comprising quantitative measures of a panel of pregnancy-related state-associated metabolites determined between the two or more time points may be indicative of a non-efficacy of the course of treatment for treating the pregnancy-related state of the subject. For example, if the pregnancy-related state was detected in the subject both at an earlier time point and at a later time point, and if the difference is a negative or zero difference (e.g., the quantitative measures of sequence reads of the dataset at a panel of pregnancy-related state-associated genomic loci (e.g., quantitative measures of RNA transcripts or DNA at the pregnancy-related state-associated genomic loci), proteomic data comprising quantitative measures of proteins of the dataset at a panel of pregnancy-related state-associated proteins, and/or metabolome data comprising quantitative measures of a panel of pregnancy-related state-associated metabolites increased or remained at a constant level from the earlier time point to the later time point), and if an efficacious treatment was indicated at an earlier time point, then the difference may be indicative of a non-efficacy of the course of treatment for treating the pregnancy-related state of the subject. A clinical action or decision may be made based on this indication of the non-efficacy of the course of treatment for treating the pregnancy-related state of the subject, e.g., ending a current therapeutic intervention and/or switching to (e.g., prescribing) a different new therapeutic intervention for the subject. The clinical action or decision may comprise recommending the subject for a secondary clinical test to confirm the non-efficacy of the course of treatment for treating the pregnancy-related state. This secondary clinical test may comprise an imaging test, a blood test, a computed tomography (CT) scan, a magnetic resonance imaging (MRI) scan, an ultrasound scan, a chest X-ray, a positron emission tomography (PET) scan, a PET-CT scan, a cell-free biological cytology, an amniocentesis, a non-invasive prenatal test (NIPT), or any combination thereof.

In another aspect, the present disclosure provides a computer-implemented method for predicting a risk of pre-term birth of a subject, comprising: (a) receiving clinical health data of the subject, wherein the clinical health data comprises a plurality of quantitative or categorical measures of said subject; (b) using a trained algorithm to process the clinical health data of the subject to determine a risk score indicative of the risk of pre-term birth of the subject; and (c) electronically outputting a report indicative of the risk score indicative of the risk of pre-term birth of the subject.

In some embodiments, for example, the clinical health data comprises one or more quantitative measures of the subject, such as age, weight, height, body mass index (BMI), blood pressure, heart rate, glucose levels, number of previous pregnancies, and number of previous births. As another example, the clinical health data can comprise one or more categorical measures, such as race, ethnicity, history of medication or other clinical treatment, history of tobacco use, history of alcohol consumption, daily activity or fitness level, genetic test results, blood test results, imaging results, and fetal screening results.

In some embodiments, the computer-implemented method for predicting a risk of pre-term birth of a subject is performed using a computer or mobile device application. For example, a subject can use a computer or mobile device application to input her own clinical health data, including quantitative and/or categorical measures. The computer or mobile device application can then use a trained algorithm to process the clinical health data to determine a risk score indicative of the risk of pre-term birth of the subject. The computer or mobile device application can then display a report indicative of the risk score indicative of the risk of pre-term birth of the subject.

In some embodiments, the risk score indicative of the risk of pre-term birth of the subject can be refined by performing one or more subsequent clinical tests for the subject. For example, the subject can be referred by a physician for one or more subsequent clinical tests (e.g., an ultrasound imaging or a blood test) based on the initial risk score. Next, the computer or mobile device application may process results from the one or more subsequent clinical tests using a trained algorithm to determine an updated risk score indicative of the risk of pre-term birth of the subject.

In some embodiments, the risk score comprises a likelihood of the subject having a pre-term birth within a pre-determined duration of time. For example, the pre-determined duration of time may be about 1 hour, about 2 hours, about 4 hours, about 6 hours, about 8 hours, about 10 hours, about 12 hours, about 14 hours, about 16 hours, about 18 hours, about 20 hours, about 22 hours, about 24 hours, about 1.5 days, about 2 days, about 2.5 days, about 3 days, about 3.5 days, about 4 days, about 4.5 days, about 5 days, about 5.5 days, about 6 days, about 6.5 days, about 7 days, about 8 days, about 9 days, about 10 days, about 12 days, about 14 days, about 3 weeks, about 4 weeks, about 5 weeks, about 6 weeks, about 7 weeks, about 8 weeks, about 9 weeks, about 10 weeks, about 11 weeks, about 12 weeks, about 13 weeks, or more than about 13 weeks.

Outputting a Report of the Pregnancy-Related State

After the pregnancy-related state is identified or an increased risk of the pregnancy-related state is monitored in the subject, a report may be electronically outputted that is indicative of (e.g., identifies or provides an indication of) the pregnancy-related state of the subject. The subject may not display a pregnancy-related state (e.g., is asymptomatic of the pregnancy-related state such as a pregnancy-related complication). The report may be presented on a graphical user interface (GUI) of an electronic device of a user. The user may be the subject, a caretaker, a physician, a nurse, or another health care worker.

The report may include one or more clinical indications such as (i) a diagnosis of the pregnancy-related state of the subject, (ii) a prognosis of the pregnancy-related state of the subject, (iii) an increased risk of the pregnancy-related state of the subject, (iv) a decreased risk of the pregnancy-related state of the subject, (v) an efficacy of the course of treatment for treating the pregnancy-related state of the subject, and (vi) a non-efficacy of the course of treatment for treating the pregnancy-related state of the subject. The report may include one or more clinical actions or decisions made based on these one or more clinical indications. Such clinical actions or decisions may be directed to therapeutic interventions, induction or inhibition of labor, or further clinical assessment or testing of the pregnancy-related state of the subject.

For example, a clinical indication of a diagnosis of the pregnancy-related state of the subject may be accompanied with a clinical action of prescribing a new therapeutic intervention for the subject. As another example, a clinical indication of an increased risk of the pregnancy-related state of the subject may be accompanied with a clinical action of prescribing a new therapeutic intervention or switching therapeutic interventions (e.g., ending a current treatment and prescribing a new treatment) for the subject. As another example, a clinical indication of a decreased risk of the pregnancy-related state of the subject may be accompanied with a clinical action of continuing or ending a current therapeutic intervention for the subject. As another example, a clinical indication of an efficacy of the course of treatment for treating the pregnancy-related state of the subject may be accompanied with a clinical action of continuing or ending a current therapeutic intervention for the subject. As another example, a clinical indication of a non-efficacy of the course of treatment for treating the pregnancy-related state of the subject may be accompanied with a clinical action of ending a current therapeutic intervention and/or switching to (e.g., prescribing) a different new therapeutic intervention for the subject.

Computer Systems

The present disclosure provides computer systems that are programmed to implement methods of the disclosure. FIG. 2 shows a computer system 201 that is programmed or otherwise configured to, for example, (i) train and test a trained algorithm, (ii) use the trained algorithm to process data to determine a pregnancy-related state of a subject, (iii) determine a quantitative measure indicative of a pregnancy-related state of a subject, (iv) identify or monitor the pregnancy-related state of the subject, and (v) electronically output a report that indicative of the pregnancy-related state of the subject.

The computer system 201 can regulate various aspects of analysis, calculation, and generation of the present disclosure, such as, for example, (i) training and testing a trained algorithm, (ii) using the trained algorithm to process data to determine a pregnancy-related state of a subject, (iii) determining a quantitative measure indicative of a pregnancy-related state of a subject, (iv) identifying or monitoring the pregnancy-related state of the subject, and (v) electronically outputting a report that indicative of the pregnancy-related state of the subject. The computer system 201 can be an electronic device of a user or a computer system that is remotely located with respect to the electronic device. The electronic device can be a mobile electronic device.

The computer system 201 includes a central processing unit (CPU, also “processor” and “computer processor” herein) 205, which can be a single core or multi core processor, or a plurality of processors for parallel processing. The computer system 201 also includes memory or memory location 210 (e.g., random-access memory, read-only memory, flash memory), electronic storage unit 215 (e.g., hard disk), communication interface 220 (e.g., network adapter) for communicating with one or more other systems, and peripheral devices 225, such as cache, other memory, data storage and/or electronic display adapters. The memory 210, storage unit 215, interface 220 and peripheral devices 225 are in communication with the CPU 205 through a communication bus (solid lines), such as a motherboard. The storage unit 215 can be a data storage unit (or data repository) for storing data. The computer system 201 can be operatively coupled to a computer network (“network”) 230 with the aid of the communication interface 220. The network 230 can be the Internet, an internet and/or extranet, or an intranet and/or extranet that is in communication with the Internet.

The network 230 in some cases is a telecommunication and/or data network. The network 230 can include one or more computer servers, which can enable distributed computing, such as cloud computing. For example, one or more computer servers may enable cloud computing over the network 230 (“the cloud”) to perform various aspects of analysis, calculation, and generation of the present disclosure, such as, for example, (i) training and testing a trained algorithm, (ii) using the trained algorithm to process data to determine a pregnancy-related state of a subject, (iii) determining a quantitative measure indicative of a pregnancy-related state of a subject, (iv) identifying or monitoring the pregnancy-related state of the subject, and (v) electronically outputting a report that indicative of the pregnancy-related state of the subject. Such cloud computing may be provided by cloud computing platforms such as, for example, Amazon Web Services (AWS), Microsoft Azure, Google Cloud Platform, and IBM cloud. The network 230, in some cases with the aid of the computer system 201, can implement a peer-to-peer network, which may enable devices coupled to the computer system 201 to behave as a client or a server.

The CPU 205 may comprise one or more computer processors and/or one or more graphics processing units (GPUs). The CPU 205 can execute a sequence of machine-readable instructions, which can be embodied in a program or software. The instructions may be stored in a memory location, such as the memory 210. The instructions can be directed to the CPU 205, which can subsequently program or otherwise configure the CPU 205 to implement methods of the present disclosure. Examples of operations performed by the CPU 205 can include fetch, decode, execute, and writeback.

The CPU 205 can be part of a circuit, such as an integrated circuit. One or more other components of the system 201 can be included in the circuit. In some cases, the circuit is an application specific integrated circuit (ASIC).

The storage unit 215 can store files, such as drivers, libraries and saved programs. The storage unit 215 can store user data, e.g., user preferences and user programs. The computer system 201 in some cases can include one or more additional data storage units that are external to the computer system 201, such as located on a remote server that is in communication with the computer system 201 through an intranet or the Internet.

The computer system 201 can communicate with one or more remote computer systems through the network 230. For instance, the computer system 201 can communicate with a remote computer system of a user. Examples of remote computer systems include personal computers (e.g., portable PC), slate or tablet PC's (e.g., Apple® iPad, Samsung® Galaxy Tab), telephones, Smart phones (e.g., Apple® iPhone, Android-enabled device, Blackberry®), or personal digital assistants. The user can access the computer system 201 via the network 230.

Methods as described herein can be implemented by way of machine (e.g., computer processor) executable code stored on an electronic storage location of the computer system 201, such as, for example, on the memory 210 or electronic storage unit 215. The machine executable or machine readable code can be provided in the form of software. During use, the code can be executed by the processor 205. In some cases, the code can be retrieved from the storage unit 215 and stored on the memory 210 for ready access by the processor 205. In some situations, the electronic storage unit 215 can be precluded, and machine-executable instructions are stored on memory 210.

The code can be pre-compiled and configured for use with a machine having a processer adapted to execute the code, or can be compiled during runtime. The code can be supplied in a programming language that can be selected to enable the code to execute in a pre-compiled or as-compiled fashion.

Aspects of the systems and methods provided herein, such as the computer system 201, can be embodied in programming. Various aspects of the technology may be thought of as “products” or “articles of manufacture” typically in the form of machine (or processor) executable code and/or associated data that is carried on or embodied in a type of machine readable medium. Machine-executable code can be stored on an electronic storage unit, such as memory (e.g., read-only memory, random-access memory, flash memory) or a hard disk. “Storage” type media can include any or all of the tangible memory of the computers, processors or the like, or associated modules thereof, such as various semiconductor memories, tape drives, disk drives and the like, which may provide non-transitory storage at any time for the software programming. All or portions of the software may at times be communicated through the Internet or various other telecommunication networks. Such communications, for example, may enable loading of the software from one computer or processor into another, for example, from a management server or host computer into the computer platform of an application server. Thus, another type of media that may bear the software elements includes optical, electrical and electromagnetic waves, such as used across physical interfaces between local devices, through wired and optical landline networks and over various air-links. The physical elements that carry such waves, such as wired or wireless links, optical links or the like, also may be considered as media bearing the software. As used herein, unless restricted to non-transitory, tangible “storage” media, terms such as computer or machine “readable medium” refer to any medium that participates in providing instructions to a processor for execution.

Hence, a machine readable medium, such as computer-executable code, may take many forms, including but not limited to, a tangible storage medium, a carrier wave medium or physical transmission medium. Non-volatile storage media include, for example, optical or magnetic disks, such as any of the storage devices in any computer(s) or the like, such as may be used to implement the databases, etc. shown in the drawings. Volatile storage media include dynamic memory, such as main memory of such a computer platform. Tangible transmission media include coaxial cables; copper wire and fiber optics, including the wires that comprise a bus within a computer system. Carrier-wave transmission media may take the form of electric or electromagnetic signals, or acoustic or light waves such as those generated during radio frequency (RF) and infrared (IR) data communications. Common forms of computer-readable media therefore include for example: a floppy disk, a flexible disk, hard disk, magnetic tape, any other magnetic medium, a CD-ROM, DVD or DVD-ROM, any other optical medium, punch cards paper tape, any other physical storage medium with patterns of holes, a RAM, a ROM, a PROM and EPROM, a FLASH-EPROM, any other memory chip or cartridge, a carrier wave transporting data or instructions, cables or links transporting such a carrier wave, or any other medium from which a computer may read programming code and/or data. Many of these forms of computer readable media may be involved in carrying one or more sequences of one or more instructions to a processor for execution.

The computer system 201 can include or be in communication with an electronic display 235 that comprises a user interface (UI) 240 for providing, for example, (i) a visual display indicative of training and testing of a trained algorithm, (ii) a visual display of data indicative of a pregnancy-related state of a subject, (iii) a quantitative measure of a pregnancy-related state of a subject, (iv) an identification of a subject as having a pregnancy-related state, or (v) an electronic report indicative of the pregnancy-related state of the subject. Examples of UIs include, without limitation, a graphical user interface (GUI) and web-based user interface.

Methods and systems of the present disclosure can be implemented by way of one or more algorithms. An algorithm can be implemented by way of software upon execution by the central processing unit 205. The algorithm can, for example, (i) train and test a trained algorithm, (ii) use the trained algorithm to process data to determine a pregnancy-related state of a subject, (iii) determine a quantitative measure indicative of a pregnancy-related state of a subject, (iv) identify or monitor the pregnancy-related state of the subject, and (v) electronically output a report that indicative of the pregnancy-related state of the subject.

EXAMPLES

Example 1: Cohorts of Subjects

As shown in FIG. 3A, a first cohort of subjects (e.g., pregnant women) was established (with patient identification numbers shown on the x-axis), from which one or more biological samples (e.g., 2 or 3 each) were collected and assayed at different time points corresponding to an estimated gestational age (shown on the y-axis, in increasing order of estimated gestational age at delivery) of a fetus of each subject, using methods and systems of the present disclosure. For example, the estimated gestational age (shown on the y-axis) may be determined using methods such as ultrasound imaging, a last menstrual period (LMP) date, or a combination thereof, and may range from 0 to about 42 weeks. The first cohort includes subjects from whom different sample types were collected for use in different studies, including studies for the prediction of delivery, prediction of due date, and prediction of actual gestational age of a fetus of each subject. FIG. 3B shows a distribution of participants in the first cohort based on each participant's age at the time of medical record abstraction. FIG. 3C shows a distribution of 100 participants in the first cohort based on each participant's race. FIG. 3D shows a distribution of collected samples in the gestational age cohort based on each participant's estimated gestational age and trimester at the time of collection of each sample. FIG. 3E shows a distribution of 225 collected samples in the first cohort based on the study sample type of the collected samples.

As shown in FIG. 4A, a second cohort of subjects (e.g., pregnant women) was established (with patient identification numbers shown on the x-axis), from which one or more biological samples (e.g., 1, 2, or 3 each) were collected and assayed at different time points corresponding to an estimated gestational age (shown on the y-axis, in increasing order of estimated gestational age at delivery) of a fetus of each subject, using methods and systems of the present disclosure. For example, the estimated gestational age (shown on the y-axis) may be determined using methods such as ultrasound imaging, a last menstrual period (LMP) date, or a combination thereof, and may range from 0 to about 42 weeks. The second cohort includes subjects from whom different sample types were collected for use in different studies, including studies for the prediction of pre-term birth, prediction of delivery, prediction of due date, and prediction of actual gestational age of a fetus of each subject. FIG. 4B shows a distribution of participants in the second cohort based on each participant's age at the time of medical record abstraction. FIG. 4C shows a distribution of 128 participants in the second cohort based on each participant's race. FIG. 4D shows a distribution of collected samples in the second cohort based on each participant's estimated gestational age and trimester at the time of collection of each sample. FIG. 4E shows a distribution of 160 collected samples in the second cohort based on the study sample type of the collected samples.

Example 2: Prediction of Due Date

As shown in FIG. 5A, a due date cohort of subjects (e.g., pregnant women) was established (with patient identification numbers shown on the x-axis), from which one or more biological samples (e.g., 1 or 2 each) were collected and assayed at different time points corresponding to an estimated gestational age (shown on the y-axis, in increasing order of estimated gestational age at delivery) of a fetus of each subject, using methods and systems of the present disclosure. The due date cohort included subjects from the first cohort and second cohort, as described in Example 1. The due date cohort includes subjects from whom different sample types were collected for use in different studies, including studies for the prediction of pre-term birth (e.g., as controls), prediction of delivery, prediction of due date, and prediction of actual gestational age of a fetus of each subject.

FIG. 5B shows a distribution of collected samples in the due date cohort based on the time between the date of sample collection and the date of delivery (time to delivery). All samples were collected in the third trimester of pregnancy, less than 12 weeks before the date of delivery, of which 59 samples had a time-to-delivery of less than 7.5 weeks and 43 samples had a time-to-delivery of less than 5 weeks. Using systems and methods of the present disclosure, a first set of predictive models was generated from the 59 samples with a time-to-delivery of less than 7.5 weeks, and a second set of predictive models was generated from the 43 samples with a time-to-delivery of less than 5 weeks. The sets of predictive models included a predictive model generated with estimated due date information (e.g., determined using estimated gestational age from ultrasound measurements) and without the estimated due date information. Each of the predictive models comprised a linear regression model with elastic net regularization. The generation of the predictive models included identifying four sets of genes which had the highest correlation with (e.g., were most predictive of) due date (e.g., as measured by time to delivery) among the respective cohorts, including (1) less than 7.5 weeks time-to-delivery with estimated due date information, (2) less than 7.5 weeks time-to-delivery without estimated due date information, (3) less than 5 weeks time-to-delivery with estimated due date information, and (4) less than 5 weeks time-to-delivery without estimated due date information. These four sets of genes that are predictive for due date are listed in Table 1.

TABLE 1
Sets of Genes Predictive for Due Date by Cohort
	Predictive Genes Included	Predictive Genes Not Included
Cohort	in Predictive Model	in Predictive Model
<7.5 weeks time-to-delivery	ACKR2, AKAP3, ANO5,	ADAMTS10, ADCY6,
with estimated due date info	C1orf21, C2orf42, CARNS1,	ATP9A, CCDC173,
	CASC15, CCDC102B,	CLIC4P1, CXorf65,
	CDC45, CDIPT, CMTM1,	KBTBD11, MKRN4P,
	collectionga, COPS8, CTD-	MKRN9P, NEXN-AS1,
	2267D19.3, CTD-2349P21.9,	SMG1P2, ST13P3, XXbac-
	DDX11L1, DGUOK,	BPG252P9.9, ZNF114
	DPAGT1, EIF4A1P2,
	FANK1, FERMT1, FKRP,
	GAMT, GOLGA6L4, KLLN,
	LINC01347, LTA, MAPK12,
	METRN, MPC2, MYL12BP1,
	NME4, NPM1P30, PCLO,
	PIF1, PTP4A3, RIMKLB,
	RP13-88F20.1, S100B,
	SIGLEC14, SLAIN1,
	SPATA33, STAT1, TFAP2C,
	TMEM94, TMSB4XP8,
	TRGV10, ZNF124, ZNF713
<7.5 weeks time-to-delivery	ACKR2, AKAP3, ANO5,	ADAMTS10, ADCY6,
without estimated due date	C1orf21, C2orf42, CARNS1,	ATP9A, CCDC173,
info	CASC15, CCDC102B,	CLIC4P1, KBTBD11,
	CDC45, CDIPT, CMTM1,	MKRN9P, NEXN-AS1,
	COPS8, CTD-2267D19.3,	SMG1P2, ST13P3, STAT1,
	CTD-2349P21.9, CXorf65,	TMEM94, XXbac-
	DDX11L1, DGUOK,	BPG252P9.9, ZNF114,
	DPAGT1, EIF4A1P2,	ZNF713
	FANK1, FERMT1, FKRP,
	GAMT, GOLGA6L4, KLLN,
	LINC01347, LTA, MAPK12,
	METRN, MKRN4P, MPC2,
	MYL12BP1, NME4,
	NPM1P30, PCLO, PIF1,
	PTP4A3, RIMKLB, RP13-
	88F20.1, S100B, SIGLEC14,
	SLAIN1, SPATA33,
	TFAP2C, TMSB4XP8,
	TRGV10, ZNF124
<5 weeks time-to-delivery	ATP6V1E1P1, ATP8A2,	AB019441.29, AC004076.9,
with estimated due date info	C2orf68, CACNB3, CD40,	ACKR2, ADAMTS10, ADM,
	CDKL4, CDKL5, CEP152,	AP5B1, APOE, AQP9,
	CLEC4D, COL18A1,	ARHGEF40, BCL3, CA4,
	collectionga, COX16, CTBS,	CCDC84, CCR3, CD177,
	CTD-2272G21.2, CXCL2,	CDPF1, CFAP46, CHST7,
	CXCL8, DHRS7B, DPPA4,	CLYBL, CMTM1, CRADD,
	EIF5A2, FERMT1, GNB1L,	CSF3R, CXCL1, DAPK2,
	IFITM3, KATNAL1, LRCH4,	DLEC1, DPAGT1, ECHDC2,
	MBD6, MIR24-2, MTSS1,	ERP27, FCGR3B, FKRP,
	MYSM1, NCK1-AS1,	FUT7, GZMM, HAUS4,
	NPIPB4, NR1H4, PDE1C,	HKDC1, HMGB1P11,
	PEMT, PEX7, PIF1,	IGLV3-21, IL18R1, IRX3,
	PPP2R3A, PXDN, RABIF,	KBTBD11, KCNJ2, KDM6B,
	SERTAD3, SIGLEC14,	LEMD2, LINC00694, LIPE-
	SLC25A53, SPANXN4,	AS1, LMF2, LMLN-AS1,
	SSH3, SUPT3H,	LPCAT4, LRG1, MAP3K10,
	TMEM150C, TNFAIP6,	MAP3K6, MAPK12,
	UPP1, XKR8, ZC2HC1C,	METTL26, MGAM,
	ZMYM1, ZNF124	MID1IP1, MIF-AS1, MME,
		MRPL23, NAP1L4P3,
		NLRP6, NPIPA5, NUP58,
		OPRL1, PADI2, PGS1, POR,
		RBKS, RNASET2,
		SDCBPP2, SHE, SUMO2,
		SUOX, SURF1, TATDN2,
		TFE3, TMCC3, TMEM8A,
		TMEM94, TOR1B, UNKL,
		ZDHHC18, ZNF668
<5 weeks time-to-delivery	C2orf68, CACNB3, CD40,	AB019441.29, AC004076.9,
without estimated due date	CDKL5, CTBS, CTD-	ACKR2, ADAMTS10, ADM,
info	2272G21.2, CXCL8,	AP5B1, APOE, AQP9,
	DHRS7B, EIF5A2, IFITM3,	ARHGEF40, ATP6V1E1P1,
	MIR24-2, MTSS1, MYSM1,	ATP8A2, BCL3, CA4,
	NCK1-AS1, NR1H4, PDE1C,	CCDC84, CCR3, CD177,
	PEMT, PEX7, PIF1,	CDKL4, CDPF1, CEP152,
	PPP2R3A, RABIF,	CFAP46, CHST7, CLEC4D,
	SIGLEC14, SLC25A53,	CLYBL, CMTM1, COL18A1,
	SPANXN4, SUPT3H,	COX16, CRADD, CSF3R,
	ZC2HC1C, ZMYM1, ZNF124	CXCL1, CXCL2, DAPK2,
		DLEC1, DPAGT1, DPPA4,
		ECHDC2, ERP27, FCGR3B,
		FERMT1, FKRP, FUT7,
		GNB1L, GZMM, HAUS4,
		HKDC1, HMGB1P11,
		IGLV3-21, IL18R1, IRX3,
		KATNAL1, KBTBD11,
		KCNJ2, KDM6B, LEMD2,
		LINC00694, LIPE-AS1,
		LMF2, LMLN-AS1,
		LPCAT4, LRCH4, LRG1,
		MAP3K10, MAP3K6,
		MAPK12, MBD6, METTL26,
		MGAM, MID1IP1, MIF-AS1,
		MME, MRPL23, NAP1L4P3,
		NLRP6, NPIPA5, NPIPB4,
		NUP58, OPRL1, PADI2,
		PGS1, POR, PXDN, RBKS,
		RNASET2, SDCBPP2,
		SERTAD3, SHE, SSH3,
		SUMO2, SUOX, SURF1,
		TATDN2, TFE3, TMCC3,
		TMEM150C, TMEM8A,
		TMEM94, TNFAIP6,
		TOR1B, UNKL, UPP1,
		XKR8, ZDHHC18, ZNF668

FIG. 5C is a Venn diagram showing the overlap of genes used in the first and second predictive models of due date. The first predictive model had a total of 51 most predictive genes, and the second predictive model had a total of 49 most predictive genes; further, only 5 genes overlapped between the two predictive models.

FIG. 5D is a plot showing the concordance between a predicted time to delivery (in weeks) and the observed (actual) time to delivery (in weeks) for the subjects in the due date cohort. The predicted time to delivery outcomes were generated using the respective predictive model based on the predictive genes listed in Table 1.

FIG. 5E shows a summary of the predictive models for predicting due date, including a predictive model using samples with a time-to-delivery of less than 5 weeks and predictive model using samples with a time-to-delivery of less than 7.5 weeks; different predictive models were generated with estimated due date information (e.g., determined using estimated gestational age from ultrasound measurements) and without the estimated due date information. A total of about 15,000 genes were evaluated for use in the predictive model (e.g., as part of the gene discovery process). Further, a total of 130 genes and 62 genes were identified as being predictive for due date among the “<5-week” and “<7.5-week” sample sets, respectively. A total of 28 and 47 genes were identified for inclusion in the predictive model for predicting due date without estimated due date information (e.g., from ultrasound) among the “<5-week” and “<7.5-week” sample sets, respectively. A total of 50 and 48 genes were identified for inclusion in the predictive model for predicting due date with estimated due date information (e.g., from ultrasound) among the “<5-week” and “<7.5-week” sample sets, respectively.

Example 3: Prediction of Gestational Age (GA)

As shown in FIG. 6A, a gestational age cohort of subjects (e.g., pregnant women) was established, from which one or more biological samples (e.g., 1 or 2 each) were collected and assayed at different time points corresponding to an estimated gestational age of a fetus of each subject, using methods and systems of the present disclosure. The gestational age cohort included subjects from the first cohort, as described in Example 1. The gestational age cohort includes subjects from whom different sample types were collected for use in different studies, including studies for the prediction of delivery, prediction of due date, and prediction of actual gestational age of a fetus of each subject.

FIG. 6B is a visual model showing mutual information of the whole transcriptome, where expression of a plurality of gestational age-associated genes varies with gestational age throughout the course of a pregnancy. As shown in the figure, different clusters of genes exhibit fluctuations (e.g., increases and decreases) during different times (e.g., at different estimated gestational ages) throughout the course of a pregnancy. For example, genes associated with innate immunity (e.g., RSAD2, HES1, HIST1H3G, CSHL1, CSH1, EXOSC4, and AXL) and genes associated with cell adhesion (e.g., PATL2, CCT6P1, ACSL4, and TUBA4A) exhibited increased expression during the latter portion of pregnancy as compared to the earlier portion of pregnancy. As another example, genes associated with cell cycle (e.g., UTRN, DOCK11, VPS50, ZMYM1, ZFAND1, FAM179B, C2CD5, and ZNF236) exhibited increased expression during the earlier portion of pregnancy as compared to the latter portion of pregnancy. As another example, genes associated with RNA processing (e.g., ZBTB4, ADK, HBS1L, EIF2D, CDK13, CCDC61, POLDIP3, and C8orf88) exhibited increased expression during the earlier and middle portions of pregnancy as compared to the latter portion of pregnancy. Therefore, different sets or clusters of genes can be assayed for use as a “molecular clock” to track and predict different gestational ages of a fetus during the course of a pregnancy. These sets of genes that are predictive for gestational age are listed in Table 2. Further, pathways that are predictive for gestational age are listed in Table 3 by cluster.

TABLE 2
Sets of Genes Predictive for Gestational Age by Cluster
Cluster Genes
1       CSHL1, CAPN6, PAPPA, LGALS14, SVEP1, VGLL3, ARMCX6, EXPH5, HDGF,
        HSD3B1, OSBP2, BEX1, CSH2, HIST1H2AL, HCFC1R1, AL773572.7, ACTG1,
        MMP8, UBE2L6, CPNE2, EFHD1, CSH1, HES1, RSAD2, RNASE3, CARD16,
        S100A12, NDUFS5, LRIF1, EXOSC4, CYP19A1, NXF3, STAT1, G6PC3, TACC2,
        HIST1H3G, BCL7B, DEFA4, OLFM4, OXTR, IF16, RDX, CAT, PLAC4,
        FAM207A, AXL, PGLYRP1
2       PATL2, NAPA, PRUNE1, ST20, ATF4, FAXDC2, BEX3, ZNF117, TCEAL3,
        EHD3, TUBA1B, GPR180, SUCNR1, OTUD5, ACSL4, PDIA3, ZBED5-AS1, VIL1,
        ITM2B, TUBA4A, CECR2, RPAP3, CCT6P1, KCNMB1
3       SCAF8, SEC24B, MYCBP2, FNDC3A, C2CD5, FRA10AC1, KIAA0368, PLOD1,
        ZNF44, SLC12A2, RARS, AUP1, NARS2, GON4L, RBL1, SPG11, C3orf62, VPS50,
        AKAP7, CEP290, WAPL, RIC1, EXOC4, UTRN, BIRC6, FASTKD1, SNRNP48,
        CEP128, BPTF, RLF, ZNF236, MAP4K3, DYRK1A, ZMYM1, TTC13, RNF121,
        REPS1, CCDC141, DOCK11, DEK, CCNL1, ATP1A1, NSD1, MIPOL1, VCAN,
        ZNRF2, ITSN2, EZH1, CACUL1, MIS18BP1, USP48, KMT5B, MCCC1, TBC1D32,
        CCDC66, ENSG00000173088, SMAD4, ATAD5, FAM179B, KPNA5, ZFAND1,
        CARNMT1, ZDHHC5, TASP1, PCGF6, PHIP
4       CCDC61, POLDIP3, IKBKE, SIPA1L1, NOC2L, PLEC, PLXND1, MAP2K2,
        HIVEP3, FAM111A, AOAH, ARHGAP30, DOCK10, FAM217B, NBPF1,
        HNRNPA1, DTX2, MTBP, SLC26A2, LRRK1, NFATC1, FLNB, MARCKS, BRD9,
        SNRPA1, TAF3, MYO1G, ZNF557, CD53, HBS1L, NFKBIE, EIF2D, PARP14,
        NCL, VPS18, ADK, PSMG4, IMP3, SH2D1B, CHTOP, NELFCD, PABPC1,
        TSHZ1, ZNF383, SDCCAG3, CDK13, TTC39C, ZBTB4, PUM2, C1orf123, GCDH,
        SGTA, NOL4L, LMCD1, KLHL2
5       GABARAPL2, RAB6C, RAB6A
6       MBNL3, MYL4, C8orf88, FTLP3, RAB2B

TABLE 3
Pathways Predictive for Gestational Age by Cluster
				Entities False
			Entities	Detection
Cluster	Pathway Identifier	Pathway Name	p Value	Rate (FDR)
1	R-HSA-909733	Interferon alpha/beta signaling	1.16E−04	0.030180579
1	R-HSA-913531	Interferon Signaling	2.08E−04	0.030180579
1	R-HSA-9013508	NOTCH3 Intracellular Domain Regulates	4.72E−04	0.037300063
		Transcription
1	R-HSA-1280215	Cytokine Signaling in Immune system	5.18E−04	0.037300063
1	R-HSA-196025	Formation of annular gap junctions	9.90E−04	0.056424803
1	R-HSA-190873	Gap junction degradation	0.001175517	0.056424803
1	R-HSA-437239	Recycling pathway of L1	0.001591097	0.060736546
1	R-HSA-8941856	RUNX3 regulates NOTCH signaling	0.002067719	0.060736546
1	R-HSA-2197563	NOTCH2 intracellular domain regulates	0.002067719	0.060736546
		transcription
1	R-HSA-1059683	Interleukin-6 signaling	0.002328072	0.060736546
1	R-HSA-9012852	Signaling by NOTCH3	0.002336021	0.060736546
1	R-HSA-446353	Cell-extracellular matrix interactions	0.002892685	0.060737316
1	R-HSA-196071	Metabolism of steroid hormones	0.003139605	0.060737316
1	R-HSA-210744	Regulation of gene expression in late	0.003196701	0.060737316
		stage (branching morphogenesis)
		pancreatic bud precursor cells
1	R-HSA-193993	Mineralocorticoid biosynthesis	0.003196701	0.060737316
1	R-HSA-6798695	Neutrophil degranulation	0.003621161	0.065180904
1	R-HSA-9013695	NOTCH4 Intracellular Domain Regulates	0.005317217	0.085315773
		Transcription
1	R-HSA-194002	Glucocorticoid biosynthesis	0.005718941	0.085315773
1	R-HSA193048	Androgen biosynthesis	0.005718941	0.085315773
1	R-HSA-912694	Regulation of IFNA signaling	0.006134158	0.085315773
1	R-HSA-982772	Growth hormone receptor signaling	0.006562752	0.085315773
1	R-HSA-6783589	Interleukin-6 family signaling	0.00700461	0.091059924
1	R-HSA-168256	Immune System	0.007818938	0.093827257
2	R-HSA-8955332	Carboxyterminal post-translational	1.49E−04	0.01808342
		modifications of tubulin
2	R-HSA-983231	Factors involved in megakaryocyte	5.42E−04	0.01808342
		development and platelet production
2	R-HSA-190840	Microtubule-dependent trafficking of	8.77E−04	0.01808342
		connexons from Golgi to the plasma
		membrane
2	R-HSA-190872	Transport of connexons to the plasma	9.58E−04	0.01808342
		membrane
2	R-HSA-389977	Post-chaperonin tubulin folding pathway	0.001128943	0.01808342
2	R-HSA-6811434	COPI-dependent Golgi-to-ER retrograde	0.001205561	0.01808342
		traffic
2	R-HSA-6807878	COPI-mediated anterograde transport	0.001205561	0.01808342
2	R-HSA-389960	Formation of tubulin folding	0.001615847	0.022621853
		intermediates by CCT/TriC
2	R-HSA-9619483	Activation of AMPK downstream of	0.002065423	0.024371102
		NMDARs
2	R-HSA-5626467	RHO GTPases activate IQGAPs	0.002309953	0.024371102
2	R-HSA-389958	Cooperation of Prefoldin and TriC/CCT	0.00243711	0.024371102
		in actin and tubulin folding
2	R-HSA-190861	Gap junction assembly	0.002978066	0.024970608
2	R-HSA-8856688	Golgi-to-ER retrograde transport	0.003023387	0.024970608
2	R-HSA-381042	PERK regulates gene expression	0.003121326	0.024970608
2	R-HSA-199977	ER to Golgi Anterograde Transport	0.004028523	0.027278879
2	R-HSA-9609736	Assembly and cell surface presentation of	0.004047319	0.027278879
		NMDA receptors
2	R-HSA-190828	Gap junction trafficking	0.004727036	0.027278879
2	R-HSA-437239	Recycling pathway of L1	0.005269036	0.027278879
2	R-HSA-5620924	Intraflagellar transport	0.005455776	0.027278879
2	R-HSA-157858	Gap junction trafficking and regulation	0.005455776	0.027278879
2	R-HSA-6811436	COPI-independent Golgi-to-ER	0.006846767	0.034233833
		retrograde traffic
2	R-HSA-983189	Kinesins	0.00792863	0.03517302
2	R-HSA-3371497	HSP90 chaperone cycle for steroid	0.008381604	0.03517302
		hormone receptors (SHR)
2	R-HSA-6811442	Intra-Golgi and retrograde Golgi-to-ER	0.008817252	0.03517302
		traffic
2	R-HSA-446203	Asparagine N-linked glycosylation	0.00885181	0.03517302
2	R-HSA-948021	Transport to the Golgi and subsequent	0.008927485	0.03517302
		modification
2	R-HSA-1445148	Translocation of SLC2A4 (GLUT4) to the	0.010560059	0.03517302
		plasma membrane
2	R-HSA-392499	Metabolism of proteins	0.0111176	0.03517302
2	R-HSA-8852276	The role of GTSE1 in G2/M progression	0.011600388	0.03517302
		after G2 checkpoint
2	R-HSA-205025	NADE modulates death signalling	0.01172434	0.03517302
2	R-HSA-438064	Post NMDA receptor activation events	0.01527754	0.045832619
2	R-HSA-380320	Recruitment of NuMA to mitotic	0.015578704	0.046736112
		centrosomes
2	R-HSA-390466	Chaperonin-mediated protein folding	0.016497529	0.049492587
2	R-HSA-434313	Intracellular metabolism of fatty acids	0.017536692	0.052610075
		regulates insulin secretion
2	R-HSA-391251	Protein folding	0.018403238	0.055209713
2	R-HSA-1296052	Ca2+ activated K+ channels	0.019466807	0.056873842
2	R-HSA-109582	Hemostasis	0.020531826	0.056873842
2	R-HSA-442755	Activation of NMDA receptors and	0.020738762	0.056873842
		postsynaptic events
2	R-HSA-5610787	Hedgehog ‘off’ state	0.024645005	0.056873842
2	R-HSA-373760	L1CAM interactions	0.026893295	0.056873842
2	R-HSA-2500257	Resolution of Sister Chromatid Cohesion	0.028436921	0.056873842
2	R-HSA-381183	ATF6 (ATF6-alpha) activates chaperone	0.029062665	0.05812533
		genes
2	R-HSA-381033	ATF6 (ATF6-alpha) activates chaperones	0.032875598	0.065751195
2	R-HSA-2132295	MHC class II antigen presentation	0.034112102	0.068224205
2	R-HSA-5663220	RHO GTPases Activate Formins	0.034533251	0.069066501
2	R-HSA-418457	cGMP effects	0.034776645	0.069553291
2	R-HSA-381119	Unfolded Protein Response (UPR)	0.037102976	0.074205952
2	R-HSA-5358351	Signaling by Hedgehog	0.042915289	0.077519335
2	R-HSA-400451	Free fatty acids regulate insulin secretion	0.051724699	0.077519335
2	R-HSA-389957	Prefoldin mediated transfer of substrate	0.055451773	0.077519335
		to CCT/TriC
2	R-HSA-2467813	Separation of Sister Chromatids	0.055478287	0.077519335
2	R-HSA-68877	Mitotic Prometaphase	0.062192558	0.077519335
2	R-HSA-5617833	Cilium Assembly	0.062720246	0.077519335
2	R-HSA-68882	Mitotic Anaphase	0.062720246	0.077519335
2	R-HSA-2555396	Mitotic Metaphase and Anaphase	0.064312651	0.077519335
2	R-HSA-380994	ATF4 activates genes in response to	0.064707762	0.077519335
		endoplasmic reticulum stress
2	R-HSA-69275	G2/M Transition	0.064846542	0.077519335
2	R-HSA-453274	Mitotic G2-G2/M phases	0.06591891	0.077519335
2	R-HSA-936440	Negative regulators of DDX58/IFIH1	0.068385614	0.077519335
		signaling
2	R-HSA-112316	Neuronal System	0.07344898	0.077519335
2	R-HSA-112314	Neurotransmitter receptors and	0.075836046	0.077519335
		postsynaptic signal transmission
2	R-HSA-901042	Calnexin/calreticulin cycle	0.077519335	0.077519335
2	R-HSA-392154	Nitric oxide stimulates guanylate cyclase	0.077519335	0.077519335
2	R-HSA-5689896	Ovarian tumor domain proteases	0.081148593	0.081148593
2	R-HSA-597592	Post-translational protein modification	0.085097153	0.085097153
2	R-HSA-6811438	Intra-Golgi traffic	0.090161601	0.090161601
2	R-HSA-75876	Synthesis of very long-chain fatty acyl-	0.095528421	0.095528421
		CoAs
2	R-HSA-5683826	Surfactant metabolism	0.099089328	0.099089328
3	R-HSA-1538133	G0 and Early G1	8.71E−04	0.206527784
3	R-HSA-1362277	Transcription of E2F targets under	0.006680493	0.291565226
		negative control by DREAM complex
3	R-HSA-453279	Mitotic G1-G1/S phases	0.010050075	0.291565226
3	R-HSA-3304347	Loss of Function of SMAD4 in Cancer	0.014424835	0.291565226
3	R-HSA-3311021	SMAD4 MH2 Domain Mutants in Cancer	0.014424835	0.291565226
3	R-HSA-3315487	SMAD2/3 MH2 Domain Mutants in	0.014424835	0.291565226
		Cancer
3	R-HSA-2173796	SMAD2/SMAD3:SMAD4 heterotrimer	0.015567079	0.291565226
		regulates transcription
3	R-HSA-3214841	PKMTs methylate histone lysines	0.023826643	0.291565226
3	R-HSA-8952158	RUNX3 regulates BCL2L11 (BIM)	0.028644567	0.291565226
		transcription
3	R-HSA-2173793	Transcriptional activity of	0.029469648	0.291565226
		SMAD2/SMAD3:SMAD4 heterotrimer
3	R-HSA-8941855	RUNX3 regulates CDKN1A transcription	0.038011863	0.291565226
3	R-HSA-3304349	Loss of Function of SMAD2/3 in Cancer	0.038011863	0.291565226
3	R-HSA-444821	Relaxin receptors	0.038011863	0.291565226
3	R-HSA-9645135	STATS Activation	0.04266207	0.291565226
3	R-HSA-3595174	Defective CHST14 causes EDS,	0.04266207	0.291565226
		musculocontractural type
3	R-HSA-3595172	Defective CHST3 causes SEDCJD	0.04266207	0.291565226
3	R-HSA-3304351	Signaling by TGF-beta Receptor Complex	0.04266207	0.291565226
		in Cancer
3	R-HSA-379724	tRNA Aminoacylation	0.043286108	0.291565226
3	R-HSA-1640170	Cell Cycle	0.04679213	0.291565226
3	R-HSA-3595177	Defective CHSY1 causes TPBS	0.047290122	0.291565226
3	R-HSA-2470946	Cohesin Loading onto Chromatin	0.047290122	0.291565226
3	R-HSA-426117	Cation-coupled Chloride cotransporters	0.047290122	0.291565226
3	R-HSA-3371599	Defective HLCS causes multiple	0.047290122	0.291565226
		carboxylase deficiency
3	R-HSA-351906	Apoptotic cleavage of cell adhesion	0.051896124	0.291565226
		proteins
3	R-HSA-176974	Unwinding of DNA	0.056480178	0.291565226
3	R-HSA-3323169	Defects in biotin (Btn) metabolism	0.056480178	0.291565226
3	R-HSA-1445148	Translocation of SLC2A4 (GLUT4) to the	0.056493106	0.291565226
		plasma membrane
3	R-HSA-69278	Cell Cycle, Mitotic	0.057847859	0.291565226
3	R-HSA-2022923	Dermatan sulfate biosynthesis	0.061042388	0.291565226
3	R-HSA-2468052	Establishment of Sister Chromatid	0.061042388	0.291565226
		Cohesion
3	R-HSA-170834	Signaling by TGF-beta Receptor Complex	0.064216491	0.291565226
3	R-HSA-68884	Mitotic Telophase/Cytokinesis	0.070101686	0.291565226
3	R-HSA-1502540	Signaling by Activin	0.070101686	0.291565226
3	R-HSA-8983432	Interleukin-15 signaling	0.074598978	0.291565226
3	R-HSA-196780	Biotin transport and metabolism	0.087962635	0.291565226
3	R-HSA-1362300	Transcription of E2F targets under	0.092374782	0.291565226
		negative control by p107 (RBL1) and
		p130 (RBL2) in complex with HDAC1
3	R-HSA-3560783	Defective B4GALT7 causes EDS,	0.096765893	0.291565226
		progeroid type
3	R-HSA-4420332	Defective B3GALT6 causes EDSP2 and	0.096765893	0.291565226
		SEMDJL1
3	R-HSA-6804114	TP53 Regulates Transcription of Genes	0.096765893	0.291565226
		Involved in G2 Cell Cycle Arrest
4	R-HSA-8953854	Metabolism of RNA	0.008040167	0.222786123
4	R-HSA-9013508	NOTCH3 Intracellular Domain Regulates	0.011600797	0.222786123
		Transcription
4	R-HSA-3304347	Loss of Function of SMAD4 in Cancer	0.013386586	0.222786123
4	R-HSA-3560792	Defective 5LC26A2 causes	0.013386586	0.222786123
		chondrodysplasias
4	R-HSA-3311021	SMAD4 MH2 Domain Mutants in Cancer	0.013386586	0.222786123
4	R-HSA-3315487	SMAD2/3 MH2 Domain Mutants in	0.013386586	0.222786123
		Cancer
4	R-HSA-73857	RNA Polymerase II Transcription	0.014524942	0.222786123
4	R-HSA-8952158	RUNX3 regulates BCL2L11 (BIM)	0.026596735	0.222786123
		transcription
4	R-HSA-72203	Processing of Capped Intron-Containing	0.028244596	0.222786123
		Pre-mRNA
4	R-HSA-72187	mRNA 3′-end processing	0.028277064	0.222786123
4	R-HSA-74160	Gene expression (Transcription)	0.02961978	0.222786123
4	R-HSA-9012852	Signaling by NOTCH3	0.032891337	0.222786123

FIG. 6C is a plot showing the concordance between a predicted gestational age (in weeks) and the measured gestational age (in weeks) for the subjects in the gestational age cohort. The subjects are stratified in the plot by major race (e.g., white, non-black Hispanic, Asian, Afro-American, Native American, mixed race (e.g., two or more races), or unknown). It is noteworthy that the data shows that, unlike many biological phenotypes, the gestational biomarkers model (e.g., prediction of gestational age based on a set of gestational age-associated biomarker genes) is independent of race or ethnicity. This observation indicates that the underlying molecular clock of pregnancy is highly conserved across races/ethnicities, which has a practical implication of making a universal assay for gestational age feasible. The predicted gestational ages were generated using a predictive model for gestational age (a Lasso model generating with a 10-fold cross-validation) based on the predictive genes listed in Table 2 and/or the predictive pathways listed in Table 3. Further, the predictive model weights of genes that are predictive for gestational age are listed in Table 4.

TABLE 4
Predictive Model Weights of Genes Predictive for Gestational Age
Gene      Weight
CGA       −2.3291809
CSH1      2.0997422
CAPN6     1.58718823
UBE2L6    0.78006933
CYP19A1   0.7495651
MCEMP1    0.66188425
STAT1     0.62796009
ANGPT2    −0.61766869
SUCNR1    0.60439183
EXPH5     0.55503889
LRMP      −0.53240046
RGS9      0.43352062
NXF3      0.40263822
DDI2      −0.39475793
PPP2CB    −0.34436392
BBX       0.34034586
FCGR2A    0.33904027
NREP      0.33265012
BEX1      0.27078087
RYR3      −0.25427064
IGHA1     −0.24225842
IL18BP    −0.22511377
SLC7A11   0.21310441
TCHH      0.2115899
SMAD5     −0.19126152
FAM114A1  −0.18288572
CCDC66    −0.18079341
PLS3      −0.17781532
BCAT1     0.17680457
RECQL     0.17503129
CD96      0.15741167
FAM214A   −0.15229302
GCNT1     0.14693661
DCAF17    −0.14675868
HIST1H2BB 0.1407058
CCT6B     0.13180261
FBXL20    −0.12456705
H19       −0.12185332
SKIL      0.11799157
ABCB10    0.11737993
FARS2     0.11728322
SERPINB10 0.11535642
MCCC1     −0.10689218
FTH1P7    0.10503966
SLC4A7    −0.10328859
TCN1      0.10244934
ARHGAP42  −0.10056675
RAC1      0.09965553
EED       −0.09795522
RAB8B     0.09392322
SOX12     −0.09281749
UBE2G1    −0.09063966
CFAP70    −0.09009795
SPA17     0.08878255
RASAL2    −0.08386265
RHAG      0.07777724
NQO2      0.07671752
NKAPL     0.07183955
SORBS2    0.07127603
BTRC      −0.07061876
LAMTOR3   0.06135476
RDX       0.06114729
APOL4     0.06043051
SVEP1     0.06015624
IGHV3-23  −0.05726866
PPCS      0.05506125
TNIP3     0.05448006
WDSUB1    −0.05228332
TMEM14A   0.0522635
SEMA3C    0.05196743
SUZ12     −0.04935669
GATSL2    −0.0426659
TMEM109   0.03944985
CPNE2     0.03713674
REEP5     0.03492848
GCSAML    0.03481997
LYRM9     0.03446721
CENPV     −0.03301296
NEK6      0.03186441
PET100    −0.03081952
FAM221A   −0.0293719
ZDHHC8    −0.02866679
IGSF21    0.02810308
FAM63B    −0.0259032
HABP4     −0.02585663
LEMD3     −0.01949602
WDR27     −0.01899405
AXL       0.01873862
SMARCA1   0.01789833
GNPAT     0.01659611
IGHV3-7   −0.01587266
DYNC2LI1  −0.01543354
PROS2P    0.01216718
ATP9A     0.01210078
HBEGF     −0.01123074
COMT      0.01102531
DYNLT3    0.00555317
TBC1D32   −0.00434216
MYL12B    0.0037807

Example 4: Prediction of Pre-Term Birth (PTB)

As shown in FIGS. 7A-7B, a pre-term birth (PTB) cohort of subjects (e.g., pregnant women) was established, from which one or more biological samples (e.g., 1, 2, 3, or more than 3 each) were collected and assayed at different time points corresponding to an estimated gestational age of a fetus of each subject, using methods and systems of the present disclosure. The pre-term birth cohort included subjects from the second cohort, as described in Example 1. The pre-term birth cohort includes subjects from whom different sample types were collected for use in different studies, including studies for the prediction of pre-term birth, prediction of delivery, prediction of due date, and prediction of actual gestational age of a fetus of each subject. As shown in the figure, a total of 160 samples from 128 pregnant subjects of the pre-term birth cohort were collected and assayed, of which 118 samples were collected from 100 pregnant subjects having full-term births and 42 samples were collected from 28 pregnant subjects having pre-term births (e.g., defined as occurring before an estimated gestational age of 37 weeks). The pre-term birth (PTB) cohort included a set of pre-term case samples (e.g., from women having pre-term births) and a set of pre-term control samples (e.g., from women having full-term births). Across the pre-term case samples and pre-term control samples, the distributions of gestational age at time of collection were similar (FIG. 7A), while the distributions of gestational age at delivery were clearly distinguishable to a statistically significant extent (FIG. 7B).

An analysis for differentially expressed genes between the pre-term case samples and pre-term control samples was performed, revealing that 151 genes were upregulated and 37 genes were downregulated. For example, FIGS. 7C-7E show differential gene expression of the B3GNT2, BP, and ELANE genes, respectively, between the pre-term case samples (left) and pre-term control samples (right). FIG. 7F shows a legend for the results from pre-term case samples and pre-term control samples shown in FIGS. 7C-7E. A set of genes that are predictive for pre-term birth (PTB) are listed in Table 5. Further, the predictive model weights of genes that are predictive for pre-term birth (PTB) are listed in Table 6.

TABLE 5
Set of Genes Predictive for Pre-Term Birth (PTB)
Gene	BaseMean	Log2FoldChange	lfcSE	Stat	P Value	P_adj
MKI67	400.830667	−0.601319668	0.108179231	32.84474216	9.98207E−09	9.05274E−05
TPX2	65.5033344	−0.581186144	0.110641746	29.0631565	7.00567E−08	0.000317672
B3GNT2	50.6724879	−0.811226454	0.166164856	24.85992629	6.16508E−07	0.001863703
TOP2A	216.98909	−0.405447156	0.086617399	22.58819561	2.00714E−06	0.004550689
CFAP45	124.955577	−0.775232315	0.16837313	21.97718654	2.75911E−06	0.005004467
RABEP1	589.967939	0.172443456	0.037329151	21.04101979	4.49555E−06	0.00502318
SPAG5	23.1133858	−0.653772557	0.145799452	20.86325357	4.93267E−06	0.00502318
MRVI1	124.226298	−0.680912281	0.155527024	20.7857985	5.13624E−06	0.00502318
HIST1H2BB	67.0856736	−0.621390031	0.142395396	20.78222285	5.14584E−06	0.00502318
IRX3	24.1768218	−1.212908431	0.274268915	20.64129438	5.53885E−06	0.00502318
PRC1	93.5892327	−0.3611091	0.081976316	19.92418748	8.05745E−06	0.006094756
ACSM3	27.2003668	−0.716459154	0.169223045	19.92251129	8.06451E−06	0.006094756
LTF	95.8462149	−1.197283648	0.285286547	19.21981298	1.16498E−05	0.008127079
CLSPN	101.400363	−0.379383578	0.088756166	18.72100697	1.51306E−05	0.009801412
ABCA13	28.4998585	−1.147381421	0.276646667	18.52138019	1.68009E−05	0.009992992
DAP3	276.946453	0.200259669	0.046325618	18.38293849	1.80668E−05	0.009992992
CLPX	260.222378	0.208245562	0.048240765	18.31405149	1.8732E−05	0.009992992
PRDM4	73.7117025	−0.280318521	0.068189159	17.43554082	2.97216E−05	0.014220995
HJURP	49.7967158	−0.48470193	0.118013732	17.43093908	2.97937E−05	0.014220995
CEACAM8	40.6294185	−1.167910698	0.291855251	17.00860876	3.72107E−05	0.016873202
WDR43	162.21835	0.201833504	0.048851646	16.90058186	3.93895E−05	0.01701064
PHGDH	64.6602039	−1.038524899	0.272984761	16.10479806	5.9932E−05	0.024705606
SPRY1	18.6318178	−0.739453446	0.191408208	15.96857116	6.44028E−05	0.025394321
COQ2	32.7210234	−0.494334868	0.129086701	15.47489359	8.36084E−05	0.031168137
SGO2	79.0913883	−0.278147351	0.071596767	15.42336324	8.59194E−05	0.031168137
FBN1	18.0266461	−0.786173751	0.199134531	15.16720482	9.83976E−05	0.034321842
GPSM2	63.6368478	−0.305850326	0.079647479	15.04158139	0.000105168	0.034781625
WASL	69.0262558	−0.314359854	0.082595598	15.00219484	0.000107386	0.034781625
C10orf88	34.4590779	−0.561281119	0.150387991	14.86051191	0.000115761	0.036201295
MAPK10	62.7246279	−0.787771018	0.214606489	14.75561567	0.000122382	0.036996225
SDAD1	119.719558	0.323236991	0.083187212	14.62160832	0.000131399	0.038440635
AP1AR	52.9450923	0.296319236	0.07703744	14.44196908	0.000144545	0.039709576
CEACAM6	17.6472741	−1.040919908	0.28533353	14.37541601	0.000149745	0.039709576
VPS9D1	31.4783536	−0.64593929	0.173835235	14.35682089	0.000151231	0.039709576
MEAF6	181.85469	0.234732787	0.061260932	14.3070259	0.000155284	0.039709576
FOXM1	20.5441036	−0.636516603	0.171727594	14.23388904	0.000161437	0.039709576
SHCBP1	21.3472375	−0.459928249	0.124085932	14.22723861	0.000162008	0.039709576
CIT	124.514777	−0.328433636	0.088967509	13.99039883	0.000183747	0.043852559
ACADVL	137.011451	−0.430868422	0.117813378	13.82728288	0.000200405	0.044288458
BCORL1	111.923293	−0.402393529	0.109550057	13.80336562	0.000202972	0.044288458
HIST1H3F	33.0009859	−0.537748862	0.147682317	13.79931363	0.000203411	0.044288458
ERI2	29.8917001	−0.429671723	0.11865343	13.70904243	0.000213424	0.044288458
ASPM	108.467082	−0.303317686	0.083048184	13.6994066	0.000214522	0.044288458
LATS2	72.1128433	−0.43419763	0.120730726	13.61286351	0.000224641	0.044288458
P4HB	308.144977	−0.467363453	0.130617695	13.59109153	0.000227261	0.044288458
RRM2	57.4816431	−0.639528628	0.178697012	13.55808795	0.000231293	0.044288458
HIST1H2AH	39.7276884	−0.738920384	0.209333866	13.55131997	0.000232128	0.044288458
TBC1D7	20.8101265	−0.491912362	0.137149751	13.53297652	0.000234408	0.044288458
ZSCAN29	85.830534	−0.403022474	0.113370078	13.47259044	0.000242074	0.044803426
MRTO4	16.8779413	0.691948182	0.183119079	13.42031428	0.000248914	0.04514802
ELANE	29.9488832	−0.86703039	0.248991041	13.32739769	0.000261556	0.045573275
CCNA2	20.5346159	−0.627654197	0.175281296	13.30323568	0.000264948	0.045573275
NXF3	21.9931399	−0.874037001	0.246746166	13.29345619	0.000266334	0.045573275
C11orf24	39.2455928	−0.422115026	0.118646242	13.24101829	0.000273889	0.045998149
NUSAP1	163.110628	−0.312315279	0.087355935	13.1574169	0.000286383	0.04722202
CPNE2	98.1394967	−0.412819488	0.115624299	13.1056335	0.000294409	0.047678502
ENPP4	21.988534	−0.702457326	0.199003539	13.00559611	0.000310561	0.049411963
TADA3	384.86541	−0.461754693	0.132540423	12.96637032	0.000317136	0.049588081
CENPJ	86.1330533	−0.400578337	0.113794638	12.91463148	0.000326024	0.049862843
BPI	70.1177976	−0.889016784	0.256224363	12.8843149	0.000331347	0.049862843
FAM117B	78.1729146	0.485833993	0.13119025	12.86163207	0.000335388	0.049862843
HIBADH	70.6973939	0.306490029	0.084559119	12.80182626	0.000346281	0.050537255
DEFA3	67.2275316	−1.117768363	0.327944883	12.7746206	0.000351354	0.050537255
TAF1A	25.0593769	0.374110248	0.103231417	12.74667933	0.000356642	0.050537255
HIST1H1B	194.721138	−0.716085762	0.209616837	12.64672494	0.000376224	0.052491955
NCAPG2	81.8608202	−0.2529091	0.072071056	12.58777256	0.000388279	0.052889151
MTG1	24.3831654	0.341740344	0.095511983	12.57598756	0.000390735	0.052889151
CKAP2L	58.9317012	−0.343643101	0.098381001	12.52409347	0.000401738	0.053578821
TRA2B	676.542908	−0.25572298	0.073568397	12.45496838	0.000416881	0.05479272
ZBTB26	19.2710753	−0.541284898	0.159692134	12.22219578	0.000472243	0.060690018
ITGAE	55.6496691	−0.580656414	0.170762602	12.19638948	0.000478821	0.060690018
TMEM204	24.0591736	−0.617192385	0.182647993	12.18471832	0.000481826	0.060690018
DNAJC9	194.988335	−0.462822231	0.13578116	12.12914118	0.0004964	0.061483925
ARG1	72.4908196	−0.796757664	0.24170391	12.07453342	0.000511153	0.061483925
TRA2A	242.818114	−0.370177056	0.10842455	12.05283964	0.000517135	0.061483925
HIST1H2AG	375.263091	−0.293447479	0.085887285	12.04075155	0.0005205	0.061483925
PPP2R5C	408.606687	0.137459246	0.039387142	12.00514553	0.000530539	0.061483925
UTP3	79.2980827	0.461692517	0.129523005	11.97005354	0.000540624	0.061483925
BMS1	183.723177	0.241018859	0.068716246	11.95976754	0.000543617	0.061483925
WHSC1	185.31172	−0.226521785	0.066425648	11.92423415	0.000554084	0.061483925
NUP133	110.269171	0.156526589	0.04522015	11.91679955	0.0005563	0.061483925
SLC25A15	42.0037796	−0.596960989	0.178414071	11.860334	0.000573423	0.061483925
MYO1E	88.9824676	0.404503129	0.114157332	11.84234693	0.000578988	0.061483925
TLE1	22.5766189	0.54382872	0.153891879	11.84212637	0.000579057	0.061483925
CENPF	286.307473	−0.601321328	0.18356237	11.81108262	0.000588792	0.061483925
HNRNPM	1750.4597	0.170158862	0.04909502	11.81061753	0.000588939	0.061483925
CCNE2	19.1264461	−0.354971369	0.104477344	11.77598515	0.000599998	0.061483925
TNKS2	219.507656	0.158809062	0.046014002	11.7758489	0.000600041	0.061483925
TYMS	62.2905051	−0.499118477	0.148971538	11.73008608	0.000614977	0.061483925
ATP1B1	66.7258463	−0.78171204	0.242172775	11.7283898	0.000615538	0.061483925
HSPA4	603.817699	0.130939432	0.038066225	11.70951895	0.000621812	0.061483925
KIF11	74.4096422	−0.291879346	0.086082108	11.68479707	0.000630129	0.061483925
GPR155	31.7649463	−0.478814886	0.143773625	11.66861505	0.000635633	0.061483925
KCTD18	81.6905015	−0.494420831	0.149178602	11.66380216	0.00063728	0.061483925
CHMP1A	78.9514046	−0.28448745	0.084366365	11.6295058	0.000649138	0.061968763
CYB5R4	245.544953	−0.240885249	0.071641203	11.58170704	0.000666038	0.062919751
SURF4	39.7092905	−0.423964499	0.127821348	11.55995935	0.000673873	0.063003677
UBFD1	23.440026	0.51702477	0.1473821	11.49849634	0.000696525	0.064457005
MS4A3	45.4722541	−0.846596609	0.259710365	11.42078505	0.00072627	0.066474938
ZNF100	72.7823971	−0.313967903	0.093889894	11.40367192	0.000732991	0.066474938
FBRSL1	157.84346	−0.423476217	0.129442424	11.34208635	0.000757702	0.067456821
HIST1H3B	160.992723	−0.563354995	0.172589487	11.33283675	0.000761485	0.067456821
JMJD1C	1173.54762	−0.321356114	0.096927602	11.32153835	0.000766132	0.067456821
HDGF	1516.62537	−0.320347942	0.097986788	11.29956087	0.000775254	0.067603661
GFOD1	46.2615555	−0.390620305	0.120574865	11.26119987	0.00079144	0.067733245
ZNF347	56.7785617	−0.483136357	0.147301017	11.24435006	0.000798658	0.067733245
NT5C2	315.658417	−0.288282573	0.087621237	11.24321471	0.000799146	0.067733245
SERPINB10	30.1641459	−0.91614822	0.286942518	11.16704123	0.000832633	0.069647542
ADCY3	131.715381	−0.755386896	0.235882849	11.15713403	0.000837091	0.069647542
HDAC6	85.9990103	−0.257845644	0.078305194	11.12402269	0.000852168	0.07025735
FNBP1L	688.822315	−0.583258432	0.179846878	11.02494984	0.000898937	0.073445592
CDCA2	27.9846514	−0.351604469	0.106383011	10.96863027	0.000926672	0.074331571
PKP2	59.0515065	−0.5919732	0.185121482	10.93505182	0.000943618	0.074331571
MAFG	62.4155814	−0.475736151	0.148504114	10.92588387	0.0009483	0.074331571
HIST1H2AL	100.449723	−0.549602282	0.171209237	10.91134298	0.000955772	0.074331571
CD109	226.319539	−0.722114926	0.221290922	10.9069803	0.000958026	0.074331571
MMP8	61.7414815	−0.963025712	0.306340595	10.89073584	0.000966464	0.074331571
ANLN	115.731414	−0.295842283	0.090850141	10.88941321	0.000967155	0.074331571
MTMR10	733.404726	−0.480452862	0.149333198	10.85233363	0.000986713	0.075197506
PMPCB	132.728427	0.238068066	0.071311803	10.80424715	0.001012675	0.076052074
ZDHHC3	66.0394411	−0.260252119	0.080306011	10.80055166	0.001014699	0.076052074
STRN4	542.589927	−0.403498387	0.125812989	10.75598871	0.001039424	0.077266708
SLC30A1	41.582641	−0.48709392	0.153134635	10.73638939	0.001050491	0.077454495
THUMPD1	309.207619	−0.406262264	0.127203679	10.67845738	0.001083904	0.079219698
UNC13D	448.751353	−0.435984447	0.136240502	10.66273958	0.001093154	0.079219698
COL6A3	229.356044	−0.871540967	0.279680555	10.64316563	0.001104784	0.079219698
DACH1	49.7307281	−0.357313535	0.109906151	10.60586614	0.001127294	0.079219698
PDZD8	154.486387	−0.257891719	0.079851585	10.59729745	0.001132531	0.079219698
MCM7	83.7976273	−0.306443012	0.09451062	10.59553298	0.001133612	0.079219698
H2AFX	26.7167358	−0.621633373	0.195620526	10.59232889	0.001135578	0.079219698
PDLIM7	380.727424	−0.505011238	0.160089466	10.53019631	0.001174397	0.080999672
XRCC2	19.1233452	−0.678008232	0.21669442	10.52303581	0.001178957	0.080999672
HIST1H2AD	97.3430238	−0.34596932	0.108676691	10.44132953	0.001232265	0.083449616
SNX2	647.453038	0.202977723	0.061821064	10.4402004	0.001233019	0.083449616
CDK1	18.0714248	−0.51816235	0.162355531	10.33963387	0.001302038	0.087226169
CCDC71L	37.33982	−0.400919901	0.127802181	10.32455688	0.001312718	0.087226169
CKLF	37.8805589	−0.462449877	0.14699266	10.29862805	0.001331292	0.087226169
NBEAL2	340.162037	−0.432033009	0.136441565	10.29489473	0.001333988	0.087226169
BLK	43.4801839	0.634035324	0.188877899	10.29085666	0.00133691	0.087226169
TBC1D17	58.4749713	−0.373545049	0.118601337	10.24113633	0.00137343	0.087484066
LEF1	151.118851	0.643948384	0.191173884	10.23488179	0.001378094	0.087484066
ZMIZ2	192.67977	−0.414950646	0.133664118	10.22724077	0.001383815	0.087484066
PROSC	153.538309	0.198924963	0.061677357	10.22540842	0.001385191	0.087484066
HBG2	345.124523	−0.918493788	0.296215427	10.21880457	0.001390159	0.087484066
G6PD	636.863085	−0.407286058	0.13130294	10.20745346	0.001398742	0.087484066
SCAMP2	67.7773099	−0.394249471	0.126956056	10.16850961	0.001428597	0.088739365
ADSL	225.751847	0.196671315	0.061110072	10.14454322	0.00144729	0.089288946
TTC14	35.3500103	−0.41643018	0.131587484	10.10593962	0.001477922	0.090562679
SNX19	56.1029379	−0.586594521	0.192975491	10.07305605	0.001504533	0.091574547
SSH1	283.720048	−0.430272183	0.139594448	10.01954535	0.001548877	0.092537718
PUDP	20.5130162	0.344091852	0.108081232	10.01828007	0.001549941	0.092537718
MECP2	485.159305	−0.330039312	0.106259251	10.01705997	0.001550968	0.092537718
CD63	369.814694	−0.370604322	0.119643987	9.97005192	0.00159107	0.093697832
KCNMB1	50.8034229	−0.621752932	0.205706399	9.966132454	0.001594461	0.093697832
MAPKAPK5	123.545681	0.16432536	0.051688944	9.958128716	0.001601407	0.093697832
GSN	1142.9619	−0.513473609	0.167530371	9.917485992	0.001637159	0.095175581
LOXHD1	199.692968	−0.731866353	0.24195628	9.90140628	0.001651525	0.095364629
RSRC2	830.686621	−0.262498114	0.084618777	9.890390225	0.001661441	0.095364629
NLRX1	30.7233614	−0.509357783	0.166698746	9.843889299	0.001703968	0.095988604
SEPT1	110.886498	0.323262856	0.101511457	9.840581353	0.001707035	0.095988604
CD69	38.0149845	−0.674155226	0.219370446	9.834226717	0.001712943	0.095988604
ZWINT	24.8850687	−0.39823044	0.128888897	9.819550962	0.001726665	0.095988604
MPZL3	113.172834	−0.654041276	0.209805319	9.802115693	0.001743112	0.095988604
C19orf60	16.0678764	0.360656348	0.114692869	9.795694668	0.001749209	0.095988604
DHRS7	141.576438	−0.39952924	0.130352818	9.792485914	0.001752264	0.095988604
HIST1H3D	53.2585736	−0.400948931	0.129905156	9.781128458	0.001763121	0.095988604
URGCP	27.7194428	0.340624969	0.106525549	9.762391628	0.00178118	0.095988604
SLFN5	215.94271	0.480638388	0.148370925	9.739063308	0.001803928	0.095988604
DENND5B	61.3148853	0.314946804	0.099031435	9.735650377	0.001807281	0.095988604
HDAC8	41.9432708	−0.268324265	0.087630995	9.735604359	0.001807326	0.095988604
MPO	58.7414306	−0.702404473	0.234008372	9.732980597	0.001809908	0.095988604
LBR	97.386483	−0.388828754	0.12690985	9.718285563	0.001824436	0.096196585
SLC25A17	26.6395003	−0.435027079	0.141781328	9.693486997	0.001849223	0.096939895
PHF10	89.6542661	0.211046689	0.067249255	9.670560543	0.001872442	0.097592955
C5orf51	85.5546517	−0.439052137	0.144932302	9.651442593	0.001892029	0.09763215
LIMA1	90.6336708	−0.243337275	0.079242036	9.61963325	0.001925082	0.09763215
KIF4A	42.6606646	−0.303097287	0.099303103	9.597227403	0.001948714	0.09763215
HOMER2	762.904045	−0.64907536	0.218124585	9.596591311	0.001949389	0.09763215
MYB	80.830462	−0.386211669	0.126466593	9.595490392	0.001950558	0.09763215
NMT2	49.2941549	0.453745355	0.141576441	9.579588804	0.001967525	0.09763215
ERICH1	445.217991	−0.412096292	0.134791355	9.570673095	0.001977103	0.09763215
LOX	38.7753467	−0.837609776	0.282800795	9.568551905	0.001979389	0.09763215
EMC7	38.9232153	−0.297068531	0.097179965	9.56836946	0.001979585	0.09763215
RNF167	143.994981	−0.28593229	0.094447548	9.567198302	0.001980849	0.09763215
SVIL	640.967988	−0.425770686	0.139799407	9.551376014	0.001997996	0.097944996
SGMS1	55.9206306	−0.461626108	0.15425216	9.533346984	0.002017718	0.098380034
IMPAD1	53.4291124	−0.579371195	0.19336976	9.502711545	0.002051685	0.099376942
MAPK6	287.705426	−0.48667072	0.162417619	9.495218971	0.00206008	0.099376942

TABLE 6
Predictive Model Weights of Genes
Predictive for Pre-Term Birth (PTB)
Gene    Weight
ELANE   0.0989222
ACSM3   0.07557269
MAPK10  0.06882871
IRX3    0.06702434
SPAG5   0.06010713
B3GNT2  0.05968447
LOX     0.05033319
H2AFX   0.04841582
ITGAE   0.03649107
ARL4A   −0.0354448
ZBTB26  0.03028558
BEX1    0.02647277
HBG2    0.02617242
SNX19   0.0248166
CCNA2   0.02240897
TLE1    −0.0213883
TMEM204 0.01798467
MRTO4   −0.0124935
PHGDH   0.01168144
IMPAD1  0.00555929
KCNMB1  0.00518973
ENPP4   0.00388786
MMP8    −0.0029393
MPZL3   0.00211636
NLRX1   0.00085898

FIG. 7G shows a receiver-operating characteristic (ROC) curve showing the performance of the predictive model for pre-term delivery across the 10-fold cross-validation. As shown in the figure, the predictive model for predicting pre-term delivery achieved a mean area under the curve (AUC) of 0.90±0.08, thereby demonstrating the excellent performance of the predictive model for predicting pre-term delivery.

Example 5: Prediction of Due Date (DD)

Using systems and methods of the present disclosure, a prediction model is developed to predict a due date of a fetus of a pregnant subject. For example, the predicted due date can be a number of days (e.g., 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, or 7 days) or weeks (e.g., 1 week, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks, 8 weeks, 9 weeks, 10 weeks, 11 weeks, 12 weeks, 13 weeks, 14 weeks, 15 weeks, 16 weeks, 17 weeks, 18 weeks, 19 weeks, 20 weeks, 21 weeks, 22 weeks, 23 weeks, 24 weeks, 25 weeks, 26 weeks, 27 weeks, 28 weeks, 29 weeks, 30 weeks, 31 weeks, 32 weeks, 33 weeks, 34 weeks, 35 weeks, 36 weeks, 37 weeks, 38 weeks, 39 weeks, 40 weeks, 41 weeks, 42 weeks, 43 weeks, 44 weeks, or 45 weeks) until an expected delivery of the fetus of the pregnant subject. As another example, the predicted due date can be a future date on which the delivery of the fetus of the pregnant subject is expected to occur.

The prediction model may be based on assaying a sample (e.g., a blood draw) of a pregnant subject at a given time point (e.g., at an estimated gestational age of 1 week, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks, 8 weeks, 9 weeks, 10 weeks, 11 weeks, 12 weeks, 13 weeks, 14 weeks, 15 weeks, 16 weeks, 17 weeks, 18 weeks, 19 weeks, 20 weeks, 21 weeks, 22 weeks, 23 weeks, 24 weeks, 25 weeks, 26 weeks, 27 weeks, 28 weeks, 29 weeks, 30 weeks, 31 weeks, 32 weeks, 33 weeks, 34 weeks, 35 weeks, 36 weeks, 37 weeks, 38 weeks, 39 weeks, 40 weeks, 41 weeks, 42 weeks, 43 weeks, 44 weeks, or 45 weeks).

FIG. 8 shows an example of a distribution of vaginal singleton births by obstetrician-estimated gestational age in the U.S. This figure shows that only 23.7% of vaginal singleton births occur at an estimated gestational age of 40 weeks, and about 67% of vaginal singleton births occur at an estimated gestational age of 39-41 weeks. Therefore, such variation of time of delivery illustrates the need for a better predictor of delivery date that uses a molecular clock, using systems and methods of the present disclosure.

FIG. 9A-9E show different methods of predicting due date for a fetus of a pregnant subject, including predicting an actual day (with error) (FIG. 9A), predicting a week (or other window) of delivery (FIG. 9B), predicting whether a delivery is expected to occur before or after a certain time boundary (FIG. 9C), predicting in which bin among a plurality of bins (e.g., 6 bins) a delivery is expected to occur (FIG. 9D), and predicting a relative risk or relative likelihood of an early delivery or a late delivery (FIG. 9E).

For example, the due date prediction model may be used to predict an actual day (with error) (FIG. 9A). For example, the predicted due date may be a number of days (e.g., 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, or 7 days) or weeks (e.g., 1 week, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks, 8 weeks, 9 weeks, 10 weeks, 11 weeks, 12 weeks, 13 weeks, 14 weeks, 15 weeks, 16 weeks, 17 weeks, 18 weeks, 19 weeks, 20 weeks, 21 weeks, 22 weeks, 23 weeks, 24 weeks, 25 weeks, 26 weeks, 27 weeks, 28 weeks, 29 weeks, 30 weeks, 31 weeks, 32 weeks, 33 weeks, 34 weeks, 35 weeks, 36 weeks, 37 weeks, 38 weeks, 39 weeks, 40 weeks, 41 weeks, 42 weeks, 43 weeks, 44 weeks, or 45 weeks) until an expected delivery of the fetus of the pregnant subject. As another example, the predicted due date may be a future date on which the delivery of the fetus of the pregnant subject is expected to occur. As another example, the predicted due date may be an estimated gestational age (e.g., 1 week, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks, 8 weeks, 9 weeks, 10 weeks, 11 weeks, 12 weeks, 13 weeks, 14 weeks, 15 weeks, 16 weeks, 17 weeks, 18 weeks, 19 weeks, 20 weeks, 21 weeks, 22 weeks, 23 weeks, 24 weeks, 25 weeks, 26 weeks, 27 weeks, 28 weeks, 29 weeks, 30 weeks, 31 weeks, 32 weeks, 33 weeks, 34 weeks, 35 weeks, 36 weeks, 37 weeks, 38 weeks, 39 weeks, 40 weeks, 41 weeks, 42 weeks, 43 weeks, 44 weeks, or 45 weeks) for which the delivery of the fetus of the pregnant subject is expected to occur. The predicted due date may be provided along with an error or confidence interval (e.g., 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 2 weeks, 3 weeks, or 4 weeks) for the predicted due date. The predicted due date may be provided along with an estimated likelihood or confidence (e.g., about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%) for the predicted due date.

As another example, the due date prediction model may be used to predict a week (or other window) of delivery (FIG. 9B). For example, the predicted due date may be a number of weeks (e.g., 1 week, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks, 8 weeks, 9 weeks, 10 weeks, 11 weeks, 12 weeks, 13 weeks, 14 weeks, 15 weeks, 16 weeks, 17 weeks, 18 weeks, 19 weeks, 20 weeks, 21 weeks, 22 weeks, 23 weeks, 24 weeks, 25 weeks, 26 weeks, 27 weeks, 28 weeks, 29 weeks, 30 weeks, 31 weeks, 32 weeks, 33 weeks, 34 weeks, 35 weeks, 36 weeks, 37 weeks, 38 weeks, 39 weeks, 40 weeks, 41 weeks, 42 weeks, 43 weeks, 44 weeks, or 45 weeks) until an expected delivery of the fetus of the pregnant subject. As another example, the predicted due date may be a future week (e.g., a week on the calendar) on which the delivery of the fetus of the pregnant subject is expected to occur. As another example, the predicted due date may be an estimated gestational age (e.g., 1 week, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks, 8 weeks, 9 weeks, 10 weeks, 11 weeks, 12 weeks, 13 weeks, 14 weeks, 15 weeks, 16 weeks, 17 weeks, 18 weeks, 19 weeks, 20 weeks, 21 weeks, 22 weeks, 23 weeks, 24 weeks, 25 weeks, 26 weeks, 27 weeks, 28 weeks, 29 weeks, 30 weeks, 31 weeks, 32 weeks, 33 weeks, 34 weeks, 35 weeks, 36 weeks, 37 weeks, 38 weeks, 39 weeks, 40 weeks, 41 weeks, 42 weeks, 43 weeks, 44 weeks, or 45 weeks) for which the delivery of the fetus of the pregnant subject is expected to occur. The predicted due date may be provided along with an estimated likelihood or confidence (e.g., about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%) for the predicted due date.

As another example, the due date prediction model may be used to predict whether a delivery is expected to occur before or after a certain time boundary (FIG. 9C). For example, the time boundary may be a number of weeks (e.g., 1 week, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks, 8 weeks, 9 weeks, 10 weeks, 11 weeks, 12 weeks, 13 weeks, 14 weeks, 15 weeks, 16 weeks, 17 weeks, 18 weeks, 19 weeks, 20 weeks, 21 weeks, 22 weeks, 23 weeks, 24 weeks, 25 weeks, 26 weeks, 27 weeks, 28 weeks, 29 weeks, 30 weeks, 31 weeks, 32 weeks, 33 weeks, 34 weeks, 35 weeks, 36 weeks, 37 weeks, 38 weeks, 39 weeks, 40 weeks, 41 weeks, 42 weeks, 43 weeks, 44 weeks, or 45 weeks) of estimated gestational age. For example, the time boundary may be an estimated gestational age of 40 weeks.

As another example, the due date prediction model may be used to predict which bin among a plurality of bins (e.g., 6 bins) a delivery is expected to occur (FIG. 9D). For example, the bins (e.g., time windows) may be equal ranges of time (e.g., 1 week, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks, 8 weeks, 9 weeks, 10 weeks, 11 weeks, 12 weeks, 13 weeks, 14 weeks, 15 weeks, 16 weeks, 17 weeks, 18 weeks, 19 weeks, 20 weeks, 21 weeks, 22 weeks, 23 weeks; or 1 month, 2 months, 3 months, 4 months, or 5 months; or a trimester among the first, second, or third trimesters). The predicted due date may be provided along with an estimated likelihood or confidence (e.g., about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%) for the predicted due date bin or time window.

As another example, the due date prediction model may be used to predict a relative risk or relative likelihood of an early delivery or a late delivery (FIG. 9E). For example, the prediction may comprise a relative risk or relative likelihood of an early delivery or a late delivery of about 10%, 20%, 30%, 40%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%. An early delivery may be defined as a due date at an estimated gestational age of less than 40 weeks, while a late delivery may be defined as a due date at an estimated gestational age of more than 40 weeks.

A due date prediction model was trained using samples collected from a gestational age (GA) cohort of pregnant subjects, all of whom had an estimated gestational age of a fetus of 34 weeks to 36 weeks. A training dataset was obtained using a cohort of 270 and 312 samples (about half of which was Caucasian and half of which was AA), of which 41 samples were designated as lab outliers and not used and 1 sample had an outlier low CPM. Further, a test dataset of 64 samples was obtained using a cohort (003_GA) of 19 samples (most of whom were Caucasian) and a cohort (009_VG) of 47 validation samples (all of whom had an estimated gestational age of a fetus of 34 weeks to 36 weeks, and most of whom were Caucasian).

Gene discovery was performed to develop the due date prediction model as follows. A set of 241 input genes, comprising candidate marker genes, was used. Using the training dataset, a subset of these candidate marker genes was identified as having a high median(log 2_CPM) value of greater than 0.5. An analysis of variance (ANOVA) was performed using a set of 248 genes (as shown in Table 7) for actual time to delivery for the training samples (e.g., −7 weeks vs. −2 weeks for the top 100 genes, and −6 weeks vs. −3 weeks for the top 100 genes). A Pearson linear correlation was performed to identify the top 100 genes among the candidate marker genes having the strongest statistical correlation to due date. A number of different prediction models were tested for prediction of time-to-delivery bins. First, the standard of care was used in which a predicted time to delivery was made based on a predicted due date at a gestational age of 40 weeks. Second, an estimated gestational age using ultrasound data only was used, using the collectionga cohort as an input to the elastic net prediction model. Third, an estimated gestational age using cfDNA only was used, using an input of log 2_CPMs of genes and confounders (e.g., parity, BMI, smoking status, etc.) as inputs to the elastic net prediction model. Fourth, an estimated gestational age using both cfDNA plus ultrasound was used, using an input of log 2 CPMs of genes, confounders, and collectionga input to the elastic net prediction model.

TABLE 7
Set of 248 Genes Used in ANOVA Model
Genes
ABCB1, AC010468.1, AC068657.2, AC078899.1, AC079250.1, AC114752.3,
ACOX1, ACTA2, ACTBP8, ACTG1P15, ADAM12, ADCK5, ADGRE1, ADGRG5,
ADGRL2, AKR1C1, AKR1E2, ALG1, ALS2, AMT, ANO5, ANP32AP1, ANP32C,
APBA3, ARFGEF3, ASMTL, ATAD3A, ATF4P3, ATP8B3, BBOF1, BBS4, BCAR3,
BCYRN1, C14orf119, C1orf228, C2orf42, C6orf106, C6orf47, C9orf3, CALM1P1,
CALM2, CAMK2D, CASC4P1, CD177, CD68, CDC27, CDC42P6, CDK5RAP2,
CFAP43, CFAP70, CHAC2, CHCHD4, CHKA, CKAP2, CLC, CLN5, CMTM3,
CNOT6LP1, CNTNAP2, COPA, CRH, CSRNP2, CSTF2, CTB-79E8.3, CXCR3,
CXXC4, CYP51A1, CYYR1, DAB2IP, DCUN1D1, DEPDC1B, DHCR24, DHTKD1,
DOCK9, DRAM1, DSC2, EEF1A1P16, EIF1AXP1, EIF3LP2, EIF4EBP3, ELMOD3,
ETFRF1, EVX2, EXO5, FAM120A, FBP1, FBXL14, FCGR3B, FGF2, FLII, FN1,
FTH1P3, FZD6, GABPA, GAS2, GATAD2B, GLIS2, GLRA4, GOLGA2, H2BFS,
HMGB1P11, HMGB3P22, HMGCS1, HNRNPKP1, HNRNPKP4, HP, HPCAL1,
HSPG2, ICAM4, ICMT, IKZF2, IL2RA, INHBA, INPP5K, INTS4, INTS6, ITGA3,
ITGB4, KCMF1, KCNK5, KIF3A, KLHDC8B, KLRC1, LRP5, MAGT1, MAPK1,
MAPK11, MAPK13, MCCC1, MCEMP1, MECP2,
Metazoa_SRP_ENSG00000278771, MGAT3, MIB1, MOB4, MORF4L1, MRRF, MT-TE,
MT-TP, MTDHP3, MUT, MYL12BP2, NAP1L1P1, NCOA1, NDUFV2P1, NEK6,
NEMP2, NRCAM, OASL, OGDH, PAK3, PAPPA, PAPPA2, PASK, PDZRN4, PERP,
PIGM, PMM1, PPIL1, PPM1H, PRICKLE4, PRKCZ, PSG9, PSMC3IP, PTMA,
RAB3GAP2, RAB43, RAP1BP1, RBBP4P1, RELL1, RFX2, RN7SL1, RN7SL396P,
RN7SL767P, RNA5SP355, RNY1, ROBO3, RP1-121G13.3, RP3-393E18.1,
RPL14P3, RPL15P2, RPL19P16, RPL5P5, RPTOR, RRN3P1, RSU1P1, SCAND1,
SEPT7P2, SERPINB9, SHISA5, SIRPG, SKOR1, SKP1P1, SLC43A1, SNRNP48,
SPCS2, SRGAP2C, SRP9P1, STAG3L2, STAT5B, STRAP, STX2, SVEP1, SYN2,
TAF6L, TANC1, TEK, TGDS, THOC3, THOC7, TIE1, TMA7, TMEM14A,
TMEM222, TMEM237, TMEM8A, TPI1P1, TRAV12-2, TRAV14DV4, TRIM36,
TTBK2, TTC28, UBE2R2, UQCRHL, VPS33B, WDR37, WDR77, WTH3DI,
Y_RNA_ENSG00000199303, Y_RNA_ENSG00000201412,
Y_RNA_ENSG00000202357, Y_RNA_ENSG00000202533,
Y_RNA_ENSG00000252891, YPEL2, ZBED5-AS1, ZBTB16, ZBTB20, ZEB2P1,
ZFY, ZNF148, ZNF319, ZNF563, ZNF696, ZNF714, ZSCAN16-AS1, ZSCAN22,
ZSCAN30

FIG. 10 shows a data workflow that is performed to develop a due date prediction model (e.g., classifier). First, the training data (n=271 samples) is randomly split up into 4 sets of 67 samples each. Next, the model is trained using different combinations of 3 of the 4 split sets that are creating by leaving out 1 split set at a time (e.g., a first combination of splits 1, 2, 3; a second combination of splits 2, 3, 4; a third combination of splits 1, 3, 4; and a fourth combination of splits 1, 2, 4; each having n=203 samples). Next, cross-validation is performed using the n=271 samples, where each of the 4 models are tested on the held-out split set (n=67 samples). Next, independent validation of each of the models is performed, whereby the models are tested on independent data (e.g., the testing dataset).

FIGS. 11A-11B show prediction error of a due date prediction model that is trained on 270 and 310 patients, respectively. The plot shows the percent of samples having a given prediction error (e.g., time to delivery bin, with a bin width of 1 week, where positive values indicate that delivery occurred after the predicted due date and negative values indicate that delivery occurred before the predicted due date). The figures show improved accuracy and lower error in due date prediction using the cfRNA-only model or the cfRNA-plus-ultrasound model, as compared to the standard-of-care (40 weeks) model and the ultrasound-only model.

Example 6: Prediction of Pre-Term Birth (PTB)

Using systems and methods of the present disclosure, a prediction model was developed to predict a risk of pre-term birth (PTB) of a pregnant subject. The dataset obtained from a cohort of Caucasian subjects (as described in Example 4) was re-analyzed with a modified gene list, as shown in Table 8. FIG. 12 shows a receiver-operator characteristic ROC) curve for the pre-term birth prediction model, using a set of 22 genes for a set of 79 samples obtained from a cohort of Caucasian subjects. Of the 79 total samples, 23 had early PTB (defined as delivery before 34 weeks of estimated gestational age). The mean area-under-the-curve (AUC) for the ROC curve was 0.91±0.10.

TABLE 8
Genes Predictive for Pre-Term Birth (PTB) (Caucasian)
Gene
SLC2A5
ESPN
LOX
IRX3
SPDYC
BEX1
ANK3
MTRNR2L12
MAPK10
B3GNT2
COL6A3
DDX11L10
NBPF3
U2AF1
MT1X
PHGDH
HBG2
RPL23AP7
CTD-3092A11.1
HLA-G
COL4A2
GSTM5

Further, FIG. 13A shows a receiver-operator characteristic ROC) curve for a pre-term birth prediction model, using a set of genes for a set of 45 samples obtained from a cohort of subjects having African or African-American ancestries (AA cohort). Of the 45 total samples, 18 had early PTB (defined as delivery before 34 weeks of estimated gestational age). The mean area-under-the-curve (AUC) for the ROC curve was 0.82±0.08.

FIG. 13B shows a gene panel for a pre-term birth prediction model for three different AA cohorts (cohort 1, cohort 2, and cohort 3), including RAB27B, RGS18, CLCN3, B3GNT2, COL24A1, CXCL8, and PTGS2.

FIG. 14A shows a workflow for performing multiple assays for assessment of a plurality of pregnancy-related conditions using a single bodily sample (e.g., a single blood draw) obtained from a pregnant subject. Several blood draws can be performed along the pregnancy to survey and test the pregnancy progression. Blood draws obtained at specific time points (e.g., T1, T2, and T3) are tested for determining the risk of specific pregnancy-related complications that may happen several weeks away. For fetal development, longitudinal testing is performed at each blood draw (T1, T2, and T3) to provide results of the progression of fetal development. For example, a first blood sample may be obtained from a pregnant subject at time T1 (e.g., during the first trimester of pregnancy), a second blood sample may be obtained from the pregnant subject at time T2 (e.g., during the second trimester of pregnancy), and a third blood sample may be obtained from the pregnant subject at time T3 (e.g., during the third trimester of pregnancy). The blood sample obtained at time T1 may be used for assaying for pregnancy-related conditions that may be detectable or predictable in early-stage pregnancy or the first trimester of pregnancy, such as pre-term birth, spontaneous abortion, PE, GDM, and fetal development. The blood sample obtained at time T2 may be used for assaying for pregnancy-related conditions that may be detectable or predictable in mid-stage pregnancy or the second trimester of pregnancy, such as pre-term birth, PE, GDM, fetal development, and IUGR. The blood sample obtained at time T3 may be used for assaying for pregnancy-related conditions that may be detectable or predictable in late-stage pregnancy or the third trimester of pregnancy, such as due date, fetal development, placenta accreta, IUGR, prenatal metabolic diseases, and neonatal metabolic genetic diseases from RNA.

FIG. 14B shows a combination of conditions which can be tested from a single blood draw along a pregnancy progression of a pregnant subject. The blood sample obtained at time T1 may be used for assaying for pregnancy-related conditions that may be detectable or predictable in early-stage pregnancy or the first trimester of pregnancy, such as pre-term birth, preeclampsia (pregnancy-related hypertensive disorders), gestational diabetes, spontaneous abortion, and fetal development (normal and abnormal). The blood sample obtained at time T2 may be used for assaying for pregnancy-related conditions that may be detectable or predictable in mid-stage pregnancy or the second trimester of pregnancy, such as gestational age, preeclampsia (pregnancy-related hypertensive disorders), gestational diabetes, spontaneous abortion, placenta previa, placenta accreta (hemorrhage or excessive bleeding delivery), premature rupture of membrane (PROM), fetal development (normal and abnormal), and intrauterine/fetal growth restriction (IUGR). The blood sample obtained at time T3 may be used for assaying for pregnancy-related conditions that may be detectable or predictable in late-stage pregnancy or the third trimester of pregnancy, such as due date, congenital disorders, placenta previa, placenta accreta (hemorrhage or excessive bleeding delivery), premature rupture of membrane (PROM), fetal development (normal and abnormal), and intrauterine/fetal growth restriction (IUGR), post-partum depression, prenatal metabolic genetic disease, post-partum cardiomyopathy, and neonatal metabolic genetic diseases from RNA.

Example 7: Prediction of Imminent Birth

Using systems and methods of the present disclosure, a prediction model was developed to detect or predict a risk of imminent birth of a pregnant subject. For example, a birth that occurs or is predicted to occur within the next 1 to 3 weeks may be considered as an imminent birth. The prediction model development comprised obtaining a cohort of subjects and training the prediction model on a training dataset corresponding to the cohort of subjects.

The cohort of subjects was obtained as follows. As shown in FIGS. 15A-15B, a Discovery 1 cohort of 310 mixed race subjects (e.g., pregnant women) and a Discovery 2 cohort of 86 Caucasian subjects, respectively, were established (with patient identification numbers shown on the x-axis). From these cohorts, one or more biological samples (e.g., 1 or 2) were collected and assayed at different time points corresponding to an estimated gestational age (shown on the y-axis, in increasing order of estimated gestational age at delivery) of a fetus of each subject, using methods and systems of the present disclosure. For example, the estimated gestational age (shown on the y-axis) may be determined using methods such as ultrasound imaging, a last menstrual period (LMP) date, or a combination thereof, and may range from 0 to about 42 weeks. The discovery cohorts includes subjects from who delivered at term and pre-term with blood collected between 1-10 weeks before delivery/birth.

FIG. 15C-15D show a distribution of participants in the Discovery 1 mixed race cohort and the Discovery 2 Caucasian cohort, respectively, based on blood sample collection gestation. FIGS. 15E-15F show a distribution of samples collection in the Discovery 1 mixed race cohort and the Discovery 2 Caucasian cohort, respectively, by weeks before birth.

Table 9 shows validation cohorts for imminent birth comprising subjects from whom different sample types were collected for use in different studies, including studies for the prediction of pre-term birth (e.g., as controls), prediction of delivery, prediction of due date, and prediction of actual gestational age of a fetus of each subject.

TABLE 9
Discovery and validation cohorts
				Vali-	Vali-
	Discovery	Discovery	Discovery	dation	dation	Discovery
	1 Mixed	1 CAU	1 AA	1 AA	2 Mixed	2 CAU
N	310	128	177	108	56	86

Differential expression analysis of the cohort data sets was performed as follows. All samples from the discovery cohort were binned in 1 to 10 weeks gestation at blood collection from birth as presented in FIG. 15E. A differential analysis for genes that are correlated to the time to delivery was performed, revealing that 9 genes show a significant correlation up to 10 weeks close to birth. A set of 9 genes (HTRA1, PAPPA2, ADCY6, PTPRB, TANGO2, IGFBP7, EFHD1, NFYB, ITGA5) that are predictive of birth 1 to 10 weeks before birth are listed in Table 10. The HTRA1 gene is particularly important. HTRA1 is a serine protease that cleaves fetal fibronectin, which may be present in vaginal secretion right before or at birth.

TABLE 10
Genes Predictive for Birth Within 1 to 3 Weeks
	Gene	Correlation	P-value
	HTRA1	−0.469584	0.000005
	PAPPA2	−0.454334	0.000011
	ADCY6	0.453381	0.000012
	PTPRB	−0.450201	0.000014
	TANGO2	0.447341	0.000016
	IGFBP7	−0.435855	0.000027
	EFHD1	−0.425501	0.000044
	NFYB	−0.415233	0.00007
	ITGA5	−0.415205	0.00007

FIG. 16A shows expression trends and significant abundance level separation for a set of top 4 genes (EFHD1, ADCY6, HTR1, PAPPA2) between samples collected at 1 week before birth. FIG. 16B shows an example of genes showing significant correlation to being close to delivery. This figure demonstrates that correlation p-value significance of log₁₀(p-value) exceeds a threshold of 1 for 3 genes (HTRA1, PAPPA2, and EFHD1) in several discovery and validation cohorts.

Example 8: Prediction of Pre-Term Birth (PTB)

Using systems and methods of the present disclosure, a prediction model was developed to detect or predict a risk of pre-term birth (PTB) of a pregnant subject. The prediction model development comprised obtaining a cohort of subjects and training the prediction model on a training dataset corresponding to the cohort of subjects.

The cohort of subjects was obtained as follows. As shown in FIG. 17A, a first cohort of 192 subjects (e.g., pregnant women) was established (with patient identification numbers shown on the x-axis). From this cohort, one or more biological samples (e.g., 1 or 2) were collected and assayed at different time points corresponding to an estimated gestational age (shown on the y-axis, in increasing order of estimated gestational age at delivery) of a fetus of each subject, using methods and systems of the present disclosure. For example, the estimated gestational age (shown on the y-axis) may be determined using methods such as ultrasound imaging, a last menstrual period (LMP) date, or a combination thereof, and may range from 0 to about 42 weeks. The first cohort includes subjects from whom different sample types (preterm, high risk preterm, miscarriages, or stillbirth) were collected for use in different types of modeling with sample classifications to identify markers associated preterm, miscarriages, or stillbirth in different subtypes or classes.

FIG. 17B shows a distribution of participants in the first cohort based on each participant's age at the time of medical record abstraction. FIG. 17C shows a distribution of 192 participants in the first cohort based on each participant's race. FIG. 17D shows a distribution of 192 collected samples in the first cohort based on the study sample type of the collected samples.

Further, as shown in FIG. 18A, a second cohort of 76 subjects (e.g., pregnant women) was established (with patient identification numbers shown on the x-axis). From this cohort, one or more biological samples (e.g., 1 or 2) were collected and assayed at different time points corresponding to an estimated gestational age (shown on the y-axis, in increasing order of estimated gestational age at delivery) of a fetus of each subject, using methods and systems of the present disclosure. For example, the estimated gestational age (shown on the y-axis) may be determined using methods such as ultrasound imaging, a last menstrual period (LMP) date, or a combination thereof, and may range from 0 to about 42 weeks.

FIG. 18B shows a distribution of 76 participants in the second cohort based on each participant's race. FIG. 18C shows a distribution of 76 collected samples (25 pre-term samples and 51 full-term controls) in the second cohort based on the study sample type of the collected samples. FIG. 18D shows a distribution of 76 collected samples (25 pre-term samples and 51 full-term controls) in the second cohort based on the study sample type of the collected samples.

Differential expression analysis of the first cohort data set was performed as follows. An analysis for differentially expressed genes between the pre-term case samples and control samples was performed, revealing a set of 100 differentially expressed genes across all cases and controls.

For example, Table 11 shows the differential gene expression between different subclasses for PTB cases. Samples were classified into a high-risk group if they were associated with having a previous history of at least one of following pregnancy complications: spontaneous PTB, PPROM, late miscarriage (e.g., after 14 weeks of gestational age), cervical surgery, and uterine anomaly. Samples were classified into a low-risk group if they were associated with a general antenatal population with none of the above risk factors. Miscarriage was characterized by having delivered before 24 weeks of gestational age.

TABLE 11
Pre-Term Birth Signal in Different Sub-Types of PTB
	Cases/	DE genes	DE genes
	Controls	up	down	Top Genes
All PTB	49/144	15	83	Shared
High risk	44/123	18	172	Shared
Low risk	5/14	0	1	Different genes
Miscarriage	14/41	0	0	Different genes
or stillbirth

A signal in pre-term birth-associated genes in different sub-types of PTB was observed to be driven by a high-risk group as shown in FIG. 19A, which shows a quantile-quantile (QQ) plot of a graphical representation of the deviation of the observed P values from the null hypothesis for individual genes. Genes which are deviated from the middle line at the log₁₀(p-value) of 3.5 are considered to be truly differentially expressed in high-risk populations relative to healthy controls. A set of top genes that are predictive for high risk pre-term birth (PTB) are listed in Table 12.

FIG. 19B shows a receiver-operator characteristic (ROC) curve for the high pre-term birth prediction model, using all differentially expressed genes from Table 11 for a set of 167 samples obtained from a high-risk subclass cohort of Caucasian subjects. Of the 167 total samples, 44 had early PTB (e.g., delivery before 34 weeks of estimated gestational age). The mean area-under-the-curve (AUC) for the ROC curve was 0.75±0.08. FIG. 19C shows a receiver-operator characteristic (ROC) curve for a set of top 9 genes (EFHD1, ABI3BP, NEAT1, HSD17B1, CDR1-AS, GCM1, DAPK2, ZCCHC7, COL3A1, and AKR7A2). The mean area-under-the-curve (AUC) for the ROC curve was 0.80±0.07, with relative contributions from each gene.

TABLE 12
Top Set of Predictive Genes for High-Risk Pre-Term Birth (PTB)
	Gene	P-adj	log2 Fold Change
	CDR1-AS	0.000006232042908	1.531899181
	COL3A1	0.0001829599367	2.296099004
	DCN	0.007756452652	1.959492728
	DAPK2	0.008577062504	−0.6538136896
	ABI3BP	0.01846895706	1.253946028
	NEAT1	0.02229732621	−0.8955349534
	ANTXR1	0.02229732621	1.307627338
	PLEKHM1P1	0.02229732621	−0.9490980614
	TNFRSF25	0.02563117996	−2.074833817
	MEGF6	0.02563117996	−1.616170492
	PGGHG	0.02563117996	−1.312523641
	TNFRSF10B	0.02728425554	−1.202142785
	LUM	0.0273958536	2.615661527
	MMP2	0.0273958536	1.511005424
	MYO18B	0.02810913316	−1.11864242
	TMC8	0.03087184347	−0.8337355677
	EME2	0.03087184347	−1.563909654
	GCM1	0.03087184347	−1.537115843
	COL14A1	0.03163361683	1.743013436
	ZCCHC7	0.0323639933	0.222285457
	EIF4A1	0.0323639933	−1.02093915
	ABCC10	0.03655742169	−1.21406946
	PABPC1L	0.03944887005	−1.272184265
	LILRA6	0.03981500296	−1.225586629
	ADCY7	0.03981500296	−0.911845995
	HSD17B1	0.03981500296	−1.112912409
	SLC24A4	0.03981500296	−1.36958566
	PIEZO1	0.03981500296	−0.7881581173
	SLC27A3	0.03981500296	−0.9788188364
	FBN2	0.03981500296	−1.075292442
	SLC12A9	0.03981500296	−0.9818661938
	SLC43A2	0.03981500296	−0.9510233821
	ABCA7	0.03981500296	−0.7356204689
	SPOCK2	0.03981500296	−0.8143930692
	AL773572.7	0.03981500296	−1.667040365
	SEC31B	0.03981500296	−1.197850588
	ARRDC5	0.03981500296	−1.690147984
	APBB3	0.03981500296	−1.393590176
	SLC11A1	0.03981500296	−0.9838153699
	APOBR	0.04450245034	−0.7589482093
	GH2	0.04450245034	−1.47585156
	TLR2	0.04636265694	−0.8826852522
	GAA	0.04636265694	−0.987530859
	NTNG2	0.04656847046	−1.541500092
	SNORD46	0.04656847046	−1.96052151
	PBXIP1	0.04656847046	−0.5065889974
	S1PR3	0.04690323503	−1.664837438
	FRAT2	0.04845006461	−0.7376686877
	FLG2	0.04845006461	−1.678849501
	CLASRP	0.04845006461	−0.6278945866
	FCGRT	0.04921060752	−0.797948221
	PDE3B	0.04951788766	−0.6367484205
	TMC6	0.04951788766	−0.718127351
	EFHD1	0.04951788766	−1.17965089
	AKR7A2	0.04958579441	0.4800853396
	ITGAM	0.05150923955	−0.3518160003
	PLXNA3	0.05220665814	−0.8351641135
	NUP210	0.05279441154	−0.5578845296
	SSH3	0.05279441154	−0.6053200011
	NPEPL1	0.05515096309	−0.9625781876
	COL9A2	0.05544088408	−0.9036988185
	SULF2	0.05931148621	−0.8282550008
	ATG16L2	0.06093047358	−0.8232810424
	LENG8	0.06137133329	−0.5229381575
	DNHD1	0.06137133329	−0.8242614989
	MYH3	0.06137133329	−1.027874258
	SIGLEC14	0.06137133329	−0.969520126
	ODF3B	0.06137133329	−0.9851026487
	CSH1	0.06167244945	−0.8095712072
	TAP1	0.06167244945	−0.5279898052
	TCIRG1	0.06167244945	−0.8389438684
	TMTC2	0.06167244945	−0.8691690267
	AOAH	0.06167244945	−0.6439585779
	TLR8	0.06663109333	−0.8023150795
	DIRC2	0.06663109333	−0.8674598547
	MPEG1	0.06663109333	−0.6624359256
	RAB44	0.06663109333	−0.8997466671
	NLRP1	0.06663109333	−0.6868095141
	UVSSA	0.06663109333	−0.6160785003
	PLXNB2	0.06663109333	−0.6271170344
	IGF2R	0.06663109333	−0.6918340652
	NOTCH1	0.06663109333	−0.4765941786
	ARPC4-
	TTLL3	0.06663109333	−0.7045393297
	CD300C	0.06663109333	−1.144634751
	SH2B1	0.06663109333	−0.578963839
	LGALS14	0.06663109333	−1.125378735
	CCDC88B	0.06663109333	−0.6836681428
	GTPBP3	0.06663109333	−0.7362739174
	ATP10A	0.06663109333	−0.7959520418
	SIGLEC7	0.06663109333	−0.6692818639
	COLGALT1	0.06663109333	−0.730199416
	SUN2	0.06663109333	−0.6109180612
	ABCA2	0.06663109333	−0.9002282272
	CSF3R	0.06663109333	−0.8347284824
	NSUN5P2	0.06678833246	−1.567214574
	LRP1	0.06678911515	−0.7509418684
	MRI1	0.06680407486	−0.8427458222
	KLC4	0.0675554476	−0.4761855735
	C1S	0.06874852119	0.8897786067
	RPS24P8	0.07310321208	−0.8139181709
	RSRP1	0.07328786935	−0.5165840992
	TMEM173	0.07328786935	−0.6198609879
	ZNF767P	0.07328786935	−1.328460916
	LILRB2	0.07328786935	−0.7255314572
	MBOAT7	0.07328786935	−0.6439778317
	EP400NL	0.07505883827	−0.5986535479
	SNORA74B	0.07505883827	−2.153171587
	COL1A1	0.07649313302	1.467807155
	NSRP1P1	0.07819752186	−0.8798559714
	ATP10D	0.07819752186	−0.5973763959
	VGLL3	0.07819752186	−0.8564161572
	POGLUT1	0.07819752186	−0.7284583558
	SENP3	0.07819752186	−0.4415204386
	RELT	0.07819752186	−0.9387042103
	MGAT1	0.07819752186	−0.5057774794
	EPPK1	0.07836403686	−0.7908834718
	SIRPB1	0.07915186374	−0.9127490872
	ZNF90	0.07915186374	0.3357861199
	CAPN13	0.07915186374	1.39545777
	POLM	0.07915186374	−0.652546798
	SIRPB2	0.07915186374	−1.001548716
	CAPN6	0.07977866418	−1.027198094
	AC004951.6	0.07977866418	1.695803913
	COL5A1	0.07977866418	1.080964445
	CCNL1	0.07977866418	−0.5394395627
	CCDC80	0.07977866418	0.7506926428
	LZTR1	0.07977866418	−0.3694662723
	CORO7	0.0823144424	−0.6671451408
	SGSM2	0.0823144424	−0.5107151598
	REC8	0.0823144424	−0.6811017805
	CSHL1	0.0823144424	−1.128469072
	PLAC4	0.0823144424	−0.9715559701
	KIFC2	0.0823144424	−1.318471383
	TRABD2A	0.08455470118	−0.916025636
	C7orf43	0.08521222818	−0.6290196123
	LTBR	0.08576238338	−0.6873265786
	NLRC5	0.08576238338	−0.3309468614
	CD93	0.08716347419	−0.7630469638
	TNFRSF1A	0.08716347419	−0.6552554162
	CDK5RAP3	0.08716347419	−0.5267137109
	FGL2	0.08828798716	−0.5520944536
	HIC2	0.08828798716	−0.8628085035
	TRAF1	0.08828798716	−0.7507113762
	DNAH1	0.08828798716	−0.6269726561
	SERINC5	0.08828798716	0.4411719721
	ITGB2	0.08828798716	−0.5961969581
	AGAP9	0.08828798716	−0.7465933148
	MYO15B	0.08871590633	−0.5886292587
	ALG2	0.08871590633	−0.5054504041
	LFNG	0.08885322846	−0.872300955
	SORL1	0.08929473343	−0.6423125952
	SLC2A6	0.09076981423	−1.013599518
	TRIM56	0.09076981423	−0.3351847824
	GGA3	0.09076981423	−0.1917226273
	ADAMTSL4	0.09076981423	−0.8144474405
	AAK1	0.09076981423	−0.2503087338
	PLEC	0.09228195226	−0.5019996265
	KLC1	0.09228195226	−0.3215539114
	SETD1B	0.09228195226	−0.3296507553
	SLC38A10	0.09228195226	−0.4899444244
	EXOC3	0.09228195226	−0.1717569971
	CSH2	0.09228195226	−0.6712648492
	P2RX7	0.09228195226	−0.8696358362
	ZNF335	0.0925066107	−0.4051906146
	TSPOAP1	0.0925066107	−0.6263300552
	MROH1	0.0925066107	−0.4067563819
	MAN2C1	0.0925066107	−0.457260922
	SCPEP1	0.0925066107	−0.58621504
	FRS3	0.09340243497	−0.7845220185
	FCN1	0.094079047	−0.6393500511
	CSRNP1	0.094079047	−0.4135881931
	CPVL	0.09479121535	−0.6477578756
	PLAC9	0.09491876413	1.510583009
	TNFRSF1B	0.09506645739	−0.7048093579
	CCDC142	0.09569299562	−0.9093263547
	PLCH2	0.09569299562	−0.9376399083
	ITGA5	0.09632706616	−0.5427180069
	ARHGAP33	0.09632706616	−0.9479851887
	MT1E	0.09715293572	0.6727425964
	OBSCN	0.09794438812	−0.5382292327
	TRPM2	0.09952076687	−0.8305205972
	MMP17	0.09960934016	−0.9364206448
	C3AR1	0.09960934016	−0.5520165487
	VIPR1	0.09960934016	−1.165669094
	SREBF1	0.09960934016	−0.6029100137
	RREB1	0.09960934016	−0.1587187676
	TMEM256-
	PLSCR3	0.09960934016	−1.22479337
	CREBZF	0.09960934016	−0.4118130094
	ADAM8	0.09999909729	−0.8574616833
	HSPA7	0.09999909729	−1.129374439

Differential expression analysis of the second cohort data set was performed as follows. Biomarker discovery was performed to identify early diagnostic markers of pre-term using cell-free RNA samples in the second cohort. In order to reduce the effect of gestational age, the sample set was reduced to 27 plasma samples from pregnant women who delivered pre-term and 53 plasma samples from matched controls that were collected at equivalent weeks of gestation (e.g., about 25 weeks of gestational age), as shown in Table 13.

TABLE 13
Demographics of Early PTB Samples in the Second Cohort
	Samples	GA at collection (weeks)	BMI
Pre-term cases	27	25.4 ± 1.0	29.5 ± 6.5
controls	53	25.4 ± 1.0	26.2 ± 8.0

FIG. 20A shows a distribution of demographic statistics for this subset of early PTB samples and controls in the second cohort that were included in the analysis. An analysis for differentially expressed genes between the pre-term case samples and pre-term control samples was performed. A set of top 30 genes that are predictive for high risk pre-term birth (PTB) were determined, as shown in Table 14.

TABLE 14
Statistical Values for Top Differentially Expressed
Genes for Early PTB in the Second Cohort
		Mean	Log2 Fold
	Gene	Expression	Change	P−value
	HRG	8.140452	1.920363	7.89E−05
	ANGPTL3	3.847834	1.83131	0.000185
	NPM1P26	0.671245	1.936622	0.000237
	HIST1H4F	20.91216	−0.47087	0.000377
	CRY	36.99376	0.257658	0.000399
	BHMT	2.291833	1.484639	0.000806
	C2orf49	57.97035	0.249506	0.000848
	OASL	26.75105	0.719533	0.001211
	SELE	1.296385	1.631514	0.001446
	CHD4	1515.132	0.15261	0.001708
	IFIT1	115.1264	0.672503	0.001787
	DHX38	418.0855	0.182905	0.00207
	DNASE1	10.21555	−0.53365	0.002209
	CEACAM6	25.49209	−0.69758	0.002253
	AGPAT4	6.973746	−0.56801	0.002335
	SERPING1	172.2336	−0.75404	0.002538
	PLCXD1	12.50904	−0.52192	0.002565
	ARFGEF3	5.735036	−0.73881	0.002608
	ERGIC2	99.542	0.222491	0.002671
	SH2D1A	33.09903	−0.48059	0.002872
	AEBP1	7.716002	−0.87421	0.00341
	SIGLEC6	4.86553	−0.90286	0.003431
	PIP5K1A	53.89827	−0.17974	0.003437
	IGHV3-48	1.871432	1.118533	0.003499
	TRBV4-2	0.981817	−1.54074	0.003557
	PHC1P1	8.194502	0.412459	0.003999
	FAM76B	128.4759	0.151824	0.004071
	PDE6H	2.829983	0.905734	0.004152
	PDAP1	670.607	0.159327	0.004326

FIG. 20B shows a QQ plot for early PTB in the second cohort, which is a graphical representation of the deviation of the observed P values from the null hypothesis for individual genes. Genes which are deviated from the middle line at the log₁₀(p-value) of 3.5 are considered to be truly differentially expressed in between case and healthy controls.

FIG. 20C shows boxplots and significant abundance level separation for the top 12 differentially expressed genes (ANGPTL3, NPM1P26, HIST1H4F, CRY1, BHMT, C2orf49, OASL, SELE, CHD4, IIFIT1, DHX38, and DNASE1) for early PTB in the second cohort. The results indicate that differential expression was not driven by ethnic differences in maternal subjects.

Example 9: Prediction of Preeclampsia (PE)

Using systems and methods of the present disclosure, a prediction model was developed to detect or predict a risk of preeclampsia (PE) of a pregnant subject. The prediction model development comprised obtaining a cohort of subjects and training the prediction model on a training dataset corresponding to the cohort of subjects.

The cohort of subjects was obtained as follows. As shown in FIG. 21, a first cohort of 18 subjects (e.g., pregnant women) was established (with delivery on the x-axis). From this cohort, one or more biological samples were collected and assayed at different time points corresponding to an estimated gestational age (shown on the x-axis, in increasing order of estimated gestational age at delivery) of a fetus of each subject, using methods and systems of the present disclosure. For example, the estimated gestational age (shown on the x- and y-axis) may be determined using methods such as ultrasound imaging, a last menstrual period (LMP) date, or a combination thereof, and may range from 0 to approximately 42 weeks. The first cohort includes 6 cases of PE with 1 subject of early onset of PE resulting in delivery before 32 weeks of gestation, and 5 subjects with late onset of PE with delivery after 36 weeks of gestation.

Further, as shown in FIG. 22A, a second cohort of 130 subjects (pregnant women) was established (with patient identification numbers shown on the x-axis). From this cohort, one or more biological samples (e.g., 1 or 2) were collected and assayed at different time points corresponding to an estimated gestational age (shown on the y-axis, in increasing order of estimated gestational age at delivery) of a fetus of each subject, using methods and systems of the present disclosure. For example, the estimated gestational age (shown on the y-axis) may be determined using methods such as ultrasound imaging, a last menstrual period (LMP) date, or a combination thereof, and may range from 0 to about 42 weeks. The first cohort includes subjects from whom different sample types were collected for use in different types of modeling with sample classifications to identify markers associated preterm in different subtypes or classes.

FIG. 22B shows a distribution of 130 participants in the second cohort based on each participant's race. FIG. 22C shows a distribution of 144 collected samples in the second cohort based on the study sample type of the collected samples.

Differential expression analysis of the first cohort data set was performed as follows. An analysis for de novo discovery for statistically significant genes between the preeclampsia case samples and healthy control samples was performed, revealing a set of 3,869 differentially expressed genes.

For example, Table 15 shows the top 20 differential expressed genes with top 4 genes (SPTB, PLGRKT, ZNF69, and KIF5C) satisfying a threshold of a Bonferroni correction of p-value less than 0.05 between cases and controls for preeclampsia.

TABLE 15
Top 20 Statistically Significant Differentially
Expressed Genes in Preeclampsia (PE)
Gene	P-value	bh adjusted	bonferroni adjusted
SPTB	7.21E−07	0.009338582	0.009338582
PLGRKT	1.61E−06	0.009585951	0.020811664
ZNF69	2.73E−06	0.009585951	0.035325024
KIF5C	2.96E−06	0.009585951	0.038343805
GLMP	5.44E−06	0.01128075	0.070507842
NFKBID	5.47E−06	0.01128075	0.070885069
SLC27A4	6.60E−06	0.01128075	0.085479797
MSANTD2	6.96E−06	0.01128075	0.090246002
ZSCAN16-AS1	8.26E−06	0.011898545	0.107086908
SLC22A17	1.18E−05	0.015324382	0.153559972
GIMAP5	1.38E−05	0.015324382	0.178203029
KNSTRN	1.47E−05	0.015324382	0.191059786
HECTD4	1.54E−05	0.015324382	0.199216971
UBE2Q1	2.04E−05	0.018495821	0.264604216
POLR2J	2.14E−05	0.018495821	0.277437317
PPM1A	2.40E−05	0.019438155	0.311010475
MAP3K13	2.78E−05	0.02120929	0.360557924
FAM157A	3.57E−05	0.02405401	0.462147561
ZNF17	3.67E−05	0.02405401	0.475265105
PROSER3	3.88E−05	0.02405401	0.503185564

FIG. 23 shows a significant abundance level separation between cases and healthy controls for the top 20 differentially expressed genes for preeclampsia (PE) in the first cohort. An additional set of 192 healthy controls with blood collection at the same gestation and similar demographic profile added as the second healthy control group to show good differential expression separation for preeclampsia subjects.

Differential expression analysis of the second cohort data set was performed as follows. We performed biomarker discovery to identify early diagnostic markers of preeclampsia using cell-free RNA in the second cohort. In order to reduce the effect of gestational age, the sample set was reduced to 36 plasma samples from pregnant women who developed preeclampsia, and 74 plasma samples from matched controls that were collected at equivalent weeks of gestation (e.g., about 25 weeks of gestational age) and comparable maternal body mass index (BMI), as shown in Table 16.

TABLE 16
Demographics of PE Samples in the Second Cohort
	Samples	GA at Collection (weeks)	BMI
	Cases	36	25.3 ± 1.0	29.8 ± 7.2
	Controls	74	25.4 ± 1.1	28.5 ± 7.2

FIG. 24A shows a distribution of demographic statistics for the subset of PE samples and controls in the second cohort that were included in the analysis. Differential expression analysis was performed between cases and controls using a Wald test, thereby obtaining a set of differentially expressed genes between pregnancies that developed preeclampsia and matched controls.

Table 17 shows the top 19 differentially expressed genes for PE. Notably, among the top genes found, several genes were associated with placental development, such as PAPPA2. It was observed that PAPPA2 showed significant statistical significance after adjustment for multiple hypothesis correction, and also showed a significant deviation from the null hypothesis in a QQ plot for differentially expressed in PE (as shown in FIG. 24B).

Additionally, as shown in the boxplots of FIG. 24C, the differences in top 12 genes (AGAP9, ANKRD1, CIS, CCDC181, CIAPIN1, EPS8L1, FBLN1, FUNDC2P2, KISS1, MLF1, PAPPA2, and TFPI2) expression were not driven by maternal ethnic differences supporting its role as early predictors of preeclampsia. The top 19 genes from differential expression analysis of the second cohort are summarized in Table 17.

TABLE 17
Top 19 Differentially Expressed Genes Predictive
of Preeclampsia (PE) in the Second Cohort
	Mean
Gene	expression	Log2 fold change	p-value
PAPPA2	10.91463	1.634397	8.49E−07
MEF2D	206.7518	−0.23456	7.2E−06
FUNDC2P2	5.743276	−1.3228	8.15E−05
CCDC181	3.281346	1.391803	0.000102
FADD	73.29945	−0.26702	0.000123
RPS4XP7	1.418757	−1.51346	0.000131
KLRC4	1.187923	−1.67053	0.000297
MLF1	2.769177	−0.80739	0.000304
ING1	97.81814	−0.21556	0.000366
ZNF800	215.7781	0.210542	0.000433
FIG4	148.146	0.135923	0.000447
UCK1	34.70849	−0.23788	0.0006
CD276	1.633719	1.027845	0.00067
PCED1B	108.4184	−0.30617	0.000909
TRIM8	236.5823	−0.16905	0.000918
TMEM129	5.657795	−0.55383	0.000937
RP13-383K5.4	1.808696	−0.95442	0.000947
CIC	428.9098	−0.18848	0.001008
CLAPIN1	26.95064	−0.26888	0.001031

Example 10: Prediction of Preeclampsia (PE) for Subjects with Blood Collected after 18 Weeks of Gestation Age and Validation Between Two Cohorts

Further, as shown in FIG. 25A, a cohort of 351 subjects (pregnant women) was established (with patient identification numbers shown on the x-axis). From this cohort, one or more biological samples (e.g., 1 or 2) were collected and assayed at different time points corresponding to an estimated gestational age (shown on the y-axis, in increasing order of estimated gestational age at delivery) of a fetus of each subject, using methods and systems of the present disclosure. For example, the estimated gestational age (shown on the y-axis) may be determined using methods such as ultrasound imaging, a last menstrual period (LMP) date, or a combination thereof, and may range from 0 to about 42 weeks. The first cohort includes subjects from whom different sample types were collected for use in different types of modeling with sample classifications to identify markers associated preterm in different subtypes or classes.

Further, a cohort of 351 subjects included 315 control subjects with delivery after 37 weeks of gestational age. 275 control subjects were classified as healthy controls, 40 control subjects had a history of chronic hypertension without preeclampsia. 36 case subjects were diagnosed with preeclampsia and delivered before 37 weeks of gestational age. 24 case subjects were diagnosed with de novo preeclampsia, and 12 case subjects had preeclampsia with a history of chronic hypertension.

Differential expression analysis of the cohort data set was performed as follows. Biomarker discovery was performed to identify early diagnostic markers of preeclampsia using cell-free RNA in the second cohort. In order to estimate the effect of chronic hypertension, two separate differential expression analyses were performed to estimate the effect of chronic hypertension. A first analysis was performed on 36 preeclampsia cases and 275 healthy controls; further, a second analysis was performed, in which 40 control subjects with chronic hypertension were added, thereby totaling 315 control subjects.

Table 18 shows the top differentially expressed genes for PE in the cohort for both comparisons including chronic hypertension and excluding chronic hypertension. The top genes from both analyses overlap, which is indicative of a signal associated with preeclampsia, and not chronic hypertension.

The PAPPA2 gene was among one of the significantly expressed gene list for both comparisons. It was observed that PAPPA2 showed significant statistical significance after adjustment for multiple hypothesis correction, and also showed a significant deviation from the null hypothesis in a QQ plots for differentially expressed in PE (as shown in FIG. 25B). Notably, the PAPPA2 gene is among the top genes found also in Example 9. Table 17 indicates its significance and consistency in preeclampsia associated signal between two different cohorts. The top genes from both differential expression analyses of the cohort are summarized in Table 18.

TABLE 18
Top Differentially Expressed Genes Predictive
of Preeclampsia (PE) in two cohort analyses
		Log2 fold		P-value
	Gene	change	P-value	(adjusted)
Including hypertension samples:
	CDCP1	1.77396	1.13E−07	0.001979
	DNAH10	0.892914	2.17E−06	0.016422
	ANXA1	0.601279	2.8E−06	0.016422
	KLF5	1.003333	4.03E−06	0.017725
	PKP1	2.050461	6.39E−06	0.022462
	RHBDL2	2.548792	2.01E−05	0.057368
	CXCL6	1.518407	2.34E−05	0.057368
	PAPPA2	1.35799	2.61E−05	0.057368
	SLPI	1.194633	4.39E−05	0.08179
Excluding hypertension samples:
	CDCP1	1.726904	5.82E−07	0.010243
	DNAH10	0.895177	2.54E−06	0.022396
	ANXA1	0.590151	6.53E−06	0.029986
	KLF5	0.984511	8.36E−06	0.029986
	PAPPA2	1.416309	8.52E−06	0.029986
	PKP1	1.986776	1.29E−05	0.037916
	SLPI	1.20008	3.25E−05	0.078277
	RHBDL2	2.44919	3.56E−05	0.078277
	CXCL6	1.472772	7.1E−05	0.138954

Additional differential expression analysis was performed on combined preeclampsia data sets for cohorts from Example 9 and current cohort totaling 72 preeclampsia cases and 452 controls.

Table 19 shows the top 13 differentially expressed genes for PE for the combined set. Notably, it was observed that PAPPA2 showed on the top with significant statistical significance after adjustment for multiple hypothesis correction.

TABLE 19
Top 13 Differentially Expressed Genes Predictive of
Preeclampsia (PE) in a combined cohort analysis
	Gene	P-value	P-value (adjusted)
	PAPPA2	1.14E−10	3.82E−06
	FABP1	9.07E−09	3.05E−04
	SNORD14A	1.56E−07	5.26E−03
	AOX1	3.01E−07	1.01E−02
	SALL1	3.29E−07	1.11E−02
	HP	3.88E−07	1.30E−02
	KIAA1211L	5.15E−07	1.73E−02
	OLFM4	6.29E−07	2.11E−02
	CLDN7	9.66E−07	3.25E−02
	ANXA1	4.43E−06	1.49E−01
	DNAH10	1.68E−05	5.63E−01
	GPSM2	3.02E−05	1.00E+00
	PKP1	1.23E−04	1.00E+00

To validate the preeclampsia prediction modeling, the PE data set (36 cases and 137 controls) from Example 9 was used for gene selection and training, and the modeling was tested for predictability using the current cohort (36 cases and 315 controls).

FIG. 25C shows a receiver-operator characteristic (ROC) curve for the preeclampsia prediction model, using all differentially expressed genes from top 10 expressed genes discovered in the training cohort. The mean area-under-the-curve (AUC) for the ROC curve for the training set was 0.75 and 0.66 for the test set, indicating a strong signal correlation.

Cross-validation PE modeling was performed on a combined cohort data set of 528 subjects. FIG. 25D shows a receiver-operator characteristic (ROC) curve for the preeclampsia prediction model, using all differentially expressed genes from Table 19. The mean area-under-the-curve (AUC) for the ROC curve was 0.76.

Example 11: Prediction of Pre-Term Birth (PTB) on Combined Multiple Cohorts

All PTB cohorts from Example 4 and Example 8 plus an additional cohort were combined in a single data set, as shown in FIG. 26A, totaling 255 case subjects with pre-term delivery before 38 weeks of gestation age and 796 healthy control subjects with delivery at gestational age after 38 weeks.

An additional cohort of subjects was obtained as follows. As shown in FIG. 26B, a cohort of 281 subjects (56 pre-term birth and 225 full-term controls) was established (with patient identification numbers shown on the x-axis). From this cohort, one or more biological samples (e.g., 1 or 2) were collected and assayed at different time points corresponding to an estimated gestational age (shown on the y-axis, in increasing order of estimated gestational age at delivery) of a fetus of each subject, using methods and systems of the present disclosure. For example, the estimated gestational age (shown on the y-axis) may be determined using methods such as ultrasound imaging, a last menstrual period (LMP) date, or a combination thereof, and may range from 0 to about 42 weeks.

In order to mitigate gestational age effects for blood collection, two separate differential expression analyses for combined cohorts were performed as follows. First, an analysis for differentially expressed genes between the pre-term birth case samples (delivered between 28 to 35 weeks) and control samples (delivered after 38 weeks) was performed for blood samples collected between 20 to 28 weeks of gestational age. In the second analysis, differentially expressed genes between the pre-term birth case samples (delivered between 28 to 35 weeks) and control samples (delivered after 38 weeks) were performed for blood samples collected between more narrow window of 23 to 28 weeks of gestational age.

Table 20 shows the top 9 differentially expressed genes for predicting pre-term births between 28 to 35 weeks with blood samples collected from subjects at between 20 to 28 weeks of gestational age, which showed significant statistical significance after adjustment for multiple hypothesis correction, and also showed a significant deviation from the null hypothesis in a QQ plot for differentially expressed in pre-term cases (as shown in FIG. 26C). Differential expression analysis was performed using EdgeR and accounting for ethnicity and cohort effects (113 PTB cases and 647 controls).

TABLE 20
Top set of genes that are predictive for preterm
births between 28-35 weeks with blood collected
between 20-28 weeks of gestational age
Genes	logFC	Log2 fold change	P-value	FDR
APOB	−1.00993	2.099877	9.01E−11	1.02E−06
FGA	−0.99345	1.545815	3.93E−10	2.23E−06
FGB	−0.94881	1.60352	8.94E−10	3.38E−06
HPD	−0.79382	1.627429	2.52E−08	7.15E−05
ALB	−0.67556	5.147333	8.32E−07	0.001887
CYP2E1	−0.57371	1.757078	4.85E−05	0.091585
FABP1	−0.57173	2.092466	5.66E−05	0.091661
OPA3	0.423862	1.482142	0.000113	0.160133
TMEM56	−0.38129	2.720486	0.000265	0.333199

Table 21 shows the top 11 differentially expressed genes for predicting pre-term births between 28 to 35 weeks with blood samples collected from subjects at between 23 to 28 weeks of gestational age, which showed significant statistical significance after adjustment for multiple hypothesis correction, and also showed a significant deviation from the null hypothesis in a QQ plot for differentially expressed in pre-term birth cases. Differential expression analysis was performed using EdgeR and accounting for ethnicity and cohort effects (73 PTB cases and 335 controls).

Only about half of the genes from Table 20 and Table 21 overlap, indicating a strong effect of gestational age at blood collection on the gene list that is predictive for pre-term birth.

TABLE 21
Top set of genes that are predictive for preterm birth between
28-35 weeks with blood collected between 23-28 week
Genes	logFC	Log2 fold change	P-value	FDR
HRG	1.3829	1.507414	2.45E−08	0.000283
APOB	−0.9663	2.503944	2.93E−07	0.001692
FGA	−0.98087	1.986942	1.11E−06	0.003309
FGB	−0.98335	1.9955	1.15E−06	0.003309
PAPPA2	−0.89151	1.504208	3.73E−06	0.008605
APOH	−0.98788	1.572287	1.02E−05	0.019636
HPD	−0.78336	2.01557	2.4E−05	0.037305
FGG	−0.9384	1.369466	2.58E−05	0.037305
ALB	−0.71179	5.593431	7.75E−05	0.099401
COL19A1	−0.66394	1.852947	9.37E−05	0.108189

Example 12: Prediction of GA on Combined Multiple Cohorts Using Training and Test Sets

The gestational age cohort includes subjects from whom different sample types were collected for use in different studies, including studies for the prediction of actual gestational age of a fetus of each subject at the time of blood collection. All healthy pregnancy samples from retrospective cohorts presented in Examples 1-11 were combined in a single data set, as shown in FIG. 27A. By combining samples from 8 prospectively collected pregnancy cohorts, we amass a set of 2,428 plasma samples from 1,652 pregnancies across a diverse set of ethnicities and covering a broad range of gestational ages. Combined data demographic is represented in Table 22. The 8 different cohorts were treated as batches and a correction was applied prior to modeling of the data.

TABLE 22
Combined data set demographic
								Range of
								Gesta-	Gesta-
								tional	tional	Gesta-	Pre-	Mother's
					%			Age at	Age at	tional	pregnancy	Age at
		Passing	%	%	His-	%	%	Blood	Blood	Age at	Body Mass	Blood
	Cohort	Count	Asian	Black	panic	White	Unknown	Draw	Draw	Delivery	Index	Draw
1	A	161	9.31	21.1	22.9	39.7	6.83	12-27.7	23.4 +/− 4.60	38.9 +/− 0.65	27.2 +/− 7.40	32.6 +/− 5.49
2	B	385	13.5	9.35	20	53.5	3.63	5.57-38.2	26.3 +/− 8.45	39.3 +/− 1.08	26.9 +/− 6.26	30.0 +/− 5.08
3	C	82	0.84	9.24	15.1	74.8	0	8.85-28.2	22.8 +/− 5.00	39.4 +/− 1.06	32.8 +/− 9.57	29.4 +/− 5.6
4	D	194	9.79	27.3	0	59.7	3.09	12.2-23.8	19.9 +/− 1.77	39.6 +/− 1.27	26.6 +/− 6.31	32.8 +/− 5.38
5	E	258	0	46.1	0	53.8	0	16.9-26.4	21.7 +/− 2.12	39.5 +/− 1.20	28.6 +/− 8.08	26.5 +/− 5.51
6	F	796	0.75	51.6	0	41.9	5.65	4.91-40.2	22.8 +/− 10.0	39.5 +/− 1.10	29.9 +/− 7.70	24.1 +/− 4.33
7	G	140	0	100	0	0	0	8-38.7	25.2 +/− 9.66	39.8 +/− 0.91	24.5 +/− 5.12	—
8	H	412	0	0	0	100	0	11.4-34.8	22.5 +/− 7.35	39.8 +/− 1.19	25.5 +/− 6.13	30.4 +/− 4.62

Three separate approaches were used to develop GA modeling based on combined cohorts.

In the first approach, the predicted gestational ages were generated using a predictive model for gestational age. The Lasso linear model predicts gestational age in the training set, with test set performance of a mean absolute error of 2.0 weeks, when using ultrasound estimated gestational age as ground truth. This model uses 494 genes listed in Table 23.

TABLE 23
Sets of 494 Genes Predictive for Gestational Age by Lasso linear model
#	Gene	P-value	P-value adjusted	#	Gene	P-value	P-value adjusted
1	CAPN6	1.86E−303	1.21E−300	247	C18orf54	1.31E−30	5.43E−28
2	CSH1	1.86E−303	1.21E−300	248	PLPP3	1.77E−30	7.33E−28
3	CSHL1	1.86E−303	1.21E−300	249	STAG3	2.10E−30	8.66E−28
4	EXPH5	1.86E−303	1.21E−300	250	CBR4	2.22E−30	9.12E−28
5	HSD17B1	1.86E−303	1.21E−300	251	GTSF1	4.17E−30	1.71E−27
6	LGALS14	1.86E−303	1.21E−300	252	ZSCAN21	1.06E−29	4.32E−27
7	PAPPA	1.86E−303	1.21E−300	253	CRCP	1.76E−29	7.16E−27
8	SVEP1	1.86E−303	1.21E−300	254	PROS2P	2.25E−29	9.15E−27
9	TACC2	1.86E−303	1.21E−300	255	ALG11	2.46E−29	9.97E−27
10	VGLL3	1.86E−303	1.21E−300	256	PSG9	2.85E−29	1.15E−26
11	HSD3B1	1.86E−303	1.21E−300	257	ARL11	5.80E−29	2.34E−26
12	NAPA	1.26E−299	8.16E−297	258	TRERF1	8.87E−29	3.57E−26
13	CYP19A1	6.06E−289	3.93E−286	259	SPATA6	1.25E−28	5.04E−26
14	MYL12B	6.60E−279	4.27E−276	260	TNFSF8	1.75E−28	7.02E−26
15	CSH2	2.72E−278	1.76E−275	261	PCSK1	1.91E−28	7.62E−26
16	PLAC4	5.84E−267	3.77E−264	262	C12orf45	2.71E−28	1.08E−25
17	BEX1	1.03E−259	6.64E−257	263	ATF4P3	4.39E−28	1.75E−25
18	OSTF1	1.62E−255	1.04E−252	264	C15orf61	7.40E−28	2.94E−25
19	CARD16	1.17E−246	7.52E−244	265	CDCA4	8.76E−28	3.47E−25
20	EFHD1	3.86E−242	2.47E−239	266	ARHGAP42	9.61E−28	3.80E−25
21	PHTF2	6.62E−239	4.24E−236	267	IFT172	1.11E−27	4.38E−25
22	TFAP2A	2.13E−231	1.36E−228	268	HCG4P5	1.19E−27	4.69E−25
23	STAT1	4.67E−230	2.98E−227	269	RPP25L	2.95E−27	1.16E−24
24	FNBP1L	3.21E−228	2.05E−225	270	SMAD1	3.82E−27	1.50E−24
25	UBE2L6	1.39E−220	8.83E−218	271	C11orf21	7.09E−27	2.77E−24
26	NTAN1	9.12E−220	5.79E−217	272	VASH1	1.09E−26	4.25E−24
27	RBM3	6.17E−209	3.91E−206	273	RNLS	1.33E−26	5.17E−24
28	ADAM12	7.37E−198	4.67E−195	274	WDR25	1.39E−26	5.37E−24
29	AP2S1	3.69E−196	2.33E−193	275	LEMD3	2.21E−26	8.52E−24
30	CDC37	1.39E−184	8.74E−182	276	TMEM56-RWDD3	7.82E−26	3.01E−23
31	NKIRAS2	1.36E−176	8.56E−174	277	WIZ	1.08E−25	4.17E−23
32	CDC16	8.09E−175	5.09E−172	278	TRIM62	1.09E−25	4.17E−23
33	FRMD4B	2.34E−173	1.47E−170	279	UPRT	1.29E−25	4.92E−23
34	SKIL	1.68E−171	1.05E−168	280	TM2D2	1.59E−25	6.04E−23
35	MMP8	1.57E−170	9.80E−168	281	SPON2	1.91E−25	7.26E−23
36	KRT8	2.82E−170	1.77E−167	282	PTPRM	2.17E−25	8.24E−23
37	RAD23B	2.76E−169	1.72E−166	283	ADSSL1	1.62E−24	6.13E−22
38	HIST1H2AI	5.59E−164	3.48E−161	284	PHLDA2	3.77E−24	1.42E−21
39	ASNA1	1.07E−153	6.66E−151	285	RRP1	3.81E−24	1.43E−21
40	COMT	2.70E−153	1.68E−150	286	TMEM184B	4.93E−24	1.85E−21
41	CPT1A	5.76E−153	3.57E−150	287	METTL1	4.97E−24	1.86E−21
42	COX17	2.71E−152	1.67E−149	288	PFAS	5.65E−24	2.11E−21
43	GPC3	1.85E−150	1.14E−147	289	MYO1B	6.63E−24	2.47E−21
44	GCNT1	2.61E−150	1.61E−147	290	TMEM53	6.81E−24	2.53E−21
45	REEP5	1.48E−149	9.10E−147	291	DDX3Y	8.21E−24	3.04E−21
46	ZSWIM7	4.83E−144	2.97E−141	292	ABL2	8.31E−24	3.07E−21
47	RAP2A	1.14E−143	7.00E−141	293	PLAU	1.25E−23	4.61E−21
48	RAB6B	2.30E−142	1.41E−139	294	MON1A	1.78E−23	6.54E−21
49	KRT18	6.62E−138	4.05E−135	295	DGAT2	2.59E−23	9.48E−21
50	ACCSL	3.97E−136	2.43E−133	296	TMEM86B	4.23E−23	1.54E−20
51	ALDH2	1.44E−135	8.76E−133	297	NR1D1	5.52E−23	2.01E−20
52	FGA	1.94E−135	1.18E−132	298	F12	6.10E−23	2.21E−20
53	MSR1	1.01E−134	6.12E−132	299	FARP1	6.70E−23	2.43E−20
54	CD36	1.91E−134	1.16E−131	300	IFT81	9.06E−23	3.27E−20
55	CD5L	1.19E−133	7.20E−131	301	KIAA1324	9.09E−23	3.27E−20
56	SLC7A5	1.97E−131	1.19E−128	302	NHLRC3	9.24E−23	3.32E−20
57	NXF3	2.08E−129	1.26E−126	303	PDSS1	1.09E−22	3.91E−20
58	CAMP	1.51E−128	9.08E−126	304	CCDC107	1.39E−22	4.96E−20
59	SERPINE1	1.29E−127	7.78E−125	305	NETO1	1.64E−22	5.83E−20
60	NREP	6.93E−127	4.17E−124	306	ASCL1	1.82E−22	6.48E−20
61	KLF10	1.76E−126	1.05E−123	307	GXYLT1	3.13E−22	1.11E−19
62	TCN1	2.65E−126	1.59E−123	308	PSG7	4.19E−22	1.48E−19
63	FABP1	1.01E−120	6.06E−118	309	ITPKC	4.51E−22	1.59E−19
64	CEACAM6	1.04E−119	6.19E−117	310	BAG2	1.35E−21	4.72E−19
65	GK	1.52E−118	9.06E−116	311	ERP27	1.56E−21	5.46E−19
66	BCL2L15	1.56E−115	9.29E−113	312	IPP	1.81E−21	6.30E−19
67	GNAI1	1.87E−115	1.11E−112	313	GALNT7	4.39E−21	1.53E−18
68	BEX4	1.24E−111	7.33E−109	314	TXLNG	8.89E−21	3.08E−18
69	TEX9	4.76E−111	2.82E−108	315	CYB5RL	9.26E−21	3.20E−18
70	PYGB	9.74E−110	5.76E−107	316	UBE3D	1.01E−20	3.50E−18
71	INHBA	3.76E−109	2.22E−106	317	CA3	1.40E−20	4.83E−18
72	ARHGAP12	7.25E−109	4.27E−106	318	WI2-1896O14.1	1.75E−20	6.01E−18
73	PSMG2	1.11E−108	6.52E−106	319	RRP9	2.10E−20	7.18E−18
74	PZP	1.67E−106	9.80E−104	320	AC108488.4	2.25E−20	7.67E−18
75	NUSAP1	1.67E−106	9.81E−104	321	ZNF174	3.02E−20	1.03E−17
76	EPSTI1	1.07E−105	6.27E−103	322	IL16	4.41E−20	1.49E−17
77	ELK3	1.47E−105	8.57E−103	323	TXNDC15	4.41E−20	1.49E−17
78	NPLOC4	3.62E−105	2.11E−102	324	MCEE	1.39E−19	4.68E−17
79	ARL6IP1	5.19E−105	3.02E−102	325	MSTO1	1.52E−19	5.10E−17
80	TPPP3	2.26E−104	1.31E−101	326	SCN9A	2.27E−19	7.59E−17
81	SLTM	5.24E−104	3.04E−101	327	YAP1	3.42E−19	1.14E−16
82	TTK	1.05E−101	6.07E−99	328	AC012507.4	8.96E−19	2.98E−16
83	SFT2D1	4.41E−100	2.55E−97	329	AQP3	8.99E−19	2.99E−16
84	CD209	4.85E−100	2.80E−97	330	NEBL	1.02E−18	3.38E−16
85	DPM3	9.22E−100	5.31E−97	331	ANGPT2	1.81E−18	5.98E−16
86	CARHSP1	1.94E−99	1.12E−96	332	DDX31	2.11E−18	6.95E−16
87	KRT7	5.26E−99	3.02E−96	333	E2F6	2.82E−18	9.24E−16
88	KIF18B	1.33E−97	7.64E−95	334	YWHAZP3	3.74E−18	1.22E−15
89	MCEMP1	1.50E−97	8.55E−95	335	CYTOR	5.21E−18	1.70E−15
90	LATS2	9.93E−96	5.67E−93	336	FBXO15	5.51E−18	1.79E−15
91	AP5M1	1.30E−95	7.40E−93	337	ZFP69	7.23E−18	2.34E−15
92	SPCS3	4.66E−95	2.65E−92	338	RCN2	7.47E−18	2.41E−15
93	WDR7	8.65E−95	4.92E−92	339	TMEM203	7.63E−18	2.46E−15
94	CMBL	1.17E−94	6.61E−92	340	MEI1	7.71E−18	2.48E−15
95	SCIN	2.40E−93	1.36E−90	341	PGAP2	7.77E−18	2.49E−15
96	GFOD1	2.72E−93	1.54E−90	342	MCCC1	1.04E−17	3.31E−15
97	FAM32A	3.19E−93	1.80E−90	343	COX18	1.27E−17	4.03E−15
98	DNAJC1	4.52E−93	2.54E−90	344	LAMP5	1.75E−17	5.55E−15
99	RIMKLB	1.48E−92	8.34E−90	345	FTH1P12	1.82E−17	5.76E−15
100	GAS2L3	4.90E−92	2.75E−89	346	MT1E	2.79E−17	8.79E−15
101	RUNDC3A	9.20E−92	5.15E−89	347	MEX3D	4.57E−17	1.44E−14
102	ASUN	5.29E−91	2.95E−88	348	TSGA10	4.69E−17	1.47E−14
103	NQO2	6.74E−90	3.76E−87	349	PDLIM1P1	5.57E−17	1.74E−14
104	NFU1	1.54E−89	8.60E−87	350	JADE3	7.26E−17	2.26E−14
105	MTHFD1L	2.59E−89	1.44E−86	351	SPR	1.60E−16	4.96E−14
106	DPY19L1	2.69E−89	1.50E−86	352	MYO18B	1.77E−16	5.46E−14
107	GCSAML	1.01E−88	5.59E−86	353	KISS1	2.49E−16	7.67E−14
108	GLTP	6.35E−88	3.51E−85	354	METTL7A	2.80E−16	8.60E−14
109	CASP7	7.14E−88	3.94E−85	355	CYB561D2	4.18E−16	1.28E−13
110	CACUL1	3.87E−87	2.13E−84	356	HLCS	4.21E−16	1.29E−13
111	ABCC1	4.99E−87	2.75E−84	357	NAIF1	4.75E−16	1.44E−13
112	FAM105A	1.52E−86	8.33E−84	358	EPHX2	5.90E−16	1.79E−13
113	RAB3IL1	2.80E−86	1.54E−83	359	COQ8B	6.23E−16	1.88E−13
114	PRKAR1B	6.96E−86	3.80E−83	360	MICA	7.49E−16	2.25E−13
115	TF	7.30E−86	3.99E−83	361	PPT2-EGFL8	8.88E−16	2.66E−13
116	MORC4	1.74E−85	9.49E−83	362	PNPLA1	1.09E−15	3.27E−13
117	NIT2	3.38E−85	1.84E−82	363	ALPK3	1.33E−15	3.96E−13
118	TMEM91	5.90E−85	3.21E−82	364	PTP4A3	2.34E−15	6.96E−13
119	DIAPH3	5.82E−84	3.15E−81	365	ZFP30	3.45E−15	1.02E−12
120	KATNB1	1.60E−81	8.63E−79	366	ZNF606	3.53E−15	1.04E−12
121	ATP1B2	1.96E−80	1.06E−77	367	ZNF229	4.74E−15	1.39E−12
122	ZMIZ2	1.74E−79	9.38E−77	368	MST1	6.33E−15	1.85E−12
123	VSIG4	4.17E−79	2.24E−76	369	RAB15	9.31E−15	2.72E−12
124	GLB1	9.18E−79	4.93E−76	370	TCL6	1.18E−14	3.44E−12
125	SLC2A1	1.16E−78	6.22E−76	371	TTLL1	1.36E−14	3.95E−12
126	OSER1	4.09E−78	2.19E−75	372	SKOR1	1.38E−14	3.98E−12
127	AMIGO2	1.06E−77	5.65E−75	373	KIAA0895L	1.78E−14	5.14E−12
128	NIPSNAP3B	1.28E−77	6.80E−75	374	CCDC58	2.61E−14	7.49E−12
129	MAP2	2.19E−77	1.17E−74	375	AMMECR1L	3.17E−14	9.05E−12
130	SMIM12	2.31E−76	1.23E−73	376	C16orf96	3.31E−14	9.45E−12
131	ACHE	2.33E−76	1.24E−73	377	IGF2	6.64E−14	1.89E−11
132	DIAPH1	4.29E−75	2.27E−72	378	CXorf40A	1.01E−13	2.85E−11
133	LYRM9	3.34E−73	1.76E−70	379	ARSG	1.07E−13	3.01E−11
134	DYNLT3	8.40E−73	4.43E−70	380	TMEM116	1.27E−13	3.56E−11
135	KCNH2	2.81E−72	1.48E−69	381	SPRY3	2.68E−13	7.50E−11
136	GINS2	3.39E−72	1.78E−69	382	BTN2A2	3.09E−13	8.64E−11
137	MOSPD3	5.36E−72	2.81E−69	383	FAM114A1	3.17E−13	8.80E−11
138	PHF5A	3.89E−70	2.03E−67	384	C4orf48	3.65E−13	1.01E−10
139	SLC16A7	1.58E−68	8.23E−66	385	HACD1	4.11E−13	1.13E−10
140	STX18	1.82E−68	9.49E−66	386	DNAJB5	4.15E−13	1.14E−10
141	ZMAT5	1.90E−68	9.86E−66	387	WASH6P	5.29E−13	1.45E−10
142	APOL4	5.51E−68	2.86E−65	388	GCSH	9.75E−13	2.66E−10
143	SLC7A11	1.17E−67	6.04E−65	389	C12orf73	1.61E−12	4.37E−10
144	CPNE4	6.51E−67	3.37E−64	390	ABTB2	1.99E−12	5.40E−10
145	NOP14	9.23E−67	4.76E−64	391	KHK	3.02E−12	8.14E−10
146	PLPP1	1.67E−65	8.60E−63	392	ZNF565	5.08E−12	1.37E−09
147	FABP3	2.37E−65	1.22E−62	393	DMD	5.21E−12	1.40E−09
148	BACE1	3.23E−65	1.66E−62	394	LINC00853	7.39E−12	1.97E−09
149	ITIH2	1.83E−63	9.36E−61	395	CALML4	8.94E−12	2.38E−09
150	HEXA	7.34E−62	3.75E−59	396	AC113189.5	9.23E−12	2.44E−09
151	KIF16B	1.03E−61	5.24E−59	397	PDGFD	9.52E−12	2.51E−09
152	PTGER2	1.74E−61	8.87E−59	398	RBPMS	1.08E−11	2.84E−09
153	HENMT1	1.81E−61	9.22E−59	399	RERG	2.78E−11	7.28E−09
154	FAM149B1	4.19E−61	2.12E−58	400	FAM84B	2.83E−11	7.39E−09
155	TMEM204	4.19E−60	2.12E−57	401	GGTA1P	2.84E−11	7.39E−09
156	MOB3C	2.79E−59	1.41E−56	402	ZSCAN12	3.51E−11	9.10E−09
157	ZBTB16	5.67E−59	2.86E−56	403	FAT4	3.79E−11	9.78E−09
158	MED16	1.81E−58	9.12E−56	404	GOLGA8R	8.50E−11	2.19E−08
159	DDX58	2.08E−58	1.04E−55	405	SHROOM2	8.51E−11	2.19E−08
160	TESK1	2.95E−57	1.48E−54	406	ZNF670	1.19E−10	3.04E−08
161	OLR1	1.91E−56	9.53E−54	407	ST7-AS1	1.24E−10	3.15E−08
162	RBM14	2.65E−56	1.32E−53	408	MXRA7	1.78E−10	4.50E−08
163	TTC28	3.22E−56	1.60E−53	409	ARHGAP22	1.81E−10	4.55E−08
164	CEBPZOS	6.36E−55	3.16E−52	410	PHKA1	1.84E−10	4.61E−08
165	IFIT1	7.00E−55	3.47E−52	411	PLCE1	2.72E−10	6.81E−08
166	PLBD2	7.06E−55	3.49E−52	412	OAZ3	2.88E−10	7.17E−08
167	FANCB	8.81E−55	4.35E−52	413	SMO	3.71E−10	9.21E−08
168	BCL2	1.12E−54	5.53E−52	414	DOLK	4.62E−10	1.14E−07
169	UBXN11	9.85E−54	4.85E−51	415	AMOT	4.82E−10	1.19E−07
170	SYPL1	1.22E−53	6.01E−51	416	SLX4IP	5.03E−10	1.23E−07
171	CCDC15	1.51E−53	7.39E−51	417	KLRC1	5.15E−10	1.26E−07
172	IL15	3.13E−53	1.53E−50	418	WDR90	5.21E−10	1.27E−07
173	TMEM14A	3.79E−53	1.85E−50	419	ATP5L2	5.89E−10	1.42E−07
174	METTL21EP	1.89E−52	9.21E−50	420	FBXL13	6.84E−10	1.65E−07
175	DSEL	5.57E−52	2.70E−49	421	SIGLEC12	7.08E−10	1.70E−07
176	STYXL1	4.94E−51	2.40E−48	422	KCND3	9.17E−10	2.19E−07
177	TMC1	1.10E−50	5.32E−48	423	ABCB8	9.84E−10	2.34E−07
178	SEC14L2	6.34E−50	3.06E−47	424	AARS2	1.18E−09	2.79E−07
179	IL1RAP	3.85E−49	1.86E−46	425	ARHGAP20	1.19E−09	2.81E−07
180	CAPN11	3.96E−49	1.91E−46	426	PRR4	1.23E−09	2.90E−07
181	SEC22C	4.44E−49	2.13E−46	427	FBXO36	1.34E−09	3.15E−07
182	PHF19	1.30E−48	6.24E−46	428	GYPB	1.50E−09	3.49E−07
183	HSPBAP1	5.04E−48	2.41E−45	429	RPP14	1.78E−09	4.14E−07
184	EXOC6B	2.62E−47	1.25E−44	430	NUDT7	2.20E−09	5.09E−07
185	KIF24	3.38E−47	1.61E−44	431	NSUN3	3.12E−09	7.18E−07
186	GLYATL1	1.01E−46	4.78E−44	432	LRIG3	3.88E−09	8.89E−07
187	ALDOC	1.82E−46	8.61E−44	433	TCEANC2	4.18E−09	9.54E−07
188	PCBD1	2.04E−46	9.65E−44	434	NME3	4.37E−09	9.92E−07
189	UBBP4	4.64E−46	2.19E−43	435	NEURL1	5.97E−09	1.35E−06
190	MYO19	1.19E−45	5.62E−43	436	MYL12AP1	1.32E−08	2.96E−06
191	NUS1	3.27E−45	1.54E−42	437	GRTP1	1.39E−08	3.12E−06
192	CAV2	5.05E−45	2.37E−42	438	PLS3	1.84E−08	4.11E−06
193	HELLS	8.27E−45	3.87E−42	439	ZNF569	2.25E−08	5.00E−06
194	PIGW	9.54E−45	4.46E−42	440	ZXDA	2.49E−08	5.51E−06
195	PSG3	5.19E−44	2.42E−41	441	ENO2	2.93E−08	6.45E−06
196	ABHD12	1.85E−43	8.60E−41	442	CA4	3.57E−08	7.83E−06
197	EFCAB2	2.09E−43	9.71E−41	443	FAM161B	4.46E−08	9.71E−06
198	DUSP4	2.25E−43	1.04E−40	444	SNX21	9.08E−08	1.97E−05
199	FASN	3.03E−43	1.40E−40	445	SYTL2	1.03E−07	2.24E−05
200	KDELC2	4.74E−43	2.19E−40	446	PLCXD1	1.07E−07	2.29E−05
201	ZMYM1	7.98E−43	3.67E−40	447	TM9SF1	1.10E−07	2.36E−05
202	PHKG2	2.23E−42	1.02E−39	448	C17orf105	1.18E−07	2.51E−05
203	VSTM1	2.36E−42	1.08E−39	449	EIF1P3	1.91E−07	4.05E−05
204	FCF1	4.12E−42	1.88E−39	450	IL 1RAPL1	2.44E−07	5.14E−05
205	NIPA1	4.57E−42	2.09E−39	451	CASKIN2	2.72E−07	5.71E−05
206	PPP2R3B	8.37E−42	3.81E−39	452	CYP2S1	3.13E−07	6.55E−05
207	SEC14L5	1.63E−41	7.39E−39	453	SNHG20	3.15E−07	6.55E−05
208	BMT2	1.65E−41	7.47E−39	454	SLC26A6	6.18E−07	0.000128
209	SMIM20	2.01E−41	9.07E−39	455	RPL23AP38	6.35E−07	0.000131
210	MMP9	2.50E−41	1.13E−38	456	CAMK4	7.60E−07	0.000156
211	QPCT	2.54E−41	1.14E−38	457	KCNN4	8.94E−07	0.000182
212	HTR2A	3.15E−41	1.41E−38	458	GCAT	9.12E−07	0.000185
213	CXCL16	6.34E−41	2.84E−38	459	KIF7	1.87E−06	0.000378
214	C19orf33	2.47E−40	1.11E−37	460	NR4A2	3.86E−06	0.000776
215	SPNS3	2.52E−40	1.13E−37	461	FAM221A	4.13E−06	0.000826
216	C17orf53	6.25E−40	2.78E−37	462	EEF1A1P11	4.53E−06	0.000902
217	ZNHIT3	1.07E−39	4.75E−37	463	FBXO40	4.58E−06	0.000906
218	GLDC	1.39E−39	6.17E−37	464	GSTM1	5.41E−06	0.001066
219	LURAP1L	1.23E−38	5.45E−36	465	SH3RF3	5.88E−06	0.001153
220	RND3	3.19E−38	1.41E−35	466	CD28	6.82E−06	0.001330
221	ZNF554	3.35E−38	1.47E−35	467	TRAV12-3	7.33E−06	0.001422
222	WRAP73	4.75E−38	2.09E−35	468	NHEJ1	7.47E−06	0.001441
223	AP1G1	5.05E−38	2.21E−35	469	ZNF19	8.37E−06	0.001606
224	NDFIP2	6.04E−38	2.64E−35	470	CCDC40	1.18E−05	0.002254
225	PTENP1	1.10E−37	4.79E−35	471	CH507-42P11.1	1.52E−05	0.002883
226	SUSD6	1.20E−37	5.22E−35	472	RPL34P27	1.56E−05	0.002946
227	FAM212B	1.96E−37	8.50E−35	473	C9orf172	2.52E−05	0.004735
228	DZIP1L	4.10E−37	1.78E−34	474	PPP1R9A	2.87E−05	0.005360
229	GABRE	1.08E−36	4.68E−34	475	CEP126	3.38E−05	0.006289
230	RARRES1	6.15E−36	2.65E−33	476	IL13RA2	3.83E−05	0.007083
231	HSPA1B	1.21E−35	5.18E−33	477	FKBP14	3.91E−05	0.007186
232	TCTA	1.54E−35	6.59E−33	478	FBXL6	4.62E−05	0.008460
233	CD68	4.23E−35	1.81E−32	479	PTPRH	4.86E−05	0.008851
234	POLR3B	5.08E−35	2.17E−32	480	GDPGP1	5.74E−05	0.010390
235	ZNF79	3.84E−34	1.63E−31	481	CFAP43	7.05E−05	0.012690
236	B4GALT2	4.89E−34	2.08E−31	482	CCDC73	7.35E−05	0.013158
237	MYLIP	1.28E−33	5.44E−31	483	SBF2-AS1	7.62E−05	0.013571
238	CAPN3	1.92E−33	8.11E−31	484	CDH5	7.88E−05	0.013943
239	FBXO28	2.20E−32	9.29E−30	485	CCDC102A	8.87E−05	0.015618
240	ZNF226	2.82E−32	1.19E−29	486	TMCO6	0.000109	0.019146
241	ATP2B2	4.97E−32	2.09E−29	487	TMEM217	0.000138	0.024093
242	TAPBPL	2.02E−31	8.45E−29	488	NKD1	0.000140	0.024259
243	CHMP6	2.50E−31	1.04E−28	489	RP5-837I24.1	0.000169	0.028995
244	ELOVL6	3.68E−31	1.54E−28	490	RPL13AP6	0.000181	0.030876
245	B4GALT7	3.68E−31	1.54E−28	491	TJP3	0.000188	0.031989
246	MRPL55	9.27E−31	3.85E−28	492	CHCHD2P6	0.000190	0.032131
247	C18orf54	1.31E−30	5.43E−28	493	OLIG1	0.000247	0.041456
248	PLPP3	1.77E−30	7.33E−28	494	RN7SL5P	0.000251	0.041953

FIG. 27B is a plot showing the relationship between a predicted gestational age (in weeks) and the measured gestational age (in weeks) for the subjects in the gestational age cohort in held-out test data. The error across the predicted range from 6 to 36 weeks is constant and does not show any correlation with GA. This is in contrast to ultrasound-based dating, which has a gradual increase in error as pregnancy progresses. Overall, the error of the model is equivalent to that of second trimester ultrasound and superior to third trimester. ANOVA analysis indicates most of the signal in the model is driven by RNA transcripts, and BMI, maternal age and race or ethnicity accounting for less than 0.5% of the signal. The gestational biomarkers model (e.g., prediction of gestational age based on a set of gestational age-associated biomarker genes) is independent of race or ethnicity.

In the second approach, whole transcriptome data from all healthy pregnancies was divided into a training set (1482 samples) and a held-out test set (495 samples), making sure to stratify by gestational age so all ranges are represented equally in training and held-out test sets.

Whole transcriptome data from the training set was subjected to a Lasso model. Table 24 shows the top 57 transcriptomic features for predicting predicted gestational ages in a training set generated using a Lasso method after restricting the space search to genes with average counts per million above 1 cpm. The model uses 54 genes and 3 additional transcriptomic features that are selected using Lasso to predict gestational age in test set performance of a mean absolute error of 2.33 weeks, when using ultrasound estimated gestational age as ground truth.

TABLE 24
Sets of 57 Transcriptomic Features Predictive
for Gestational Age by Lasso Method
					BH-
	Transcriptomic	Feature			corrected
#	features	type	Correlation	P-value	P-value
1	CAPN6	gene	0.584328	2.04E−136	1.17E−134
2	LGALS14	gene	0.556407	3.24E−121	9.23E−120
3	SVEP1	gene	0.54131	1.40E−113	2.58E−112
4	CSHL1	gene	0.541084	1.81E−113	2.58E−112
5	EXPH5	gene	0.533408	9.75E−110	1.11E−108
6	PAPPA	gene	0.508472	2.97E−98	2.82E−97
7	VGLL3	gene	0.489895	2.68E−90	2.19E−89
8	BEX1	gene	0.489431	4.18E−90	2.98E−89
9	TACC2	gene	0.450982	3.85E−75	2.44E−74
10	STAT1	gene	0.419325	3.50E−64	1.99E−63
11	PLAC4	gene	0.369908	2.87E−49	1.49E−48
12	UBE2L6	gene	0.363607	1.52E−47	7.21E−47
13	% ERCC	QC	−0.356695	1.07E−45	4.67E−45
		metrics
14	CPNE2	gene	0.339643	2.46E−41	1.00E−40
15	NXF3	gene	0.337411	8.77E−41	3.33E−40
16	PAPPA2	gene	0.315658	1.21E−35	4.31E−35
17	CSH1	gene	0.313818	3.15E−35	1.06E−34
18	SLC7A5	gene	0.290907	2.71E−30	8.57E−30
19	LTF	gene	0.279006	6.65E−28	2.00E−27
20	TMSB10P1	gene	0.273393	8.13E−27	2.32E−26
21	SEC14L2	gene	0.271602	1.79E−26	4.85E−26
22	SKIL	gene	0.258285	5.16E−24	1.34E−23
23	FABP1	gene	0.254356	2.58E−23	6.40E−23
24	MEF2A	gene	0.253145	4.22E−23	1.00E−22
25	SLC7A11	gene	0.23882	1.15E−20	2.62E−20
26	Unique_reads	QC	0.229539	3.59E−19	7.88E−19
		metrics
27	ANXA11	gene	0.186124	5.11E−13	1.08E−12
28	IFIT1	gene	0.169894	4.62E−11	9.40E−11
29	MYL12B	gene	0.168367	6.90E−11	1.36E−10
30	ANGPT2	gene	−0.168225	7.17E−11	1.36E−10
31	MCEMP1	gene	0.157461	1.10E−09	2.02E−09
32	IGF2	gene	−0.154093	2.48E−09	4.42E−09
33	RNLS	gene	0.153744	2.70E−09	4.66E−09
34	MYCNOS	gene	0.149773	6.89E−09	1.15E−08
35	PSG3	gene	0.131688	3.63E−07	5.91E−07
36	CXCR4	gene	0.124867	1.42E−06	2.25E−06
37	JCHAIN	gene	−0.117279	5.99E−06	9.23E−06
38	KLK1	gene	−0.108699	2.75E−05	4.12E−05
39	PLS3	gene	−0.098127	1.55E−04	2.23E−04
40	TNFAIP6	gene	0.098058	1.56E−04	2.23E−04
41	DDX58	gene	0.089527	5.60E−04	7.78E−04
42	IGHA1	gene	−0.085325	1.01E−03	1.37E−03
43	CH507-9B2.5	gene	−0.082546	1.47E−03	1.95E−03
44	RGPD2	gene	−0.079216	2.27E−03	2.95E−03
45	OIT3	gene	−0.068552	8.29E−03	1.05E−02
46	NR4A1	gene	−0.065645	1.15E−02	1.42E−02
47	CACUL1	gene	−0.064953	1.24E−02	1.50E−02
48	KISS1	gene	0.060214	2.04E−02	2.43E−02
49	RASIP1	gene	−0.060011	2.09E−02	2.43E−02
50	CGA	gene	−0.059406	2.22E−02	2.53E−02
51	CCDC15	gene	0.047547	6.73E−02	7.52E−02
52	%	QC	−0.039872	1.25E−01	1.37E−01
	mithocondrial	metrics
	RNA
53	SH2D1B	gene	−0.030152	2.46E−01	2.65E−01
54	PARGP1	gene	0.021481	4.09E−01	4.31E−01
55	MYLIP	gene	0.020002	4.42E−01	4.58E−01
56	C18orf8	gene	−0.018013	4.88E−01	4.97E−01
57	PPM1H	gene	0.016917	5.15E−01	5.15E−01

In the third approach, genes predictive of gestational age were identified by recursive feature elimination (RFE). A combined dataset of healthy individuals from 5 cohorts (cohorts with less than 100 samples were excluded, e.g. B, C, and F) was randomly split into 80% training (2390 samples) and 20% testing sets (478 samples) making sure to stratify by gestational age so all ranges are represented equally in training and held-out testing sets. Outliers identified by lab QC metrics were removed prior to modeling. Expression levels were converted to log 2 CPM levels. A linear model fit to gene features by ordinary least squares predicted gestational age at blood draw. Features were selected by performing feature ranking with RFE, which recursively reduces the feature set by pruning features with the least importance based on the estimated coefficients in the linear model. Prior to recursive feature elimination, gene features were filtered for transcripts whose expression levels had a minimum strength of relationship to gestational age. Spearman rank correlation coefficients were computed for the pairwise relationships of raw gene counts with gestational age at blood draw to assess the strength of each gene in predicting gestational age in the linear model. Based on the threshold set for the minimum Spearman rank correlation, e.g. 0.3, 0.4, 0.5, or 0.6, the whole transcriptome is down-selected to a pool of genes analyzed by RFE. A 5-fold cross validation tuned the hyperparameter with respect to the number of genes to target by RFE. The final linear model was trained on the training set by RFE set to the best number of genes identified by cross validation. Models were evaluated based on root mean squared error, mean absolute error (MAE), median absolute error performance between the estimated and observed gestational age on the testing dataset.

Table 25 shows the top 70 genes model identified for predicting predicted gestational ages in a training set generated using the RFE method with Spearman threshold of 0.4. This 70 gene linear model identified by RFE predicted gestational age in the testing set with a mean absolute error performance of 2.5 weeks, when using ultrasound estimated gestational age as ground truth.

TABLE 25
70 Genes from the Linear Model fit by
RFE Predictive for Gestational Age
#	Gene	P-value
1	ALS2CR12	1.58E−05
2	ANGPT2	2.18E−26
3	APOBEC3G	0.01150902
4	BCAP29	0.00052699
5	BLOC1S3	0.00011045
6	C1orf115	1.31E−08
7	CAPN6	1.14E−18
8	CAPNS1	0.03519931
9	CARMIL2	2.18E−05
10	CBWD5	2.38E−05
11	CEP152	0.00166964
12	CGA	4.40E−73
13	CMC1	0.03732266
14	CSH1	1.14E−17
15	CSH2	0.00019274
16	CXCR4	2.28E−08
17	CYP19A1	9.74E−05
18	DDX58	7.24E−15
19	DYNLT3	1.87E−09
20	EXPH5	5.48E−07
21	FGG	7.86E−16
22	GCLC	0.00401303
23	GP9	2.05E−06
24	GPR65	0.00102721
25	HIST1H3G	8.21E−09
26	HMGB3	0.00977082
27	HSPB1	0.0021566
28	KISS1	3.52E−07
29	KRT8	0.00010513
30	KRTCAP2	9.90E−05
31	LAP3	0.0004834
32	LEMD3	3.36E−05
33	LIMS1	5.85E−17
34	LRSAM1	0.00082994
35	MCM6	6.27E−05
36	MCM9	8.71E−05
37	MEIS1	0.00455709
38	METTL7A	0.0001903
39	MICB	0.00049999
40	MIGA1	0.00308384
41	MPLKIP	0.00023848
42	MS4A3	8.93E−10
43	PAPPA	6.57E−10
44	PITHD1	2.54E−13
45	PLAC4	5.82E−08
46	PNKD	0.00632914
47	PRDX2	9.14E−08
48	PSG3	6.65E−05
49	PTGER2	0.00031855
50	RGP1	0.02456697
51	RN7SL1	0.00022625
52	RNLS	2.66E−05
53	RRAGD	4.00E−06
54	RTTN	0.00220346
55	SIMC1	0.01018069
56	SLC7A11	9.86E−06
57	STAG3L3	9.77E−05
58	STAT1	3.25E−27
59	STOM	9.27E−12
60	SVEP1	7.84E−09
61	TACC2	1.56E−05
62	TAF3	0.00247011
63	TBC1D22B	0.00336354
64	TCTA	0.00020092
65	TFEC	0.01982375
66	TPTEP1	2.08E−07
67	TRERF1	0.00075604
68	VGLL3	1.17E−08
69	ZNF189	0.00149201
70	ZNF79	0.00061504

FIG. 27D is a plot showing the concordance between a predicted gestational age (in weeks) and the measured gestational age (in weeks) for the subjects in the gestational age cohort in the held-out testing data for RFE gestation age modeling.

In the other approach, a linear regression model was developed to predict gestational age as a function of transcript expression levels in more narrow gestation age. A single cohort whole transcriptome dataset was collected focusing on the first trimester between 6-16 weeks. A single cohort whole transcriptome dataset was collected focusing on the first trimester. The data was split into 80% training data (164 samples) and 20% held-out testing data (33 samples), making sure to stratify by gestational age so all ranges are represented equally in training and held-out test sets. The training dataset was used in a 5-fold cross validation to select gene features and perform modeling with linear regression fit by ordinary least squares. Feature selection was performed by hierarchical clustering. First, the whole transcriptome was filtered based on a minimal magnitude of the Pearson correlation coefficient threshold to gestational age, e.g. |R|≥0.2 would reduce the genes to 3.7% of the whole transcriptome to 547 genes for clustering. The filtered genes are then clustered based on gene-to-gene similarity across the observations as calculated by pairwise Pearson correlation coefficients. A cutoff was then identified to trim the hierarchical clustering to reduce the features to a target number of clusters. A representative gene feature is the selected or computed for each cluster. Cluster representatives can be selected based on identifying a single gene with the largest Pearson correlation coefficient magnitude to gestational age or could be an aggregate measurement representing the mean or median of all genes within the cluster. In each round of cross validation, the identified features are then used to train a linear regression on the training folds and the model evaluated on the fold not used for training. The final features were identified based on the minimal RMSE performance between the observed and predicted gestational from the linear model.

Table 26 shows the 20 predictive genes for gestational age in a linear model as identified by hierarchical clustering. The linear model to predict gestational age in the first trimester (6 to 16 weeks) had a test set performance of a RMSE of 2.1 weeks, when using ultrasound estimated gestational age as ground truth.

TABLE 26
Set of 20 Genes Predictive for Gestational Age
identified by hierarchical clustering in samples
collected between 6-16 weeks of gestation.
#	Gene	Pearson Correlation Coefficient
1	ARL6IP1	0.290774
2	HMGB3	0.327823
3	NLRC3	−0.345206
4	TRAF5	−0.29844
5	CD44	−0.274007
6	CSH1	0.713144
7	CCDC157	−0.301364
8	ANLN	0.328642
9	RCHY1	0.256837
10	PRRC2C	−0.270451
11	CYFIP1	0.284176
12	SERPINB1	0.294268
13	GPR18	−0.267355
14	TRIM58	0.279979
15	NCOA4	0.298769
16	C1QA	0.346268
17	AMMECR1L	−0.261443
18	GPC3	0.339435
19	EOGT	−0.226626
20	CTSB	0.249796

FIG. 27E is a plot showing the concordance between a predicted gestational age (in weeks) and the measured gestational age (in weeks) for the subjects in the gestational age cohort in held-out test data in first trimester modeling.

Example 13: Prediction of Preeclampsia (PE) Using Genes Selected by Medium-to-High Level Expression Genes

Further, whole transcriptome data from two cohorts described in Examples 9 and 10 were combined and analyzed by the abundant gene search method. The combined cohort of 541 samples contains 469 control samples with gestational age at blood draw of at least 17 weeks and delivery as low as 21 weeks of gestational age. Additionally, this combined cohort contains 72 case samples diagnosed with preeclampsia with gestational age at blood draw of at least 18 weeks and deliveries as early as 26 weeks of gestational age.

Logistic regression was performed to model the probability of preeclampsia in a pregnant individual from transcript expression data. Selection methods were applied to identify genes predictive of preeclampsia that are expressed at medium-to-high abundance. Genes were filtered based on a minimal median fold change of raw counts per gene between individuals with and without preeclampsia prior to modeling. One embodiment includes filtering for genes that have a median fold change in expression between case and control of <=0.5 and >1.5 to include abundant genes that are both upregulated and downregulated in preeclampsia. Additionally, genes are filtered to have a minimum number of reads across a set percentage of the training data. One embodiment filters genes with at least 5 reads in more than 50% of the training samples. These two filters are applied to reduce the transcriptome to an initial gene pool of abundant genes that are then ranked as features for the logistic model through recursive feature elimination (RFE). Prior to modeling, raw gene counts are converted to standardized log 2 CPM levels.

Nested resampling is performed to estimate the performance of abundant gene sets identified by RFE without data leakage between training and testing required to tune the best number of features to target by RFE. The outer resampling loop is used to test performance of logistic models trained on identified gene features by RFE whereas the inner resampling loop is used to tune the target number of features needed for RFE. The combined dataset of from 2 cohorts was randomly split one hundred times into 80% training (432 samples) and 20% held-out testing (109 samples) to comprise the outer resampling loop, making sure to stratify by case and control, gestational age, and cohort to ensure each are represented equally in both the training and held-out testing sets.

For each training and testing outer split, the training data was further split into 80% training (345 samples) and 20% held-out testing (87 samples) sets to comprise the inner resampling loop. This inner resampling split was randomly performed one hundred times to estimate the robustness of the gene features identified in a given training/testing split.

To identify the abundant gene features for a given inner training/testing dataset split, cross validation (CV) was performed on the inner resampling loop to identify the best number of features prior to training a logistic model on the outer training dataset. A 4-fold cross validation (CV) is performed on each inner training dataset to identify the best number of features for training a logistic model by RFE by maximizing the AUC performance on a test set. In each CV round, the target number of genes is optimized by performing RFE from 1 to a maximum number of features. In one embodiment, the maximum number of features was set to 20 to reduce overfitting given the size of the training dataset. A mean AUC is computed across the 4 CV test folds for each of the number of RFE features used, and the best number of features is selected based on the maximum mean AUC across the 4 CV folds. Then the full inner training set is used to train a logistic regression model by RFE with the best number of features to identify the abundant genes, and the AUC performance of the model is calculated on paired inner testing dataset. The frequency of abundant genes was computed across the one hundred random inner splits, and these data were filtered to generate the final gene features used to train a final logistic model on the outer training dataset. Performance of features sets were then compared by evaluating the trained logistic models on the held-out outer testing dataset. Cutoffs to identify gene features include selection based on most frequently observed across the inner loops, e.g. selecting the top two most frequently identified genes, or based on those abundant genes that showed significant differential expression between preeclampsia cases versus controls as computed by the Mann-Whitney rank test with p-values corrected for multiple tests via the Holm step-down method using Bonferroni adjustments.

Table 27 shows the 132 genes identified in the abundant gene search across the one hundred inner resampling training and test splits.

TABLE 27
132 genes identified in the abundant gene search across the
one hundred inner resampling training and test splits.
#	Gene	P-value_mw	P-value_adjusted_holm
1	FABP1	6.23E−07	8.23E−05
2	CDCA2	3.14E−06	0.00041104
3	HMGB3	0.00010898	0.01416703
4	ELANE	0.00012196	0.01573288
5	CDC20	0.00015193	0.01944651
6	SHCBP1	0.00020189	0.02563957
7	OLFM4	0.00027466	0.03460665
8	S100A9	0.00034386	0.04298208
9	S100A12	0.00039749	0.04928901
10	STK33	0.00045608	0.05609825
11	PLS1	0.00046166	0.056323
12	APOB	0.00048905	0.05917536
13	PCNA	0.00121359	0.14563076
14	S100A16	0.0014132	0.16817071
15	DEFA3	0.00142513	0.16817071
16	PLEKHA6	0.00201857	0.23617235
17	CDR1-AS	0.00216043	0.25060948
18	KIF20A	0.00229895	0.26437936
19	CLC	0.00244557	0.27879471
20	PEG10	0.00256623	0.28998356
21	CEACAM6	0.00294602	0.32995372
22	HIST1H3G	0.00297726	0.3304754
23	KIF18B	0.00308089	0.3388975
24	ABCA13	0.00325526	0.35482292
25	PRDM5	0.00344753	0.37233343
26	KRT23	0.004504	0.48192809
27	PLAC4	0.00461967	0.48968489
28	CEACAM8	0.00465489	0.48968489
29	HIST1H2BM	0.00482249	0.50153917
30	TRMT10A	0.00485911	0.50153917
31	CAMP	0.00543939	0.55481806
32	TCN1	0.0058169	0.58750665
33	SULT1B1	0.00594789	0.59478851
34	RETN	0.00617211	0.61103934
35	HIST1H4H	0.00679116	0.66553325
36	MGST1	0.00759263	0.73648489
37	BPI	0.00790964	0.75932584
38	MYO1B	0.00833748	0.79206037
39	RNASE2	0.00903946	0.84970968
40	PLK1	0.00908236	0.84970968
41	FOXM1	0.00927762	0.85354118
42	HIST1H2AH	0.00988609	0.89963399
43	ENSG00000188206	0.01021538	0.91938418
44	MMP8	0.01100497	0.97944234
45	NLRP2	0.01147255	1
46	CTSG	0.0121512	1
47	ANXA3	0.01243247	1
48	AKR1C3	0.01349336	1
49	KLRG1	0.01352394	1
50	TEK	0.01389568	1
51	AC078883.3	0.01389568	1
52	SELENOP	0.01408491	1
53	TRPM6	0.01443775	1
54	ARG1	0.01450273	1
55	CEACAM1	0.01460069	1
56	ROBO1	0.01473221	1
57	AZU1	0.01493144	1
58	CLIC5	0.01496488	1
59	CHMP4C	0.01499838	1
60	FCGR1A	0.01705805	1
61	ALPK3	0.01724672	1
62	LTF	0.01857887	1
63	U2AF1	0.01861938	1
64	ALDH1L2	0.01886405	1
65	MPO	0.02240514	1
66	PRTN3	0.02352466	1
67	BCL6B	0.02397577	1
68	SMAD5	0.02428066	1
69	JAKMIP1	0.02751905	1
70	TNNT1	0.03006317	1
71	CDH6	0.03347483	1
72	PHGDH	0.03381315	1
73	DSP	0.03540731	1
74	HIST1H2AL	0.03583358	1
75	AFMID	0.03691843	1
76	PGLYRP1	0.03736014	1
77	ASL	0.04310444	1
78	MUC3A	0.0442874	1
79	ME1	0.04514905	1
80	SNAPC2	0.04576058	1
81	LAMP5	0.0471846	1
82	PHACTR1	0.0480934	1
83	MYOM2	0.04836889	1
84	PRR16	0.05207253	1
85	HACD3	0.05590646	1
86	JUN	0.05877114	1
87	CEBPE	0.06063659	1
88	MS4A3	0.06097083	1
89	METTL17	0.07353507	1
90	KCNN3	0.07471534	1
91	TCL1A	0.07604486	1
92	MRAS	0.07739361	1
93	FMO2	0.07931455	1
94	STEAP1B	0.07945323	1
95	SERPINB10	0.08042952	1
96	MT-TI	0.08241133	1
97	TMEM176B	0.0884438	1
98	FPR3	0.08859527	1
99	MT-TT	0.11415812	1
100	MT-TG	0.12956794	1
101	CTSW	0.14995411	1
102	RSAD1	0.15133406	1
103	RELN	0.17681601	1
104	SLC43A2	0.17995066	1
105	CHI3L1	0.18661349	1
106	BTBD11	0.18932905	1
107	SULT1A1	0.20048273	1
108	ALPL	0.24393954	1
109	RPL23AP7	0.25526013	1
110	DDAH1	0.26624377	1
111	MT-TC	0.27540426	1
112	RIPK3	0.28223297	1
113	RPL23AP82	0.28623848	1
114	VSIG4	0.33770179	1
115	DDX11L10	0.35259587	1
116	FFAR2	0.42464406	1
117	BTLA	0.43505175	1
118	FOSB	0.46417303	1
119	FCGBP	0.46714367	1
120	GSTM1	0.48114512	1
121	TLE1P1	0.50050691	1
122	GSTA1	0.50205287	1
123	SORBS2	0.50722428	1
124	SERTAD3	0.514511	1
125	MMP25	0.52290481	1
126	RPL23AP97	0.55662534	1
127	OVOS2	0.55771295	1
128	TRHDE	0.61336971	1
129	RAP1GAP	0.61450747	1
130	HLA-DQA2	0.69692228	1
131	CTD-3088G3.8	0.81560517	1
132	EMCN	0.92709603	1

FABP1 was among the top significantly expressed genes for both Examples 9 and 10 and this analysis. It was observed that FABP1 showed significant statistical significance after adjustment for multiple hypothesis correction, and also showed a significant deviation from the null hypothesis in a QQ plots for differentially expressed in PE (as shown in FIG. 28A).

To evaluate the preeclampsia prediction modeling, the multiples splits of PE data into 80% training and 20% held-out testing (87 samples) were used to build predictive linear modeling with estimation of AUC on testing sets. Single FABP1 gene modeling in one hundreds splits produced the area-under-the-curve (AUC) for the ROC curve values with mean at 0.67 (FIG. 28B).

Combining best gene PAPPA2 from Examples 9 and 10 with the nine abundant genes include FABP1, CDCA2, HMGB3, ELANE, CDC20, SHCBP1, OLFM4, S100A9, S100A12 with significant differential expression (adjusted p-value<0.05) from Table 27 provide significant increase in predictive modeling with the mean AUC across the outer testing sets is 0.73 (FIG. 28C)

Example 14: Detection and Monitoring Fetal Organ Development in Mother Plasma Across Pregnancy Progression Using Gene Sets

Using systems and methods of the present disclosure, a method of detection and measurement of the fetal organ transcriptional RNA signals in mother plasma were developed to monitor various fetal developmental stages during pregnancy.

The transcriptome data obtained from cohorts A, B, G and H as described in Example 12 (FIG. 27A) were split into a training set (cohort H) and a held-out test set (cohorts A, B, and G). The training set contains four longitudinal blood samples per subject collected at approximate gestational ages of 12, 20, 25 and 32 weeks.

Cell-type specific gene sets represented in Table 28 were derived from a publicly available database of gene ontologies (gsea-msigdb.org) and used to identify the fetal organ development signal in plasma of pregnant subjects.

TABLE 28
Cell-type specific gene set collections (C8)
used in the gene set enrichment analysis
	Number of
Focus organ	cell types	Adult or fetal	PMID
Liver	31	adult	31292543
Developing heart	25	Fetal 5-25 w	31292543
Olfactory	26	adult	32066986
Embryonic cortex	31	fetal 22-23 w	29867213
Esophagus	4	fetal 25 w	29802404
Large intestine	9	fetal 24 w	29802404
Large intestine	7	adult	29802404
Small intestine	7	fetal 24 w	29802404
Stomach	5	fetal 24 w	29802404
Bone marrow	29	adult	30243574
Fetal retina	11	fetal 5-25 w	31269016
Kidney	30	adult	31249312
Kidney	11	fetal 12-19 w	30166318
Midbrain	26	fetal and progenitor	27716510
Pancreas	9	adult	27693023
Cord blood	10	adult and progenitor	29545397
Prefrontal cortex	31	fetal 8-26 w	29539641

Samples collected from early and late pregnancy (12 and 32 weeks, respectively) were compared across 302 cell-type specific gene sets (Table 28). 80 of those gene sets were identified as significantly enriched, including 31 upregulated and 4 downregulated fetal cell types (Table 29). Discovered gene sets associated with cell participating in fetal organ development of heart, large and small intestine, retina, prefrontal cortex, midbrain, kidney, and esophagus. To further evaluate changes in activity of significantly enriched fetal organ gene sets in the course of pregnancy, normalized transcriptome fraction for each of the sets was calculated for every cfRNA sample and the fraction was modeled as a linear function of the recorded gestational age. As a result, 19 out of those 31 significantly enriched fetal gene sets were found to have significant temporal upward trends along the pregnancy timeline, and 3 out 4—significant downward trend.

TABLE 30
Fetal organ gene sets significantly enriched in the comparison between samples collected at 32 and 12 weeks
of gestation age; P-value was adjusted using Benjamini-Hochberg correction; NES (normalized enrichment score)
	P-value
Gene set	adjusted	NES3	Trend
CUI_DEVELOPING_HEART_C6_EPICARDIAL_CELL	1.46E−03	1.67	upward
CUI_DEVELOPING_HEART_C8_MACROPHAGE	4.17E−06	1.75	upward
FAN EMBRYONIC CTX BIG GROUPS CAJAL RETZIUS	1.11E−03	1.49	upward
FAN_EMBRYONIC_CTX_BIG_GROUPS_MICROGLIA	1.37E−09	1.9	upward
FAN_EMBRYONIC_CTX_MICROGLIA_1	1.37E−09	2.43	upward
FAN_EMBRYONIC_CTX_MICROGLIA_3	7.12E−03	1.78	upward
FAN_EMBRYONIC_CTX_NSC_2	1.37E−09	2.3	upward
GAO_LARGE_INTESTINE_24W_C11_PANETH_LIKE_CELL	1.46E−03	1.51	upward
GAO_SMALL_INTESTINE_24W_C3_ENTEROCYTE_PROGENITOR_SUBTYPE_1	3.90E−04	1.93	upward
GAO_SMALL_INTESTINE_24W_C4_ENTEROCYTE_PROGENITOR_SUBTYPE_2	3.33E−06	2.06	upward
HU_FETAL_RETINA_BLOOD	2.91E−08	1.89	upward
HU_FETAL_RETINA_MICROGLIA	8.18E−09	1.8	upward
HU_FETAL_RETINA_RGC	1.23E−04	1.57	upward
HU_FETAL_RETINA_RPC	6.55E−03	1.63	upward
HU_FETAL_RETINA_RPE	8.32E−03	1.48	upward
MANNO MIDBRAIN NEUROTYPES HMGL	2.37E−05	1.53	upward
MANNO_MIDBRAIN_NEUROTYPES_HNPROG	3.93E−04	1.73	upward
MANNO_MIDBRAIN_NEUROTYPES_HPROGBP	1.37E−09	2	upward
MANNO MIDBRAIN NEUROTYPES HPROGFPL	1.37E−09	2.03	upward
MANNO MIDBRAIN NEUROTYPES HPROGFPM	3.02E−08	1.86	upward
MANNO_MIDBRAIN_NEUROTYPES_HPROGM	4.56E−06	1.79	upward
MENON_FETAL_KIDNEY_5_PROXIMAL_TUBULE_CELLS	2.36E−03	1.69	upward
MENON_FETAL_KIDNEY_7_LOOPOF_HENLE_CELLS_DISTAL	4.13E−05	1.71	upward
MENON_FETAL_KIDNEY_8_CONNECTING_TUBULE_CELLS	9.01E−03	1.49	upward
ZHONG_PFC_C1_MICROGLIA	1.37E−09	2.02	upward
ZHONG_PFC_C1_OPC	1.37E−09	2.31	upward
ZHONG_PFC_C2_UNKNOWN_NPC	1.37E−09	2.31	upward
ZHONG PFC C3 UNKNOWN INP	4.25E−04	1.96	upward
ZHONG_PFC_C8_ORG_PROLIFERATING	3.96E−07	2.15	upward
ZHONG_PFC_MAJOR_TYPES_MICROGLIA	4.24E−08	1.75	upward
ZHONG_PFC_MAJOR_TYPES_NPCS	1.37E−09	2.17	upward
ZHONG_PFC_C4_UNKNOWN_INP	5.28E−03	−1.82	downward
FAN_EMBRYONIC_CTX_BRAIN_B_CELL	5.32E−03	−1.6	downward
GAO_ESOPHAGUS_25W_C4_FGFR1HIGH_EPITHELIAL_CELLS	5.81E−03	−1.42	downward
MENON_FETAL_KIDNEY_2_NEPHRON_PROGENITOR_CELLS	7.23E−03	−0.91	downward

Top three fetal organ gene sets with the most significant upward trends (based on the p-value of the collection age coefficient at a confidence level of 0.05) are depicted in FIG. 29A. Those sets are “24-week small intestine enterocyte progenitor cell”, “fetal retina microglia”, and “developing heart C6 epicardial cell”.

To verify if the fetal cell-type signature trends can be generalized from training cohort to held out test cohorts (A, B, and G). The selected fetal cell-type signatures were models as a linear function of gestational age in held-out cohorts. FIG. 29B shows indistinguishable trends for each the signatures gene sets in trained and tested cohorts.

In addition, 3 fetal organ gene sets were independently identified as having significant downward trajectories in the transcriptome fraction space (3 of those were also significantly enriched in samples collected at 12 weeks of gestation age compared to sample from 32 weeks). It indicates that these analyses, gene set enrichment in the individual gene space and analysis of linear trends in the transcriptome fraction space) are not equivalent in tracking fetal fractions. FIG. 29C shows the verification modeling of the top three downward trending gene sets with gestation age (kidney nephron progenitor cells, esophagus C4 epithelial cells, and prefrontal cortex brain C4 cells in held out test cohorts A, B, and G.

Example 15: Human cfRNA Profiling from Liquid Biopsies Provide a Molecular Window into Maternal-Fetal Health

A liquid biopsy of the maternal circulation offers a non-invasive window into the biological progression of the maternal-fetal dyad [Koh et al]. We show that cell-free RNA (cfRNA) signatures from such liquid biopsy provide accurate information on gestational age, on monitoring the progression of fetal organ development and offer an early warning of potential risk of developing preeclampsia.

Results center on a comprehensive transcriptome data set from eight independent prospectively collected cohorts comprising 1,724 racially and ethnically diverse pregnancies, and retrospective analysis of 2,536 banked blood plasma samples. This data set includes samples from 72 patients with preeclampsia matched to 469 non-cases obtained from two independent cohorts. Liquid biopsies were collected 14.5 weeks (SD 4.5 weeks) prior to delivery.

We show that cfRNA signatures can accurately date gestation with a mean absolute error of 15 days across the entire pregnancy. Importantly, the molecular signatures are independent of clinical factors, such as BMI, maternal age, and race or ethnicity, which cumulatively account for less than 1% of model variance, the model is overwhelmingly driven by transcripts (p<2e-16). Additionally, using longitudinal samples at 4 gestational time points, we show an increase in fetal signals from heart, kidney and small intestine as gestation progresses; an observation confirmed in three other cohorts with longitudinal data (p<1e-5). Further, we have identified a cfRNA signature with biologically relevant gene features (p<1e-12) to enable early detection of preeclampsia with a sensitivity of 75% and a positive predictive value of 30% given our study incidence rate of 13%.

A cfRNA profile can be analyzed to provide a non-invasive method to assess maternal-fetal health as well as assess the risk for perinatal pathologies like preeclampsia. This approach overcomes biases from the risk assumptions based on clinical factors, including race. Thus, the test is broadly applicable and provides new opportunities to identify at-risk pregnancies allowing for more precision based therapeutic approaches and improved maternal-fetal health outcomes.

Contemporary obstetrics has a long and successful history of minimally invasive screening for fetal aneuploidy (Rose et al 2020). As a result, aneuploidy screening may be a common aspect of prenatal care despite its low incidence (estimated <1%, Nussbaum et al 2016) compared to the more frequent rates of early delivery due either to preterm labor or preeclampsia which occur over ten-fold more frequently (5-18% of deliveries globally, Blencowe et al, 2102). These obstetric complications are the leading cause of maternal and neonatal morbidity and mortality worldwide (WHO). An early detection cfRNA test, aimed at these more frequent complications, may represent a long overdue advance to obstetric practice with implications for maternal and child health globally.

Beyond this potential for developing a more effective stratification of prenatal risk, cfRNA analyses may also provide a deeper understanding of molecular intricacies and biologic systematics, particularly those that vary longitudinally with the progression of pregnancy. The dynamic and complex nature of pregnancy necessitates assessment of a tissue-specific molecular analyte, such as RNA, to adequately capture the molecular messaging from maternal, placental and fetal cells. Such an examination may enable avenues of diagnostic and therapeutic intervention that are presently not available.

In this work, we demonstrate that cfRNA signatures may meet these multiple objectives by both providing accurate information on gestational age progression, time dependent process of fetal organ development and identification of individual's risk for adverse pregnancy outcomes such as preeclampsia.

The study design is described as follows. Other studies may use cfRNA to monitor pregnancy and detect or diagnose adverse pregnancy outcomes such as preeclampsia (Koh et al 2014, Ngo et al 2018, Munchel et al 2020, Del Vecchio et al 2020, Moufarrej et al 2021). A common limitation of these and other studies has been the use of relatively small sample sizes with low ethnic & racial diversity, with incomplete validation, has hindered use in the clinical setting. In this study, generalizability has been improved by applying the techniques to a larger and more diverse sample set. Combination of samples from eight prospectively collected pregnancy cohorts provided n=2,536 plasma samples from n=1,652 pregnancies across a diverse set of ethnicities and covering a broad range of gestational ages (FIG. 30). The broad demography of our data (Table 31) enabled us to test if initial findings could be applied widely. All study procedures involving human subjects were reviewed and approved by the appropriate local institutional review board. All samples were collected under controlled conditions and only included samples with a time from collection to spin down and freezer storage less than 8 hrs. All plasma samples were processed following main laboratory protocol with minor variations (supplementary methods) and a standardized bioinformatic pipeline to measure gene counts and multiple sample quality metrics for each cfRNA sample. The eight different cohorts were treated as batches and a correction was applied prior to modeling of the data. A more detailed description of each cohort and the correction method is available in the supplementary information.

TABLE 31
Summary of samples collected from different cohorts
				Pre-
		Gestational		pregnancy	Mother's
		Age at	Gestational	Body	Age at
		Blood	Age at	Mass	Blood
cohort	count	Draw	Delivery	Index	Draw
A	161	23.4 +/− 4.60	38.9 +/− 0.65	NA	NA
B	385	26.3 +/− 8.45	39.3 +/− 1.08	NA	NA
C	70	22.5 +/− 5.00	39.3 +/− 1.08	33.5 +/− 9.27	29.8 +/− 5.16
D	194	19.9 +/− 1.77	39.6 +/− 1.27	26.6 +/− 6.31	32.8 +/− 5.38
E	282	21.8 +/− 2.16	39.5 +/− 1.22	28.6 +/− 7.94	26.4 +/− 5.52
F	594	27.1 +/− 7.78	39.5 +/− 1.11	NA	NA
G	140	25.2 +/− 9.66	39.9 +/− 0.91	24.5 +/− 5.12	NA
H	412	22.5 +/− 7.35	39.8 +/− 1.19	25.5 +/− 6.13	NA
					Pre-
			Gestational		pregnancy	Mother's
			Age at	Gestational	Body	Age at
	Sample		Blood	Age at	Mass	Blood
Cohort	Type	Count	Draw	Delivery	Index	Draw
A	case	46	22.6 +/− 5.17	36.2 +/− 2.42	NA	NA
A	control	88	22.8 +/− 5.00	39.0 +/− 0.57	27.5 +/− 7.19	NA
E	case	39	22.5 +/− 2.53	34.6 +/− 3.97	29.8 +/− 7.31	26.2 +/− 5.86
E	control	271	21.8 +/− 2.09	39.5 +/− 1.34	28.5 +/− 8.06	26.7 +/− 5.56

It was observed that molecular signature of gestational age is independent of clinical factors. While gestational age may be predicted using multiple samples over a pregnancy (Ngo et al 2018), we aimed to test performance using a single blood sample to predict gestational age. The potential to create a predictive model for gestational age given the transcription counts for a sample, can be seen in a principal components analyses (FIG. 34). In FIG. 34, the first principal component separates the samples by the gestational age at sample collection, indicating that gestational age is one of main driver of transcriptomic variability across the dataset. Before beginning to develop a machine-learning model to capture this signal, we divided our data from all full-term pregnancies without preeclampsia into a training set (n=1,924 samples) and a held-out test set (n=480 samples), making sure to stratify by gestational age so all age bands were represented equally in both sets.

Prior to modeling the counts for each gene were first normalized to account for variation due to sequencing depth and then transformed so that the mean of each gene is the same across cohorts (see Supplementary text for details). We limited our feature space to genes with a median expression greater than zero across all samples (14,628 genes). A Lasso linear model was fitted to predict gestational age in the training set, with test set performance of a mean absolute error of 15 days (SD 1 day) (FIG. 31A), when using first trimester fetal ultrasound biometry as the gold standard measurement. Of note, we model against ultrasound as the true gestational age, thus the known error of 5-7 days when measured in first trimester (Hadlock et al, 1987) in ultrasound estimated gestational age is a limitation to assess the true performance of our model. The model uses 699 of the available gene features, although this includes a long tail of features with low contribution. Using the top-50 most informative features, it was possible to train a linear model to achieve a mean absolute error of 2.3 weeks.

To assess whether adding further samples to our data set would increase model learning, modeling was repeated with progressively smaller subsets of the data to construct a learning curve (FIG. 31C). The continued reduction in error as we reached our complete training set of n=1,924 samples, indicated that model learning was not exhausted and additional samples would increase our performance. Notably, as seen in FIG. 31C, the similar performance in cross-validation and on the independent held-out test data indicated that the model was not overfit. To determine how far the model could be extrapolated, a final model was built using all data, this gave a mean absolute error of 13 days across the entire data set, improvements beyond adding more samples could come from samples with known conception date, e.g. from in vitro fertilized pregnancies. Compared to prior published results (Ngo et al 2018), this model outperforms the accuracy across all trimesters. In our data set, the error in cfRNA gestational dating was consistent across the predicted range from 6 to 36 weeks (FIG. 31A). This result is in contrast to ultrasound-based dating, which has a gradual increase in error as pregnancy progresses, increasing to over 20 days in the third trimester (Skupski et al 2017). Overall, the error of our model is equivalent to that of second trimester ultrasound and superior to third trimester ultrasound (Skupski et al 2017).

Next, we explored if the inclusion of clinical factors improved the performance of the model. By analysis of variance (ANOVA), we showed that the model was driven almost entirely by information from the cfRNA transcripts with body mass index, maternal age and race/ethnicity accounting for less than 1% of total variance (FIG. 31B). A liquid biopsy test based on molecular signatures, therefore, worked independently of clinical factors and could help reduce biases introduced from risk assumptions based on clinical and demographic factors.

These data indicate that a simple blood test that can be shipped to a central lab has broad applicability and may be used as the primary assessment of gestational age in low resources settings, where timely access to trained ultrasonographers may be limited, and the high proportion of small for gestational age pregnancies further degrades accuracy of the translation of fetal ultrasound biometry to gestational age estimates. There may also be an adjunct value for suboptimally dated pregnancies where a confirmatory ultrasound was not able to be obtained before third trimester.

Further, we observed molecular signature for fetal organ development. We explored whether transcripts found in maternal circulation during pregnancy encode information regarding fetal organ development. As individual transcripts from the fetus are relatively rare in the maternal plasma, we investigated fetal organ signal by analyzing gene sets and by targeting gene sets discovered in human embryonic cells for this analysis. We used longitudinal samples from the cohort H (Gybel-Brask et al 2014), where pregnant individuals were sampled up to four times during pregnancy. A total of 91 women had data available for all four collections, which were carried out at gestational weeks 12, 20, 25, and 32 (within a given std dev).

Based on a pairwise comparison between samples from early and late pregnancy (collections at 12 and 32 weeks), we identified 80 cell-type specific gene sets that were significantly enriched (Table 32). Of these, 33 sets were characteristic of embryonic cell types of which 19 showed significant temporal upward trends along the pregnancy timeline. Of all the analyzed gene sets, including fetal and adult, the “24-week small intestine enterocyte progenitor cell” type (Gao et al 2018) showed the most significant trend (FIG. 32A) For the small intestine gene set we evaluated how many of the samples monotonically increased over the four time points and identified 36 study participants that followed this strict criterion (p<2e-16). Another example of increasing signal with gestational age was observed from “developing heart C6 epicardial cell” (FIG. 32B, Cui et al 2019). Of the remaining gene sets thirteen displayed downward trajectories, examples of a gene sets that decrease in expression were kidney nephron progenitor cells (FIG. 32C, Menon et al 2018), which aligns with the decreasing nephrogenic zone width as a function of gestational age (Ryan et al 2018). Additionally, for these gene sets, we confirmed the directional change in expression in three other cohorts: A, B and G, where at least 2 longitudinal samples were processed (FIG. 36).

TABLE 32
Cell-type specific gene set collections (C8)
used in the gene set enrichment analysis
Primary		Number of
author	Focus organ	cell types	Adult or fetal	PMID
Aizarani	Liver	31	adult	31292543
Cui	Developing heart	25	Fetal 5-25 w	31292543
Durante	Olfactory	26	adult	32066986
Fan	Embryonic cortex	31	fetal 22-23 w	29867213
Gao	Esophagus	4	fetal 25 w	29802404
Gao	Large intestine	9	fetal 24 w	29802404
Gao	Large intestine	7	adult	29802404
Gao	Small intestine	7	fetal 24 w	29802404
Gao	Stomach	5	fetal 24 w	29802404
Hay	Bone marrow	29	adult	30243574
Hu	Fetal retina	11	fetal 5-25 w	31269016
Lake	Kidney	30	adult	31249312
Menon	Kidney	11	fetal 12-19 w	30166318
Manno	Midbrain	26	fetal and	27716510
			progenitor
Muraro	Pancreas	9	adult	27693023
Zheng	Cord blood	10	adult and	29545397
			progenitor
Zhong	Prefrontal cortex	31	fetal 8-26 w	29539641

Using a gene ontology (GO) collection of gene sets, we identified seven pregnancy related sets that were significantly enriched in the comparison between early and late pregnancy samples (FIGS. 35A-35B). Three gene sets in the gonadotropin and estrogen pathways exhibited significant changes consistent with their known physiology (Tal et al 2015).

We next compared the observed collection time labels to a set of randomly permuted collection time labels. This comparison certified that all selected gene sets were, in fact, associated with the longitudinal progression of pregnancy (FIG. 37). Furthermore, we repeated the gene set analyses after removing all 699 genes used in the gestational age model and rediscovered the same 80 gene sets were differentially expressed. As changes in gene sets, up or down, were only significant in the context of gestational age, with or without the gestational age model genes, we showed the first window into fetal development from a maternal liquid biopsy sample.

Preeclampsia is a leading cause of maternal morbidity and mortality. A diagnosis of preeclampsia confers a lifetime increased risk for cardiovascular disease for the mother (Haug et al, 2018). Yet, despite the signification health implications of this diagnosis for a woman's pregnancy and her lifetime, there remains challenges to developing reliable methods to identify women at risk early in pregnancy.

We evaluated the predictability of preeclampsia from molecular signatures measured in blood draws taken during the second trimester (16-27 weeks), on average 14.5 weeks (SD 4.5 weeks) before delivery. A case-control study with 72 cases of preeclampsia and 469 matched non-cases selected from two independent cohorts (cohorts A and E) was performed. Cohort E included 34 controls with chronic hypertension and 19 with gestational hypertension, both cohorts included preterm birth samples in the non-case population. Preeclampsia was defined by criteria consistent with those of the 2013 Task Force on Hypertension in Pregnancy (ACOG 2013), and each case was adjudicated by two board certified physicians. Blood samples were collected at gestational weeks 16-27, before the onset of signs or symptoms of preeclampsia. As before, a cohort correction was applied prior to modeling.

We used Spearman correlation tests to identify transcriptional signatures that can differentially separate the preeclampsia cases and controls presented in Table 33.

TABLE 33
Set of 38 Differentially Expressed Transcriptional
Features Predictive of Preeclampsia (PE)
	Transcriptional feature	P-value	P-value adj
	CLDN7	4.20E−10	1.40E−05
	PAPPA2	3.94E−09	1.32E−04
	SNORD14A	1.17E−08	3.91E−04
	PLEKHH1	3.76E−08	0.0012570947
	MAGEA10	1.86E−07	0.006203178738
	IGKV2OR22-4	3.76E−07	0.01257256125
	CH17-335B8.4	3.76E−07	0.01257503174
	TLE6	4.82E−07	0.01610065186
	FABP1	6.32E−07	0.02112300951
	AC015977.5	9.57E−07	0.03196867232
	GJC1	2.53E−06	0.08459648949
	PTPRQ	3.10E−06	0.1035580684
	GJD4	4.79E−06	0.1599066029
	TEAD3	6.09E−06	0.2033532195
	RNA5SP71	6.64E−06	0.2217167558
	SALL1	7.90E−06	0.2638484427
	GPSM2	8.20E−06	0.2737536288
	SLC27A2	8.52E−06	0.2845032434
	CRH	8.53E−06	0.2847182052
	TRIM29	8.84E−06	0.2953097559
	GTSF1L	9.41E−06	0.3143403365
	DEFB132	1.18E−05	0.3929372843
	OR7E158P	1.18E−05	0.3929372843
	RNU6-708P	1.18E−05	0.3929372843
	SAA2-SAA4	1.18E−05	0.3929372843
	HP	1.29E−05	0.4322689364
	ITGB6	1.34E−05	0.4480987694
	KIAA1211L	1.39E−05	0.4638821437
	OR4S1	1.41E−05	0.4721774325
	NOC2LP1	1.45E−05	0.4849266379
	HRH4	1.53E−05	0.5103650892
	CFAP57	1.95E−05	0.649835203
	THEM6	2.11E−05	0.7046812124
	S100A14	2.18E−05	0.7271782584
	DPCR1	2.39E−05	0.7967427421
	GPC1	2.58E−05	0.8613470703
	MYOM3	2.69E−05	0.8978677978
	BHMT2	2.79E−05	0.9319628309

During in each round of cross-validation we kept features with adjusted p-value below 0.05 and consistently identified seven genes: CLDN7, PAPPA2, SNORD14A, PLEKHH1, MAGEA10, TLE6 and FABP1 (FIG. 33A). Each of the seven genes selected for modeling may have a function relevant to preeclampsia or fetal development. PAPPA2, or pregnancy associated plasma protein 2, is expressed primarily in placenta (Uhlén et al 2015) and specifically in trophoblast cells. It may be linked to the development of preeclampsia (Kramer et al 2016, Chen et al 2019), and associated with inhibition of trophoblast migration, invasion and tube formation. PAPPA2 is a protease that cleaves insulin growth factor binding protein 5 (IGFBP5) and impacts the pathway of insulin growth factor 2 in which higher levels lead to increased fetal growth (White et al 2018). Claudin 7 (CLDN7) a protein involved in tight cell junction formation, may be implicated in blastocyst implantation; in a healthy pregnancies CLDN7 is reduced in response to estrogen at time of implantation (Poon et al 2013). Fatty acid Binding Protein 1 (FABP1) may be detected and purified from human cytotrophoblasts and may be highly expressed in fetal liver, it is critical for fatty acid uptake and transport (Wang et al 2020) and is upregulated 3-fold when cytotrophoblasts differentiate to syncytiotrophoblasts around the time of implantation (Cunningham and McDermott 2009).

Based on these identified gene features, a logistic regression model, in a leave-one-out cross validation setup, was used to estimate the likelihood of preeclampsia. At a sensitivity of 75%, our model achieves a positive predictive value of 32.3% (SD 3%) given a 13.7% occurrence in our study; AUC for the model is 0.82 (FIG. 33B). Similar to the gestational age model, adding in clinical factors (BMI, maternal age, and race/ethnicity) has no significant effect and account for less than 1% of variance based on ANOVA analyses.

To further understand the molecular signature changes and how they might reflect the pathophysiology driving preeclampsia, a differential gene set analysis was performed. The top upregulated gene sets are dominated by structural cell functions including desmosome, blood vessel morphogenesis and vasculature development (FIG. 38A), while the vast majority of downregulated gene sets were related to immune pathways (FIG. 38B). Both aligned well with what is known about preeclampsia pathophysiology (Redman & Sargent, 2005).

The control group contained both normotensive women (n=416) and women with chronic hypertension (n=34) and gestational hypertension (n=19). Comparison of the chronic or gestational hypertensive groups to the normotensive group, showed no overlap with genes significant for preeclampsia (no gene achieved an adjusted p-value below 0.05). While others have published studies designed to determine the effect of hypertension per se on gene expression (e.g. Zeller et al 2017), here we demonstrate that the signal for preeclampsia, is independent of any signal associated with chronic or gestational hypertension. As preeclampsia and spontaneous preterm birth are theorized by some to have overlapping molecular pathways (REF), we also excluded samples with delivery prior to gestational week 37 (n=89) from the non-case group. Removal of preterm delivery samples had no impact on our model performance (supplementary methods), indicating that our signature can separate preeclampsia from spontaneous preterm delivery. We report a stand-alone molecular predictor that has the potential to be a reliable, early detection of preeclampsia, that is based entirely on transcripts and is independent of clinical factors such as body mass index, maternal age and race/ethnicity.

The transcriptome data set presented here shows that comprehensive molecular profiling from liquid biopsies can provide a robust window into maternal-fetal health. We have shown that transcript signatures from a single liquid biopsy can: (i) accurately estimate gestational age at performance levels comparable to ultrasound, making it a viable option for rural and low-resource settings, as well as to confirm gestational age beyond the first trimester where ultrasound accuracy is limited (Skupski et al 2017), (ii) provide non-invasive monitoring of fetal organ development including the fetal heart, small intestine and kidney, and (iii) has the potential to reliably identify risk of preeclampsia prior to onset of disease using novel transcript signatures, whose biological significance adds further rigor to our findings.

These findings expand on other studies from tens of pregnancies (Koh et al 2014, Ngo et al 2018) by moving to over a thousand pregnancies. This scale allows us to non-invasively assess molecular foundation of pregnancy health, with the ability to develop signatures from specific fetal organs that may give an early warning of birth defects such as congenital heart disease. We further improved the accuracy of gestational age assessment to be equivalent to ultrasound. The generalizability of these results is afforded by the large and racially diverse cohorts utilized in this work.

We establish specific transcript signatures that inform the early identification of the risk of preeclampsia. However, we do not replicate the differential gene expression for preeclampsia seen in Moufarraj et al (2021) (collected before week 16) in the samples used for preeclampsia modeling (collected week 16-27). Nor did we replicate the final genes selected in Munchel et al (2020)(collected at time of diagnosis, typically after week 34). Comparison of differential gene expression across studies may be confounded by varying trimesters of sample collection.

The data presented here are strengthened by the study size and the use of geographically distinct cohorts. This ensures diversity in our sample composition and generalizability of our conclusions. However, due to small differences in collection protocols for the different cohorts required cohort correction, prospective studies may combine diversity and size with a consistent framework for collecting samples, for clinical validation and utility studies.

The presented results demonstrate improved methods to overcome current limitations in our ability to assess maternal-fetal health during a pregnancy. Importantly, a liquid biopsy approach overcomes biases introduced by risk assumption based only clinical factors, including race and BMI. As such, molecular tests, based on cfRNA, are broadly applicable and provide new opportunities to identify at-risk pregnancies allowing for more precision based therapeutic approaches and improved maternal-fetal health outcomes. A cfRNA platform enables early detection of multiple clinically relevant endpoints (e.g. gestational age and preeclampsia) from a single sample without the need of local specialized point-of-care testing facilities.

In addition to a more effective approach to risk stratification for adverse pregnancy outcomes, liquid biopsies of the maternal-fetal-placental transcriptome also present a vehicle by which understanding of the biological underpinnings of maternal-fetal health and disease can be improved and provide novel insight into interactions across maternal-fetal dyad. This holds the promise of more effective, precision therapeutic interventions that can then target molecular subtypes of preeclampsia and preterm birth.

The impact from the use of non-invasive assessment of molecular signatures can be appreciated from its role in advancing breast cancer diagnosis (Alimirzale et al, 2019). We now have the opportunity to similarly advance the field of maternal and child health by identifying those at risk for adverse outcomes such as preeclampsia, preterm birth and gestational diabetes in this decade. Given the 60 million women who experience some form of pregnancy complication each year, a molecular, precision diagnostic and precision medicine approach has the potential to transform many lives.

In this work, we have demonstrated the potential of obtaining transcript signatures obtained in pregnancy allow us insight into three novel aspects of pregnancy: The estimation of gestational age, the monitoring of fetal organ development, and the assessment of risk for preeclampsia later in gestation. These insights were all obtained via a single liquid biopsy obtained on average 14.5 weeks before delivery.

Cohort Descriptions

Cohort A (BWH)

LIFECODES is a prospective pregnancy biorespository that has been recruiting pregnant women in the greater Boston, MA area since 2006. Women 18 yrs. and older and plan to deliver at Brigham and Women's Hospital are eligible. Higher order pregnancies (triplets or greater) are excluded. To date N=5,569 pregnant women have been enrolled and followed, providing longitudinal samples and data, through delivery. Racial and ethnic makeup of LIFECODES follows the general US trend with 55% being Caucasian, 14.8% African American, 7.3% Asian, 18.4% Hispanic, and 4.5% Mixed/Other. The medical record for each subject in LIFECODES is independently reviewed by two certified Maternal Fetal Medicine physicians. Complications and outcomes for each subject are coded using a structured coding tool. The codes from each reviewer are then compared with disagreement in either pregnancy outcome or complication and is decided by a review committee. Ref PMID 25797229

Cohort B (GAPPS)

The Global Alliance to Prevent Prematurity and Stillbirth (GAPPS) (www.gapps.org) has developed a continually recruiting cohort of pregnant women and their babies designed to combat the deficit of pregnancy-related specimens and accompanying data available for research. Participants for this study were enrolled at all gestational ages from obstetric and antepartum clinic sites in Washington State under the Advarra IRB (FWA00023875) protocol number Pro00036408. Written informed consent was obtained from all participants and parental permission and assent were obtained for participating minors aged at least 15 years. A repository of biospecimens collected longitudinally at each trimester of pregnancy and the postpartum period are linked to comprehensive patient data across the gestation. Biospecimens were collected from ten maternal body sites (vaginal, cervical, buccal and rectal mucosa, blood, urine, chest, dominant palm, antecubital fossa and nares), five types of birth products (amniotic fluid, cord blood, placental membranes, placental tissue and umbilical cord) and seven infant body sites (right palm, buccal and rectal mucosa, meconium/stool, chest, nares and respiratory secretions if intubated). All blood is processed and stored at −80C within two hours of collection. The data repository was developed with the goal of supporting prematurity and stillbirth research and to better understand associated risk factors.

Pregnant women were provided literature describing the repository project and invited to participate in the study. Women who were incapable of understanding the informed consent or assent forms or were incarcerated were excluded from the study. Comprehensive demographic, health history and dietary assessment surveys were administered, and relevant clinical data (for example, gestational age, height, weight, blood pressure, vaginal pH, diagnosis) were recorded. Relevant clinical information was obtained from neonates at birth and discharge and six weeks postpartum.

At subsequent prenatal visits, labor and delivery, and at discharge, characterizing surveys were administered, relevant clinical data were recorded and samples were collected. Vaginal and rectal samples were not collected at labor and delivery or at discharge. Women with any of the following conditions were excluded from sampling at a given visit: (1) Incapable of self-sampling due to mental, emotional or physical limitations; (2) More than minimal vaginal bleeding as judged by the clinician; (3) Ruptured membranes before 37 weeks; (4) Active herpes lesions in the vulvovaginal region; and (5) Experiencing active labor.

Cohort C (IO)

Informed consent for sample and data collection was obtained at the University of Iowa by the Maternal Fetal Tissue Bank (IRB #200910784). Blood samples were collected in ACD-A tubes (Becton Dickinson). Plasma was aliquoted, snap frozen, and stored at −80C. All freezers are alarmed with temperature monitors. Time of sample collection and processing are recorded within the research information system managed by the UI Bioshare service (Labmatrix, Biofortis). All samples are coded and are annotated with clinical information. (PMID: 24965987)

Cohort D (KCL)

INSIGHT: Biomarkers to predict premature birth is an ongoing observational cohort study designed to study women at high risk of spontaneous preterm birth (sPTB) compared to low-risk controls. Plasma samples (taken between 16-23⁺⁶ weeks of gestation) provided for the current analyses were obtained from women with singleton pregnancies participants recruited from four tertiary antenatal clinics in the UK. High-risk pregnancies are defined by at least one of; prior sPTB or late miscarriage (between 16 to 37 weeks of gestation), previous destructive cervical surgery or incidental finding of a cervical length <25 mm on transvaginal ultrasound scan. Women with no risk factors for sPTB and otherwise well at the time of recruitment are recruited as low-risk controls from either routine antenatal or ultrasonography clinics at these centres. Exclusion criteria for both the high and low risk groups were multiple pregnancy, known major congenital fetal abnormality, rupture of membranes or current vaginal bleeding. Approval from London City and East Research Ethics Committee was granted (13/LO/1393). Informed written consent was obtained from all participants.

Reference: PMID: 32694552, Cervicovaginal natural antimicrobial expression in pregnancy and association with spontaneous preterm birth (Hezelgrave et al., 2020) is incorporated by reference herein in its entirety.

Reference: Hezelgrave N L, Seed P T, Chin-Smith E C, Ridout A E, Shennan A H, Tribe R M. Cervicovaginal natural antimicrobial expression in pregnancy and association with spontaneous preterm birth. Sci Rep. 2020 Jul. 21; 10(1):12018. doi: 10.1038/s41598-020-68329-z is incorporated by reference herein in its entirety.

Cohort E (MSU)

The Pregnancy Outcomes and Community Health (POUCH) Study cohort includes 3,019 pregnant women enrolled at 16-27 weeks' gestation (1998-2004) from 52 clinics in five Michigan communities. Eligibility included singleton pregnancy and no known congenital anomaly, maternal age ≥15, maternal serum alpha-fetoprotein (MSAFP) screening, no pre-pregnancy diabetes mellitus, and English speaking. At enrollment study nurses interviewed participants and collected biologic samples (blood, urine, hair, vaginal fluid). An additional at-home data collection protocol included ambulatory blood pressure monitoring and three consecutive days of saliva and urine collection for measuring stress hormones. To conserve resources, a sub-cohort of 1,371 participants were studied in greater depth, i.e., medical records abstracted, biological samples analyzed, and placentas examined.¹ The sub-cohort is 42% primiparous, 57% 20-30 years of age, 42% African American and 49% non-Hispanic white, and 57% were insured through Medicaid.

Holzman C, Senagore P K, Wang J. Mononuclear leukocyte infiltrate in the extra-placental membranes and preterm delivery. Am J Epidemiol 2013; 177(10):1053-64. PMCID: PMC3649632 is incorporated by reference herein in its entirety.

Cohort F (PITT)

Samples were provided from biobanks collected in association with NIH P01 HD HD030367. These samples were part of 3 successive renewals of the PPG and collected between 2001 and 2012. In all cases samples were collected longitudinally across pregnancy from low risk pregnant women cared for at Magee-Womens Hospital Pittsburgh Pennsylvania. Exclusion criteria were pre-existing hypertension, diabetes, multiple gestation or renal disease. Charts were abstracted and reviewed by a jury of 5 clinicians. The population was approximately 50% African American, 50% Caucasian with very few other race/ethnicities included.

Powers R W, Roberts J M, Plymire D A, Pucci D, Datwyler S A, Laird D M, Sogin D C, Jeyabalan A, Hubel C A, Gandley R E. Low Placental Growth Factor Across Pregnancy Identifies a Subset of Women With Preterm Preeclampsia Type 1 Versus Type 2 Preeclampsia? Hypertension. 2012; 60:239-46 is incorporated by reference herein in its entirety.

Cohort G (PM)

The Pemba Pregnancy and Discovery Cohort (PPNDC) study is being undertaken in Pemba Island, Zanzibar, Tanzania. This ongoing study is follow-up continuation with methods similar to the AMANHI bio-repository study which involved 3 sites (Pakistan, Bangladesh and Pemba), methods already published (ref: DOI: 10.7189/jogh. 07.021202 is incorporated by reference herein in its entirety).

Demography: The population is a mix of Arab and original Waswahili inhabitants of the island. A significant portion of the population also identifies as Shirazi people.

Study Goal: The main purpose of the study is to identify important biomarkers as predictors of important pregnancy-related outcomes and to extend bio-bank in Pemba (started with AMANHI) for future research as new methods and technologies become available.

Study Participants: Women of Reproductive Age (18-49 years), resident of the island who intended to stay in the study areas for the entire duration of follow-up and consented for collection of epidemiological data as well as biological samples are being enrolled in the study

Method: Trained women fieldworkers (FWs), performed home visits every 2-3 months to all women of reproductive age in the study area to enquire about pregnancy. If a woman reported two or more consecutive missed period or suspected a pregnancy, FWs conducted a urine pregnancy test to confirm it. Pregnant women who provided consent underwent a screening ultrasound to date the pregnancy. All women in their early pregnancies with ultrasound confirmed gestational age between 8 and 19 weeks were consented for participation in the study. Women were randomized for antenatal maternal sample collection at either 24-28 weeks or 32-36 weeks gestation. The fathers of the babies also consented for their saliva sample collection.

A trained study worker conducted four home visits to all women in the cohort; at baseline (immediately after enrolment), at 24-28 weeks, 32-36 weeks and after 37 completed weeks of pregnancy to collect self-reported morbidity data from these women. Blood pressure and protein urea was measured by the study staff during these visits.

Bio-specimens (blood and urine) were collected from the pregnant women at the time of enrollment (between 8 and 19 weeks) and once during the antenatal period (24-28 or 32-26 weeks of gestation.

Reference: AMANHI (Alliance for Maternal and Newborn Health Improvement) Bio-banking Study group); Understanding biological mechanisms underlying adverse birth outcomes in developing (PMID: 29163938) is incorporated by reference herein in its entirety.

Cohort H (RS)

This prospectively collected cohort from Roskilde hospital in Denmark, sampled participants 4 times during pregnancy at weeks 12, 20, 25 and 32. All Danish-speaking women over the age of 18 were eligible for inclusion. At each visit a blood sample was collected and we performed a detailed ultrasound examination. At end of collection in 2010 the cohort included 1,214 participants.

Reference: Gybel-Brask, D., Hegdall, E., Johansen, J., Christensen, I. J. & Skibsted, L. Serum YKL-40 and uterine artery Doppler—a prospective cohort study, with focus on preeclampsia and small-for-gestational-age. Acta Obstet Gynecol Scand 93, 817-824 (2014) is incorporated by reference herein in its entirety.

Methods

cfRNA Isolation

Plasma samples received on dry ice from our collaborators were stored at −80° C. until further processing. Total circulating nucleic acid was extracted from plasma ranging in volume from ˜215 ul to 1 ml, using a column-based commercially available extraction kit, following the manufacturer's instructions (Plasma/Serum Circulating and Exosomal RNA purification kit, Norgen, cat 42800). We added in spike-in control RNA during extraction to monitor the yield.

Following extraction cfDNA was digested using Baseline-ZERO DNase (Epicentre) and the remaining cfRNA purified using RNA Clean and Concentrator-5 kit (Zymo, cat R1016) or RNeasy MinElute Cleanup Kit (Qiagen, cat 74204).

RT-qPCR Assay

We developed a RT-qPCR based method to assess the relative amount of cfRNA extracted from each sample. We measured and compared the threshold Cycles (Ct) values from each RNA extraction using a 3 color multiplex qPCR assay using TaqPath™ 1-Step Multiplex Master Mix kit (Catalog A28526) and Quant Studio 5 system. We measured the Ct values for an endogenous housekeeping gene (ACTB; Thermofisher Scientific, cat 4351368) and a spike-in control RNA as well as an assay to monitor presence of DNA contamination (IDT).

cfRNA Library Preparation

cfRNA libraries were prepared using the SMARTer Stranded Total RNAseq-Pico Input Mammalian kit (Takara, Cat 634418). following the manufacturer's instructions except we did not use ribo depletion. Library quality was assessed by RT-qPCR following the method described for assessing RNA extraction and Fragment analyzer analysis 5300 (Agilent Technologies).

Enrichment and Sequencing

Libraries were normalized before pooling for target capture. We used SureSelect Target Enrichment kit (Agilent Technologies, cat 5190-8645) and followed the manufacturer's instructions for hybrid capture. Samples were quantitated and 50 base-pair, paired-end sequencing was performed on a Novaseq S2. Between 98 and 144 samples were pooled and sequenced per sequencing run.

Analysis for Outliers

qPCR of ACTB and a spike-in control RNA as well as MultiQC sequencing metrics were monitored to eliminate sample outliers before performing gene expression analyses. Individual samples more than 3 standard deviations from the mean were removed as outliers. A set of samples were removed following this filtering.

Feature Normalization

For each gene, its relationship to total counts per sample is measured and corrected for using linear model residuals (e.g., gene ACTB). We also thought to correct the genes such that each cohort has the same mean value for each gene. However, the cohorts come from different parts of the gestational age spectrum. Therefore, only cohort effects orthogonal to the gestational age effect are corrected (e.g., gene CAPN6). Each cohort has its own color. The benefit of this correction becomes clearer if we zoom in to the second trimester. In this range, the CAPN6 counts from the bright green-colored cohort were unusually high and in the corrected version, this effect has been removed.

Mathematical Details

The steps for the above correction are as follows.

For each gene, model its counts as a function of total counts, cohort and gestational age. This gets a linear model gene=β₀+β₁totcounts+β₂cohort+β₃GA.

Once this model is fit, we can correct for the effect of these variables by taking the model residuals as the corrected values.

However, we don't want to correct for the gestational age effect (we want that to remain in the data because it's a variable of interest). To avoid doing so, set the coefficient 3 to zero before calculating fitted values and residuals.

Gestational Age Model without Cohort Correction

In this approach, we selected all samples from healthy pregnancies and split the dataset into a training set (1482 samples, 75% of data) and a test set (495 samples, 25% of data), in which samples were stratified by cohort. Samples that did not pass QC filtering based on basic sequencing metrics had been previously excluded from analysis (70 samples, 3.5% of total). We trained a Lasso model to predict the gestational age at collection for each sample using the mean absolute error as optimization metric and 10-fold cross-validation in the training set. We used all genes with mean log 2(CPM+1)>1 (12894 genes) plus a set of sequencing metrics as features for training. Modeling was performed in log 2(CPM+1) space and all data was centered and scaled prior to modeling using the training set statistics. This led to a model with mean absolute error of 15.9 days in the with-hold test set using 455 transcriptomic features. We then selected the top 55 features of this model and retrained the Lasso using the same approach described above achieving a mean absolute error of 16.3 days in the withhold test set.

Gene Set Enrichment Analysis (GSEA)

GSEA<PMIDs: 12808457, 16199517> was done with fast gsea algorithm <doi: doi.org/10.1101/060012> using Bioconductor fgsea package <DOI: 10.18129/B9.bioc.fgsea>. Gene sets were compiled from the Molecular Signatures Database (MSigDB)<21546393, 16199517> using CRAN msigdbr v7.2 API. We focused on two collections of gene sets: Gene Ontology (GO) sub-collection of the ontology gene sets, C5:GO, and the cell type signature gene sets, C8 (Table 32). Genes were ranked based on their log-fold change and associated Wald-test p-value obtained from the analysis of differential expression using Bioconductor's DESeq2, DOI: 10.18129/B9.bioc.DESeq2, <25516281> as a −log₁₀(p-value)*shrunkenLFC. GSEA was carried out on 364 samples from the Roskilde cohort collected from 91 women with healthy pregnancies over 4 time intervals during pregnancy, 11-14 weeks, 17-xxx w, xxx-xxx w, and xxx-xxx w. Log-fold changes and corresponding p-values were obtained from pairwise comparisons between collections 1 and 2, 1 and 3, and 1 and 4. Significantly enriched gene sets (Benjamini-Hochberg adjusted p-value<0.01), whose number varied predictably with the distance between the comparators (e.g., Table 33), were used in downstream analyses, including analysis of plasma transcriptome partitioning and set-specific longitudinal trends.

Evaluating Changes in Plasma Transcriptome Partitioning

Plasma transcriptome can be phenomenologically viewed as being partitioned between characteristic sets of genes. We assessed this partitioning in each RNAseq sample by converting raw gene counts to counts per million (CPM) and summing these CPMs over all genes in each of the sets. The resulting cumulative CPM score, which is a relative measure of abundance of each gene set in the overall transcriptome, was used to directly compare gene sets across collection time points. Cumulative CPM scores for all gene sets significantly enriched between collections 1 and 4 were calculated for every RNAseq sample. The scores for each sample were regressed onto the recorded gestational age (in weeks) using a linear model. Gene sets with an adjusted p-value for the gestational age coefficient <0.01 were considered to be having a significant (positive or negative) trend in their relative abundance. The association of these trends with the time component in the data was further verified by scrambling the temporal structure and re-examining the trends along the original time variable. For each mother we also evaluated the monotonicity of the cumulative CPM score function along the collection times. Since there are 24 possible permutations of order of the 4 collection times and only one of those permutations allows for a monotonic upward trend (and one—for downward), we were able to analytically assess the significance of observed number monotonic trends among 91 mothers using a Chi-squared test.

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Example 16: Prediction of Very Early Pre-Term Birth (ePTB) on Combined Multiple Cohorts

All PTB cohorts from Example 4 and Example 8 were combined in a single data set, as shown in FIG. 26A, totaling 58 case subjects with very early preterm delivery and 487 full-term deliveries. Very early Pre-term Birth (ePTB) was defined as deliveries occurring after 16 weeks of gestation and before 32 weeks of gestation (including cases of late miscarriages).

As shown in FIG. 26B, a cohort of 545 subjects (58 very early pre-term and 487 full-term controls) was established (with patient identification numbers shown on the x-axis). From this cohort, one or more biological samples (e.g., 1 or 2) were collected and assayed at different time points corresponding to an estimated gestational age (shown on the y-axis, in increasing order of estimated gestational age at delivery) of a fetus of each subject, using methods and systems of the present disclosure. For example, the estimated gestational age (shown on the y-axis) may be determined using methods such as ultrasound imaging, a last menstrual period (LMP) date, or a combination thereof, and may range from 0 to about 42 weeks

In order to mitigate the gestational age effect for blood collection in this analysis, only samples collected between 16 and 27 weeks of gestational age were included. Table 34 shows the top 30 differentially expressed genes for predicting very early preterm birth between 16 to 32 weeks with blood collected between 16 to 27 weeks, with significant statistical significance after adjustment for multiple hypothesis correction; the results summarized in this table also showed a significant deviation from the null hypothesis in a QQ plot for differential expression in very early pre-term cases (as shown in FIG. 39). Differential expression analysis was performed using EdgeR, and accounting for ethnicity and cohort effects (58 ePTB cases and 487 controls).

TABLE 34
Top set of genes that are predictive for ePTB between
16 and 32 weeks of gestational age with blood samples
collected between 16 and 27 weeks of gestational age
Gene	logFC	log(CPM)	P-Value	FDR
COL3A1	−1.554608	2.721233	4.30E−07	0.004491
COL1A2	−1.476499	2.139572	7.32E−07	0.004491
COL1A1	−1.60053	2.71966	1.51E−06	0.006179
EPB41L4A	−0.580864	2.971978	2.75E−06	0.008421
CDR1-AS	−0.983948	3.04125	4.57E−06	0.011204
MMP2	−1.182085	1.154661	1.94E−05	0.039687
ATP5F1	−0.130342	6.243824	1.23E−04	0.214913
CDCA7L	−0.294654	5.140473	3.23E−04	0.495809
CLSPN	−0.241616	4.865637	4.15E−04	0.504392
RRM2	−0.408065	4.269675	4.44E−04	0.504392
ZCCHC7	−0.144083	6.964859	4.52E−04	0.504392
PDHA1	−0.177542	5.60246	5.97E−04	0.574045
TK1	−0.528352	1.51427	7.36E−04	0.574045
CCNA2	−0.381202	2.852578	8.17E−04	0.574045
TIPRL	−0.151145	5.006339	8.29E−04	0.574045
TYMS	−0.330468	4.326804	8.35E−04	0.574045
SNRPD3	−0.14252	6.572218	8.62E−04	0.574045
PSMD14	−0.166879	4.365445	8.62E−04	0.574045
CCDC80	−0.773546	3.143176	8.89E−04	0.574045
TUBB2A	−0.782378	3.745655	9.52E−04	0.583731
C1S	−0.715219	0.853868	1.08E−03	0.633619
CEP68	0.248055	4.095732	1.18E−03	0.636236
TIMELESS	−0.261195	3.754269	1.19E−03	0.636236
PER3	0.281305	4.239084	1.35E−03	0.668346
RTEL1P1	1.337333	1.13544	1.38E−03	0.668346
DCN	−1.031659	1.625258	1.46E−03	0.668346
CD96	−0.447194	5.016654	1.47E−03	0.668346
LRRC23	−0.288526	2.094129	1.63E−03	0.708272
TRIM23	0.223815	5.477493	1.73E−03	0.708272
TOP2A	−0.225064	5.946619	1.73E−03	0.708272

Example 17: Prediction of Gestational Diabetes Mellitus (GDM) on Combined Multiple Cohorts

Using systems and methods of the present disclosure, a prediction model was developed to detect or predict a risk of gestational diabetes mellitus (GDM) of a pregnant subject. The prediction model development comprised obtaining a cohort of subjects and training the prediction model on a training dataset corresponding to the cohort of subjects represented in Table 35.

Further, whole transcriptome data from four cohorts were analyzed by the abundant gene search method. The three (K, M, P) cohorts contain combined 49 GDM samples and 430 control samples with gestational age at blood draw having a median of 21 weeks. Additionally, the R cohort comprised blood samples collected from 11 participants diagnosed with gestational diabetes and 119 healthy participants with multiple blood draws at gestational age of about 13, 20, 26, and 32 weeks.

TABLE 35
GDM cases & controls by cohort
	Cohort	Cases	Controls
	K	18	164
	M	12	187
	P	19	79
	R, Draw 1 (about13 weeks)	9	105
	R, Draw 2 (about 20 weeks)	8	109
	R, Draw 3 (about 26 weeks)	11	119
	R. Draw 4 (about 32 weeks)	9	116

Genes Predictive of GDM Determined by Differential Expression Analysis

Differential expression analysis was performed with DESeq on gene expression data from a training dataset comprising three combined cohorts (P, M, and K). The training set comprised 49 GDM cases and 430 healthy controls. The top 4 differentially expressed genes were identified by QQ plot, as shown in FIG. 40. Log 2 RPM expression levels of the top 4 genes from the training set were used as features to train a logistic model (L2 penalty), where individual models were developed for each gene. The test set comprised an independent cohort (R) with multiple blood draws from a group of maternal subjects. The trained models were evaluated on draws 3 & 4 in the test cohort to yield AUC metrics at about 26 and 32 weeks of gestational age, respectively, as shown in Table 36.

TABLE 36
Performance of models developed for each of the top 4 genes identified
by differential expression evaluated on an independent test
cohort (R) at about 26 and 32 weeks gestational age
			Test AUC	Test AUC
			RS Draw 3,	RS Draw 4,
	Log2 fold		about	about
Gene	change	P-value	26 weeks	32 weeks
SPTA1	0.564	0.0000248	0.58	0.51
RTN4IP1	−0.324	0.0000564	0.55	0.48
ALDOB	0.945	0.0000716	0.62	0.77
FABP1	0.732	0.0001020	0.52	0.75

Genes Predictive of GDM Discovered by a Leave-One-Cohort-Out Analysis

Robust feature discovery was performed on a training dataset by identifying genes that are consistently predictive of GDM from cohort to cohort. For a group of cohorts that comprise a training dataset, each cohort is held out as an independent test set, while the remaining cohorts are reserved for training. Gene expression values are expressed as standardized Log 2 RPM and combined from three cohorts (K, M, and P) with a total of 49 GDM cases and 430 controls with a median gestational age of 21 weeks, as shown in Table 35. In each round, two cohorts were used to train, while the remaining cohort was reserved for testing. Features were selected by filtering for genes with Mann Whitney p-values<0.05 when comparing GDM cases versus controls. Genes were then further filtered for those whose absolute GDM effect size had a mean value >0.5 and a coefficient of variation <0.5 across the training cohorts. Genes were then further filtered based on whether the trained logistic model (L2 penalty) for the gene had a mean AUC>0.6 when each training cohort was reserved for testing to further improve feature robustness across each cohort. The top 5 performing genes were then combined, and gene filtering was repeated as described above. Further, a leave-one-out analysis was performed across the full training set (3 cohorts combined), and a final AUC>0.6 threshold was applied. Seven genes were identified from the leave-one-cohort analysis across the training dataset, as shown in Table 37.

TABLE 37
Top 8 GDM genes identified by a leave-one-cohort-
out analysis within the training dataset
# Gene Name
1 TMEM101
2 FCHO2
3 PPP1R15A
4 NOMO3
5 ANKRD54
6 MT-TH
7 OARD1
8 UBE2Q2

A logistic model (L2 penalty) based on the 8 genes was trained on the full 3-cohort training set and evaluated on an independent cohort RS (Table 35). Evaluation of the model on the independent test showed an AUC of 0.55 when predicting at about 20 weeks gestational age (Draw 2) and 0.57 at about 26 weeks gestational age (Draw 3).

Genes Predictive of GDM Discovered by Effect Size

A leave-one-out cross validation was performed on a small training set from one cohort with samples at about 13 weeks gestational age (R, Draw 1). The training set comprised 9 GDM cases and 105 controls. Gene collections that are upregulated and downregulated in GDM were selected from the training data as follows. Gene expression values were transformed into Log 2 counts. A gene collection was identified by finding the optimal gene set where the sum of counts maximized the GDM effect size. A grid search over the effect size threshold was performed to tune the hyperparameter used to select the highest effect genes based on the maximal GDM effect of the resultant summed collection. A gene collection was generated for both upregulated (n=7) and downregulated (n=2) GDM effects (Table 38). These two gene collections were then used as features in a logistic model (L2 penalty) trained on samples from R Draw 1 at about 13 weeks gestation and tested on sample collected at a later gestational age of about 20 weeks from the same cohort (R Draw 2 with 8 cases and 109 controls). Performance on the test set was observed with an AUC of 0.60.

TABLE 38
Genes comprising the upregulated and downregulated gene collections
identified from the first trimester (~13 weeks gestation)
#	Gene Name	GDM Effect Size Collection
1	C1QTNF6	Upregulated
2	AZIN2	Upregulated
3	NEAT1	Upregulated
4	PHYHD1	Upregulated
5	PINK1-AS	Upregulated
6	NPIPA5	Upregulated
7	PGS1	Upregulated
8	ADIRF	Downregulated
9	PALMD	Downregulated

PCA Components Predictive of GDM

Features were identified from a training set comprised of Log 2 RPM gene expression data from three cohorts (P, M, and K, ˜21 weeks gestation). Seventy percent of the training data was split into a training set (36 cases and 299 controls), while the remaining 30% was used as a test set (13 cases and 131 controls) for feature engineering. Candidate genes were selected for an upregulated effect size in GDM greater than an effect size threshold. Principal component analysis (PCA) was performed and trained on standardized Log 2 RPM counts from controls in the training set. The full training and test sets were then PCA transformed. A logistic model (L1 penalty) was trained on the PCA components calculated from the training data and then applied to principal components similarly calculated from the test dataset. The hyperparameters for the effect size threshold and the PCA variance threshold were optimized by a grid search based on optimizing the AUC on the test set. The effect size threshold was set to 0.6, yielding 15 high effect genes shown in Table 39, and the PCA variance threshold was set to 0.6, yielding 3 principal components after transforming the 15 high effect genes.

TABLE 39
15 high effect genes comprising the principal
component features in the GDM model
#  Gene Name
1  SRP14
2  ATP6V1G1
3  METTL9
4  OARD1
5  HNRNPA2B1
6  PPP1CB
7  FUNDC2
8  BDH2
9  C18orf32
10 COPS3
11 ALDOB
12 SMDT1
13 VKORC1
14 UBE2J1
15 RHOA

The final principal component transformation based on the 15 high effect genes was retrained on the full training dataset (P, M, and K) with 49 GDM cases and 430 controls, and then used as features in a logistic model trained on the full training dataset. The model was evaluated on an independent cohort (R), and performance was observed with an AUC of 0.59 for Draw 2 (8 cases and 109 controls at about 20 weeks) and an AUC of 0.60 for Draw 3 (11 cases and 119 controls at about 26 weeks).

Example 18: Clinical Intervention Care Pathway to Improve Early Pre-Term Birth (ePTB) Outcomes Based on Prediction Test Administer in Second Trimester

Using systems and methods of the present disclosure, a clinical intervention care plan algorithm was developed to improve early pre-term birth outcomes following results of predictive tests administered in the second trimester, as shown in FIG. 41.

Currently, there is no early pre-term test available for an asymptomatic general population without prior preterm history, and a majority of pregnancies are followed to routine prenatal care pathway. An ePTB prediction test is applied at early stage of pregnancy (13 to 26 weeks of gestational age), pregnant subjects who test positive are provided with two arm approaches. For a first arm, pregnant subjects who test positive at a second trimester are referred for increased surveillance with cervical length ultrasound and low dose aspirin treatment regimen. The pregnant subjects with short cervix then proceed for possible treatment with vaginal progesterone or surgical cerclage. In the first arm of the treatment, about 30-40% of spontaneous ePTB can be reduced or delayed.

On a second arm, pregnant subjects who test positive at a third trimester are referred for increased surveillance for preterm labor symptoms and routine fetal fibronectin testing (fFN) in cervical secretions. The pregnant subjects with active labor presentation and positive fFN test have a lower threshold for providing antennal steroid treatment to improve neonatal outcomes. In the second arm of the treatment, about 22% of neonatal death can be reduced.

REFERENCES

• Senarath, Sachintha; Ades, Alex; FRANZCOG; Nanayakkara, Pavitra; MRANZCOG, Cervical Cerclage: A Review and Rethinking of Current Practice, Obstetrical & Gynecological Survey: December 2020-Volume 75-Issue 12-p 757-765 is incorporated by reference in its entirety.
• Child T, Leonard S A, Evans J S, Lass A. Systematic review of the clinical efficacy of vaginal progesterone for luteal phase support in assisted reproductive technology cycles. Reprod Biomed Online. 2018 June; 36(6):630-645. doi: 10.1016/j.rbmo.2018.02.001. Epub 2018 Feb. 22. PMID: 29550390 is incorporated by reference in its entirety.
• McGoldrick E, Stewart F, Parker R, Dalziel S R. Antenatal corticosteroids for accelerating fetal lung maturation for women at risk of preterm birth. Cochrane Database of Systematic Reviews 2020, Issue 12. Art. No.: CD004454. DOI: 10.1002/14651858.CD004454.pub4. Accessed 20 Jul. 2021 is incorporated by reference in its entirety.

Example 19: Clinical Intervention Care Pathway to Improve Preeclampsia (PE) Outcomes Based on Prediction Test Administer in Second Trimester

Using systems and methods of the present disclosure, a clinical intervention care plan algorithm was developed to improve preeclampsia outcomes following results of predictive tests administered in the second trimester, as shown in FIG. 42.

Currently, there is no preeclampsia test available for an asymptomatic general population without prior history of hypertension or prior preeclampsia, and a majority of pregnancies are followed to routine prenatal care pathway. If a PE prediction test is performed for subjects at an early stage of pregnancy (13 to 20 weeks of gestational age), pregnant subjects who test positive are provided three arm approaches. For a first arm, pregnant subjects who test positive at an early second trimester (13 to 16 weeks of gestation) are treated with low dose aspirin regime, which can result in a 24% reduction of early onset of preeclampsia.

In a second arm, pregnant subjects who test positive at a second or third trimester are referred for increased surveillance for home blood pressure monitoring and low dose aspirin treatment. In a third arm, pregnant subjects with elevated blood pregnancies proceed with serial blood tests for liver or renal dysfunction and treatment with anti-hypertension medications (e.g., hydralazine, labetalol and oral nifedipine), which can reduce incident of PE by 45%. By recommending the preeclampsia subjects with positive blood test for liver and renal dysfunctions for a combination of antenatal observation, indication for delivery, and possible lower threshold for antenatal steroid treatment, this can result in estimated 22% reduction in neonatal death.

REFERENCES

• Yeo Jin Choi, Sooyoung Shin, Aspirin Prophylaxis During Pregnancy: A Systematic Review and Meta-Analysis; Am J Prev Med, 2021 Jul; 61(1):e31-e45 is incorporated by reference in its entirety.
• Eva G. Mulder, Chahinda Ghossein-Doha, Ella Cauffman, Veronica A. Lopes van Balen, Veronique M. M. M. Schiffer, Robert-Jan Alers, Jolien Oben, Luc Smits, Sander M. J. van Kuijk, Marc E. A. Spaanderman; Preventing Recurrent Preeclampsia by Tailored Treatment of Nonphysiologic Hemodynamic Adjustments to Pregnancy, Hypertension. 2021; 77:2045-2053 is incorporated by reference in its entirety.
• McGoldrick E, Stewart F, Parker R, Dalziel S R. Antenatal corticosteroids for accelerating fetal lung maturation for women at risk of preterm birth. Cochrane Database Syst Rev. 2020 Dec. 25; 12(12):CD004454. doi: 10.1002/14651858.CD004454.pub4. PMID: 33368142; PMCID: PMC8094626 is incorporated by reference in its entirety.

Example 20: Clinical Intervention Care Pathway to Improve Gestational Diabetes Mellitus (GDM) Outcomes Based on Prediction Test Administer in Second Trimester

Using systems and methods of the present disclosure, a clinical intervention care plan algorithm was developed to improve GDM outcomes following results of predictive tests administered in the second trimester, as shown in FIG. 43.

Currently, there is no gestational diabetes mellitus test available for an asymptomatic general population in early second trimester and a majority of pregnancies are followed to routine prenatal care pathway with diagnostic oral glucose tolerance test at 24-28 weeks of gestational age. If a gestational diabetes prediction test is performed for subjects at an early stage of pregnancy (13 to 20 weeks of gestational age), pregnant subjects who test positive are provided two arm approaches. For a first arm, pregnant subjects who test negative at an early second trimester (13 to 16 weeks of gestation) are not recommended to take an oral glucose tolerance test at 24-28 weeks of gestational age.

In a second arm, pregnant subjects who test positive at a second trimester are recommended to skip a 1-hour glucose tolerance test and to proceed with taking a 3-hour glucose tolerance test for improved accuracy of diagnosis.

Example 21: Prediction of Pre-Term Birth (PTB) on Combined Multiple Cohorts

All PTB cohorts from Examples 4, 8, and 11, plus an additional cohort (P), were combined in a single data set, as shown in FIG. 44A, totaling 255 samples from subjects with preterm delivery before 35 weeks of gestation age and 1269 samples from healthy control subjects with delivery gestation age after 37 weeks.

An additional cohort (P) of subjects was obtained as follows. As shown in FIG. 44B, a cohort of 150 subjects (54 pre-term and 96 full-term controls) was established (with patient identification numbers shown on the x-axis). From this cohort, one or more biological samples (e.g., 1 or 2) were collected and assayed at different time points corresponding to an estimated gestational age (shown on the y-axis, in increasing order of estimated gestational age at delivery) of a fetus of each subject, using methods and systems of the present disclosure. For example, the estimated gestational age (shown on the y-axis) may be determined using methods such as ultrasound imaging, a last menstrual period (LMP) date, or a combination thereof, and may range from 0 to about 42 weeks.

In order to mitigate gestational age effects for blood collection, three separate differential expression analyses for combined cohorts were performed as follows. First, an analysis for differentially expressed genes between the pre-term birth case samples (delivered before 35 weeks) and control samples (delivered at or after 37 weeks) was performed for blood samples collected between 17-28 weeks of gestational age (190 cases and 859 controls). In the second analysis, differentially expressed genes between the pre-term birth case samples (delivered earlier than 35 weeks) and control samples (delivered after or at 37 weeks) were performed for blood samples collected between a narrow window of 23-26 weeks of gestational age (60 cases and 271 controls). In a third analysis, differentially expressed genes between the pre-term birth case samples (delivered earlier than 35 weeks) and control samples (delivered after or at 37 weeks) were performed for blood samples collected between at an earlier window between 17-23 weeks of gestational age (111 cases and 505 controls).

First differential expression analysis of predicting preterm birth earlier than 35 weeks of gestational age, with blood samples collected between 17-28 weeks of gestational age, was performed using EdgeR and accounting for ethnicity, and cohort effects and gestational age at collection (190 PTB cases and 859 controls). Table 40 shows a set of top 19 genes with p-value<0.1 after adjustment from multiple hypothesis correction (FDR value), and also showed a significant deviation from the null hypothesis in a QQ plot for differentially expressed in pre-term birth cases (as shown in FIG. 44C). Table 41 shows an additional set of genes with p-value<0.1 for predicting preterm birth earlier than 35 weeks of gestation, with blood samples collected between 17-28 weeks of gestational age. Genes are ordered according to their statistical significance (P-values).

TABLE 40
Top 19 genes with p-value < 0.1 after adjustment from multiple
hypothesis correction (FDR value), that are predictive for
preterm birth earlier than 35 weeks of gestation with blood
samples collected between 17-28 weeks of gestational age
#	Gene	logFC	P-Value	FDR
1	FGA	−1.04779	2.04E−15	1.46E−11
2	HRG	−1.14768	2.49E−15	1.46E−11
3	FGB	−0.84237	1.60E−11	6.21E−08
4	APOB	−0.78279	7.49E−11	2.19E−07
5	APOH	−0.82927	5.19E−10	1.21E−06
6	COL3A1	−0.98584	3.76E−08	7.31E−05
7	ALB	−0.57285	5.51E−08	8.32E−05
8	HPD	−0.59372	5.70E−08	8.32E−05
9	COL1A1	−1.00293	1.84E−07	0.00023915
10	FABP1	−0.56313	2.94E−07	0.0003184
11	CFH	−0.42425	3.00E−07	0.0003184
12	COL1A2	−0.81295	3.19E−06	0.00309871
13	CYP2E1	−0.47476	9.33E−06	0.00837437
14	MUC3A	−0.5149	1.25E−05	0.01042708
15	CDR1-	−0.537	1.34E−05	0.01043626
	AS
16	ALDOB	−0.48986	1.56E−05	0.01136251
17	ADH1B	−0.46998	5.00E−05	0.03435136
18	HP	−0.42634	0.0001198	0.07769152
19	DCN	−0.66171	0.00014101	0.08662964

TABLE 41
Additional set of genes with p-value < 0.1 for predicting
preterm birth earlier than 35 weeks of gestation with blood
samples collected between 17-28 weeks of gestational age
#	Gene	logFC	P-Value	FDR
1	INHBA	−0.37162	0.00024695	0.13632815
2	MYH11	−0.26583	0.00025577	0.13632815
3	CCDC80	−0.47289	0.00025694	0.13632815
4	PLXNA3	0.43233	0.00032064	0.16273233
5	HIST1H2AI	−0.17725	0.00039821	0.18855433
6	AHNAK2	−0.3859	0.00040383	0.18855433
7	CCNA2	−0.22972	0.00046407	0.2083505
8	PRG4	−0.43682	0.00053207	0.21732697
9	1-Mar	0.347134	0.00053818	0.21732697
10	CCR2	0.383962	0.00053992	0.21732697
11	EZH1	0.090991	0.00056513	0.21989261
12	MALAT1	0.384296	0.00063344	0.23852244
13	KLF5	−0.28811	0.00067648	0.24676558
14	PLSCR1	−0.13343	0.00084663	0.29328991
15	UNK	0.096595	0.00085524	0.29328991
16	PAPPA2	−0.40533	0.00090333	0.29328991
17	PER3	0.171607	0.00090616	0.29328991
18	CAMKK1	0.227011	0.00092964	0.29328991
19	TMEM43	0.263695	0.00095742	0.29377879
20	NBPF10	0.175322	0.00098153	0.29377879
21	NELL2	0.356349	0.00109303	0.3034526
22	ARG1	−0.2776	0.00112046	0.3034526
23	TEX30	−0.19148	0.00112999	0.3034526
24	TCN1	−0.36384	0.00116198	0.3034526
25	TK1	−0.29507	0.0011672	0.3034526
26	TMEM56	−0.27078	0.00118023	0.3034526
27	CLCN6	0.380015	0.00119582	0.3034526
28	RNASE3	−0.36576	0.00129822	0.31937455
29	IL2RB	0.220493	0.00134056	0.31937455
30	DIRC2	0.317528	0.00139892	0.31937455
31	PTGR1	−0.19462	0.00140719	0.31937455
32	ABCA13	−0.30061	0.00142353	0.31937455
33	PDE3B	0.264993	0.00143959	0.31937455
34	HSPA1B	0.28971	0.00145009	0.31937455
35	SH3BP5	−0.13924	0.00149536	0.3232475
36	SLC2A5	−0.30138	0.0015704	0.33197687
37	GPX3	−0.24256	0.00161509	0.33197687
38	PABPC1L	0.456285	0.00162106	0.33197687
39	ITGB7	0.287416	0.00167524	0.33715669
40	MMP8	−0.34981	0.00173049	0.33889101
41	FERMT2	−0.17972	0.0017688	0.33889101
42	ATP10D	0.248288	0.00179581	0.33889101
43	PLK1	−0.22723	0.00179999	0.33889101
44	TYMS	−0.17849	0.00186307	0.34062912
45	RRM2	−0.21162	0.00186758	0.34062912
46	ZBTB25	0.14581	0.00192423	0.34483979
47	CD7	0.210869	0.00194975	0.34483979
48	MTHFS	−0.11498	0.00205892	0.34711434
49	IGFBP2	−0.40481	0.002075	0.34711434
50	PDK4	−0.20835	0.00208199	0.34711434
51	TTC14	0.287065	0.0020842	0.34711434
52	CCNE2	−0.17035	0.00213535	0.34711434
53	EMB	−0.09234	0.00214103	0.34711434
54	BEX1	−0.26041	0.00217897	0.34842594
55	TNNI2	0.242586	0.00225168	0.35053589
56	DHX34	0.305572	0.00225222	0.35053589
57	RETN	−0.3173	0.00232144	0.35239745
58	CRISP3	−0.36534	0.00234073	0.35239745
59	CHPF2	0.296714	0.00235475	0.35239745
60	CDH6	0.446673	0.00244603	0.3527879
61	PGGHG	0.451204	0.00247897	0.3527879
62	SAYSD1	−0.15461	0.0024981	0.3527879
63	CANT1	0.189086	0.00250317	0.3527879
64	TRIM8	0.088478	0.00250847	0.3527879
65	ARHGEF18	0.184928	0.0025668	0.35669386
66	GALNT7	0.171836	0.00266696	0.36327936
67	LTF	−0.29442	0.00267643	0.36327936
68	CEACAM8	−0.29635	0.00272645	0.36581387
69	PKP4	−0.09544	0.00276342	0.36656121
70	LENG8	0.264807	0.00283865	0.36910855
71	ARL1	−0.08755	0.00284586	0.36910855
72	AZI2	−0.07627	0.00296502	0.3803368
73	SLC15A4	0.139099	0.00302285	0.38354039
74	CCDC141	0.352908	0.00329923	0.40507236
75	ANKRD36	0.143622	0.00330275	0.40507236
76	APOC1	−0.24152	0.00337521	0.40507236
77	ZNF692	0.314622	0.0034314	0.40507236
78	IL7R	0.153439	0.00343657	0.40507236
79	FN1	−0.22938	0.0034427	0.40507236
80	CKAP2L	−0.1414	0.00346852	0.40507236
81	THBD	0.31222	0.00355915	0.40507236
82	OBSCN	0.257153	0.00357239	0.40507236
83	SELENOP	−0.2075	0.00358074	0.40507236
84	PSMA3	−0.07338	0.00358329	0.40507236
85	PKD1	0.287392	0.00362194	0.40507236
86	OLFM4	−0.33973	0.00364367	0.40507236
87	MANSC1	−0.19999	0.00372481	0.40804253
88	ACTA2	−0.20389	0.0037403	0.40804253
89	TMEM39A	0.187568	0.00389507	0.42099242
90	PLCH2	0.372379	0.00398863	0.42714967
91	APBB3	0.429175	0.00413909	0.43923276
92	ITGA9	−0.22658	0.0041947	0.44112422
93	EXOG	0.166132	0.00429892	0.44263471
94	HIST1H2AL	−0.15415	0.00431358	0.44263471
95	CAMP	−0.29659	0.00432283	0.44263471
96	MIB2	0.168881	0.00454601	0.4614398
97	CCDC144B	0.264578	0.00466679	0.46961576
98	C1R	−0.35317	0.00470707	0.4696207
99	SNX19	−0.17109	0.00481307	0.47612692
100	MEGF6	0.4601	0.00485623	0.47635988
101	MNT	0.09461	0.00492665	0.47700017
102	RNF169	0.065814	0.00506902	0.47700017
103	EPHB6	0.307981	0.00511012	0.47700017
104	ITGA5	0.228836	0.0051295	0.47700017
105	KIAA1143	−0.07632	0.00513876	0.47700017
106	RPS6KA5	0.107865	0.00519912	0.47700017
107	C7orf31	0.095471	0.00523239	0.47700017
108	VPS29	−0.0608	0.00528375	0.47700017
109	NUP210	0.223982	0.00530044	0.47700017
110	ABCA7	0.306445	0.00534237	0.47700017
111	KDM4B	0.106133	0.00535228	0.47700017
112	GALT	0.229845	0.00535763	0.47700017
113	NBPF26	0.170399	0.00543232	0.47700017
114	HSPA1A	0.178078	0.00543485	0.47700017
115	FOXM1	−0.18776	0.00569004	0.49567006
116	TTN	0.361796	0.00578995	0.50063788
117	LUC7L3	0.076295	0.00588639	0.50106547
118	SPOCK2	0.271026	0.00590797	0.50106547
119	TESC	−0.11835	0.00594812	0.50106547
120	NMRAL1	0.10644	0.0059666	0.50106547
121	SERPINB10	−0.27926	0.00603985	0.50359371
122	S100A12	−0.18638	0.00622577	0.51103623
123	ATAD3B	0.318935	0.00623391	0.51103623
124	HELLS	−0.09181	0.00627331	0.51103623
125	HIST1H3F	−0.14879	0.00630422	0.51103623
126	NBPF8	0.167509	0.00652976	0.52466391
127	FLT1	−0.11643	0.00656771	0.52466391
128	GINS2	−0.26903	0.00660718	0.52466391
129	COX20	−0.08568	0.00680829	0.53399289
130	SMIM20	−0.12782	0.00681615	0.53399289
131	PSMD14	−0.07958	0.00689023	0.5361977
132	CEACAM6	−0.25445	0.00697169	0.53894431
133	RPH3AL	−0.21896	0.0071488	0.54783785
134	TRABD2A	0.301776	0.0071806	0.54783785
135	C3	−0.18217	0.00732683	0.55510284
136	PBXIP1	0.199065	0.00741578	0.55510284
137	SULF2	0.258541	0.00741849	0.55510284
138	NOTCH1	0.267867	0.00751332	0.55861766
139	SMIM24	−0.19888	0.00761332	0.56247034
140	ERCC6L	−0.20093	0.00781274	0.56427079
141	UNKL	0.223599	0.00788269	0.56427079
142	NBPF11	0.1189	0.00789503	0.56427079
143	KRT8	0.193337	0.00795669	0.56427079
144	MAST3	0.089153	0.00796759	0.56427079
145	KCNH2	−0.25824	0.00798896	0.56427079
146	AC024560.3	0.202427	0.00803	0.56427079
147	POLR2A	0.050504	0.00808068	0.56427079
148	DEFA3	−0.32174	0.00814568	0.56427079
149	SGSM3	0.101151	0.00829395	0.56427079
150	LMTK2	0.161143	0.00832376	0.56427079
151	SLC12A6	0.139805	0.00834325	0.56427079
152	TOP2A	−0.10845	0.0083509	0.56427079
153	MPO	−0.20111	0.00836113	0.56427079
154	UVSSA	0.2368	0.00836279	0.56427079
155	ZNF865	0.175801	0.0084319	0.56550092
156	TACC2	0.266062	0.00856314	0.56550092
157	TMEM2	0.172006	0.00860142	0.56550092
158	IDI1	−0.07782	0.00860486	0.56550092
159	HSPA7	0.400728	0.00877046	0.56550092
160	HSPG2	−0.1904	0.00877754	0.56550092
161	RCN3	0.464299	0.00880775	0.56550092
162	CAPN15	0.168296	0.00881938	0.56550092
163	CAMLG	−0.06238	0.00887155	0.56550092
164	DDX39B	0.295788	0.00891392	0.56550092
165	TOX4	0.047401	0.00892093	0.56550092
166	NLRP1	0.236209	0.00899511	0.56550092
167	VTI1A	0.090232	0.00907805	0.56550092
168	STIM2	0.112881	0.00911269	0.56550092
169	AFF2	−0.14313	0.00917015	0.56550092
170	CYSTM1	−0.1873	0.00920811	0.56550092
171	ABCA2	0.32242	0.00920901	0.56550092
172	TARBP2	0.189071	0.00925303	0.56550092
173	EIF4A1	0.26069	0.00945454	0.57464107
174	FCHO1	0.127726	0.00951062	0.57464107
175	TMC6	0.223573	0.00956686	0.57464107
176	CLEC4E	−0.18421	0.0095995	0.57464107
177	THAP12	−0.05666	0.0097045	0.57525432
178	NFU1	−0.07127	0.00973334	0.57525432
179	KIAA0141	0.132062	0.0098395	0.57525432
180	MS4A14	0.284113	0.00987025	0.57525432
181	SLC25A30	0.135501	0.00988115	0.57525432
182	FCGR2C	0.369137	0.0099791	0.57525432
183	ATP10A	0.24706	0.01001119	0.57525432
184	NINJ1	0.109417	0.01004847	0.57525432
185	SEC31B	0.370585	0.01005328	0.57525432
186	FAM107A	−0.19884	0.01019154	0.57594247
187	AGER	0.330009	0.0102037	0.57594247
188	IKBKB	0.074524	0.01024932	0.57594247
189	RPL3P4	0.290315	0.01026266	0.57594247
190	DNMT3A	0.092337	0.0104197	0.58195786
191	ANKRD11	0.122861	0.01048561	0.58220313
192	LILRA4	0.180795	0.01052385	0.58220313
193	CPEB3	0.132065	0.01069118	0.58867045
194	STRIP1	0.127331	0.01076033	0.58969665
195	CLASRP	0.216493	0.01096388	0.59804356
196	CHMP4BP1	0.214505	0.0110522	0.59821642
197	IFI6	−0.258	0.0111135	0.59821642
198	GAA	0.270265	0.01112828	0.59821642
199	HIKESHI	−0.09654	0.01117204	0.59821642
200	ZNF276	0.149414	0.01129951	0.60227919
201	ARIH1	0.077238	0.01140323	0.6034841
202	NBPF9	0.147874	0.01149254	0.6034841
203	GYG1	−0.09593	0.01159812	0.6034841
204	KCNC3	0.279616	0.01160066	0.6034841
205	CEP68	0.118344	0.01160072	0.6034841
206	AKAP17A	0.179066	0.01166187	0.6034841
207	RNF111	0.043219	0.01168401	0.6034841
208	CCNL2	0.207683	0.0118058	0.6070888
209	EP400NL	0.218649	0.01187441	0.60793866
210	FCRL5	0.305718	0.01196743	0.60908546
211	IGF2R	0.268732	0.01203031	0.60908546
212	SMCR8	0.062574	0.01221539	0.60908546
213	KLHL35	0.365873	0.012227	0.60908546
214	VGLL3	0.286155	0.01225075	0.60908546
215	PLPPR2	0.248368	0.01232664	0.60908546
216	HBG1	0.488888	0.01237353	0.60908546
217	CEACAM1	−0.2294	0.01242269	0.60908546
218	SELPLG	0.172377	0.0124516	0.60908546
219	TMEM106A	0.235544	0.01247414	0.60908546
220	SPAG5	−0.13343	0.01250929	0.60908546
221	IL6R	0.235819	0.01253686	0.60908546
222	RELT	0.320346	0.0126367	0.60908546
223	CAPN10	0.241909	0.01267804	0.60908546
224	UBR2	0.05001	0.0126795	0.60908546
225	BPI	−0.23487	0.01306896	0.61980568
226	CPNE3	−0.08843	0.01312473	0.61980568
227	ITPRIP	0.333223	0.01319897	0.61980568
228	SUSD6	0.143109	0.01330757	0.61980568
229	MYH3	0.319441	0.01337869	0.61980568
230	NPIPB11	0.225074	0.01338374	0.61980568
231	HIST1H2AH	−0.16579	0.01339516	0.61980568
232	ARAP1	0.113937	0.01340864	0.61980568
233	TNFRSF1B	0.236397	0.01341026	0.61980568
234	COQ7	−0.10226	0.01343364	0.61980568
235	NCKIPSD	−0.16181	0.01355632	0.62228365
236	SORBS1	−0.12546	0.01366928	0.62228365
237	SLC11A2	0.131949	0.01367015	0.62228365
238	ANXA1	−0.12078	0.01370058	0.62228365
239	DDX31	0.149845	0.01376824	0.62293282
240	TSPYL2	0.152066	0.01392207	0.62746062
241	MIA3	0.112725	0.01401485	0.62921269
242	SRCAP	0.087386	0.01421777	0.63587761
243	TMUB2	0.179351	0.01427441	0.635974
244	RICTOR	0.047912	0.01443204	0.63701257
245	B3GNT2	−0.14535	0.0144994	0.63701257
246	CLSPN	−0.09817	0.01450526	0.63701257
247	RPRD2	0.046718	0.01451601	0.63701257
248	KIFC1	−0.18671	0.01460628	0.63717368
249	ATG2A	0.173904	0.01467416	0.63717368
250	RAD51B	0.182219	0.01477235	0.63717368
251	KIF20A	−0.181	0.01482021	0.63717368
252	MT2A	−0.1039	0.01487899	0.63717368
253	LFNG	0.284885	0.01494183	0.63717368
254	TPD52L1	−0.22667	0.01497767	0.63717368
255	ADGRES	0.179919	0.01500528	0.63717368
256	EXO1	−0.14261	0.01505712	0.63717368
257	KLHL12	0.072157	0.01511598	0.63717368
258	ZNF641	0.11215	0.01514451	0.63717368
259	DCUN1D1	0.09413	0.01522795	0.63717368
260	ATP2B1	0.125617	0.01522929	0.63717368
261	ZCRB1	−0.07944	0.01553718	0.63898806
262	MKI67	−0.11168	0.01563439	0.63898806
263	NOTCH2	0.225099	0.01567665	0.63898806
264	ELL2P1	−0.28705	0.0156776	0.63898806
265	TRAPPC12	0.078491	0.01568194	0.63898806
266	ITPR3	0.184525	0.01570768	0.63898806
267	PDPR	0.159366	0.01572536	0.63898806
268	C17orf80	−0.0737	0.01574463	0.63898806
269	KLC1	0.116093	0.01581611	0.63898806
270	SUN2	0.2067	0.01585866	0.63898806
271	ZNF587	0.148131	0.01590788	0.63898806
272	SIGLEC7	0.193033	0.01592954	0.63898806
273	SPC24	−0.14702	0.01599473	0.63940564
274	HIST1H3D	−0.10572	0.01613502	0.64281254
275	PSMA3-AS1	0.156466	0.01629385	0.64451294
276	IL1R1	−0.15503	0.01635679	0.64451294
277	GIGYF1	0.173191	0.01640429	0.64451294
278	SLC43A2	0.271739	0.01642484	0.64451294
279	IFIT1	−0.20819	0.01645377	0.64451294
280	EEF1E1	−0.09811	0.01652464	0.64512425
281	CAMK2G	0.077266	0.01663281	0.64718269
282	CPD	0.150082	0.01669924	0.64760864
283	NEK2	−0.19375	0.01678854	0.6489159
284	TUBGCP6	0.22681	0.01698933	0.65450974
285	PIK3IP1	0.22368	0.0171141	0.65595108
286	ARPC4-	0.195999	0.01719787	0.65595108
	TTLL3
287	HMCN1	−0.22912	0.0171991	0.65595108
288	DLK1	0.406847	0.01725152	0.65595108
289	ISG15	−0.19497	0.01732315	0.65653607
290	CBX7	0.114646	0.01739648	0.65718171
291	HCFC1R1	−0.09912	0.0175175	0.65961868
292	NEAT1	0.273427	0.01776116	0.6615242
293	OTUD7B	−0.07552	0.01777955	0.6615242
294	PLEKHM1P1	0.266675	0.01778405	0.6615242
295	ZNF880	−0.11044	0.01787496	0.6615242
296	CD19	0.254783	0.01790047	0.6615242
297	HIST1H2BL	−0.12878	0.01790813	0.6615242
298	AUH	0.099883	0.01821664	0.67079755
299	DEF8	0.134343	0.01833732	0.67311793
300	SLC19A1	0.300927	0.01844905	0.67481727
301	SZT2	0.152443	0.01868453	0.67481727
302	P2RY8	0.261269	0.01870759	0.67481727
303	ADNP2	0.08817	0.01870974	0.67481727
304	QSOX2	0.200001	0.01872196	0.67481727
305	MYBL2	−0.12281	0.01873047	0.67481727
306	PCNX1	0.128145	0.01881993	0.67489532
307	MCM4	−0.0977	0.01901543	0.67489532
308	PLA2G6	0.270264	0.01907223	0.67489532
309	MAPK8IP3	0.168985	0.01914121	0.67489532
310	ZNF628	0.201732	0.01915175	0.67489532
311	LPCAT1	0.169393	0.01933296	0.67489532
312	NCSTN	0.142595	0.01937521	0.67489532
313	FNBP4	0.080692	0.01938271	0.67489532
314	NBN	−0.04407	0.01946149	0.67489532
315	KMT2A	0.046935	0.01964344	0.67489532
316	DGKA	0.12424	0.01965792	0.67489532
317	RILPL1	0.110835	0.0197448	0.67489532
318	TBL1X	0.09656	0.01980309	0.67489532
319	CNPY3	0.075107	0.01983667	0.67489532
320	SLC12A9	0.299377	0.01992008	0.67489532
321	BUB1B	−0.09969	0.0199485	0.67489532
322	SLC25A17	−0.11684	0.01999033	0.67489532
323	PANX2	0.284076	0.02004928	0.67489532
324	HEATR5A	−0.09643	0.02005246	0.67489532
325	MYLIP	0.104019	0.02006079	0.67489532
326	RBMS3	−0.19762	0.02006373	0.67489532
327	ADAM28	0.183931	0.02013975	0.67489532
328	UBR5	0.038568	0.02034022	0.67489532
329	USP18	−0.19703	0.02041136	0.67489532
330	FAM161B	0.182304	0.02043321	0.67489532
331	CCDC84	0.26184	0.02043381	0.67489532
332	PLCXD1	0.198888	0.02051062	0.67489532
333	CLSTN3	0.237424	0.02051223	0.67489532
334	C15orf39	0.105977	0.02052644	0.67489532
335	GABBR1	0.284971	0.02052952	0.67489532
336	PLCB2	0.17458	0.02053626	0.67489532
337	ATG16L2	0.296619	0.0206175	0.67489532
338	PRKCZ	0.163892	0.02064059	0.67489532
339	WBSCR22	0.085443	0.02076199	0.67696851
340	TMCO6	0.173505	0.02091538	0.67883629
341	PGLYRP1	−0.22309	0.02093558	0.67883629
342	TCIRG1	0.295107	0.02124424	0.68693636
343	EGLN2	0.161778	0.02138346	0.689528
344	MRPS36	−0.07868	0.02158738	0.69271736
345	SLC43A1	−0.1344	0.02175011	0.69271736
346	IFIT2	−0.14909	0.02182304	0.69271736
347	H2AFX	−0.1496	0.02184128	0.69271736
348	TNFRSF8	0.174519	0.0218725	0.69271736
349	NRROS	0.12798	0.02193378	0.69271736
350	EEPD1	0.225546	0.02195508	0.69271736
351	EIF2AK3	0.147126	0.02205429	0.69271736
352	POR	0.219464	0.02205949	0.69271736
353	PHF5A	−0.07449	0.0221504	0.69271736
354	NQO1	−0.20608	0.02220612	0.69271736
355	PAN2	0.184904	0.02224324	0.69271736
356	CD99P1	−0.13373	0.02227539	0.69271736
357	SLC45A4	0.118013	0.02236131	0.69271736
358	LILRA6	0.307306	0.02240705	0.69271736
359	SETD1B	0.123318	0.0224899	0.69271736
360	ZNF746	0.141649	0.02254211	0.69271736
361	TDP2	−0.05474	0.02255055	0.69271736
362	CARS2	0.108206	0.02262887	0.6932987
363	TMC8	0.212077	0.02273431	0.6934895
364	ABHD11	0.115085	0.02291834	0.6934895
365	UBE4A	0.112898	0.02293195	0.6934895
366	SREBF1	0.22463	0.02298465	0.6934895
367	BBC3	0.136315	0.02300575	0.6934895
368	IFIT3	−0.17453	0.0230222	0.6934895
369	DIDO1	0.101033	0.02306184	0.6934895
370	BCAS4	0.156649	0.02311038	0.6934895
371	FGD3	0.093298	0.0236161	0.70211107
372	IGFBP7	−0.15367	0.02372217	0.70211107
373	MED12	0.053554	0.02378065	0.70211107
374	NLRC4	−0.11586	0.02380693	0.70211107
375	SLC16A3	0.228567	0.02388297	0.70211107
376	KXD1	0.051909	0.02391767	0.70211107
377	FAM103A1	−0.09355	0.02403275	0.70211107
378	CDK5RAP3	0.165733	0.02404738	0.70211107
379	IL17RA	0.184535	0.02412421	0.70211107
380	SLAMF1	0.217307	0.02413338	0.70211107

Second differential expression analysis of predicting preterm birth earlier than 35 weeks of gestational age, with blood samples collected between 23-26 weeks of gestational age, was performed using EdgeR and accounting for ethnicity, and cohort effects and gestational age at collection (60 PTB cases and 271 controls). Table 42 shows a set of top 17 genes with p-value<0.1 after adjustment from multiple hypothesis correction (FDR value), and also showed a significant deviation from the null hypothesis in a QQ plot for differentially expressed in pre-term birth cases (as shown in FIG. 44D). Table 43 shows an additional set of genes with p-value<0.1 for predicting preterm birth earlier than 35 weeks of gestation with blood samples collected between 23-26 weeks of gestational age. Genes are ordered according to their statistical significance (P-values).

TABLE 42
Top 17 genes with p-value < 0.1 after adjustment from multiple
hypothesis correction (FDR value), that are predictive for
preterm birth earlier than 35 weeks of gestation with blood
samples collected between 23-26 weeks of gestational age
#	Gene	logFC	P-Value	FDR
1	HRG	−2.0501607	1.04E−13	1.21E−09
2	APOH	−1.5623334	4.11E−10	2.38E−06
3	HPD	−1.2263966	1.87E−09	7.21E−06
4	FGA	−1.4396986	2.49E−09	7.21E−06
5	FGB	−1.3687247	5.31E−09	1.23E−05
6	ALB	−1.1326035	4.58E−08	8.85E−05
7	FGG	−1.3587488	1.43E−07	0.000236
8	APOB	−1.2053038	1.87E−07	0.000271
9	FABP1	−1.0001499	5.02E−07	0.000647
10	ADH1B	−1.0046253	7.37E−07	0.000855
11	CYP2E1	−0.9826505	1.33E−06	0.001402
12	PDK4	−0.5034507	3.24E−05	0.030923
13	SH3PXD2A	−0.2910378	3.47E−05	0.030923
14	MUC3A	−0.8112918	6.09E−05	0.04865
15	PCGF2	−0.8084937	6.29E−05	0.04865
16	LZTS2	−0.3533705	0.00011954	0.08215
17	APOC1	−0.5631767	0.00012038	0.08215

TABLE 43
Additional set of genes with p-value < 0.1 for predicting
preterm birth earlier than 35 weeks of gestation with blood
samples collected between 23-26 weeks of gestational age
#	Gene	logFC	P-Value	FDR
1	DLGAP4	−0.1826629	0.00025723	0.15917
2	PTGS2	0.84128363	0.00026069	0.15917
3	PAPPA2	−0.7793313	0.00038856	0.225385
4	EMILIN1	−0.4481043	0.00059221	0.327151
5	KIAA1143	−0.1572862	0.00082778	0.436505
6	CLEC4E	−0.4112452	0.00097681	0.492696
7	MBNL3	0.22423002	0.00111498	0.538953
8	NUP98	0.09665667	0.00123335	0.572325
9	C19orf43	−0.0918831	0.00129597	0.578253
10	RPH3AL	−0.4402562	0.00142451	0.612065
11	FAM9C	−0.7142533	0.00159475	0.649768
12	FKBP5	−0.2820347	0.00167331	0.649768
13	CFH	−0.4469532	0.00168029	0.649768
14	YOD1	0.33247661	0.00192385	0.719956
15	DPH3	−0.1658585	0.00241433	0.875271
16	FO538757.1	−0.4227779	0.00289461	0.975219
17	TXNDC5	−0.3194514	0.00290269	0.975219
18	ZNF483	−0.3604009	0.00297885	0.975219
19	SH2D1A	0.31281166	0.00302628	0.975219
20	PKP4	−0.167658	0.00341057	0.999823
21	KCTD2	−0.2160454	0.00382209	0.999823
22	CTD-	0.88326474	0.00399624	0.999823
	3088G3.8
23	TM4SF1	0.40428082	0.00426688	0.999823
24	UBE2B	0.16850547	0.00435697	0.999823
25	C3	−0.3254057	0.00473421	0.999823
26	KIAA0430	0.14144464	0.00478614	0.999823
27	GPX3	−0.3665209	0.00480981	0.999823
28	ZBTB16	−0.242741	0.00496256	0.999823
29	UBR2	0.09842027	0.00508955	0.999823
30	ARMC2	0.22755852	0.00517468	0.999823
31	AIFM3	0.48184268	0.00521153	0.999823
32	SOCS2	−0.2791332	0.00547838	0.999823
33	OPA1	0.16331524	0.0057958	0.999823
34	PIP5K1B	0.20202821	0.00581586	0.999823
35	ERICH6	−0.3921927	0.00593558	0.999823
36	SESN1	−0.1998035	0.00652404	0.999823
37	ZNF462	−0.1864143	0.00671098	0.999823
38	IFI27L1	−0.452319	0.00677637	0.999823
39	REC8	0.4129679	0.00717734	0.999823
40	ENG	−0.2243093	0.00726122	0.999823
41	SLC18B1	0.39411126	0.00735385	0.999823
42	MALAT1	0.5093659	0.00756213	0.999823
43	TCP11L2	0.32943455	0.0076547	0.999823
44	FECH	0.33308949	0.00780277	0.999823
45	ZNF518B	−0.1696499	0.00789717	0.999823
46	CGNL1	−0.3124707	0.00796199	0.999823
47	MANSC1	−0.3228849	0.00804338	0.999823
48	ABCG2	0.38123408	0.00809224	0.999823
49	CMKLR1	−0.3742352	0.00819591	0.999823
50	HIST1H2BB	−0.2704749	0.00846588	0.999823
51	DHX34	0.39787335	0.00862585	0.999823
52	MTHFS	−0.1745955	0.00871068	0.999823
53	CNTROB	−0.1665571	0.00886627	0.999823
54	ZBTB4	−0.1300612	0.00887294	0.999823
55	IGHA1	−0.3745478	0.00991255	0.999823
56	ATN1	−0.1616119	0.00997235	0.999823
57	TNFRSF8	0.34514822	0.01023486	0.999823
58	SF3B6	−0.1206185	0.01026664	0.999823
59	ERCC6L	−0.3636561	0.01036967	0.999823
60	ZNF282	−0.1812759	0.01062498	0.999823
61	VPS53	0.11170753	0.0106913	0.999823
62	ZNF768	−0.1353357	0.01077038	0.999823
63	RNF145	−0.1914913	0.01079595	0.999823
64	CCDC134	0.25411934	0.01083317	0.999823
65	MICALCL	0.3554645	0.01092668	0.999823
66	SH3BP5	−0.171843	0.01098901	0.999823
67	ACACB	−0.2045808	0.01119203	0.999823
68	ETFB	−0.1510851	0.01121339	0.999823
69	TRIM23	0.18470962	0.01121431	0.999823
70	TDP2	−0.1055306	0.01160123	0.999823
71	RBFA	−0.1873702	0.01162321	0.999823
72	ACD	−0.1391661	0.01181329	0.999823
73	ITPRIP	0.51076938	0.0119837	0.999823
74	ZNF582	−0.3109977	0.01200289	0.999823
75	NAXD	0.20887993	0.01206603	0.999823
76	ULK2	0.13622427	0.01230707	0.999823
77	B3GNT2	−0.280015	0.01240541	0.999823
78	ZNF354A	−0.2219853	0.01256182	0.999823
79	AMOT	−0.2021322	0.01290087	0.999823
80	RNF169	0.10073219	0.01297084	0.999823
81	STAG3	−0.4021953	0.01315327	0.999823
82	NCR1	0.34775107	0.01385312	0.999823
83	FAM46C	0.23767656	0.01404483	0.999823
84	BIRC2	0.14715869	0.01425473	0.999823
85	COL3A1	−0.7793199	0.01472776	0.999823
86	NSRP1	−0.1201089	0.01473527	0.999823
87	FASLG	0.39523963	0.01478741	0.999823
88	ZMYND15	0.34817106	0.01480891	0.999823
89	NCKIPSD	−0.2858192	0.01483803	0.999823
90	MMP25	0.61695067	0.01504564	0.999823
91	RNF14	0.17065401	0.01507707	0.999823
92	TAF6L	0.33757278	0.01508158	0.999823
93	GHR	−0.4175955	0.01518602	0.999823
94	PIAS4	−0.1382704	0.01536949	0.999823
95	CELF1	0.10670906	0.01545935	0.999823
96	FOXO3B	0.28663588	0.01577862	0.999823
97	ZNF880	−0.1974472	0.01578517	0.999823
98	SOX6	0.3209163	0.01579766	0.999823
99	PRG4	−0.5432311	0.0159479	0.999823
100	UCK1	−0.1613335	0.01620986	0.999823
101	C7orf31	0.14545571	0.01648371	0.999823
102	PLA2G7	0.31700117	0.01648608	0.999823
103	OTUD7B	−0.129247	0.01659747	0.999823
104	DYM	0.11498399	0.01661968	0.999823
105	LMTK2	0.22610005	0.01689268	0.999823
106	DMPK	−0.3229673	0.01693248	0.999823
107	FAM107A	−0.3305965	0.01696118	0.999823
108	FGD5	−0.2571516	0.01704237	0.999823
109	INHBA	−0.417118	0.01716363	0.999823
110	MOSPD3	−0.2189547	0.01723402	0.999823
111	CAMLG	−0.0990098	0.01729544	0.999823
112	APOBEC3C	−0.1071202	0.01738431	0.999823
113	CHMP4BP1	0.33535436	0.01759232	0.999823
114	KLHL9	0.12519507	0.01767043	0.999823
115	NOTCH1	0.37680237	0.01779583	0.999823
116	ADGRE5	0.28079719	0.01796911	0.999823
117	PLEKHM3	0.1673145	0.01808403	0.999823
118	ITGAX	0.47545536	0.01830889	0.999823
119	NEUROD2	−0.3566226	0.01847832	0.999823
120	FRY	0.15403656	0.01856121	0.999823
121	MAGI2	−0.4263608	0.0187085	0.999823
122	PTDSS2	−0.3127907	0.01872473	0.999823
123	SORBS1	−0.2354539	0.01902384	0.999823
124	ARFGAP3	0.08070118	0.01908572	0.999823
125	SLC9A8	0.27458933	0.01951124	0.999823
126	FLT1	−0.1862232	0.01956642	0.999823
127	FAM206A	−0.1844597	0.01976687	0.999823
128	SNX8	−0.1606373	0.01992467	0.999823
129	EGR2	0.40055113	0.02001137	0.999823
130	CRIP2	−0.2769295	0.02007045	0.999823
131	FBXO18	−0.0995458	0.02013104	0.999823
132	THBD	0.40966091	0.02015288	0.999823
133	SACS	0.13073475	0.02017999	0.999823
134	LPIN2	0.1659817	0.02018442	0.999823
135	ATG16L2	0.47066975	0.0203194	0.999823
136	DAP3	0.08230965	0.0206098	0.999823
137	NBPF26	0.21725083	0.02068397	0.999823
138	SKI	−0.1495791	0.02079017	0.999823
139	ZNF628	0.33399888	0.02092355	0.999823
140	LILRA6	0.50709887	0.02103163	0.999823
141	AKAP10	0.11183522	0.02103648	0.999823
142	EED	0.14941401	0.02104887	0.999823
143	IGLV2-14	−0.4599037	0.02118479	0.999823
144	CUL4A	0.19550185	0.02120272	0.999823
145	SESN3	0.21352389	0.02122431	0.999823
146	GGH	−0.286244	0.02123904	0.999823
147	RBMS3	−0.3370053	0.02131978	0.999823
148	EPG5	0.12765985	0.02167255	0.999823
149	ROMO1	−0.1350013	0.02170047	0.999823
150	PSMA2	−0.1500424	0.02176662	0.999823
151	JCHAIN	−0.2717374	0.0218627	0.999823
152	TCF4	−0.1022857	0.02194006	0.999823
153	ANPEP	0.40564921	0.02206361	0.999823
154	GNL1	−0.0997968	0.02226215	0.999823
155	IFITM2	−0.1759504	0.0225286	0.999823
156	C19orf47	0.21854524	0.02262179	0.999823
157	NUS1	0.14799733	0.02271065	0.999823
158	RCN3	0.68134501	0.02306315	0.999823
159	THAP12	−0.0859371	0.02311962	0.999823
160	MICU3	0.28981943	0.02338403	0.999823
161	PLTP	−0.2540581	0.0234384	0.999823
162	SOX12	−0.225235	0.02344202	0.999823
163	NFKBID	0.49807675	0.0236816	0.999823
164	SPAG1	−0.2060284	0.02381805	0.999823
165	GCLC	0.25921593	0.02387105	0.999823
166	SMPD1	−0.3658053	0.02409033	0.999823
167	CYP19A1	0.31658844	0.02416579	0.999823
168	IGF2R	0.37123383	0.02422257	0.999823
169	SRGAP2C	−0.2674164	0.02428598	0.999823
170	NBPF10	0.21328924	0.02445397	0.999823
171	ZNF706	−0.1029408	0.02454303	0.999823
172	SLC11A1	0.47849014	0.0246525	0.999823
173	NEAT1	0.44914561	0.02469506	0.999823
174	RP3-	−0.2996412	0.02479862	0.999823
	370M22.8
175	MPRIP	−0.1062469	0.02481405	0.999823
176	CYP4F3	0.48971249	0.02494545	0.999823
177	SF3A2	−0.1064816	0.02501017	0.999823
178	HP	−0.4687396	0.02506622	0.999823
179	IGFBP7	−0.2605503	0.02517671	0.999823
180	RAB11FIP3	−0.181872	0.02531611	0.999823
181	ALDOB	−0.4368653	0.025317	0.999823
182	BCL7A	−0.2317492	0.02552236	0.999823
183	SOCS4	−0.1297161	0.02559725	0.999823
184	ANAPC15	−0.1113047	0.02562734	0.999823
185	PRICKLE1	−0.1549395	0.02592533	0.999823
186	CEP55	−0.2088249	0.02594296	0.999823
187	BCKDHA	0.27552704	0.02596038	0.999823
188	PLCXD1	0.30232113	0.02636879	0.999823
189	USP53	−0.2299264	0.02639874	0.999823
190	FAM103A1	−0.1655768	0.02640089	0.999823
191	ARHGEF10	−0.2302561	0.02654062	0.999823
192	ASS1	−0.3371256	0.0266732	0.999823
193	CAMKMT	0.18688262	0.02713489	0.999823
194	PRR13	−0.118958	0.02756679	0.999823
195	PTGIR	−0.2526015	0.02759952	0.999823
196	ADPGK	0.22144726	0.02760505	0.999823
197	TSEN2	0.17037095	0.02765733	0.999823
198	ADAM8	0.52818264	0.02769841	0.999823
199	MARK3	0.10173154	0.02771626	0.999823
200	TVP23C	−0.2478444	0.02772386	0.999823
201	TMEM232	0.3877995	0.027959	0.999823
202	ATG2A	0.24751798	0.02811799	0.999823
203	ADHFE1	0.28113267	0.02824963	0.999823
204	CCDC6	−0.0907515	0.02831569	0.999823
205	CCR2	0.40104756	0.02845943	0.999823
206	HIST1H3F	−0.2252338	0.02846834	0.999823
207	TIMP3	−0.3519568	0.0285298	0.999823
208	DIRC2	0.35441835	0.02860835	0.999823
209	TCEB3	−0.0868661	0.02863146	0.999823
210	ZNF175	−0.23782	0.02873465	0.999823
211	DCUN1D1	0.14426954	0.02884704	0.999823
212	PITPNM3	−0.3213807	0.02888684	0.999823
213	FOSB	0.6135836	0.02896411	0.999823
214	AQR	0.06441042	0.02897575	0.999823
215	GINS2	−0.3871113	0.02900555	0.999823
216	COPB1	0.06632984	0.02901851	0.999823
217	IFIT1B	0.32407614	0.02902811	0.999823
218	CHMP6	−0.2003379	0.02908907	0.999823
219	NES	−0.2500724	0.02911141	0.999823
220	CLSPN	−0.1648583	0.02920979	0.999823
221	ZNF688	−0.1424407	0.02923402	0.999823
222	FAM69B	−0.3101323	0.02924848	0.999823
223	APOE	−0.3243643	0.02940223	0.999823
224	IGHG2	−0.3336143	0.02945943	0.999823
225	SLC25A32	0.13035519	0.02956385	0.999823
226	APBB3	0.53377928	0.02960979	0.999823
227	ARG1	−0.3553876	0.02985572	0.999823
228	SLC43A2	0.3769808	0.02989364	0.999823
229	FABP4	−0.2559567	0.02991405	0.999823
230	HABP4	0.24172857	0.03005608	0.999823
231	C2CD3	0.10120882	0.03017285	0.999823
232	ORAI2	−0.1762831	0.03018521	0.999823
233	PER3	0.21521013	0.03029788	0.999823
234	AC093673.5	−0.2891258	0.03051499	0.999823
235	KIF20A	−0.2844225	0.03053083	0.999823
236	TBCK	0.16579385	0.03066786	0.999823
237	MT2A	−0.1566396	0.03087897	0.999823
238	ALG8	0.20954186	0.03090105	0.999823
239	LIN52	0.26231885	0.03095795	0.999823
240	EPN2	−0.3096568	0.03100399	0.999823
241	ARIH1	0.09621805	0.0310866	0.999823
242	ALDH1A1	0.22786487	0.0312975	0.999823
243	ZNF703	0.27576921	0.03137979	0.999823
244	ACPP	0.29430814	0.03144763	0.999823
245	TMEM234	0.28955944	0.03163473	0.999823
246	RORA	0.18907074	0.03167226	0.999823
247	PSMA7	−0.0670017	0.03173471	0.999823
248	ING2	−0.1277887	0.03182283	0.999823
249	DUS3L	−0.2256817	0.03187092	0.999823
250	SFMBT2	0.11771092	0.03207741	0.999823
251	DDI2	0.10736217	0.03228297	0.999823
252	AATK	0.38287082	0.03238781	0.999823
253	EOMES	0.25204548	0.03245533	0.999823
254	UNKL	0.28483329	0.03253455	0.999823
255	RACGAP1	−0.1425339	0.03254637	0.999823
256	MICALL2	−0.2695713	0.03298099	0.999823
257	CHTF8	−0.0944541	0.03303854	0.999823
258	EML2	0.12500876	0.03315582	0.999823
259	VTI1A	0.11874312	0.03326678	0.999823
260	CKLF	−0.1923901	0.03339663	0.999823
261	VWF	−0.3119939	0.03341445	0.999823
262	AHNAK2	−0.3975013	0.03341731	0.999823
263	BET1L	−0.1441156	0.03349439	0.999823
264	ENOX2	0.11686247	0.03380531	0.999823
265	ZNF280C	0.14656363	0.03385665	0.999823
266	DNAJB4	0.15647994	0.03396513	0.999823
267	FAM96B	−0.0996577	0.03432174	0.999823
268	PRX	−0.2526297	0.0344957	0.999823
269	RNF5	−0.1396363	0.03478149	0.999823
270	FAM212A	−0.1897578	0.03483004	0.999823
271	DOCK10	0.10839726	0.0350643	0.999823
272	PFN2	−0.3192937	0.03507091	0.999823
273	TGFBR3	0.25019499	0.03509169	0.999823
274	C7orf50	−0.1730759	0.03510597	0.999823
275	OXSR1	0.10426307	0.03514952	0.999823
276	PLSCR1	−0.1539301	0.0352033	0.999823
277	CDKN3	−0.1793994	0.03526916	0.999823
278	PTPRG	−0.2728392	0.03529744	0.999823
279	SLC24A1	−0.1781733	0.03535686	0.999823
280	TFEC	0.13865261	0.03540698	0.999823
281	LFNG	0.41498618	0.03546648	0.999823
282	FOLR3	−0.4824429	0.0356224	0.999823
283	TCIRG1	0.42460234	0.03566012	0.999823
284	ZNF248	−0.1482991	0.03607008	0.999823
285	SYTL2	0.22099325	0.03625104	0.999823
286	GABARAP	−0.0681237	0.03665675	0.999823
287	LYL1	−0.1235543	0.03691445	0.999823
288	ABHD8	0.27374966	0.03696402	0.999823
289	ATL2	0.10911832	0.03696907	0.999823
290	VAC14	0.12159626	0.03727137	0.999823
291	MCM7	−0.133427	0.03753042	0.999823
292	WLS	0.31920592	0.03777635	0.999823
293	GMFG	−0.0762437	0.03777639	0.999823
294	MIPEP	0.19756689	0.0378531	0.999823
295	MYBL1	0.13609471	0.03788196	0.999823
296	CENPP	−0.1775462	0.03806583	0.999823
297	C15orf52	−0.2739874	0.03807024	0.999823
298	PLK1	−0.2821968	0.03807628	0.999823
299	KIAA1324	0.38983772	0.03836171	0.999823
300	TNNI2	0.28261991	0.03837332	0.999823
301	ZNF629	−0.2118135	0.03841179	0.999823
302	ARHGEF10L	0.28102719	0.03850904	0.999823
303	SUSD6	0.19967273	0.0388163	0.999823
304	MYL4	−0.3963638	0.03884241	0.999823
305	SMIM12	−0.1271663	0.03896514	0.999823
306	SREBF1	0.32605041	0.03909875	0.999823
307	SVIL-AS1	−0.2266914	0.03923228	0.999823
308	ZFP91	−0.1216083	0.03933035	0.999823
309	SH3RF1	0.15044488	0.03937422	0.999823
310	ATXN10	0.10995568	0.03956122	0.999823
311	CSF3R	0.40657663	0.03957007	0.999823
312	ZNF362	0.09743055	0.03961429	0.999823
313	NFU1	−0.100997	0.03985893	0.999823
314	PLXNB3	−0.3310656	0.04054132	0.999823
315	ARL2	−0.161297	0.04070359	0.999823
316	IGFBP2	−0.5246938	0.04072204	0.999823
317	APEX2	−0.1420479	0.04090007	0.999823
318	TMF1	−0.0636947	0.04102724	0.999823
319	SLC15A4	0.16273554	0.04117683	0.999823
320	ANKRD33B	−0.2529753	0.04118417	0.999823
321	ALG5	0.22362176	0.04129761	0.999823
322	IGKV4-1	−0.2543051	0.04167867	0.999823
323	SNPH	−0.3155746	0.04194896	0.999823
324	DNAJC24	−0.1508193	0.04197652	0.999823
325	TACC3	−0.1476047	0.04202318	0.999823
326	GK5	0.16735486	0.04214779	0.999823
327	ALKBH5	−0.0874234	0.04218493	0.999823
328	CLEC7A	0.21728275	0.04220416	0.999823
329	KANK1	−0.2255087	0.0422137	0.999823
330	RNF8	−0.1465837	0.04278441	0.999823
331	COA5	−0.0930276	0.04296264	0.999823
332	TSPYL4	−0.1347864	0.04312105	0.999823
333	PID1	0.23786205	0.04317041	0.999823
334	FAM32A	−0.1070765	0.04322635	0.999823
335	YWHAZP4	0.22146435	0.04349002	0.999823
336	SDHAP1	0.32501671	0.04367187	0.999823
337	ADAP1	0.29057012	0.04368926	0.999823
338	KIF26B	−0.3342392	0.04382832	0.999823
339	RRN3P1	0.2103656	0.04410024	0.999823
340	SIGIRR	0.21434437	0.04419149	0.999823
341	FAM127B	−0.1588417	0.0442788	0.999823
342	COX8A	−0.1234086	0.04430464	0.999823
343	BRI3BP	0.26908104	0.04451084	0.999823
344	GOLGA2	−0.1421676	0.04455463	0.999823
345	LNX2	0.13956437	0.04463541	0.999823
346	RELT	0.42035408	0.04485223	0.999823
347	AMPD2	0.16253961	0.04491238	0.999823
348	COL1A1	−0.6942388	0.04500516	0.999823
349	PRDM4	−0.1005633	0.04520397	0.999823
350	MAZ	−0.1086896	0.04529317	0.999823
351	ERCC1	−0.1098209	0.04537037	0.999823
352	MXI1	0.23509908	0.04549618	0.999823
353	THOC1	0.09635068	0.04565955	0.999823
354	AK1	−0.211156	0.04577507	0.999823
355	ADGRF5	−0.2657715	0.04607249	0.999823
356	HELLS	−0.1233562	0.04608852	0.999823
357	H2AFV	−0.1114127	0.04633008	0.999823
358	SAMD14	−0.2708931	0.04634534	0.999823
359	RAB13	−0.1397459	0.0466095	0.999823
360	ITLN1	0.32354922	0.04674951	0.999823
361	TTC39C	0.09049556	0.04675678	0.999823
362	IL2RB	0.23545479	0.04691262	0.999823
363	TMEM43	0.25763206	0.04733173	0.999823
364	LDLRAD4	−0.1447728	0.04766856	0.999823
365	ZNF333	0.20134639	0.04775679	0.999823
366	PLPP3	−0.2300937	0.04776469	0.999823
367	CRY1	−0.1198904	0.04788717	0.999823
368	TTC30B	−0.2580155	0.04798778	0.999823
369	MEIS2	−0.3392974	0.04815618	0.999823
370	RBM17	−0.0958349	0.04818096	0.999823
371	MLEC	−0.2367412	0.04843225	0.999823
372	UBE2R2	−0.0875255	0.04870795	0.999823
373	LTN1	0.07955132	0.04882314	0.999823
374	KIAA1211	−0.2514489	0.04887108	0.999823
375	FGD6	0.14050951	0.04888819	0.999823
376	FOXO3	0.21676256	0.04899547	0.999823
377	CISD2	0.17691071	0.04913734	0.999823
378	PAFAH2	0.22118013	0.04915197	0.999823
379	LMBRD2	0.18522972	0.0492318	0.999823
380	ZNF720	−0.0931394	0.04930151	0.999823
381	CHN2	0.18167055	0.04944251	0.999823
382	RTEL1P1	0.65717329	0.04949181	0.999823
383	DGAT2	0.41471623	0.04958542	0.999823
384	CHMP3	−0.1236621	0.04981575	0.999823
385	CEP295NL	0.64735357	0.04994012	0.999823

Third differential expression analysis of predicting preterm birth earlier than 35 weeks of gestational age, with blood samples collected between 17-23 weeks of gestational age, was performed using EdgeR and accounting for ethnicity, and cohort effects and gestational age at collection (111 PTB cases and 505 controls). Table 44 shows a set of top 6 genes with p-value<0.1 after adjustment from multiple hypothesis correction (FDR value), and also showed a significant deviation from the null hypothesis in a QQ plot for differentially expressed in pre-term birth cases (as shown in FIG. 44E). Table 45 shows an additional set of genes with p-value<0.1 for predicting preterm birth earlier than 35 weeks of gestation with blood samples collected between 17-23 weeks of gestational age. Genes are ordered according to their statistical significance (P-values).

TABLE 44
Top 6 genes with p-value < 0.1 after adjustment from multiple
hypothesis correction (FDR value), that are predictive for
preterm birth earlier than 35 weeks of gestation with blood
samples collected between 17-23 weeks of gestational age
#	Gene	logFC	P-Value	FDR
1	FGA	−0.8922522	2.07E−07	0.002408
2	COL3A1	−1.1822498	7.06E−07	0.004095
3	COL1A1	−1.2205151	1.51E−06	0.005844
4	COL1A2	−1.0088068	1.09E−05	0.031216
5	CDR1-	−0.7115165	1.35E−05	0.031216
	AS
6	HSPA1B	0.57245175	1.74E−05	0.03368

TABLE 45
Additional set of genes with p-value < 0.1 for predicting
preterm birth earlier than 35 weeks of gestation with blood
samples collected between 17-23 weeks of gestational age
#	Gene	logFC	P-Value	FDR
1	APOB	−0.5826059	0.00018491	0.306558
2	NUP62CL	0.36283704	0.00039242	0.569258
3	CFH	−0.3925453	0.00064396	0.718794
4	EZH1	0.10917121	0.00064612	0.718794
5	FGB	−0.5417924	0.00071031	0.718794
6	CPNE3	−0.1598343	0.00075069	0.718794
7	HIST1H2AI	−0.2214732	0.0008052	0.718794
8	ABCA13	−0.4106282	0.00115275	0.925144
9	PLXNA3	0.53018951	0.00130431	0.925144
10	KLF5	−0.3693255	0.00135386	0.925144
11	DCN	−0.7354785	0.00135523	0.925144
12	ZBTB25	0.21316372	0.00146636	0.945397
13	BEX1	−0.3482247	0.00180193	0.999753
14	PTGR1	−0.2413271	0.00205964	0.999753
15	CCDC80	−0.5093286	0.00221921	0.999753
16	FABP1	−0.4395804	0.00232075	0.999753
17	NABP2	−0.2123718	0.00240932	0.999753
18	MMP8	−0.4528477	0.00248249	0.999753
19	TMEM56	−0.3358729	0.00262098	0.999753
20	UNK	0.10740632	0.00278715	0.999753
21	CEACAM8	−0.3912624	0.00290442	0.999753
22	TK1	−0.3710566	0.0029977	0.999753
23	OLFM4	−0.4569144	0.00307192	0.999753
24	RETN	−0.4096121	0.00313118	0.999753
25	POSTN	−0.4541202	0.0033519	0.999753
26	POLR2A	0.07393081	0.00360939	0.999753
27	AMT	0.23843514	0.00368187	0.999753
28	ERLEC1	0.12130672	0.00377886	0.999753
29	ALB	−0.3771048	0.00382494	0.999753
30	GALNT7	0.22055918	0.00397611	0.999753
31	TCN1	−0.4369808	0.00418378	0.999753
32	SEMA3C	−0.3609237	0.00437721	0.999753
33	TYMS	−0.2121301	0.00439571	0.999753
34	SERPINB10	−0.3835561	0.00446509	0.999753
35	KXD1	0.08832161	0.0046164	0.999753
36	CRISP3	−0.4517656	0.00464372	0.999753
37	DLK1	0.61460928	0.00470334	0.999753
38	APOH	−0.4805561	0.00477496	0.999753
39	LTF	−0.3761597	0.00483032	0.999753
40	IRAK2	0.19067454	0.0050855	0.999753
41	CAMP	0.3878126	0.00516332	0.999753
42	CNPY3	0.11633546	0.00517313	0.999753
43	VPS37B	0.15814742	0.00518814	0.999753
44	SAYSD1	−0.1950745	0.00519864	0.999753
45	AC005795.1	0.20057776	0.00526874	0.999753
46	PSMD14	−0.1158157	0.00538832	0.999753
47	CST7	−0.5217516	0.00539692	0.999753
48	CAMKK1	0.26063751	0.00549614	0.999753
49	VPS29	−0.0830259	0.00560881	0.999753
50	ARL1	−0.1206514	0.00564317	0.999753
51	PIAS4	0.11228955	0.00579437	0.999753
52	ARPC4-TTLL3	0.2947005	0.00579671	0.999753
53	CEACAM6	−0.3567903	0.00583167	0.999753
54	CCDC18-AS1	0.28958197	0.00632943	0.999753
55	SF3A1	0.0783621	0.00639703	0.999753
56	SLC2A5	−0.3531257	0.00649409	0.999753
57	IDI1	−0.1187531	0.00657305	0.999753
58	HSPA1A	0.25560927	0.00674572	0.999753
59	AHNAK2	0.391944	0.00690585	0.999753
60	TPT1P4	0.23092184	0.00696854	0.999753
61	ANXA1	−0.1853844	0.00745635	0.999753
62	TACC3	0.12955759	0.00747907	0.999753
63	HBG1	0.6911507	0.00751888	0.999753
64	NEK3	−0.1559149	0.00776413	0.999753
65	1-Mar	0.35690649	0.00795965	0.999753
66	TMEM14C	−0.1709381	0.0079713	0.999753
67	CCNA2	−0.2263652	0.00801614	0.999753
68	MTX2	−0.1547208	0.0081661	0.999753
69	IRS2	0.20766438	0.00820013	0.999753
70	COQ7	−0.1466541	0.00833708	0.999753
71	S100B	−0.3287938	0.00861007	0.999753
72	TSC22D4	0.11843984	0.00864383	0.999753
73	OBSCN	0.32640506	0.00888143	0.999753
74	TPPP3	−0.2379465	0.00899679	0.999753
75	HIST1H4I	−0.1672515	0.00903644	0.999753
76	PLD1	−0.1847271	0.00992616	0.999753
77	PER3	0.17292321	0.01018427	0.999753
78	CTB-50L17.10	0.10225093	0.01026921	0.999753
79	TEX30	−0.2110864	0.01047769	0.999753
80	AFF2	−0.19233	0.01048049	0.999753
81	INHBA	−0.3622862	0.01049335	0.999753
82	RNF111	0.05623506	0.01080035	0.999753
83	PABPC1L	0.49410783	0.01080075	0.999753
84	GPBP1L1	0.05507902	0.01090532	0.999753
85	BPI	−0.3221364	0.01104231	0.999753
86	SLC3A2	0.18156536	0.0112006	0.999753
87	MYH11	−0.254936	0.01126761	0.999753
88	ALDH1A2	−0.2305017	0.0113409	0.999753
89	TTN	0.46246546	0.01139138	0.999753
90	ABHD16A	0.20970139	0.01140776	0.999753
91	GS1-44D20.1	0.17063532	0.0114796	0.999753
92	NR1D2	0.10785231	0.0115101	0.999753
93	RNASE3	−0.3866944	0.01159032	0.999753
94	TRAPPC12	0.1120295	0.01183535	0.999753
95	RAD51B	0.2566469	0.01191832	0.999753
96	POLR2K	−0.1549786	0.01203891	0.999753
97	CDH6	0.47160832	0.01203921	0.999753
98	ANKRD36	0.15136038	0.01212896	0.999753
99	ZNF550	0.30399132	0.01222071	0.999753
100	SNX19	−0.1850206	0.0123524	0.999753
101	PSMA3	−0.0935928	0.01294008	0.999753
102	SF3A2	0.0822754	0.01294752	0.999753
103	PDE3B	0.30101247	0.01297583	0.999753
104	NELL2	0.3861488	0.01304957	0.999753
105	KATNA1	−0.0912704	0.01308488	0.999753
106	WASH6P	0.45059223	0.01322944	0.999753
107	ITGA9	−0.2609704	0.0134086	0.999753
108	LGALS1	−0.1618404	0.01363949	0.999753
109	GALT	0.29467619	0.01376172	0.999753
110	TRIM8	0.09716423	0.01403662	0.999753
111	NICN1	−0.2172396	0.01419089	0.999753
112	FERMT2	−0.1951171	0.01422377	0.999753
113	PDIA4	0.09664602	0.01450684	0.999753
114	EPB42	−0.2430774	0.01452652	0.999753
115	RIPK2	−0.110475	0.01457411	0.999753
116	PELI2	0.14817975	0.01479923	0.999753
117	KLHL35	0.46532872	0.01484529	0.999753
118	SLC15A4	0.14721116	0.01489834	0.999753
119	TGFB2	0.28472572	0.01507659	0.999753
120	RUNDC3A	−0.2992381	0.01523721	0.999753
121	SGSM3	0.12690997	0.01548659	0.999753
122	LTA4H	−0.1483382	0.01558966	0.999753
123	CANT1	0.20605193	0.01570725	0.999753
124	PPP1R35	0.18021209	0.01616723	0.999753
125	MPO	−0.2474597	0.01617706	0.999753
126	FOXJ2	0.11503104	0.01621339	0.999753
127	SELENBP1	−0.2532564	0.01622888	0.999753
128	CCDC173	0.37753916	0.01632994	0.999753
129	CTDSP2	0.07518886	0.01636667	0.999753
130	NUDT9	−0.1365469	0.01656297	0.999753
131	ATP10D	0.26481636	0.01656597	0.999753
132	AZI2	−0.086938	0.01659226	0.999753
133	FUCA2	0.14782949	0.01669051	0.999753
134	PRRC2C	0.05896815	0.01677844	0.999753
135	DEFA4	−0.3046262	0.01684177	0.999753
136	ZNF257	0.18123619	0.01690074	0.999753
137	H3F3B	0.0730957	0.01711348	0.999753
138	FGGY	−0.1220351	0.01712126	0.999753
139	TTC38	−0.1944937	0.01714651	0.999753
140	PGM2	−0.0807912	0.01752113	0.999753
141	SH3BP5	−0.1490668	0.0175562	0.999753
142	FAM133B	0.12698846	0.01767701	0.999753
143	ARHGEF18	0.20558778	0.01790049	0.999753
144	SREK1	0.07846238	0.017972	0.999753
145	C7orf31	0.10246202	0.01799207	0.999753
146	CTD-2017F17.2	0.46727872	0.0183904	0.999753
147	STIM2	0.12847968	0.01859262	0.999753
148	EP400NL	0.28376719	0.01862442	0.999753
149	NUDCD2	−0.165063	0.01909539	0.999753
150	ZBTB16	0.13331658	0.01913721	0.999753
151	GRPEL2	−0.1877752	0.01927475	0.999753
152	NLRC4	−0.1701506	0.0195017	0.999753
153	HIST1H3I	−0.1866323	0.01966998	0.999753
154	IL2RB	0.22901014	0.01978275	0.999753
155	IL7R	0.17493298	0.02021919	0.999753
156	TMEM43	0.25352755	0.02060582	0.999753
157	NBPF11	0.1485556	0.02075834	0.999753
158	ANKRD36B	0.1927486	0.02126847	0.999753
159	HIKESHI	−0.1211526	0.02130131	0.999753
160	ADSS	−0.0950366	0.02138402	0.999753
161	CCDC141	0.3919521	0.02152967	0.999753
162	PKD1	0.30833702	0.02177052	0.999753
163	CCR2	0.34638257	0.02194942	0.999753
164	MS4A3	−0.2869229	0.02244994	0.999753
165	MUT	−0.1097854	0.02273149	0.999753
166	IGF1R	0.1945484	0.02282841	0.999753
167	CASS4	0.12014184	0.02291597	0.999753
168	DLD	−0.0865122	0.02300047	0.999753
169	NFXL1	−0.1051861	0.02334338	0.999753
170	QSOX2	0.26727564	0.0235745	0.999753
171	MSNP1	0.15424572	0.02358748	0.999753
172	GPAT4	0.14540808	0.02361456	0.999753
173	GSKIP	−0.1367002	0.02403918	0.999753
174	RHOU	−0.149483	0.02406404	0.999753
175	TKFC	0.12691977	0.02437814	0.999753
176	ATP10A	0.30508566	0.02446292	0.999753
177	PTP4A3	0.1449434	0.02472307	0.999753
178	MEI1	−0.2446254	0.02495366	0.999753
179	IL7	0.18042937	0.02506084	0.999753
180	HIST1H3D	−0.1312724	0.02506997	0.999753
181	SMIM20	−0.1498791	0.02509728	0.999753
182	AK5	0.2135572	0.02522872	0.999753
183	ARG1	−0.2523013	0.02529551	0.999753
184	MLLT11	0.2563372	0.02546545	0.999753
185	CTD-2319112.10	0.21588609	0.02551335	0.999753
186	EEF1E1	−0.1263748	0.02554448	0.999753
187	CKAP2L	−0.1360314	0.0255639	0.999753
188	SLC4A4	−0.2360361	0.02587196	0.999753
189	NMRAL1	0.12247516	0.02597727	0.999753
190	PRG4	−0.3738295	0.02605235	0.999753
191	SELPLG	0.21964904	0.02605785	0.999753
192	MALAT1	0.33881384	0.02614156	0.999753
193	EIF4HP1	0.25442345	0.02616057	0.999753
194	COX5A	−0.0822105	0.02621488	0.999753
195	SPOCK2	0.31101424	0.02634448	0.999753
196	RILPL1	0.12949377	0.02640549	0.999753
197	CHD2	0.05277056	0.02651847	0.999753
198	TCTN3	0.23335682	0.02665692	0.999753
199	STYXL1	0.10093585	0.02710051	0.999753
200	TM2D3	0.11782763	0.02742488	0.999753
201	HIST1H2AH	−0.1930756	0.0277185	0.999753
202	C1orf123	−0.1423279	0.0277822	0.999753
203	B3GNT5	−0.2444396	0.02804637	0.999753
204	TPD52L1	−0.2825496	0.0282404	0.999753
205	MIER3	−0.1124144	0.02851633	0.999753
206	TMEM35B	0.20806256	0.02864175	0.999753
207	TSPYL2	0.1697368	0.02864491	0.999753
208	ADA	−0.1589866	0.02866328	0.999753
209	ARID1B	0.0528842	0.02870548	0.999753
210	FN1	−0.2404726	0.02905857	0.999753
211	SELENOP	−0.2151347	0.0291476	0.999753
212	RBM6	0.07373482	0.02920453	0.999753
213	CEP68	0.14191808	0.02945737	0.999753
214	MTCL1	0.18237028	0.02957545	0.999753
215	ALAS2	−0.2291027	0.02974141	0.999753
216	EXOG	0.1727914	0.02989632	0.999753
217	GLTSCR1	0.19245341	0.02998657	0.999753
218	PGLYRP1	−0.2830829	0.02998786	0.999753
219	SMIM5	0.20149599	0.0300126	0.999753
220	CDC6	−0.1658365	0.0300815	0.999753
221	CAV2	0.21059274	0.03018762	0.999753
222	NBPF9	0.17983382	0.0302083	0.999753
223	PTGIR	0.17136031	0.0304244	0.999753
224	SNRPG	−0.1371207	0.03044173	0.999753
225	WBP1L	0.12104254	0.03044713	0.999753
226	TOR1AIP2	0.08360512	0.03048316	0.999753
227	EMB	−0.0897702	0.0305139	0.999753
228	AVPR1A	0.21704274	0.03059684	0.999753
229	P4HA2	0.37243812	0.03060348	0.999753
230	GYG1	−0.1125703	0.03083176	0.999753
231	C3	−0.1993848	0.03100619	0.999753
232	DOC2B	−0.2537712	0.03104329	0.999753
233	HEATR5A	−0.1057825	0.03105816	0.999753
234	G2E3	−0.0844544	0.03111066	0.999753
235	PCNT	0.06710106	0.03115947	0.999753
236	CYP2E1	−0.2906311	0.03118366	0.999753
237	ZDHHC5	0.09675558	0.03122839	0.999753
238	KDM4B	0.11555829	0.03124625	0.999753
239	TIPRL	−0.0841239	0.03126632	0.999753
240	PIWIL4	−0.1441967	0.03128178	0.999753
241	TOX4	0.05298922	0.03128257	0.999753
242	CYB5D2	0.17434026	0.03151201	0.999753
243	MCTS1	−0.1283583	0.03162187	0.999753
244	ARPC1A	−0.0762396	0.03166386	0.999753
245	GAB1	0.10675688	0.03177612	0.999753
246	KIAA1328	0.08801699	0.03179623	0.999753
247	CBX7	0.14747089	0.03216422	0.999753
248	MYBL2	−0.1459055	0.03222052	0.999753
249	COX20	−0.0940038	0.03228853	0.999753
250	S100A12	−0.2026783	0.0324576	0.999753
251	DCUN1D1	0.10810631	0.03255478	0.999753
252	CEP97	−0.1203253	0.03257225	0.999753
253	CCR7	0.27413875	0.03272345	0.999753
254	IGFBP2	−0.3549402	0.03305778	0.999753
255	PROSER2	0.18257741	0.03312428	0.999753
256	POLE4	−0.1296828	0.03313182	0.999753
257	CIC	0.10838803	0.03321301	0.999753
258	ING1	0.08081968	0.03322562	0.999753
259	PPIL1	−0.1927958	0.03327341	0.999753
260	C3orf14	−0.2563693	0.03333526	0.999753
261	SF3B5	−0.116132	0.03338042	0.999753
262	ISCU	0.08400156	0.03338527	0.999753
263	IGHG2	0.26195808	0.03380502	0.999753
264	CHPF2	0.28256794	0.03383726	0.999753
265	E2F8	−0.2465367	0.03388536	0.999753
266	Metazoa_SRP_ENSG00000278771	−0.2058012	0.033919	0.999753
267	MIB2	0.17694897	0.03404959	0.999753
268	CCNK	0.0529718	0.03421768	0.999753
269	ZNF292	0.06953068	0.03431769	0.999753
270	PPP1R15A	0.13124538	0.0343715	0.999753
271	ATP7B	0.21466598	0.03451874	0.999753
272	ANKS6	0.24689062	0.03469057	0.999753
273	PCP2	0.22564137	0.03478878	0.999753
274	RRM2	−0.1881119	0.03494304	0.999753
275	CPEB3	0.15049772	0.03504406	0.999753
276	FOXM1	−0.1910254	0.03513846	0.999753
277	HIST1H2AL	−0.1450165	0.03532496	0.999753
278	NEFH	−0.1914372	0.035411	0.999753
279	MAST3	0.10031607	0.03547816	0.999753
280	ZFAT	0.12262196	0.03593907	0.999753
281	CUL3	−0.0453055	0.03610051	0.999753
282	BBC3	0.17360764	0.03631048	0.999753
283	TAOK2	0.10209633	0.03647822	0.999753
284	BICD1	0.11544926	0.03677942	0.999753
285	AC006116.22	0.2292784	0.03678963	0.999753
286	ING4	0.09297105	0.03695455	0.999753
287	MT-TP	−0.2835665	0.03697	0.999753
288	DNAJB1	0.1476015	0.03700129	0.999753
289	ADAP2	−0.1722998	0.03712279	0.999753
290	PREP	−0.1098884	0.0379176	0.999753
291	FAM49B	−0.0952589	0.0379976	0.999753
292	PLK1	−0.2051848	0.03801488	0.999753
293	SYNJ2	0.13699949	0.03801954	0.999753
294	INO80C	−0.1330365	0.03804286	0.999753
295	HBE1	0.42870509	0.03830571	0.999753
296	USP11	0.06798314	0.03840566	0.999753
297	MCM6	0.15356415	0.03843693	0.999753
298	MRPL36	−0.134445	0.03855475	0.999753
299	BBOF1	0.13716434	0.0385769	0.999753
300	TTC14	0.26365258	0.03869701	0.999753
301	ZNF746	0.18539114	0.0388262	0.999753
302	SMCR8	0.07266396	0.03890485	0.999753
303	DGKA	0.16075717	0.03895777	0.999753
304	C3orf58	0.13596494	0.03904565	0.999753
305	CD7	0.20770221	0.03920229	0.999753
306	EPPK1	0.3359978	0.03929967	0.999753
307	ATAD3B	0.33834265	0.03931759	0.999753
308	APBB1	0.19196402	0.03941002	0.999753
309	UBR5	0.03721083	0.03951333	0.999753
310	SLC14A1	−0.2118413	0.03955782	0.999753
311	GOLGA8R	0.20030818	0.03963813	0.999753
312	S100A4	−0.1270935	0.03978126	0.999753
313	NAT1	−0.1691511	0.04054604	0.999753
314	CASP5	−0.1777435	0.04055036	0.999753
315	DDX31	0.17809076	0.04063238	0.999753
316	LUC7L3	0.07402997	0.04065676	0.999753
317	PSMA3-AS1	0.18324627	0.04089756	0.999753
318	MUC3A	−0.3375097	0.04093926	0.999753
319	PRR5L	−0.0957441	0.04096973	0.999753
320	SETD4	0.18086207	0.04126734	0.999753
321	PRPSAP1	−0.1033051	0.04149971	0.999753
322	MRPL51	−0.0994934	0.04151102	0.999753
323	LENG8	0.24702492	0.04167004	0.999753
324	TMEM55B	0.12862126	0.04179192	0.999753
325	UBXN4	0.07134072	0.04180286	0.999753
326	PABPN1	0.07244813	0.04195609	0.999753
327	TRAFD1	0.06658772	0.04213277	0.999753
328	SNTB2	−0.1100601	0.04233428	0.999753
329	MRPL48	−0.1195106	0.04241753	0.999753
330	SPATA5	0.09150062	0.04246213	0.999753
331	H2AFX	−0.1776987	0.04275797	0.999753
332	IGFBP4	−0.2246328	0.04288488	0.999753
333	GFI1	−0.2316195	0.04296089	0.999753
334	HBS1L	−0.0546702	0.04320669	0.999753
335	TMUB2	0.19402025	0.04323319	0.999753
336	QRSL1	−0.1400253	0.04327588	0.999753
337	MKI67	−0.1150793	0.04343116	0.999753
338	SMIM24	−0.2066749	0.04344628	0.999753
339	FAM78A	0.09176017	0.04368267	0.999753
340	AHR	−0.0810842	0.0439174	0.999753
341	PLXNA2	0.17677215	0.04405629	0.999753
342	ANKMY1	0.12999115	0.0440723	0.999753
343	MEGF6	0.44577879	0.0443392	0.999753
344	NBPF10	0.14614391	0.04464845	0.999753
345	TMEM206	0.1606816	0.04479684	0.999753
346	CD24	−0.2078109	0.04489029	0.999753
347	RPAP3	0.08627224	0.0450221	0.999753
348	KLHL12	0.07504398	0.04508842	0.999753
349	FAM208A	−0.0419344	0.04534657	0.999753
350	FAM26E	0.18269354	0.04536151	0.999753
351	C10orf11	−0.153169	0.04553543	0.999753
352	COPS5	−0.0541677	0.04564979	0.999753
353	SNX29	0.08506495	0.04565399	0.999753
354	SLC7A6	0.21035707	0.04576956	0.999753
355	CD19	0.29589004	0.04584316	0.999753
356	CNNM4	0.22034199	0.04589658	0.999753
357	NIF3L1	−0.1567129	0.04591594	0.999753
358	PBX2	0.09040127	0.04600611	0.999753
359	MAPK1IP1L	0.08569724	0.04627337	0.999753
360	EFCAB5	0.17026595	0.0462916	0.999753
361	MISP3	0.19341489	0.04640056	0.999753
362	PAICS	−0.1323756	0.0466355	0.999753
363	NBN	−0.0542005	0.04667697	0.999753
364	PIK3IP1	0.26921035	0.046751	0.999753
365	TMEM106B	0.0814957	0.04676457	0.999753
366	ANP32B	0.07359856	0.04691678	0.999753
367	NBEAL1	0.0661075	0.04723681	0.999753
368	FPGT	−0.1115372	0.04771241	0.999753
369	MYLIP	0.12467534	0.04805567	0.999753
370	SDHA	0.09790987	0.04806401	0.999753
371	STX11	0.09670973	0.04819952	0.999753
372	MT-TM	−0.2647748	0.04824865	0.999753
373	ZNF865	0.18795028	0.04828377	0.999753
374	FAN1	0.12049483	0.04840424	0.999753
375	CYSLTR1	−0.1743521	0.04873218	0.999753
376	CACNB4	−0.2114985	0.04891416	0.999753
377	HPD	−0.2728785	0.04892793	0.999753
378	ZNF630	−0.1900738	0.04907291	0.999753
379	RPA3	−0.1355575	0.04911536	0.999753
380	ADRA2A	0.24629972	0.04914611	0.999753
381	PTMAP2	0.18200957	0.04963155	0.999753
382	ZW10	−0.0832316	0.04969237	0.999753
383	ADAM28	0.22059564	0.04971214	0.999753
384	FAM175B	0.06386437	0.04988883	0.999753
385	ARHGAP45	0.09866914	0.04996179	0.999753
386	TCEA1	0.05831703	0.04999775	0.999753
387	NIPA2	−0.1265798	0.05021501	0.999753
388	PTMA	0.10851123	0.05038825	0.999753
389	MEF2D	0.06287954	0.05041783	0.999753
390	S100A8	−0.1731034	0.05043263	0.999753
391	UST	0.19855501	0.05059008	0.999753
392	TOP1	0.07870085	0.0506117	0.999753
393	ZNF587	0.17157982	0.0506316	0.999753

Example 22: Prediction of Pre-Term Birth (PTB) on Combined Multiple Cohorts Using an Effect Size

Features were identified from a training set comprising Log 2 RPM gene expression data from six cohorts (FIG. 44A), collected at about 25 weeks gestation). Seventy percent of the training data was split into a training set (38 cases and 186 controls), while the remaining 30% was used as a test set (18 cases and 79 controls) for feature engineering. Candidate genes were selected for an upregulated effect size in PTB greater than an effect size threshold. Principal component analysis (PCA) was trained on standardized Log 2 CPM counts from controls in the training set. The full training and test sets were then PCA transformed. A logistic model (L1 penalty) was trained on the PCA components calculated from the training data and then applied to principal components similarly calculated from the test dataset. The hyperparameters for the effect size threshold and the PCA variance threshold were optimized by a grid search based on optimizing the AUC on the test set. The effect size threshold was set to 0.3, yielding 837 high effect genes, and the PCA variance threshold was set to 0.6, obtaining an AUC of 0.56 in the test set using the aforementioned logistic regression model obtained from the training set.

Table 46 shows a set of top 50 genes contributing to 20% of the total PTB model weight. Table 47 shows the remaining 787 genes contributing to 80% of the model weight. Genes are sorted by total weight in the modeling, which is obtained as the matrix multiplication between PCA components and weights of the logistic regression model.

TABLE 46
Top 50 high effect genes identified using an effect size
threshold of 0.3 and contributing 20% of total PTB model
weight. Genes are sorted by total weight in the model.
Top 50 genes contribute to 20% of total model weight.
#	Gene	Weight
1	EGFL7	0.03915196
2	FAM65C	0.03236397
3	FAM212A	0.03105369
4	RNF8	0.02983798
5	EPHX2	0.02916541
6	SPCS2	0.02810884
7	ACOT8	0.02800098
8	RPS19BP1	0.02520334
9	SMIM12	0.0245331
10	TNFSF13	0.0243419
11	SF3A2	0.02431467
12	TRPM6	0.02420862
13	C20orf96	0.02384787
14	C1orf43	0.02382509
15	SGMS1	0.02375853
16	CCDC28B	0.02329786
17	DOLPP1	0.0223773
18	TNFAIP8L1	0.0218296
19	TRIP10	0.02178185
20	SMIM1	0.02162177
21	RER1	0.02157154
22	ZNF429	0.02134285
23	TATDN2	0.02073552
24	FBXO18	0.02071262
25	DNMT3B	0.02065702
26	VPS28	0.02052528
27	FAM189B	0.02015087
28	BCL7B	0.01989426
29	OBSL1	0.01979065
30	HERC6	0.01978811
31	MYEF2	0.01938121
32	APOC1	0.01933969
33	TRA2B	0.01901918
34	ARAF	0.01895693
35	FGA	0.01895179
36	RNF181	0.01877974
37	SERPINH1	0.01844746
38	MAPK13	0.01829422
39	RALY	0.01829161
40	RAB11FIP3	0.01819169
41	NQO1	0.01815695
42	ULK3	0.01806994
43	C8orf76	0.01794826
44	C1orf174	0.01780182
45	BEND7	0.01764843
46	AP1B1	0.01759565
47	TRNAU1AP	0.01749675
48	ING2	0.01749674
49	CHMP5	0.01733394
50	SRSF3	0.01723014

TABLE 47
Remaining 787 high effect genes identified using
an effect size threshold of 0.3 and contributing
the remaining 80% of PTB model weight
#	Gene	Weight
1	HEXIM1	0.01721642
2	IFI44	0.01721479
3	PIAS4	0.01712305
4	SLC31A1	0.01692751
5	ZDHHC12	0.01663261
6	GTF2H5	0.01655058
7	PAQR7	0.01628653
8	UFD1L	0.01623378
9	RFESD	0.01622693
10	CDK16	0.01605331
11	XPNPEP3	0.01599098
12	SLC3A2	0.01592603
13	ENSG00000281457	0.01589179
14	FGFR1OP	0.01573999
15	MBIP	0.01572768
16	CNTROB	0.01568919
17	EPSTI1	0.01554056
18	ANKRD9	0.01553828
19	C11orf68	0.01553649
20	PANX2	0.01550303
21	KLC3	0.01542868
22	RHOF	0.01542195
23	SURF4	0.01521329
24	STUB1	0.01517591
25	C12orf57	0.01515882
26	ZC3H4	0.01506663
27	SURF1	0.01501501
28	FABP1	0.01491422
29	NMI	0.01490726
30	TNNI3	0.01465785
31	PRG4	0.01450515
32	CYP 20.00	0.01438684
33	APOH	0.01435591
34	MRVI1	0.01431809
35	CDH5	0.01423431
36	BSDC1	0.01422665
37	SNED1	0.01412338
38	ZNF470	0.01407822
39	SEMA3D	0.0140655
40	KATNA1	0.01406457
41	UCK1	0.01398802
42	NEUROD2	0.0139867
43	LZTS2	0.01388412
44	TDRKH	0.0138581
45	TRMT2B	0.01377213
46	ZNF738	0.01375493
47	FHOD1	0.01368045
48	RSAD2	0.01365854
49	ZNF235	0.01362804
50	MYSM1	0.01360496
51	ALB	0.01360188
52	NDUFB7	0.01347576
53	HEXA	0.01341841
54	RNF7	0.01333575
55	MT-TI	0.01330716
56	TCEA2	0.01326231
57	GATA2	0.01325527
58	TOR1A	0.0131401
59	CLP 1	0.01313316
60	PLPP3	0.01308848
61	NFE2	0.0130462
62	FAM212B	0.01288717
63	PLB1	0.01282596
64	TMEM126B	0.01276746
65	ZNF316	0.01269329
66	TMEM173	0.01267247
67	PFKP	0.01259505
68	SLC35A5	0.01246928
69	SHARPIN	0.01239333
70	ZBED5	0.01238414
71	MPST	0.0123601
72	INHBA	0.01234872
73	ZNF426	0.01226576
74	FRRS1	0.01224469
75	PTGIR	0.01215383
76	RERE	0.01208942
77	CHADL	0.01204215
78	GALNT14	0.01201084
79	RNF103	0.01200383
80	RFX1	0.0120024
81	MT-TR	0.01199505
82	TSTA3	0.01194721
83	TCEAL8	0.01192295
84	GPS2	0.01189976
85	ADGRG1	0.01189662
86	ZNF688	0.01185935
87	C16orf45	0.01185113
88	PTS	0.01178986
89	APOB	0.0117698
90	NDUFB6	0.01173206
91	TMEM241	0.01170914
92	TCTA	0.0116774
93	DCTN3	0.01166422
94	DPPA4	0.01166093
95	WBP4	0.01162894
96	SNX8	0.01162428
97	SPTB	0.01161443
98	APBB1	0.01160381
99	CACTIN	0.01157742
100	ABCB6	0.01152498
101	SKI	0.01151656
102	BAHCC1	0.01148244
103	MAFK	0.01141461
104	ORAI2	0.01130337
105	ENG	0.01126375
106	CLPTM1L	0.01125244
107	EPHB1	0.01120639
108	MT-TV	0.01118425
109	COL9A3	0.01115156
110	FAM98C	0.011115
111	CHCHD2	0.01108176
112	PSRC1	0.01108028
113	RPTOR	0.01106756
114	AP5S1	0.01106511
115	BPI	0.01104209
116	BAX	0.01092365
117	FKBP8	0.01087398
118	RMND5B	0.01083154
119	RITA1	0.01080038
120	PFN2	0.01074414
121	C14orf37	0.01073079
122	SCPEP1	0.01072412
123	GLMP	0.01069927
124	LRRC23	0.01069669
125	HHEX	0.01069015
126	ZNF790	0.01066268
127	PIH1D1	0.01063902
128	OIT3	0.01059278
129	USP20	0.01056321
130	WDR48	0.01054698
131	BAG5	0.01053765
132	MRPL41	0.01051548
133	TACC3	0.01050731
134	EBF1	0.01049728
135	GLTSCR1	0.01048172
136	CHMP6	0.0104744
137	LRP3	0.01046161
138	MT-TL2	0.01040473
139	JAG1	0.01037697
140	ZNF577	0.01030925
141	UBA3	0.01029964
142	ANKRD6	0.01027499
143	EBAG9	0.01027133
144	CDC37	0.01021894
145	TCEAL9	0.01019624
146	NUCKS1	0.01017028
147	LRIG2	0.01016899
148	TNNT1	0.01012428
149	SPSB1	0.01005599
150	CDC25A	0.0099944
151	FAM174A	0.00991168
152	CH507-9B2.3	0.00988169
153	SNUPN	0.00982907
154	ARL5B	0.00979701
155	ASB16-AS1	0.00976137
156	ACSL5	0.00974051
157	SF3B6	0.00972095
158	NDUFAF5	0.00970246
159	RHAG	0.00969147
160	RILP	0.00965655
161	WDR34	0.00964694
162	MRPL49	0.00955667
163	PNRC2	0.00950779
164	MAP3K9	0.00950116
165	ATG9A	0.00949969
166	ATN1	0.00945919
167	PRDM8	0.00945394
168	SYT11	0.00944026
169	ADH4	0.0094169
170	BAIAP2-AS1	0.00936576
171	SLC35B2	0.00934654
172	BCORL1	0.00934404
173	ZNF281	0.00928822
174	MT-TS2	0.00927669
175	IFNLR1	0.00927275
176	CD163	0.0092677
177	PGP	0.00926172
178	GNG7	0.00921657
179	CSRP1	0.00919699
180	C6orf106	0.009185
181	CASP9	0.00918328
182	ATP5S	0.00918088
183	RRNAD1	0.00917771
184	ZNF221	0.00913142
185	ACOX1	0.00910253
186	SNX12	0.00909081
187	PIGQ	0.00907831
188	SIRT3	0.00896525
189	CCR7	0.0089525
190	RBM25	0.00894769
191	NIT2	0.00894521
192	PTMS	0.00893852
193	ZNF563	0.00889911
194	TRMT1	0.00889782
195	RBM17	0.00889295
196	B3GNT2	0.00887035
197	SH2D4A	0.00886797
198	ZNF205	0.00884385
199	HPD	0.0088162
200	RTFDC1	0.00880671
201	ZNF267	0.00876904
202	DLG3	0.00876036
203	SRSF4	0.00872258
204	UPP1	0.00871042
205	TNFRSF10A	0.00868123
206	ZNF862	0.00867379
207	SRBD1	0.00866858
208	SCRIB	0.00861318
209	WASL	0.0085974
210	LIMA1	0.00857368
211	SUMF1	0.00856865
212	PHF13	0.00852661
213	KMT5B	0.00847853
214	ZNF783	0.00842612
215	ZNF668	0.00839873
216	NINL	0.00835549
217	REXO1	0.00835175
218	EXTL3	0.00834063
219	FBXW4	0.00832495
220	PCYT2	0.00831598
221	NMT2	0.00828096
222	F2RL3	0.00826484
223	ARHGEF5	0.00825034
224	ZFPM1	0.00819933
225	FAM134A	0.00814859
226	CNPPD1	0.00814028
227	MUC3A	0.0081174
228	ZNF76	0.00810961
229	DONSON	0.00808845
230	ZNF35	0.00806021
231	SOCS4	0.00797538
232	ACADVL	0.00795214
233	914K2A	0.00792301
234	HJURP	0.00791244
235	RHOC	0.00789077
236	AK1	0.00783309
237	HIP1R	0.00779878
238	VPS39	0.00779387
239	ZSCAN29	0.0077435
240	KCNH2	0.00769522
241	IQGAP3	0.00768821
242	PAIP2B	0.00768409
243	KCNK6	0.00767881
244	PDRG1	0.00767842
245	TRAPPC3	0.00766951
246	HMGN3	0.00766543
247	CIRBP	0.00762058
248	EAPP	0.00761623
249	HBD	0.00757263
250	GARNL3	0.00756375
251	ZNF71	0.00749732
252	TRIM3	0.00749069
253	FBXW5	0.00747122
254	TRAPPC2B	0.00746991
255	FAM103A1	0.00745236
256	VSIG10	0.00743924
257	SNW1	0.00743495
258	ST14	0.00742482
259	PPP1R35	0.00737414
260	CWC15	0.00736713
261	DNAAF3	0.00733761
262	CDH1	0.00733675
263	PSMA7	0.00733262
264	TOP 1.00	0.00721997
265	IGHV3-30	0.00719987
266	KATNB1	0.0071801
267	ENTPD7	0.00717934
268	TBC1D10B	0.00717475
269	CRACR2B	0.00716528
270	CAPN10	0.00713475
271	HERC2	0.00708978
272	CTC1	0.00701121
273	ELMSAN1	0.00700645
274	KCNQ4	0.00698507
275	TONSL	0.00698371
276	PELP1	0.00695813
277	ZNHIT3	0.00695297
278	TRAM2	0.00693132
279	SRSF10	0.00687069
280	ANP32B	0.00686986
281	SAMD12	0.00684181
282	KIN	0.00683122
283	ZNF257	0.00681605
284	ATP6V0D1	0.00680417
285	CKAP2L	0.00680053
286	TSPYL4	0.0067654
287	EIF1AD	0.00675332
288	ZNF518B	0.00675167
289	HNRNPL	0.00674865
290	TNPO2	0.00672039
291	MIER3	0.00671229
292	C21orf2	0.00669982
293	CNTNAP2	0.00665981
294	SYNE3	0.00662893
295	RACGAP1	0.00662596
296	PEX16	0.00661942
297	GPANK1	0.00661331
298	SRGAP2C	0.00660625
299	IRF2BP1	0.00659663
300	GFER	0.00655544
301	EPS8L2	0.00653381
302	CBX4	0.00647188
303	PPP1R26	0.00644835
304	PIK3R6	0.00642804
305	IFT122	0.00642399
306	MRPL22	0.00638506
307	PDAP1	0.00638494
308	TTN	0.00638015
309	GABBR1	0.00637569
310	LRRC59	0.00635053
311	CAD	0.00634658
312	ABHD15	0.00632624
313	P4HB	0.00631207
314	PATL1	0.00630895
315	DCUN1D2	0.00630072
316	ZNF394	0.00629403
317	MORC2	0.00628119
318	HIST1H2BB	0.00626976
319	ZCCHC6	0.00625588
320	P2RX5	0.00625104
321	DNAJB5	0.00624363
322	ZNF629	0.00623278
323	PTDSS2	0.00623102
324	CCL3L3	0.00620529
325	RRBP1	0.00618936
326	RAB24	0.00616838
327	UXT	0.00614935
328	NFATC1	0.00614695
329	ZCWPW1	0.00612475
330	ZNF678	0.00609963
331	ADAM12	0.00607422
332	WDR53	0.00599808
333	CD19	0.00598854
334	SMYD5	0.00598828
335	FAM214B	0.00597508
336	CDC42SE1	0.0059579
337	SLX4	0.00595597
338	NEMP1	0.00595561
339	HMGB2	0.00592168
340	MRI1	0.00588256
341	NAT6	0.00586786
342	XRCC1	0.00585168
343	IRF9	0.00583976
344	OSGIN2	0.00583503
345	MRNIP	0.00582855
346	RSRC2	0.0058153
347	ZNF598	0.00577474
348	PIK3IP1	0.00575823
349	KIAA0922	0.00571143
350	MRPL28	0.00567637
351	ZNF326	0.00566734
352	PDSS2	0.00566216
353	ZC3H12A	0.00565495
354	MORN3	0.0056501
355	RNF31	0.00561533
356	KIAA1147	0.00560077
357	CLCN7	0.00558628
358	EVPL	0.00557115
359	CTSL	0.00556813
360	HP	0.00556605
361	HSPA1L	0.00555607
362	EMILIN1	0.00551661
363	TSC22D4	0.00548898
364	ORM1	0.00548706
365	RASAL2-AS1	0.00546787
366	APEX2	0.00546566
367	CENPP	0.00543941
368	C7orf50	0.00543674
369	MICAL3	0.00542727
370	SNAPC4	0.00542409
371	ZBTB39	0.00539849
372	SELENOP	0.00539036
373	TBC1D25	0.00538649
374	WDR73	0.00538553
375	NPIPA5	0.0053847
376	PARP6	0.0053542
377	AHDC1	0.0053378
378	PATJ	0.00533587
379	DHX37	0.00533578
380	PPID	0.00531605
381	SMIM24	0.00531315
382	ANKRD45	0.0053085
383	TAF3	0.00528601
384	POLM	0.0052713
385	DNAJB2	0.00525996
386	GFAP	0.00524745
387	TOR1AIP2	0.00522342
388	MICALL2	0.00520235
389	GINS2	0.00516785
390	CRHBP	0.00516767
391	MTIF2	0.00514099
392	TRAF1	0.00513172
393	HTRA2	0.0051272
394	DUSP3	0.00511558
395	NET1	0.00509752
396	MEIS2	0.00508531
397	ATG4D	0.00503696
398	CDADC1	0.00503346
399	FBRSL1	0.00500885
400	SWSAP1	0.00500631
401	MTRNR2L8	0.00498493
402	FTCDNL1	0.00498196
403	PTGDS	0.0049811
404	ST3GAL1	0.00496821
405	TRIM10	0.00496727
406	NECTIN1	0.00494824
407	NUF2	0.00494803
408	SH3PXD2B	0.00487005
409	HNRNPH3	0.00485432
410	TNFRSF21	0.00485095
411	FBXL19	0.00482935
412	C3orf38	0.00482822
413	ERLEC1	0.00481757
414	RAPGEF6	0.00481753
415	FAM134B	0.00476877
416	NEK2	0.00476605
417	PIGC	0.00474254
418	HDAC10	0.00467651
419	RETN	0.00467019
420	AUNIP	0.00465792
421	CLSPN	0.00463933
422	SMC3	0.00463566
423	TICRR	0.00462759
424	BCAR1	0.00455823
425	TNK2	0.00451586
426	NLRC3	0.00450598
427	PGRMC2	0.0044856
428	ITPKB	0.00448118
429	GAS8	0.00447802
430	MFAP1	0.00445902
431	KIAA1549	0.00445435
432	STK36	0.0044393
433	MSANTD2	0.00440631
434	MID1IP1	0.00439898
435	HLA-DQA2	0.00438787
436	KIAA0232	0.00438699
437	ZCCHC3	0.0043752
438	ZDHHC5	0.00436213
439	TCEAL1	0.00436064
440	MCM7	0.00434985
441	ZYG11B	0.00432486
442	HIST1H2BL	0.00430363
443	EMC7	0.0042997
444	SOX12	0.00426019
445	PSMC1	0.00425978
446	PSENEN	0.00424307
447	FGFR1	0.00422946
448	CIR1	0.00419353
449	PLTP	0.00418576
450	CCNB2	0.00416864
451	DOK1	0.00415016
452	RNF145	0.00415008
453	TBC1D22A	0.00411891
454	PLIN2	0.00408977
455	P2RY8	0.00405717
456	ROMO1	0.00403507
457	HIST1H3F	0.00403297
458	MAD1L1	0.00402509
459	DMTF1	0.0040051
460	LONP1	0.00399071
461	CMBL	0.0039846
462	METAP2	0.00398148
463	BDH1	0.00397872
464	CEP95	0.00397779
465	SYS1	0.00397486
466	BCDIN3D	0.0039398
467	NDC80	0.00391798
468	SLC35F5	0.00390787
469	ZNHIT6	0.00390234
470	BNIP1	0.00390142
471	PLIN3	0.00390095
472	CHMP4A	0.00389975
473	SPHK2	0.00389825
474	RALA	0.00387198
475	POMC	0.00384375
476	FXR2	0.00383397
477	RRP15	0.00379515
478	CNPY3	0.00379038
479	FASTKD3	0.00378887
480	RABL3	0.00376548
481	SLC39A13	0.00374723
482	ZBTB5	0.00374536
483	SLC7A6OS	0.0037395
484	SNX21	0.00373102
485	FAM171A1	0.00372713
486	EHMT2	0.00367873
487	GTPBP6	0.00367428
488	44258	0.00366069
489	SCAF1	0.00365522
490	ALDH18A1	0.00365454
491	RABL2B	0.00364771
492	PCGF3	0.00364631
493	FBRS	0.00364104
494	SFMBT1	0.00363168
495	ZBTB41	0.00362658
496	TMF1	0.00361566
497	IRAK1BP1	0.00361537
498	ZNF550	0.00359616
499	RNF26	0.00356074
500	ATRN	0.0035562
501	POLDIP3	0.00353106
502	FAM32A	0.0035253
503	RBM19	0.00349255
504	PLEKHA7	0.00349242
505	BRF1	0.00349014
506	EFTUD2	0.00348959
507	ZDHHC13	0.00348433
508	AKAP9	0.00346468
509	DDRGK1	0.00338493
510	ZBTB17	0.00338478
511	C19orf43	0.00336635
512	SUGP2	0.00334684
513	CHID1	0.00331867
514	MKL1	0.00330825
515	IGLC3	0.00326331
516	HOXB3	0.00325705
517	PSMG1	0.00325184
518	TRMT13	0.00324839
519	GOLGA2	0.00324633
520	RNASE3	0.00323686
521	AXIN2	0.00323191
522	GPAA1	0.00322351
523	ZNF317	0.00321854
524	HIST1H2AD	0.00320508
525	WRAP73	0.00320307
526	NOD1	0.00319479
527	HMGXB4	0.00318399
528	ABL2	0.00314609
529	SYNGAP1	0.00312749
530	TSPAN31	0.00306728
531	SLU7	0.0030589
532	SPRED2	0.00302972
533	FBXL15	0.00302544
534	DNAJC14	0.00301706
535	MAZ	0.00301373
536	AKT1	0.00300904
537	EPS8L1	0.00298856
538	ESPL1	0.00298083
539	FAM50B	0.00297548
540	RLIM	0.00296119
541	SYMPK	0.00294351
542	DNHD1	0.00293687
543	SDF2	0.00293563
544	DUSP23	0.00292554
545	C2CD2L	0.0029136
546	WHSC1	0.00290877
547	NSRP1	0.00290313
548	TSHZ2	0.00288423
549	HIC1	0.00287728
550	PLXNB2	0.0028503
551	FOLR3	0.00283506
552	CTB-50L17.10	0.0028331
553	ZRSR2	0.0028224
554	APBA2	0.00281752
555	FEN1	0.00281398
556	MAGEE1	0.00281389
557	KLF16	0.0028058
558	EPB41L5	0.00279834
559	PPP4C	0.00274163
560	DCUN1D3	0.00273349
561	GSDMB	0.0027255
562	AMY2B	0.00271999
563	FLT3	0.00271279
564	MUT	0.00269531
565	FAM107B	0.00269214
566	CCDC88C	0.00267412
567	PPP1R12C	0.00266498
568	NAV2	0.00264828
569	SH3GL1	0.00264045
570	CEP83	0.00263927
571	RANGAP1	0.00262376
572	SIRT6	0.00262223
573	SREK1	0.00261003
574	CDCA2	0.00258655
575	KAT2A	0.00258023
576	NUDCD3	0.00255822
577	CSF1	0.00254994
578	ZNF865	0.00253668
579	TOB1	0.00251809
580	BET1L	0.00251733
581	GJA4	0.00251321
582	C11orf95	0.0024976
583	ZNF182	0.00249399
584	COQ5	0.00247868
585	HIST1H4B	0.00247098
586	MR1	0.00247081
587	MYO5A	0.00246957
588	DTX2P1-UPK3BP1-	0.00243386
	PMS2P11
589	GFOD1	0.00241489
590	RINL	0.00241422
591	ING1	0.00241211
592	SMARCC2	0.0023985
593	ZBTB7A	0.00238074
594	MYCN	0.00236136
595	SHQ1	0.00235142
596	CCDC3	0.00234966
597	PDE2A	0.00234651
598	ERCC6L	0.00233006
599	DPH1	0.00231002
600	NFKBIA	0.0022911
601	RP5-862P8.2	0.00227093
602	ZDHHC6	0.00225623
603	ZNF432	0.00225097
604	CEP104	0.00224807
605	ARRDC4	0.00224182
606	H1FX	0.00223116
607	LMBR1L	0.00222269
608	USP8	0.0021974
609	MED9	0.00219293
610	TDP2	0.00217073
611	DNTTIP1	0.00216686
612	RILPL2	0.00214484
613	SH3BP5	0.00214274
614	MYO7A	0.00212784
615	NCOR2	0.00212433
616	GTPBP8	0.00212003
617	FO538757.1	0.00211862
618	CXXC1	0.00211442
619	AKAP8	0.00211194
620	ZNRF1	0.00210383
621	ULK1	0.0020961
622	AVEN	0.00209074
623	ABCC10	0.00207338
624	HIST2H2AC	0.00203952
625	FAN1	0.00203669
626	OSBP	0.00202982
627	GOLM1	0.00202069
628	P3H1	0.00201862
629	CCDC71	0.00201133
630	RPUSD1	0.00200975
631	LZTR1	0.00197951
632	NAPRT	0.00196389
633	EPN1	0.00196033
634	LTB4R	0.00194123
635	PNKP	0.0019049
636	ZNF264	0.00189308
637	GTSE1	0.00188309
638	HIST1H2AL	0.00188158
639	IGLV1-47	0.00184976
640	NAIF1	0.00184679
641	TLE1	0.00183477
642	CCDC96	0.00182908
643	TFR2	0.00181797
644	YTHDC1	0.00181123
645	HDX	0.00178841
646	TAPT1	0.00178501
647	SPA17	0.00177161
648	FAM9C	0.00176343
649	FAM43A	0.0017418
650	ANKLE2	0.00173128
651	ZNF496	0.00171209
652	PARD6B	0.00170735
653	AKAP8L	0.00169481
654	LIAS	0.00166417
655	DBF4B	0.00165354
656	PLK1	0.00165293
657	RAB3IL1	0.00163743
658	OGG1	0.00162467
659	FOXM1	0.00161892
660	MT-RNR2	0.00160061
661	GPIHBP1	0.00158073
662	FOXO1	0.00157252
663	ITGA9	0.00156769
664	SDF4	0.00155878
665	KLC2	0.00154916
666	ANXA4	0.00153646
667	CCHCR1	0.00152904
668	ZNF282	0.00151814
669	TSPYL1	0.00147807
670	BAP1	0.0014725
671	BBS10	0.00146978
672	ZBTB48	0.00145997
673	BRD9	0.00145826
674	NLRX1	0.00142502
675	YDJC	0.00141928
676	ZBTB7B	0.00141311
677	BRD1	0.00140997
678	MNS1	0.00140356
679	ABCD4	0.00139032
680	MEX3C	0.00138039
681	ZNF219	0.00137284
682	CCDC12	0.00136843
683	SPATA2	0.00136746
684	ZNF528	0.00135979
685	SH3PXD2A	0.00135844
686	OLFML2B	0.00133113
687	C2orf49	0.00127454
688	HMGN2	0.00125333
689	POLE3	0.0012327
690	MDM4	0.00119826
691	INMT	0.00117138
692	MAN2C1	0.00114471
693	PPARA	0.00113824
694	BPNT1	0.0011324
695	IRS2	0.00112693
696	TBC1D13	0.00109838
697	SYF2	0.00109755
698	RAPGEF3	0.00108811
699	RPL41	0.00108174
700	TMEM259	0.00108088
701	CDK10	0.00107791
702	ZNF420	0.00107789
703	JAGN1	0.00107556
704	SPRTN	0.00106533
705	CD79B	0.00106206
706	B3GAT3	0.00106058
707	MYL4	0.00105931
708	TCN1	0.00103934
709	GNA12	0.00102483
710	EFNB2	0.00102043
711	OASL	0.00100613
712	SLC22A4	0.0009892
713	TAF7	0.00096694
714	ECHDC2	0.00095397
715	CENPB	0.0009517
716	C15orf57	0.00094717
717	PLCB3	0.00093872
718	SYVN1	0.00092311
719	TRIM62	0.00091832
720	SMG9	0.00090996
721	SCAPER	0.00090709
722	DMPK	0.00089951
723	DGKQ	0.00089441
724	NOC2L	0.00088618
725	ZNF341	0.0008737
726	HDAC1	0.000863
727	MZF1	0.00086231
728	NT5C3B	0.00085006
729	GCHFR	0.0008309
730	RALB	0.00082971
731	TSGA10	0.00082398
732	PPP6R1	0.00082136
733	NBPF20	0.00081391
734	ZNF595	0.00081372
735	MROH1	0.00081248
736	PPAT	0.00081043
737	KDM2B	0.00080194
738	CRISP3	0.00080069
739	ZNF70	0.00077202
740	PLP2	0.00076753
741	IFT57	0.00075833
742	HBQ1	0.00073992
743	ZBTB4	0.00072527
744	ASF1B	0.0006931
745	GNE	0.00067357
746	ODF3B	0.00067249
747	FAM184A	0.00066331
748	PDE12	0.00064095
749	IL3RA	0.00063461
750	DIXDC1	0.00060502
751	ANP32A	0.00059486
752	MAP3K12	0.00059293
753	GOLGB1	0.00058282
754	PPP4R2	0.00057197
755	ENPP2	0.000558
756	RPH3AL	0.00055265
757	ZNF791	0.00053816
758	NPIPB4	0.00050393
759	ZNF615	0.00048048
760	CHAC2	0.00046328
761	DDX43	0.00046102
762	GMPPB	0.0004581
763	TNRC6A	0.00045704
764	LENG1	0.00045275
765	TMEM218	0.00045032
766	FUT4	0.00043039
767	PRKCE	0.00033648
768	TMA7	0.00033279
769	BTBD6	0.00031161
770	ZFP30	0.00028603
771	ATXN7L3	0.00028551
772	FLVCR2	0.00028409
773	P4HA2	0.00028193
774	IP6K2	0.00027222
775	CTSG	0.00025912
776	TMEM14A	0.00024798
777	RNF157	0.0002095
778	ECD	0.00020545
779	KIF20A	0.00018898
780	MXD3	0.00018339
781	SLC39A7	0.00017198
782	ZNF787	0.00012374
783	DUS3L	5.1952E−05
784	ALG3	3.8399E−05
785	BCKDHB	2.9225E−05
786	CLN5	2.2305E−05
787	DLGAP4	5.8398E−06

While preferred embodiments of the present invention have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. It is not intended that the invention be limited by the specific examples provided within the specification. While the invention has been described with reference to the aforementioned specification, the descriptions and illustrations of the embodiments herein are not meant to be construed in a limiting sense. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the invention. Furthermore, it shall be understood that all aspects of the invention are not limited to the specific depictions, configurations or relative proportions set forth herein which depend upon a variety of conditions and variables. It should be understood that various alternatives to the embodiments of the invention described herein may be employed in practicing the invention. It is therefore contemplated that the invention shall also cover any such alternatives, modifications, variations or equivalents. It is intended that the following claims define the scope of the invention and that methods and structures within the scope of these claims and their equivalents be covered thereby.

Claims

1.-191. (canceled)

192. A method comprising: (a) assaying a cell-free blood sample of a pregnant subject to determine at least one expression level of at least one pregnancy-associated gene, wherein said at least one pregnancy-associated gene is differentially expressed in a first population of subjects having a pregnancy-related hypertensive disorder as compared to a second population of subjects not having said pregnancy-related hypertensive disorder;(b) computer processing said at least one expression level of said at least one pregnancy-associated gene determined in (a) (i) against at least one reference expression level of said at least one pregnancy-associated gene or (ii) with a trained machine learning algorithm;(c) determining, based at least in part on said computer processing in (b), that said pregnant subject has an elevated risk of having said pregnancy-related hypertensive disorder; and(d) based at least in part on said determining in (c), providing a treatment plan to said pregnant subject for said elevated risk of having said pregnancy-related hypertensive disorder.

193. The method of claim 192, wherein said treatment plan comprises a prophylactic intervention that reduces said elevated risk of having said pregnancy-related hypertensive disorder.

194. The method of claim 192, wherein said prophylactic intervention comprises providing medical monitoring to said pregnant subject.

195. The method of claim 194, wherein said medical monitoring comprises monitoring a blood pressure of said pregnant subject.

196. The method of claim 192, wherein said prophylactic intervention comprises providing a nutritional supplement to said pregnant subject.

197. The method of claim 196, wherein said nutritional supplement comprises calcium, vitamin D, vitamin B3, or docosahexaenoic acid (DHA).

198. The method of claim 192, wherein said prophylactic intervention comprises providing a lifestyle modification to said pregnant subject.

199. The method of claim 198, wherein said lifestyle modification comprises an exercise regimen, nutrition counseling, meditation, stress relief, weight loss or maintenance, or improving sleep quality.

200. The method of claim 192, further comprising performing a liver or renal dysfunction test on said pregnant subject.

201. The method of claim 192, wherein said treatment plan comprises a therapeutic intervention for said pregnancy-related hypertensive disorder or said elevated risk of having said pregnancy-related hypertensive disorder.

202. The method of claim 201, wherein said therapeutic intervention comprises administering a drug to said pregnant subject.

203. The method of claim 202, wherein said drug is selected from the group consisting of an antihypertensive drug, aspirin, progesterone, a corticosteroid, an antibiotic, a tocolytic drug, a cyclo-oxygenase inhibitor, an oxytocin antagonist, a betamimetic drug, magnesium sulfate, magnesium chloride, and magnesium oxide.

204. The method of claim 202, wherein said drug is selected from the group consisting of a cholesterol medication, a heartburn medication, an angiotensin II receptor antagonist, a calcium channel blocker, a diabetes medication, metformin, and an erectile dysfunction medication.

205. The method of claim 192, wherein (c) further comprises determining that said pregnant subject has an elevated risk of having a molecular subtype of said pregnancy-related hypertensive disorder, and wherein (d) further comprises providing said treatment plan to said pregnant subject for said molecular subtype of said pregnancy-related hypertensive disorder.

206. The method of claim 205, wherein said molecular subtype of said pregnancy-related hypertensive disorder is selected from the group consisting of: preeclampsia, mild preeclampsia, severe preeclampsia, preeclampsia determined at less than 34 weeks gestational age, preeclampsia determined at greater than 34 weeks gestational age, preeclampsia determined at less than 37 weeks gestational age, preeclampsia determined at greater than 37 weeks gestational age, preeclampsia with clinical indication of delivery at less than 34 weeks gestational age, preeclampsia with clinical indication of delivery at greater than 34 weeks gestational age, preeclampsia with clinical indication of delivery at less than 37 weeks gestational age, preeclampsia with clinical indication of delivery at greater than 37 weeks gestational age, eclampsia, chronic or pre-existing hypertension, gestational hypertension, and HELLP (hemolysis, elevated liver enzymes, and low platelets) syndrome.

207. The method of claim 206, wherein said molecular subtype of said pregnancy-related hypertensive disorder is preeclampsia.

208. The method of claim 192, wherein (a) further comprises determining at least one RNA level of said at least one pregnancy-associated gene, and wherein (b) further comprises computer processing said at least one RNA level of said at least one pregnancy-associated gene.

209. The method of claim 208, wherein (a) further comprises reverse transcribing ribonucleic acid (RNA) molecules from said cell-free blood sample to produce complementary deoxyribonucleic acid (cDNA) molecules; and assaying said cDNA molecules to determine said at least one RNA level of said at least one pregnancy-associated gene.

210. The method of claim 208, wherein said assaying further comprises nucleic acid sequencing.

211. The method of claim 208, wherein said assaying further comprises array hybridization.

212. The method of claim 208, wherein said assaying further comprises polymerase chain reaction (PCR).

213. The method of claim 212, wherein said PCR comprises digital PCR or digital droplet PCR.

214. The method of claim 208, wherein (a) further comprises selectively enriching nucleic acid molecules from said cell-free blood sample.

215. The method of claim 208, wherein (a) further comprises assaying nucleic acid molecules from said cell-free blood sample without selectively enriching said nucleic acid molecules.

216. The method of claim 192, wherein said cell-free blood sample comprises a plasma sample.

217. The method of claim 192, wherein said pregnant subject is asymptomatic for said pregnancy-related hypertensive disorder.

218. The method of claim 192, wherein said computer processing in (b) comprises said trained machine learning algorithm.

219. The method of claim 218, wherein said trained machine learning algorithm is selected from the group consisting of a linear regression, a logistic regression, an analysis of variance (ANOVA) model, a deep learning algorithm, a support vector machine (SVM), a neural network, a Random Forest, and a combination thereof.

220. The method of claim 192, further comprising monitoring said pregnant subject for risk of having said pregnancy-related hypertensive disorder, wherein said monitoring comprises determining whether said pregnant subject has an elevated risk of having said pregnancy-related hypertensive disorder at each of a plurality of time points.

221. The method of claim 220, wherein a difference in said determining whether said pregnant subject has said elevated risk of having said pregnancy-related hypertensive disorder at each of said plurality of time points is indicative of one or more clinical indications selected from the group consisting of: (i) a diagnosis of said pregnancy-related hypertensive disorder of said pregnant subject, (ii) a prognosis of said pregnancy-related hypertensive disorder of said pregnant subject, (iii) an efficacy or non-efficacy of a therapeutic intervention for treating said pregnancy-related hypertensive disorder of said pregnant subject, and (iv) an efficacy or non-efficacy of a prophylactic intervention for reducing said elevated risk of having said pregnancy-related hypertensive disorder of said pregnant subject.