Patent Application
20080176237
This invention relates generally to the isolation of fetal nucleic acid and prenatal screening or testing of genetic and chromosomal abnormalities.
Prenatal testing or screening is usually performed to determine the gender of the fetus or to detect genetic disorders and/or chromosomal abnormalities in the fetus during pregnancy. As of today, over 4000 genetic disorders, caused by one or more faulty genes, have been recognized. Some examples include Cystic Fibrosis, Huntington's Disease, Beta Thalassaemia, Myotonic Dystrophy, Sickle Cell Anemia, Porphyria, and Fragile-X-Syndrome. Chromosomal abnormality is caused by aberrations in chromosome numbers, duplication or absence of chromosomal material, and by defects in chromosome structure. Some examples of chromosomal abnormalities are trisomies, namely trisomy 16, a major cause of miscarriage in the first trimester, trisomy 21 (Down syndrome), trisomy 13 (Patau syndrome), trisomy 18 (Edwards syndrome), Klinefelter's syndrome (47, XXY), (47, XYY), and (47, XXX); the absence of chromosomes (monosomy), e.g., Turner syndrome (45, X0); chromosomal translocations, deletions and/or microdeletions, e.g., Robertsonian translocation, Angelman syndrome, DiGeorge syndrome and Wolf-Hirschhorn Syndrome.
Currently available prenatal genetic tests usually involve invasive procedures. For example, chorionic villous sampling (CVS) performed on a pregnant woman around 10-12 weeks into the pregnancy and amniocentesis performed at around 14-16 weeks all contain invasive procedures to obtain the sample for testing chromosomal abnormalities in a fetus. Fetal cells obtained via these sampling procedures are usually tested for chromosomal abnormalities using cytogenetic or fluorescent in situ hybridization (FISH) analyses.
While these procedures can be useful for detecting chromosomal aberrations, they have been shown to be associated with the risk of miscarriage. Therefore amniocentesis or CVS is only offered to women perceived to be at increased risk, including those of advanced maternal age (>35 years), those with abnormal maternal serum screening or those who have had a previous fetal chromosomal abnormality. As a result of these tests the percentage of women over the age of 35 who give birth to babies with chromosomal aberrations such as Down syndrome has drastically reduced. However, lack of appropriate or relatively safe prenatal testing or screening for the majority of pregnant women has resulted in about 80% of Down syndrome babies born to women under 35 years of age.
Thus there is a need for diagnostic screening tests for the general population of pregnant women, especially tests directed to identifying fetal chromosomal aberrations as well as other genetic variations or defects.
The present invention is based, in part, on the discovery that cervical mucous is a good natural reservoir for migrated placental cells, e.g., fetal cells as well as for isolating fetal nucleic acids. Accordingly the present invention provides methods and kits useful for testing or screening for genetic abnormalities in fetuses using fetal nucleic acids isolated from cervical mucus samples. In addition, the present invention provides primers and probes useful for nucleic acid amplification of, e.g. genetic markers, especially using relatively small size amplicons in fetal genetic screening.
In one embodiment of the invention, it provides a method for conducting a genetic test of a fetus. The method comprises isolating a nucleic acid sample from a cervical mucus sample obtained from a female subject containing the fetus, wherein the nucleic acid sample consists essentially of polynucleotides in a size ranging from about 50 base pairs to about 300 base pairs and wherein the result of a genetic test on the nucleic acid sample is indicative of a genetic composition of the fetus.
In another embodiment of the invention, it provides a method of isolating a fetal nucleic acid sample. The method comprises isolating a nucleic acid sample consisting essentially of polynucleotides of about 50 base pairs to about 300 base pairs in length from a cervical mucus sample obtained from a female subject containing the fetus.
In yet another embodiment of the invention, it provides a genetic testing kit suitable for testing the genetic composition of a fetus. The kit comprises a pair of primers suitable for amplifying a desired allele or genetic marker, wherein the amplified nucleotide fragment is less than about 200 base pairs and wherein the desired allele is not uniquely associated with the Y chromosome. In other embodiments, the kit comprises an isolated DNA sample from a cervical mucus sample obtained from a female subject containing the fetus. The DNA sample consists essentially of polynucleotides in a size ranging from about 50 base pairs to about 200 base pairs.
In still another embodiment of the invention, it provides an isolated DNA sample useful for genetic testing of a fetus. The DNA sample can be obtained by isolating DNA fragments in a size ranging from about 50 base pairs to about 200 base pairs from a cervical mucus sample obtained from a female subject containing the fetus.
It is the discovery of the present invention that cervical mucus samples can be a great source for fetal cells as well as fetal nucleic acids. Accordingly, the present invention provides methods, reagents and kits useful for testing or screening fetus for genetic abnormalities using nucleic acids isolated from cervical mucus samples.
In addition, the present invention provides primers and probes useful for nucleic acid amplification, e.g. of genetic markers, especially using relatively small size amplicons in fetal genetic screening.
According to one aspect of the present invention, it provides methods for conducting genetic tests of a fetus by isolating one or more nucleic acid samples from one or more cervical mucus samples obtained from a female subject containing the fetus. In general, the nucleic acid sample useful for the methods of the present invention can be a DNA sample, RNA sample, or a combination thereof including any DNA, cDNA, or RNA derived from one or more nucleic acid samples isolated from one or more cervical mucus samples.
In one embodiment, the nucleic acid sample useful for the methods of the present invention is a DNA sample. In another embodiment, the nucleic acid sample useful for the methods of the present invention is substantially free of proteins or polypeptides. In yet another embodiment, the nucleic acid sample useful for the methods of the present invention is isolated by any known or later discovered size fractionation method including, but not limited to, gel electrophoresis, capillary electrophoresis, size exclusion matrixes, and size fractionation columns.
In still another embodiment, the nucleic acid sample useful for the methods of the present invention is in a size range representative of, or substantially associated, with fetal nucleic acid. In still another embodiment, the nucleic acid sample useful for the methods of the present invention is in a size range substantially free of nucleic acid from the host of the fetus. For example, the nucleic acid sample useful for the methods of the present invention can be in a size range from about 50 to about 1000 base pairs, from about 50 to about 500 base pairs, from about 50 to about 400 base pairs, from about 50 to about 300 base pairs, from about 50 to about 250 base pairs, from about 50 to about 200 base pairs, from about 50 to about 150 base pairs, or from about 50 to about 100 base pairs or a combination thereof, and optionally, does not contain a substantial amount, e.g. more than 0.5%, 1%, 2%, 3%, 4%, or 5% of nucleic acids from any other size range or source.
According to the present invention, the nucleic acid sample useful for the methods of the present invention can be isolated from a cervical mucus sample from the host of a fetus, e.g., a pregnant woman. The cervical mucus sample of the present invention can be obtained from the host of a fetus, at any time during the pregnancy, for example, during the first or second trimester, by any means now known or later discovered in the art. In general, a cervical mucus sample, e.g., an endocervical mucus sample, can be obtained using techniques such as transcervical swabs, endocervical lavage, scrapes, cytobrush, aspiration, intrauterine lavage, or a combination thereof.
In one embodiment, the cervical mucus sample of the present invention is a fresh sample, e.g. without substantial preservation or processing. In another embodiment, the cervical mucus sample is a sample preserved from a fresh sample, e.g., preserved in a suitable aqueous preservation or transportation medium, or alternatively, a sample of a medium containing nucleic acids leached from one or more cervical mucus samples. Without being bound to any theory, it is believed that nucleic acid will diffuse out from the cervical mucus into a fluid that is in contact with the mucus. Fetal nucleic acid will thus be present both in the cervical mucus sample as well as in the media in which the sample is stored and/or transported. Accordingly, the nucleic acid sample useful for the methods of the present invention can be obtained directly from the cervical mucus sample, or from the medium, for example, preservation medium, transportation medium, or any aqueous medium, that is in contact with the cervical mucus. Examples of transportation media include, but are not limited to, any tissue culture medium known to one of skill in the art, e.g. RPMI-1640 medium. In yet another embodiment, the cervical mucus sample of the present invention is maintained or stored between about 4° C. and about 20° C., e.g., in a low calcium basal medium.
In still another embodiment, the cervical mucus sample of the present invention is a treated sample, e.g., a fresh sample or preserved sample treated with any suitable reagent(s) to facilitate mucous dissolution which in turn, assists in isolation of nucleic acid components from the sample. For example, the cervical mucus sample can be a sample treated with mucolytic agent(s) or mucinase(s), e.g. N-acetyl-L-cysteine, L-cysteine, dithiothreitol (DTT), brornhexine hydrochloride, and any of the hyaluronidases, including hyaluronate lyase, hyaluronoglucosarninidase, and hyaluronglucuronidase. In another example, the cervical mucus sample of the present invention is a sample treated with enzyme(s), e.g., sugar hydrolysis enzyme(s) such as P-galactosidase or invertase, or proteinase, or pepsin or combinations thereof. The cervical mucus sample may also be treated with chemicals known in the art to induce apoptosis to release fetal nucleic acid.
In another embodiment, the cervical mucus sample of the present invention is a sample treated to enrich fetal nucleic acid and/or reduce maternal nucleic acid content. For example, the cervical mucus sample can be treated to reduce or degrade any nucleic acid, e.g., DNA that is characteristic of maternal DNA. One of such nucleic acid is hypermethylated maternal DNA. Any means to reduce, degrade, or selectively remove hypermethylated maternal DNA can be used including, without any limitation, methylation specific restriction enzymes such as McrBC (BioLabs), antibodies specific for hypermethylated maternal DNA such as anti-5′-methyl-cytosine antibodies and/or anti-methylCpG binding protein-2 (MeCP2) antibodies, or ligands or proteins such as MeCP2 that specifically bind methylated CpG islands in maternal DNA.
Alternatively fetal nucleic acid can be enriched using markers specific for fetal nucleic acids. For example, hypomethylated maspin DNA can be used as a marker for fetal DNA. In one instance, one can treat total cervical mucous DNA with sodium bisulfite, which can induce chemical changes in the hypomethylated fetal DNA whereby unmethylated cytosine of fetal DNA is converted into uridine (U). Such change can be used to preferentially isolate or enrich fetal DNA, e.g., to preferentially amplify fetal DNA containing uridine(s) converted from cytosine(s).
According to the present invention, the nucleic acid sample of the present invention can be used to conduct genetic tests or screening of a fetus. In particular, the nucleic acid sample of the present invention can be used to test or screen the genetic composition of a fetus, e.g. chromosomal composition, gene composition, or genetic marker or finger printing pattern of a fetus. In one embodiment, testing or screening a genetic composition of a fetus includes probing for chromosomal abnormalities including, without any limitation, monosomy, partial monosomy, trisomy, partial trisomy, chromosomal translocation, chromosomal duplication, chromosomal deletion or microdeletion, and chromosomal inversion.
In general, the term “monosomy” refers to the presence of only one chromosome from a pair of chromosomes. Monosomy is a type of aneuploidy. Partial monosomy occurs when the long or short arm of a chromosome is missing. Common human genetic disorders arising from monosomy include: X0, only one X chromosome instead of the usual two (XX) seen in a normal female (also known as Turner syndrome); cri du chat syndrome, a partial monosomy caused by a deletion of the end of the short p (from the word petit, French for small) arm of chromosome 5; and 1p36 Deletion Syndrome, a partial monosomy caused by a deletion at the end of the short p arm of chromosome 1.
In contrast, the term “trisomy” refers to the presence of three, instead of the normal two, chromosomes of a particular numbered type in an organism. Thus the presence of an extra chromosome 21 is called trisomy 21. Most trisomies, like most other abnormalities in chromosome number, result in distinctive birth defects. Many trisomies result in miscarriage or death at an early age. A partial trisomy occurs when part of an extra chromosome is attached to one of the other chromosomes, or if one of the chromosomes has two copies of part of its chromosome. A mosaic trisomy is a condition where extra chromosomal material exists in only some of the organism's cells. While a trisomy can occur with any chromosome, few babies survive to birth with most trisomies. The most common types that survive without spontaneous abortion in humans include: Trisomy 21 (Down syndrome); Trisomy 18 (Edwards syndrome); Trisomy 13 (Patau syndrome); Trisomy 9; Trisomy 8 (Warkany syndrome 2); Trisomy 16 (which is the most common trisomy in humans, occurring in more than 1% of pregnancies. This condition, however, usually results in spontaneous miscarriage in the first trimester). Trisomy involving sex chromosomes include: XXX (Triple X syndrome); XXY (Klinefelter's syndrome); and XYY (XYY syndrome).
In another embodiment, testing or screening a genetic composition of a fetus includes probing for allele or gene abnormalities, e.g., one or more mutations such as point mutations, insertions, deletions in one or more genes.
In yet another embodiment, testing or screening a genetic composition of a fetus includes probing for one or more polymorphism patterns or genetic markers, e.g., short tandem repeat sequences (STRs), single nucleotide polymorphisms (SNPs), etc.
In still another embodiment, testing or screening a genetic composition of a fetus includes probing for any genetic abnormality corresponding to or associated with a condition or disorder, e.g. Cystic Fibrosis, Sickle-Cell Anemia, Phenylketonuria, Tay-Sachs Disease, Adrenal Hyperplasia, Fanconi Anemia, Spinal Muscularatrophy, Duchenne's Muscular Dystrophy, Huntington's Disease, Beta Thalassaemia, Myotonic Dystrophy, Fragile-X Syndrome, Down Syndrome, Edwards Syndrome, Patau Syndrome, Klinefelter's Syndrome, Triple X syndrome, XYY syndrome, Trisomy 8, Trisomy 16, Turner Syndrome, Robertsonian translocation, Angelman syndrome, DiGeorge Syndrome, Wolf-Hirschhom Syndrome, RhD Syndrome, Tuberous Sclerosis, Ataxia Telangieltasia, and Prader-Willi syndrome.
In still another embodiment, testing or screening a genetic composition of a fetus includes probing for any genetic abnormality that is not uniquely associated with Y chromosome.
In still another embodiment, testing or screening a genetic composition of a fetus includes probing for any genetic condition corresponding to or associated with gender or paternity of the fetus.
Usually genetic tests provided by the present invention use the nucleic acid sample of the present invention either directly or as templates for “amplification-based” genetic composition testing assays, including without any limitation, polymerase chain reaction (“PCR”), real-time polymerase chain reaction (“RT-PCR”), ligase chain reaction (“LCR”), self-sustained sequence replication (“3SR”) also known as nucleic acid sequence based amplification (“NASBA”), Q-B-Replicase amplification, rolling circle amplification (“RCA”), transcription mediated amplification (“TMA”), linker-aided DNA amplification (“LADA”), multiple displacement amplification (“MDA”), invader and strand displacement amplification (“SDA”). Amplification of a nucleotide fragment using a pair of primers specific for an allele indicates the presence of the allele.
In one embodiment, the “amplification-based” genetic composition testing assays of the present invention include using primers to generate amplicons less than about 200 base pairs, less than about 150 base pairs, or between about 75 to about 150 base pairs. Exemplary primers of the invention used in the amplification-based assays are provided herein. In one embodiment, the primers of the invention include, but are not limited to, the pairs of primers of SEQ ID NOs: 1 and 2; SEQ ID NOs: 3 and 4; SEQ ID NOs: 5 and 6; SEQ ID NOs: 9 and 10; SEQ ID NOs: 11 and 12; and SEQ ID NOs: 13 and 14. In another embodiment, exemplary primers of the invention include, but are not limited to, the primer sets listed in Tables 2, 3, 4 and 5.
According to another aspect of the present invention, it provides a method of isolating a fetal nucleic acid sample. The method comprises isolating one or more nucleic acid samples from a cervical mucus sample obtained from a maternal host of a fetus in a size range enriched with fetal nucleic acids. Examples of such size range include without any limitation from about 50 to about 1000 base pairs, from about 50 to about 500 base pairs, from about 50 to about 400 base pairs, from about 50 to about 300 base pairs, from about 50 to about 250 base pairs, from about 50 to about 200 base pairs, from about 50 to about 150 base pairs, or from about 50 to about 100 base pairs or a combination thereof. In one embodiment, the nucleic acid sample does not contain a substantial amount, e.g. more than 0.5%, 1%, 2%, 3%, 4%, or 5% of nucleic acids from any other size range or source.
According to yet another aspect of the present invention, it provides an isolated nucleic acid sample useful for genetic testing of a fetus. The nucleic acid sample, e.g. a DNA sample, can be obtained by isolating nucleic acid fragments of from about 50 base pairs to about 100, 200, 300, 400, 500, or 1000 base pairs in length from a cervical mucus sample obtained from a female subject containing the fetus. In one embodiment, these nucleic acid fragments are obtained from the total nucleic acid isolated from the cervical mucus sample by a size fractionation method. In another embodiment, the isolated nucleic acid is substantially free of non-nucleic acid components.
According to still another aspect of the present invention, it provides kits useful for genetic testing or screening of a fetus. In one embodiment, the kit provided by the present invention contains one or more pairs of primers useful for genetic composition testing assays and optionally one or more probes useful for detecting the amplified product(s) by the primers. In another embodiment, the kit provided by the present invention contains one or more pairs of primers useful for testing one or more polymorphisms or genetic markers of a fetus. In yet another embodiment, the kit provided by the present invention contains one or more pairs of primers which are useful for generating amplicons less than about 200 base pairs, less than about 150 base pairs, or between about 75 to about 150 base pairs. In still another embodiment, the kit provided by the present invention contains one or more pairs of primers for one or more designated chromosomes and the primers are selected from the primer sets listed in Tables 2, 3, 4 or 5. In a further embodiment, the kit of the invention contains the pairs of primers of SEQ ID NOs: 1 and 2; SEQ ID NOs: 3 and 4; SEQ ID NOs: 5 and 6; SEQ ID NOs: 9 and 10; SEQ ID NOs: 11 and 12; SEQ ID NOs: 13 and 14; or a combination thereof. The kit can also optionally contain one or more probes and/or other suitable reagents useful for detecting the amplified product(s) by the primers. Further, the kit can comprise instructions for using the pair of primers to test the genetic composition of a fetus.
In still another embodiment, the kit of the present invention contains one or more nucleic acid samples of the present invention. In a further embodiment, the kit provided by the present invention contains the cervical mucus sample of the present invention and an instruction for isolating the nucleic acid sample of the present invention from the cervical mucus sample.
The following examples are intended to illustrate but not to limit the invention in any manner, shape, or form, either explicitly or implicitly. While they are typical of those that might be used, other procedures, methodologies, or techniques known to those skilled in the art may alternatively be used.
This Example describes the collection and isolation of fetal DNA from pregnant women.
Cervical mucous samples were collected from patients, after due consent, by cytobrush method. In the cytobrush method, a Pap smear cytobrush (e.g. MedScand-AB, Malmo, Sweden) was inserted to a maximum depth of 2 cm and removed while rotating it a full turn (i.e., 360°). In order to remove the transcervical cells caught on the brush, the brush was shaken into a test tube containing 2-3 ml of a tissue culture medium (e.g., RPMI-1640 medium, available ATCC, Virginia) in the presence of 1% Penicillin Streptomycin antibiotic. In order to concentrate the transcervical cells on microscopic slides cytospin slides were prepared using e.g. a Cytofunnel Chamber Cytocentrifuge (Thermo-Shandon, England). The conditions used for cytocentrifugation are dependent on the murkiness of the transcervical specimen; if the specimen contained only a few cells, the cells are first centrifuged for five minutes and then suspended with 1 ml of fresh medium. Once prepared, the cytospin slides can be kept in 95% alcohol until further use.
DNA was extracted from fetal tissues, mucous samples or the transport media using Roche's Apoptotic DNA-Ladder Kit following manufacturer's protocol with slight modification. Mucous samples were incubated with equal volume of lysis buffer for 30 minutes to 2 hours or until all the mucous had been dissolved. Some samples needed to be homogenized with a 21 gauze 1.5 inch long needle to facilitate complete mucous dissolution. Total mucous DNA was then size fractionated on 10% PAGE, also known as 10% TBE gel (Invitrogen) under non-denaturing conditions, and the small, 100-250 base pair long DNA band (see
This Example demonstrates that the DNA obtained from the cervical mucous samples after PAGE purification is indeed fetal DNA.
The total DNA obtained from the cervical swap was size fractionated on 10% PAGE, and the small, 50-250 base pair DNA band (see
10-20 ng of this size-fractionated DNA was amplified by PCR with primers designed to amplify short STR regions (e.g., D22S1045, CSF1P0, D2S441 see Table 1 for detail).
Typical PCR cycle consisted of: Denaturation temperature of 94° C. for 30 sec, annealing temperature varied from 56 to 62° C. depending upon the primer length, extension was done at 72° C. Number of cycles used ranged from 26 to 40.
These primers were also used for PCR reaction with the DNA extracted from fetal tissues and the total, unfractionated, mucous DNA. Shown in
This Example demonstrates that the mini-STR markers detect fetal alleles.
Mini-STR markers of the invention were used to detect fetal alleles from DNA extracted from clinical cervical mucous samples. Table 1, below, summarizes the results obtained. D1S1677-F and -R, D22S1045-F and -R, DIOS1248-F and -R, TPOX, Mini-LFG33-F and -R, and Mini-LFG34-F and -R are exemplary primers of the invention.
Although the invention has been described with reference to the presently preferred embodiment, it should be understood that various modifications can be made without departing from the spirit of the invention. Accordingly, the invention is limited only by the following claims.
| Number | Date | Country | |
|---|---|---|---|
| 60869090 | Dec 2006 | US |
