Patent Application
20200385796
The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Dec. 16, 2016, is named AGB-7003-UT_SL.txt and is 332,274 bytes in size.
Mitochondria are the energy center of the cell. Every cell has about 100 to 200 mitochondria and every mitochondria contains 1-10 copies of mitochondrial DNA. Qualitative changes in mitochondrial DNA (mtDNA), such as mutations and deletions, have been implicated in many diseases such as diabetes mellitus and cancer. Mitochondria are also vulnerable to oxidative stress.
Provided are methods and kits for determining dosage of mitochondrial nucleic acid relative to genomic nucleic acid.
Provided in certain aspects are multiplex methods for determining dosage of mitochondrial nucleic acid relative to genomic nucleic acid for a sample from a subject including: (a) amplifying sets of mitochondrial polynucleotides and genomic polynucleotides from nucleic acid for a sample under amplification conditions, wherein: (i) each set comprises a mitochondrial polynucleotide and a genomic polynucleotide; (ii) the mitochondrial polynucleotide and the genomic polynucleotide are native; (iii) the mitochondrial polynucleotide of a set differs from the mitochondrial polynucleotide of the other sets and the genomic polynucleotide of a set differs from the genomic polynucleotide of the other sets; (iv) the mitochondrial polynucleotide and the genomic polynucleotide of a set are defined by formula 5′X—V—Y3′; (v) 5′X—V—Y3′ represents a contiguous sequence of nucleotides present in the mitochondrial polynucleotide and the genomic polynucleotide; (vi) X and Y of the mitochondrial polynucleotide are identical to X and Y, respectively, of the genomic polynucleotide in each set; (vii) V is one or more nucleotide positions at which a nucleotide of the mitochondrial polynucleotide differs from the corresponding nucleotide of the genomic polynucleotide in a set; thereby providing a plurality of amplified sets each comprising amplicons corresponding to all or a portion of the mitochondrial polynucleotide and amplified genomic polynucleotide in the set; (b) comparing (i) the amplicons corresponding to the mitochondrial polynucleotide, to (ii) the amplicons corresponding to the genomic polynucleotide for each set, thereby generating a comparison; and (c) determining the relative dosage of mitochondrial nucleic acid to genomic nucleic acid in the sample based on the comparison.
Provided in other aspects, are kits including amplification primer pairs that comprise polynucleotides chosen from polynucleotides in Table 2 and Table 4, or portions thereof.
Provided in another aspect, is a multiplex method for determining dosage of extrachromosomal nucleic acid relative to genomic nucleic acid for a sample from a subject including: (a) amplifying sets of extrachromosomal polynucleotides and genomic polynucleotides from nucleic acid for a sample under amplification conditions, wherein: (i) each set comprises an extrachromosomal polynucleotide and a genomic polynucleotide; (ii) the extrachromosomal polynucleotide and the genomic polynucleotide are native; (iii) the extrachromosomal polynucleotide of a set differs from the extrachromosomal polynucleotide of the other sets and the genomic polynucleotide of a set differs from the genomic polynucleotide of the other sets; (iv) the extrachromosomal polynucleotide and the genomic polynucleotide of a set are defined by formula 5′X—V—Y3′; (v) 5′X—V—Y3′ represents a contiguous sequence of nucleotides present in the extrachromosomal polynucleotide and the genomic polynucleotide; (vi) X and Y of the extrachromosomal polynucleotide are identical to X and Y, respectively, of the genomic polynucleotide in each set; (vii) V is one or more nucleotide positions at which a nucleotide of the extrachromosomal polynucleotide differs from the corresponding nucleotide of the genomic polynucleotide in a set; thereby providing a plurality of amplified sets each comprising amplicons corresponding to all or a portion of the extrachromosomal polynucleotide and amplified genomic polynucleotide in the set; (b) comparing (i) the amplicons corresponding to the extrachromosomal polynucleotide, to (ii) the amplicons corresponding to the genomic polynucleotide for each set, thereby generating a comparison; and (c) determining the relative dosage of extrachromosomal nucleic acid to genomic nucleic acid in the sample based on the comparison.
Provided in another aspect, is a multiplex method for determining dosage of extrachromosomal nucleic acid relative to genomic nucleic acid for a sample from a subject including: (a) amplifying sets of extrachromosomal polynucleotides and genomic polynucleotides from nucleic acid for a sample under amplification conditions, wherein: (i) each set comprises an extrachromosomal polynucleotide and a genomic polynucleotide; (ii) the extrachromosomal polynucleotide and the genomic polynucleotide are native; (iii) the extrachromosomal polynucleotide of a set differs from the extrachromosomal polynucleotide of the other sets and the genomic polynucleotide of a set differs from the genomic polynucleotide of the other sets; (iv) the extrachromosomal polynucleotide and the genomic polynucleotide of a set are defined by formula 5′X—V—Y3′; (v) the 5′X—V—Y3′ represents a contiguous sequence of nucleotides present in the extrachromosomal polynucleotide and the genomic polynucleotide; (vi) X and Y of the extrachromosomal polynucleotide are identical to X and Y, respectively, of the genomic polynucleotide in each set; (vii) V is one or more nucleotide positions at which a nucleotide of the extrachromosomal polynucleotide differs from the corresponding nucleotide of the genomic polynucleotide in a set; thereby providing a plurality of amplified sets each comprising amplicons corresponding to all or a portion of the extrachromosomal polynucleotide and amplified genomic polynucleotide in the set; (b) comparing (i) the amplicons corresponding to the extrachromosomal polynucleotide, to (ii) the amplicons corresponding to the genomic polynucleotide for each set, thereby generating a comparison; and (c) determining the relative dosage of extrachromosomal nucleic acid to genomic nucleic acid in the sample based on the comparison.
Provided in another aspect, is a multiplex method for determining dosage of mitochondrial nucleic acid relative to nuclear nucleic acid for a sample from a subject, including: (a) contacting nucleic acid of a sample from a subject comprising nucleic acid of a first species comprising a nuclear genome and a mitochondrial genome with nucleic acid of a second species comprising nucleic acid of a nuclear genome and a mitochondrial genome for which the copy number of the mitochondrial genome and the copy number of the nuclear genome are known, wherein the nuclear genome of the first species has regions that are paralogous to regions of the nuclear genome of the second species and the mitochondrial genome of the first species has regions that are paralogous to regions of the mitochondrial genome of the second species; (b) amplifying sets of nuclear polynucleotides of paralogous regions of the nuclear genome of the first species and the nuclear genome of the second species and sets of mitochondrial polynucleotides of paralogous regions of the mitochondrial genome of the first species and the mitochondrial genome of the second species from the nucleic acid of (a) under amplification conditions, wherein: (i) each set comprises a polynucleotide of the nuclear genome of the first species and a polynucleotide of the nuclear genome of the second species or each set comprises a polynucleotide of the mitochondrial genome of the first species and a polynucleotide of the mitochondrial genome of the second species; (ii) the mitochondrial polynucleotides and the nuclear polynucleotides are native; (iii) the mitochondrial polynucleotides of a set differ from the mitochondrial polynucleotides of the other sets and the nuclear polynucleotides of a set differ from the nuclear polynucleotides of the other sets; (iv) the mitochondrial polynucleotides of a set and the nuclear polynucleotides of a set are defined by formula 5′J-V—K3′; (v) 5′J-V—K3′ represents a contiguous sequence of nucleotides present in the mitochondrial polynucleotides or in the nuclear polynucleotides; (vi) J and K of the mitochondrial polynucleotides of a set are identical and J and K of the nuclear polynucleotides of a set are identical; and (vii) V is one or more nucleotide positions at which a nucleotide of the mitochondrial polynucleotides of the first and second species of a set differ or V is one or more nucleotide positions at which a nucleotide of the nuclear polynucleotides of the first and second species of a set differ; thereby providing a plurality of amplified sets each comprising amplicons corresponding to all or a portion of the mitochondrial polynucleotides of a set or amplicons corresponding to all or a portion of the amplified nuclear polynucleotides of a set; (c) comparing the amplicons corresponding to the mitochondrial polynucleotide of the second species to the amplicons corresponding to mitochondrial polynucleotide of the first species in a set and comparing the amplicons corresponding to the nuclear polynucleotide of the second species to the amplicons corresponding to the nuclear polynucleotide of the first species in a set, thereby generating comparisons; and (d) determining the relative dosage of mitochondrial nucleic acid to the nuclear nucleic acid in the sample from the subject based on comparisons of (c) for all sets. In certain embodiments, the comparisons in (c) are a ratio of the amount of the amplicons corresponding to the polynucleotide of the mitochondrial genome of the second species to the amount of amplicons corresponding to polynucleotide of the mitochondrial genome of the first species in a set and a ratio of the amount of the amplicons corresponding to the polynucleotide of the nuclear genome of the second species to the amount of amplicons corresponding to the polynucleotide of the nuclear genome of the first species in a set, and determining the relative dosage of mitochondrial nucleic acid to nuclear nucleic acid in the sample from the subject in (d) is based on the ratios. In certain aspects, the first species is human. In some aspects, the second species is chimpanzee.
Provided in other aspects, are kits including amplification primer pairs that comprise polynucleotides chosen from polynucleotides in Table 7, or portions thereof.
Certain embodiments are described further in the following description, examples, claims and drawings.
The drawings illustrate certain embodiments of the technology and are not limiting. For clarity and ease of illustration, the drawings are not made to scale and, in some instances, various aspects may be shown exaggerated or enlarged to facilitate an understanding of particular embodiments.
Certain of methods and kits provided herein enable the interrogation of both mitochondrial nucleic acid and genomic nucleic acid in a single reaction and do not require control samples or internal standards in order to compare amplicons representing these species. Certain methods and kits provided herein also do not require positive controls.
Certain of methods and kits provided herein enable the interrogation of both mitochondrial nucleic acid and nuclear (genomic) nucleic acid in a single reaction and utilize an internal standard that simulates the huge difference in copy number between the mitochondrial genome and the nuclear genome, as well as allowing for multiplex assays requiring little to no optimization. Certain methods and kits provided herein also utilize an internal standard.
The multiplex methods and kits provided herein by examining multiple regions of the mitochondrial DNA genome allow for both the determination of mitochondrial dosage and the detection of mitochondrial deletions in a single reaction. The examination of multiple locations of the mitochondrial genome also minimizes technical variability, allowing for a more accurate assessment of mitochondrial dosage.
Technology described herein can be utilized to assess a state of a cell, tissue, body function, medical condition (e.g., disease) or disorder, progression of a medical condition or disorder or treatment of a medical condition or disorder, for example. Certain embodiments of the technology are useful for (i) determining the likelihood a test subject has a medical condition or disorder or is pre-disposed to having a medical condition or disorder, (ii) determining the presence or absence of a progression of a medical condition or disorder in a test subject, (iii) determining the presence or absence of a response to a therapy administered to a test subject having the medical condition or disorder, (iv) determining whether a dosage of a therapeutic agent administered to a test subject should be increased, decreased or maintained; the like or combination of the foregoing. Various aspects and embodiments of the technology are described hereafter.
Nucleic Acid
Provided in part herein are methods for nucleic acid quantification. The terms “nucleic acid”, “nucleic acid molecule” and “polynucleotide” may be used interchangeably throughout the disclosure. Non-limiting examples of nucleic acid include deoxyribonucleic acid (DNA, e.g., complementary DNA (cDNA), genomic DNA (gDNA) also referred to as nuclear DNA, mitochondrial DNA (mtDNA), episomal DNA, and the like), ribonucleic acid (RNA, e.g., message RNA (mRNA), short inhibitory RNA (siRNA), ribosomal RNA (rRNA), transfer RNA (tRNA), microRNA, RNA highly expressed by the fetus or placenta, and the like), DNA or RNA analogs (e.g., containing base analogs, sugar analogs and/or a non-native backbone and the like), RNA/DNA hybrids and polyamide nucleic acids (PNAs). A nucleic acid can be in single-stranded or double-stranded form, and unless otherwise limited, can encompass known analogs of natural nucleotides that can function in a similar manner as naturally occurring nucleotides.
A nucleic acid can be in any form useful for conducting processes herein (e.g., linear, circular, supercoiled, single-stranded, double-stranded and the like). A nucleic acid may be, or may be from, mitochondria, a plasmid, phage, virus, an episomal or extrachromosomal element, a chloroplast, a plastid, autonomously replicating sequence (ARS), centromere, artificial chromosome, chromosome, or other nucleic acid able to replicate or be replicated in vitro or in a host cell, a cell, a cell nucleus or cytoplasm of a cell, in certain embodiments. A nucleic acid in some embodiments can be from a single chromosome (e.g., a nucleic acid sample may be from one chromosome of a sample obtained from a diploid organism). The term also may include, as equivalents, derivatives, variants and analogs of RNA or DNA synthesized from nucleotide analogs, single-stranded (e.g., “sense” or “antisense”, “plus” strand or “minus” strand, “forward” reading frame or “reverse” reading frame) and double-stranded polynucleotides. Deoxyribonucleotides include deoxyadenosine, deoxycytidine, deoxyguanosine and deoxythymidine. For RNA, the base thymine is replaced with uracil. A nucleic acid may be prepared using a nucleic acid obtained from a subject.
Circulating Cell-Free Nucleic Acid
Nucleic acid can be circulating cell-free nucleic acid in certain embodiments. The terms “circulating cell-free nucleic acid,” “extracellular nucleic acid” and “cell free nucleic acid” as used herein refer to nucleic acid isolated from a source having substantially no cells. Circulating cell-free nucleic acid (ccfNA, ccfDNA) can be present in and obtained from blood. Circulating cell-free nucleic acid often includes no detectable cells and may contain cellular elements or cellular remnants. Non-limiting examples of acellular sources for extracellular nucleic acid are blood, blood plasma, blood serum, cerebrospinal fluid, spinal fluid, and urine. Obtaining circulating cell-free nucleic acid includes obtaining a sample directly (e.g., collecting a sample, e.g., a test sample) or obtaining a sample from another who has collected a sample. Without being limited by theory, circulating cell-free nucleic acid may be a product of cell apoptosis and cell breakdown, which provides basis for extracellular nucleic acid often having a series of lengths across a spectrum (e.g., a “ladder”).
Circulating cell-free nucleic acid can include different nucleic acid species, and therefore is referred to herein as “heterogeneous.” For example, blood serum or plasma from a person having cancer can include nucleic acid from cancer cells and nucleic acid from non-cancer cells. In another non-limiting example, blood serum or plasma from a pregnant female can include maternal nucleic acid and fetal nucleic acid. In another non-limiting example, blood serum or plasma from a pregnant female can include maternal nucleic acid, placental nucleic acid and fetal nucleic acid. In another non-limiting example, blood serum or plasma can include nuclear or genomic nucleic acid and mitochondrial nucleic acid. At least two different nucleic acid species can exist in different amounts in circulating cell-free nucleic acid and sometimes are referred to as minority species and majority species. In certain instances, a minority species of nucleic acid is from an affected cell type (e.g., cancer cell, wasting cell, cell attacked by immune system). In some instances, a minority species of circulating cell-free nucleic acid sometimes is about 1% to about 40% of the overall nucleic acid (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39 or 40% of the nucleic acid is minority species nucleic acid). In circulating cell-free nucleic acid mitochondrial nucleic acid can be present in greater amounts than genomic or nuclear nucleic acid and can be considered the majority species. In some embodiments, a minority species of circulating cell-free nucleic acid is of a length of about 500 base pairs or less (e.g., about 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% of minority species nucleic acid is of a length of about 500 base pairs or less). In some embodiments, a minority species of circulating cell-free nucleic acid is of a length of about 300 base pairs or less (e.g., about 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% of minority species nucleic acid is of a length of about 300 base pairs or less). In some embodiments, a minority species of circulating cell-free nucleic acid is of a length of about 200 base pairs or less (e.g., about 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% of minority species nucleic acid is of a length of about 200 base pairs or less). In some embodiments, a minority species of circulating cell-free nucleic acid is of a length of about 150 base pairs or less (e.g., about 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% of minority species nucleic acid is of a length of about 150 base pairs or less). In some embodiments, the majority nucleic acid species of circulating cell-free nucleic acid (mitochondrial) is of a length that is less than the length of the minority nucleic acid species of circulating cell-free nucleic acid (nuclear or genomic). In some embodiments, the length of the majority nucleic acid species (mitochondrial) is about 50 base pairs and the length of the minority nucleic acid species (genomic or nuclear) is about 166 base pairs.
Cellular Nucleic Acid
Nucleic acid can be cellular nucleic acid in certain embodiments. The term “cellular nucleic acid” as used herein refers to nucleic acid isolated from a source having intact cells. Non-limiting examples of sources for cellular nucleic acid are blood cells, tissue cells, organ cells, tumor cells, hair cells, skin cells, and bone cells.
In some embodiments, nucleic acid is from peripheral blood mononuclear cells (PBMC). A PBMC is any blood cell having a round nucleus, such as, for example, lymphocytes, monocytes or macrophages. These cells can be extracted from whole blood, for example, using ficoll, a hydrophilic polysaccharide that separates layers of blood, with PBMCs forming a buffy coat under a layer of plasma. Additionally, PBMCs can be extracted from whole blood using a hypotonic lysis which preferentially lyses red blood cells and leaves PBMCs intact, and/or can be extracted using a differential centrifugation process known in the art.
Mitochondrial DNA can be extracted from whole blood using standard methods for DNA extraction from whole blood. Mitochondrial DNA can be enriched using a protocol as described in BioTechniques 55:133-136 (September 2013), hereby incorporated in its entirety by reference.
Using standard methods of DNA extraction both mitochondrial and nuclear DNA can be obtained from a sample. For example, standard DNA extraction kits can be used with buffy coat or buccal swaps for both mitochondrial and nuclear DNA and the corresponding kits when targeting circulating cell free DNA.
Nucleic Acid for Internal Standard
In some embodiments the copy number or genomic equivalents of the mitochondrial genome and the nuclear genome of nucleic acid of a second species is known or can be determined. The known equivalents of the mitochondrial genome and the nuclear genome for the nucleic acid of the second species serve as internal standards that can be used in conjunction with paralog assay results in determining the copy number of the mitochondrial genome and the copy number of the nuclear genome of the nucleic acid of the first species. The copy number of the mitochondrial nucleic acid and the copy number of the nuclear nucleic acid can be used to determine the mitochondrial/nuclear ratio for the nucleic acid of the sample from a subject (i.e., dosage). The exact amounts of mitochondrial and nuclear genomic equivalents or copy numbers for the nucleic acid of a second species (e.g., chimpanzee) that is utilized in an assay can be determined using methods such digital PCR. In some embodiments, the method is digital droplet PCR with a mitochondrial specific primer pair and a nuclear specific primer pair. In certain embodiments, ratios for mitochondrial to nuclear genomic equivalents for the internal standard species can be from approximately 500 to approximately 5000. A standard ratio for a chimpanzee is approximately 1200. As described below the nucleic acid for the internal standard is obtained from a genome (species) with regions in its mitochondrial and nuclear genome that are paralogs with regions of the mitochondrial and nuclear genome of the nucleic acid of the sample from a subject.
Samples
Nucleic acid in or from a suitable sample can be utilized in a method described herein. A mixture of nucleic acids can comprise two or more nucleic acid fragment species having different nucleotide sequences, different fragment lengths, different origins (e.g., genomic origin, mitochondrial vs nuclear (genomic) origin, fetal vs. maternal origin, cell or tissue origin, cancer vs. non-cancer origin, tumor vs. non-tumor origin, sample origin, subject origin, and the like), or combinations thereof. In some embodiments, nucleic acid is analyzed in situ (e.g., in a sample; in a subject), in vivo, ex vivo or in vitro.
Nucleic acid often is isolated from a sample obtained from a subject. A subject can be any living or non-living organism, including but not limited to a human, a non-human animal, a plant, a bacterium, a fungus or a protist. Any human or non-human animal can be selected, including but not limited to mammal, reptile, avian, amphibian, fish, ungulate, ruminant, bovine (e.g., cattle), equine (e.g., horse), caprine and ovine (e.g., sheep, goat), swine (e.g., pig), camelid (e.g., camel, llama, alpaca), monkey, ape (e.g., gorilla, chimpanzee), ursid (e.g., bear), poultry, dog, cat, mouse, rat, fish, dolphin, whale and shark. A subject may be male or female.
Nucleic acid may be isolated from any type of suitable biological specimen or sample (e.g., a test sample). A sample or test sample can be any specimen that is isolated or obtained from a subject (e.g., a human subject, a pregnant female or a non-human subject). Non-limiting examples of specimens include fluid or tissue from a subject, including, without limitation, cerebrospinal fluid, spinal fluid, lavage fluid (e.g., bronchoalveolar, gastric, peritoneal, ductal, ear, arthroscopic), urine, feces, sputum, saliva, nasal mucous, prostate fluid, lavage, semen, lymphatic fluid, bile, tears, sweat, breast milk, breast fluid, biopsy sample (e.g., cancer biopsy), cell or tissue sample (e.g., from the liver, lung, spleen, pancreas, colon, skin, bladder, eye, brain, esophagus, head, neck, ovary, testes, prostate, the like or combination thereof). In some embodiments, a biological sample may be blood and sometimes a blood fraction (e.g., plasma or serum). As used herein, the term “blood” encompasses whole blood or any fractions of blood, such as serum and plasma as conventionally defined, for example. Blood or fractions thereof often comprise nucleosomes (e.g., maternal and/or fetal nucleosomes). Nucleosomes comprise nucleic acids and are sometimes cell-free or intracellular. Blood also comprises buffy coats. Buffy coats sometimes are isolated by utilizing a ficoll gradient. Buffy coats can comprise white blood cells (e.g., leukocytes, T-cells, B-cells, platelets, and the like). In some embodiments, buffy coats comprise maternal and/or fetal nucleic acid. Blood plasma refers to the fraction of whole blood resulting from centrifugation of blood treated with anticoagulants. Blood serum refers to the watery portion of fluid remaining after a blood sample has coagulated. Fluid or tissue samples often are collected in accordance with standard protocols hospitals or clinics generally follow. For blood, an appropriate amount of peripheral blood (e.g., between 3-40 milliliters) often is collected and can be stored according to standard procedures prior to or after preparation. A fluid or tissue sample from which nucleic acid is extracted may be acellular (e.g., cell-free). In some embodiments, a fluid or tissue sample may contain cellular elements or cellular remnants. In some embodiments cancer cells may be included in the sample.
Nucleic Acid Isolation and Processing
Nucleic acid can be isolated using any suitable technique. Cell lysis procedures and reagents are known in the art and may generally be performed by chemical (e.g., detergent, hypotonic solutions, enzymatic procedures, and the like, or combination thereof), physical (e.g., French press, sonication, and the like), or electrolytic lysis methods. Any suitable lysis procedure can be utilized. For example, chemical methods generally employ lysing agents to disrupt cells and extract the nucleic acids from the cells, followed by treatment with chaotropic salts. Physical methods such as freeze/thaw followed by grinding, the use of cell presses and the like also are useful. High salt lysis procedures also are commonly used. For example, an alkaline lysis procedure may be utilized. The latter procedure traditionally incorporates the use of phenol-chloroform solutions, and an alternative phenol-chloroform-free procedure involving three solutions can be utilized. In the latter procedures, one solution can contain 15 mM Tris, pH 8.0; 10 mM EDTA and 100 ug/ml Rnase A; a second solution can contain 0.2N NaOH and 1% SDS; and a third solution can contain 3M KOAc, pH 5.5. These procedures can be found in Current Protocols in Molecular Biology, John Wiley & Sons, N.Y., 6.3.1-6.3.6 (1989), incorporated herein in its entirety.
Nucleic acid may be isolated at a different time point as compared to another nucleic acid, where each of the samples is from the same or a different source. A nucleic acid may be from a nucleic acid library, such as a cDNA or RNA library, for example. A nucleic acid may be a result of nucleic acid purification or isolation and/or amplification of nucleic acid molecules from the sample. Nucleic acid provided for processes described herein may contain nucleic acid from one sample or from two or more samples (e.g., from 1 or more, 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 11 or more, 12 or more, 13 or more, 14 or more, 15 or more, 16 or more, 17 or more, 18 or more, 19 or more, or 20 or more samples).
Nucleic acid may be provided for conducting methods described herein without processing of the sample(s) containing the nucleic acid, in certain embodiments. In some embodiments, nucleic acid is provided for conducting methods described herein after processing of the sample(s) containing the nucleic acid. For example, a nucleic acid can be extracted, isolated, purified, partially purified or amplified from the sample(s). The term “isolated” as used herein refers to nucleic acid removed from its original environment (e.g., the natural environment if it is naturally occurring, or a host cell if expressed exogenously), and thus is altered by human intervention (e.g., “by the hand of man”) from its original environment. The term “isolated nucleic acid” as used herein can refer to a nucleic acid removed from a subject (e.g., a human subject). An isolated nucleic acid can be provided with fewer non-nucleic acid components (e.g., protein, lipid) than the amount of components present in a source sample. A composition comprising isolated nucleic acid can be about 50% to greater than 99% free of non-nucleic acid components. A composition comprising isolated nucleic acid can be about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or greater than 99% free of non-nucleic acid components. The term “purified” as used herein can refer to a nucleic acid provided that contains fewer non-nucleic acid components (e.g., protein, lipid, carbohydrate) than the amount of non-nucleic acid components present prior to subjecting the nucleic acid to a purification procedure. A composition comprising purified nucleic acid may be about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or greater than 99% free of other non-nucleic acid components. The term “purified” as used herein can refer to a nucleic acid provided that contains fewer nucleic acid species than in the sample source from which the nucleic acid is derived. A composition comprising purified nucleic acid may be about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or greater than 99% free of other nucleic acid species. For example, cancer cell nucleic acid can be purified from a mixture comprising cancer cell and non-cancer cell nucleic acid. In certain examples, nucleosomes comprising small fragments of cancer cell nucleic acid can be purified from a mixture of larger nucleosome complexes comprising larger fragments of non-cancer nucleic acid.
Mitochondrial and Genomic (Nuclear) Nucleic Acid
Provided herein are methods to determine the dosage of mitochondrial nucleic acid relative to genomic (nuclear) nucleic acid in a sample. In some embodiments, the nucleic acid is DNA.
Mitochondrial/Genomic (Nuclear) Paralogs
In some embodiments, mitochondrial and genomic polynucleotides are analyzed in sets of polynucleotides. In some embodiments the mitochondrial polynucleotide and the genomic polynucleotide of a set are referred to as a mitochondrial/genomic (nuclear) paralog. A mitochondrial/genomic (nuclear) paralog is a region in the mitochondrial genome with a similar or nearly identical region in the nuclear genome. The paralogous sequence can be any size but must contain one or more regions that are identical in the mitochondrial genome and the nuclear genome and one or more nucleotides that are different in the mitochondria genome and the nuclear genome. In some embodiments, the paralogous sequence includes one or two base pair mismatches.
As used herein, the term “set” can refer to a mitochondrial polynucleotide and a corresponding genomic polynucleotide (paralogs) that have the following characteristics: (i) a set comprises a mitochondrial polynucleotide and a genomic polynucleotide; (ii) the mitochondrial polynucleotide and the genomic polynucleotide of a set are native; (iii) the mitochondrial polynucleotide is different from the genomic polynucleotide in a set; (iv) the mitochondrial polynucleotide and the genomic polynucleotide of a set are defined by formula 5′X—V—Y3′ and (v) the mitochondrial polynucleotide of a set differs from the mitochondrial polynucleotide of the other sets and the genomic polynucleotide of a set differs from the genomic polynucleotide of the other sets.
The term “native” as used herein refers to the sequence of nucleotides as it is present in a mitochrondrial genome or nuclear genome and that has not been modified, altered or rearranged.
As used herein the term “multiplex” refers to the analysis of more than one set of a mitochondrial polynucleotide and a genomic polynucleotide in a single reaction. The polynucleotides represent distinct and different regions of the mitochondrial genome and distinct and different regions of the nuclear genome.
In some embodiments, 5′X—V—Y3′ represents a contiguous sequence of nucleotides present in the mitochondrial polynucleotide and the genomic polynucleotide and X and Y of the mitochondrial polynucleotide are identical to X and Y, respectively, of the genomic polynucleotide in each set. V is one or more nucleotide positions at which a nucleotide of the mitochondrial polynucleotide differs from the corresponding nucleotide of the genomic polynucleotide in a set (e.g., a mismatch, single nucleotide polymorphisms (SNPs)). V can also be an insertion or a deletion. In certain embodiments, V is a single nucleotide position.
As used herein, the term “identical” refers to defined portions (specific length) of mitochondrial and genomic polynucleotides for which the nucleotide sequence does not differ at any position. 5′X—V—Y3′ can be any length or number of nucleotides. In some embodiments, 5′X—V—Y3 is about 30 to about 300 base pairs in length.
In some embodiments “dosage” is determined based on a comparison of mitochondrial nucleic acid (from mitochondrial genome) to genomic nucleic acid. In some embodiments “dosage” is a ratio of mitochondrial DNA to genomic DNA for a sample. In some embodiments “dosage” is a ratio of the amount of mitochondrial DNA to the amount of genomic DNA for a sample. In some embodiments, the comparison is a ratio of (i) the amount of the amplicons corresponding to the mitochondrial polynucleotide, to (ii) the amount of the amplicons corresponding to the genomic polynucleotide, in each set. A ratio could be either a comparison of the amount of the amplicons corresponding to the mitochondrial polynucleotide to the amount of the amplicons corresponding to the genomic polynucleotide or a comparison of the amount of the amplicons corresponding to the genomic polynucleotide to the amount of the amplicons corresponding to the mitochondrial polynucleotide. Sometimes dosage represents the copy number of mitochondrial DNA relative to the copy number of genomic DNA in a sample.
The term “amount” as used herein with respect to amplicons refers to any suitable measurement, including, but not limited to, copy number, weight (e.g., grams) and concentration (e.g., grams per unit volume (e.g., milliliter); molar units). In some embodiments, “amount” is determined based on analysis of a detectable parameter that correlates with amount; such as the quantification of a specific nucleotide at a defined position in a mitochondrial or a genomic polynucleotide (e.g., “V”).
Mitochondrial/Mitochondrial Paralogs-Nuclear/Nuclear Paralogs
In some embodiments, mitochondrial polynucleotides of a first species present in a sample and mitochondrial polynucleotides of a second species provided as an internal standard are analyzed in sets of polynucleotides and nuclear polynucleotides of a first species present in a sample and nuclear polynucleotides of a second species provided as an internal standard are analyzed in sets of polynucleotides. In some embodiments, the mitochondrial polynucleotides of a set are referred to as a mitochondrial/mitochondrial paralog. In some embodiments, the nuclear polynucleotides of a set are referred to as a nuclear/nuclear paralog. A mitochondrial/mitochondrial paralog is a region in the mitochondrial genome of a first species with a similar or nearly identical region in the mitochondrial genome of a second species. A nuclear/nuclear paralog is a region in the nuclear genome of a first species with a similar or nearly identical region in the nuclear genome of a second species. The paralogous sequence can be any size but must contain one or more regions that are identical in the two mitochondrial genomes and one or more nucleotides that are different in the two mitochondrial genomes. For nuclear genomes, the paralogous sequence can be any size but must contain one or more regions that are identical in the two nuclear genomes and one or more nucleotides that are different in the two nuclear genomes. In some embodiments, the paralogous sequence includes one or two base pair mismatches.
The species of polynucleotides of a set can represent any two species where paralog regions occur in the mitochondrial genomes of the two species and where paralog regions occur in the nuclear genomes of the two species. In certain embodiments, the first species is human and second species is non-human. In some embodiments, the second species is chimpanzee. In certain embodiments, the nucleic acid of a sample from a subject is the first species and the nucleic acid providing an internal standard is the second species.
The term “set” can refer to a mitochondrial polynucleotide of a first species and a corresponding mitochondrial polynucleotide of a second species (paralogs) or can refer to a nuclear polynucleotide of a first species and a corresponding nuclear polynucleotide of a second species (paralogs) that have the following characteristics: (i) each set comprises a polynucleotide of the nuclear genome of the first species and a polynucleotide of the nuclear genome of the second species or each set comprises a polynucleotide of the mitochondrial genome of the first species and a polynucleotide of the mitochondrial genome of the second species; (ii) the mitochondrial polynucleotides and the nuclear polynucleotides are native; (iii) the mitochondrial polynucleotides of a set differ from the mitochondrial polynucleotides of the other sets and the nuclear polynucleotides of a set differ from the nuclear polynucleotides of the other sets; (iv) the mitochondrial polynucleotides of a set and the nuclear polynucleotides of a set are defined by formula 5′J-V—K3′; (v) 5′J-V—K3′ represents a contiguous sequence of nucleotides present in the mitochondrial polynucleotides or in the nuclear polynucleotides; (vi) J and K of the mitochondrial polynucleotides of a set are identical and J and K of the nuclear polynucleotides of a set are identical; and (vii) V is one or more nucleotide positions at which a nucleotide of the mitochondrial polynucleotides of the first and second species of a set differ or V is one or more nucleotide positions at which a nucleotide of the nuclear polynucleotides of the first and second species of a set differ.
The term “native” as used herein refers to the sequence of nucleotides as it is present in a mitochrondrial genome or nuclear genome and that has not been modified, altered or rearranged.
The term “multiplex” refers to the analysis of more than one set of a mitochondrial polynucleotide of a first species and a corresponding mitochondrial polynucleotide of a second species in a single reaction or more than one set of a nuclear polynucleotide of a first species and a corresponding nuclear polynucleotide of a second species in a single reaction. In some embodiments, the more than one set of mitochondrial polynucleotides and the more than one set of nuclear polynucleotides are in a single reaction. In some embodiments, the more than one set of mitochondrial polynucleotides and the more than one set of nuclear polynucleotides are in different reactions.
The mitochondrial polynucleotides of a set of a mitochondrial polynucleotide of a first species and a corresponding mitochondrial polynucleotide of a second species differs from the mitochondrial polynucleotides of other sets of mitochondrial polynucleotides. The nuclear polynucleotides of a set of a nuclear polynucleotide of a first species and a corresponding nuclear polynucleotide of a second species differs from the nuclear polynucleotides of other sets of nuclear polynucleotides. The polynucleotides represent distinct and different regions of the mitochondrial genomes and distinct and different regions of the nuclear genomes.
In some embodiments, 5′J-V—K3′ represents a contiguous sequence of nucleotides present in the mitochondrial polynucleotides and J and K of the mitochondrial polynucleotides are identical in each set. In some embodiments, 5′J-V—K3′ represents a contiguous sequence of nucleotides present in the nuclear polynucleotides and J and K of the nuclear polynucleotides are identical in each set. V is one or more nucleotide positions at which a nucleotide of the mitochondrial polynucleotides in a set differ or one or more nucleotide positions at which a nucleotide of the nuclear polynucleotides in a set differ. In some aspects V can be a mismatch or single nucleotide polymorphism (SNP). V can also be an insertion or a deletion. In certain embodiments, V is a single nucleotide position.
As used herein, the term “identical” refers to defined portions (specific length) of mitochondrial polynucleotides of a set or nuclear polynucleotides of a set for which the nucleotide sequences do not differ at any position.
5′J-V—K3′ can be any length or number of nucleotides. In some embodiments, 5′J-V—K3′ is about 30 to about 300 base pairs in length.
In certain embodiments, a first species/second species paralog are analyzed together in an assay. In some embodiments, assays target nuclear paralogs. In some embodiments, assays target mitochondrial paralogs. In some embodiments, the first species/second species paralogs are human/chimpanzee paralogs. In some embodiments, an assay consists of a set of a mitochondrial polynucleotide of a first species and a corresponding mitochondrial polynucleotide of a second species that analyzed together. In some embodiments, an assay consists of set of a nuclear polynucleotide of a first species and a corresponding nuclear polynucleotide of a second species that are analyzed together. Certain ratios are based on the amounts of amplicons of a first and a second species determined in the assays that target mitochondrial paralogs. Certain ratios are based on the amounts of amplicons of a first and a second species determined in the assays that target nuclear paralogs.
In some embodiments “dosage” is determined based on a comparison of mitochondrial nucleic acid (from the mitochondrial genome) to nuclear nucleic acid (from the nuclear genome) for a first species. In some embodiments “dosage” is a ratio of mitochondrial DNA to nuclear DNA for a sample from a subject. In some embodiments “dosage” is a ratio of the amount of mitochondrial DNA to the amount of nuclear DNA for a sample from a subject. In some embodiments “dosage” is a ratio of the copy number of mitochondrial DNA to the copy number of nuclear DNA for a sample from a subject (e.g., first species or human). In some embodiments, the mitochondrial copy number for the nucleic acid of a first species can be derived based on the ratio of the amount of the mitochondrial polynucleotide of the first species and the amount of the mitochondrial polynucleotide of the second species as determined by assays targeting mitochondrial paralogs, in conjunction with the known value for the copy number of the mitochondrial nucleic acid (genome) of the second species. In some embodiments, the nuclear copy number for the nucleic acid of a first species can be derived based on the ratio of the amount of the nuclear polynucleotide of the first species and the amount of the nuclear polynucleotide of the second species as determined by assays targeting nuclear paralogs, in conjunction with the known value for the copy number of the nuclear nucleic acid (genome) of the second species.
In some embodiments, the subject is human and accordingly the nucleic acid of the first species is human and the nucleic acid of the second species is chimpanzee.
The term “amount” as used herein with respect to amplicons refers to any suitable measurement, including, but not limited to, copy number, weight (e.g., grams) and concentration (e.g., grams per unit volume (e.g., milliliter); molar units). In some embodiments, “amount” is determined based on analysis of a detectable parameter that correlates with amount; such as the quantification of a specific nucleotide at a defined position in a mitochondrial or a nuclear polynucleotide (e.g., “V”).
Identification of Paralogs
The mitochondrial genome is a circular genome of about 16.5 Kb and contains 37 genes, 13 of which encode proteins. The mitochondrial genome can be is divided into short fragments of any length that is amenable to carrying out sequence comparison (e.g., 100 bp). Alignment techniques and sequence identity assessment methodology are known. Such analyses can be performed by using mathematical algorithms.
Mitochondrial/Genomic (Nuclear) Paralogs (5′X—V—Y3)
Fragments of the mitochondrial genome are aligned with and compared to regions of a human genome based on defined criteria, such as, but not limited to, the number of mismatches that are allowed in the sequence (e.g., 1 mismatch, 2 mismatches, 5 mismatches, 10 mismatches, 15 mismatches, 20 mismatches, 25 mismatches) to identify similar or nearly identical regions. From these regions, those regions that fulfil the criteria specified for (5′X—V—Y3′) and the other criteria that define a set, as discussed above, are selected. A sufficient number of regions are chosen from different locations in the mitochondrial genome in order to span the mitochondrial genome and to provide a sufficient number of measurements to minimize technical variability. In some embodiments, regions are chosen so that at least one region is located in specific mitochondrial genes of interest. In some embodiments the number of sets is about 2 sets to about 20 sets. In some embodiments the number of sets is about 2 sets to about 10 sets. In some embodiments the number of sets is 10 sets. In some embodiments the number of sets is a least 5 sets.
In some embodiments, sets of mitochondrial and genomic polynucleotides are described in Table 1.
Mitochondrial/Mitochondrial Paralogs-Nuclear/Nuclear Paralogs (5′J-V—K3)
Fragments of a mitochondrial genome of a first species are aligned with and compared to regions of a mitochondrial genome of a second species and fragments of a nuclear genome of a first species are aligned with and compared to regions of a nuclear genome of a second species based on defined criteria, such as, but not limited to, the number of mismatches that are allowed in the sequence (e.g., 1 mismatch, 2 mismatches, 5 mismatches, 10 mismatches, 15 mismatches, 20 mismatches, 25 mismatches) to identify similar or nearly identical regions. From these regions, those regions that fulfil the criteria specified for (5′J-V—K3′) and the other criteria that define a set, as discussed above, are selected. A sufficient number of regions are chosen from different locations in the mitochondrial genome in order to span the mitochondrial genome and to provide a sufficient number of measurements to minimize technical variability. In some embodiments, regions are chosen so that at least one region is located in specific mitochondrial genes of interest. A sufficient number of regions are chosen from different locations in the nuclear genome in order to provide a sufficient number of measurements to minimize technical variability. In some embodiments the number of sets of mitochondrial/mitochondrial paralogs and nuclear/nuclear paralogs are each about 2 sets to about 20 sets. In some embodiments, the number of sets of mitochondrial/mitochondrial paralogs and nuclear/nuclear paralogs are each about 2 sets to about 10 sets. In some embodiments, the number of sets is 10 sets. In some embodiments, the number of sets is a least 5 sets. In other embodiments, the number of sets of nuclear/nuclear paralogs is greater than the number of sets of mitochondrial/mitochondrial paralogs. For example, the number of sets of mitochondrial/mitochondrial paralogs and nuclear/nuclear paralogs are each about 1, 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, 80, 85, 90, 95, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475 or 500 sets, in some embodiments.
In some embodiments, sets of mitochondrial paralogs are described in Table 6.
Amplification
Often sets of mitochondrial polynucleotides and genomic polynucleotides from nucleic acid for a sample are amplified and then analyzed. Sometimes only a portion of a paralog 5′X—V—Y3′ is amplified. In some embodiments, the length of an amplicon is about 30 base pairs to about 300 base pairs. An amplicon often includes at least a portion of X and Y regions and includes V. In some embodiments, an amplicon includes regions of a polynucleotide 5′ of X and 3′ of Y.
In some embodiments, sets of mitochondrial polynucleotides and sets of nuclear polynucleotides from nucleic acid for a sample and an added internal standard are amplified and then analyzed. Sometimes only a portion of a paralog 5′J-V—K3′ is amplified. In some embodiments, the length of an amplicon is about 30 base pairs to about 300 base pairs. An amplicon often includes at least a portion of J and K regions and includes V.
Amplification primers are chosen as described below. In some embodiments, amplifying is by a polymerase chain reaction (PCR) process.
Amplification conditions are known and can be selected for a particular nucleic acid that will be amplified. Amplification conditions include certain reagents some of which can include, without limitation, nucleotides (e.g., nucleotide triphosphates), modified nucleotides, oligonucleotides (e.g., primer oligonucleotides for polymerase-based amplification and oligonucleotide building blocks for ligase-based amplification), one or more salts (e.g., magnesium-containing salt), one or more buffers, one or more polymerizing agents (e.g., ligase enzyme, polymerase enzyme), one or more nicking enzymes (e.g., an enzyme that cleaves one strand of a double-stranded nucleic acid) and one or more nucleases (e.g., exonuclease, endonuclease, RNase). Any polymerase suitable for amplification may be utilized, such as a polymerase with or without exonuclease activity, DNA polymerase and RNA polymerase, mutant forms of these enzymes, for example. Any ligase suitable for joining the 5′ of one oligonucleotide to the 3′ end of another oligonucleotide can be utilized. Amplification conditions also can include certain reaction conditions, such as isothermal or temperature cycle conditions. Methods for cycling temperature in an amplification process are known, such as by using a thermocycle device. The term “cycling” refers to amplification (e.g. an amplification reaction or extension reaction) utilizing a single amplification primer pair or multiple amplification primer pairs where temperature cycling is used. In some embodiments, about 25 PCR amplification cycles to about 45 PCR amplification cycles are performed in. Amplification conditions also can, in some embodiments, include an emulsion agent (e.g., oil) that can be utilized to form multiple reaction compartments within which single nucleic acid molecule species can be amplified. Amplification is sometimes an exponential product generating process and sometimes is a linear product generating process.
Any suitable amplification technique and amplification conditions can be selected for a particular nucleic acid for amplification. Known amplification processes include, without limitation, polymerase chain reaction (PCR), extension and ligation, ligation amplification (or ligase chain reaction (LCR)) and amplification methods based on the use of Q-beta replicase or template-dependent polymerase (see US Patent Publication Number US20050287592). Also useful are strand displacement amplification (SDA), thermophilic SDA, nucleic acid sequence based amplification (3SR or NASBA) and transcription-associated amplification (TAA). Reagents, apparatus and hardware for conducting amplification processes are commercially available, and amplification conditions are known and can be selected for the target nucleic acid at hand.
Amplification Primers
Primers useful for amplification of mitochondrial and genomic polynucleotides are provided. In some embodiments primers are used in sets, where a set contains at least a pair. In some embodiments a plurality of primer sets, each set comprising pair(s) of primers, may be used. The term “primer” as used herein refers to a nucleic acid that comprises a nucleotide sequence capable of hybridizing or annealing to a polynucleotide, at or near (e.g., adjacent to) a specific region of interest. A primer may be naturally occurring or synthetic. The term “specific” or “specificity”, as used herein, refers to the binding or hybridization of one molecule to another molecule, such as a primer for a polynucleotide. That is, “specific” or “specificity” refers to the recognition, contact, and formation of a stable complex between two molecules, as compared to substantially less recognition, contact, or complex formation of either of those two molecules with other molecules. As used herein, the term “anneal” refers to the formation of a stable complex between two molecules. The terms “primer”, “oligo”, or “oligonucleotide” may be used interchangeably throughout the document, when referring to primers.
A primer nucleic acid can be designed and synthesized using suitable processes, and may be of any length suitable for hybridizing to a nucleotide sequence of interest (e.g., where the nucleic acid is in liquid phase or bound to a solid support) and performing analysis processes described herein. Primers may be designed based upon a target nucleotide sequence. A primer in some embodiments may be about 10 to about 100 nucleotides, about 10 to about 70 nucleotides, about 10 to about 50 nucleotides, about 15 to about 30 nucleotides, or about 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 or 100 nucleotides in length. A primer may be composed of naturally occurring and/or non-naturally occurring nucleotides (e.g., labeled nucleotides), or a mixture thereof. Primers suitable for use with embodiments described herein, may be synthesized and labeled using known techniques. Oligonucleotides (e.g., primers) may be chemically synthesized according to the solid phase phosphoramidite triester method first described by Beaucage and Caruthers, Tetrahedron Letts., 22:1859-1862, 1981, using an automated synthesizer, as described in Needham-VanDevanter et al., Nucleic Acids Res. 12:6159-6168, 1984. Purification of oligonucleotides can be effected by native acrylamide gel electrophoresis or by anion-exchange high-performance liquid chromatography (HPLC), for example, as described in Pearson and Regnier, J. Chrom., 255:137-149, 1983.
All or a portion of a primer nucleic acid sequence (naturally occurring or synthetic) may be substantially complementary to a target nucleic acid, in some embodiments. As referred to herein, “substantially complementary” with respect to sequences refers to nucleotide sequences that will hybridize with each other. The stringency of the hybridization conditions can be altered to tolerate varying amounts of sequence mismatch. Included are regions of counterpart, target and capture nucleotide sequences 55% or more, 56% or more, 57% or more, 58% or more, 59% or more, 60% or more, 61% or more, 62% or more, 63% or more, 64% or more, 65% or more, 66% or more, 67% or more, 68% or more, 69% or more, 70% or more, 71% or more, 72% or more, 73% or more, 74% or more, 75% or more, 76% or more, 77% or more, 78% or more, 79% or more, 80% or more, 81% or more, 82% or more, 83% or more, 84% or more, 85% or more, 86% or more, 87% or more, 88% or more, 89% or more, 90% or more, 91% or more, 92% or more, 93% or more, 94% or more, 95% or more, 96% or more, 97% or more, 98% or more or 99% or more complementary to each other.
Primers that are substantially complimentary to a target nucleic acid sequence are also substantially identical to the compliment of the target nucleic acid sequence. That is, primers are substantially identical to the anti-sense strand of the nucleic acid. As referred to herein, “substantially identical” with respect to sequences refers to nucleotide sequences that are 55% or more, 56% or more, 57% or more, 58% or more, 59% or more, 60% or more, 61% or more, 62% or more, 63% or more, 64% or more, 65% or more, 66% or more, 67% or more, 68% or more, 69% or more, 70% or more, 71% or more, 72% or more, 73% or more, 74% or more, 75% or more, 76% or more, 77% or more, 78% or more, 79% or more, 80% or more, 81% or more, 82% or more, 83% or more, 84% or more, 85% or more, 86% or more, 87% or more, 88% or more, 89% or more, 90% or more, 91% or more, 92% or more, 93% or more, 94% or more, 95% or more, 96% or more, 97% or more, 98% or more or 99% or more identical to each other. One test for determining whether two nucleotide sequences are substantially identical is to determine the percent of identical nucleotide sequences shared.
Amplification primer sequence, primer length and mismatches with the target nucleic acid are some of the parameters that affect amplification primer annealing to target nucleic acid sequences. By adjusting these parameters and others amplification primers can be designed that minimize annealing and accordingly inhibit elongation.
As used herein, the phrase “hybridizing” or grammatical variations thereof, refers to binding of a first nucleic acid molecule to a second nucleic acid molecule under nucleic acid synthesis conditions. Hybridizing can include instances where a first nucleic acid molecule binds to a second nucleic acid molecule, where the first and second nucleic acid molecules are complementary. As used herein, “specifically hybridizes” refers to preferential hybridization under nucleic acid synthesis conditions of a primer, to a nucleic acid molecule having a sequence complementary to the primer compared to hybridization to a nucleic acid molecule not having a complementary sequence. For example, specific hybridization includes the hybridization of a primer to a target nucleic acid sequence that is complementary to the primer.
A primer, in certain embodiments, may contain a modification such as inosines, abasic sites, locked nucleic acids, minor groove binders, duplex stabilizers (e.g., acridine, spermidine), Tm modifiers or any modifier that changes the binding properties of the primers or probes.
In some embodiments, amplification primers are designed to result in amplicons of about 30 base pairs to about 300 base pairs. In some embodiments, when the sample comprises circulating cell free nucleic acid, amplification primers are designed to result in amplicons greater than about 50 base pairs and less than about 166 pairs. Circulating cell free genomic nucleic acid (DNA) is less degraded (the mean is about 166 bp) than circulating cell free mitochondrial nucleic acid (DNA) (the mean is about 50 bp), Designing primers so amplicons are in the size range of greater than about 50 base pairs to less than about 166 base pairs results in amplification of a large portion of circulating cell free genomic nucleic acid and amplification of a smaller portion of the circulating cell free mitochondrial nucleic acid. This selective amplification can allow for the detection and quantitation of genomic nucleic acid in the same assay as mitochondrial nucleic acid. In some embodiments, the size of the amplicons is greater than about 60 bp and less than about 100 bp. In some embodiments, the size of the amplicons is greater than about 70 bp and less than about 100 bp.
In some embodiments, amplification primers are designed to amplify a paralog 5′X—V—Y3′ and the mitochondrial polynucleotide and the genomic polynucleotide of a set are reproducibly amplified relative to each other by a single pair of amplification primers that hybridize to an internal polynucleotide within X and Y. One primer in the pair hybridizes to a polynucleotide within X and the other primer in the pair hybridizes to another polynucleotide within Y. The mitochondrial polynucleotide of a set is co-amplified with the genomic polynucleotide of a set using a single primer pair that binds to regions upstream and downstream of V. In some embodiments, mitochondrial and genomic polynucleotides are amplified under conditions that amplify each species at a “substantially reproducible level”. In certain embodiments, a “substantially reproducible level” varies by about 1% or less. In some embodiments, a substantially reproducible level varies by 10%, 5%, 4%, 3%, 2%, 1.5%, 1%, 0.5%, 0.1%, 0.05%, 0.01%, 0.005% or 0.001%. Unbiased amplification of the mitochondrial and genomic polynucleotides of a set allows for a direct comparison of the amplicons in a single reaction and without the need for an internal standard. In some embodiments, determining the identity and quantity of the nucleotide at V is a good marker for relative copy number quantification.
In some embodiments, amplification primers are designed so the mitochondrial polynucleotide and the genomic polynucleotide of a set are amplified by different species specific pairs of amplification primers. The amplification primers are designed to hybridize to flanking polynucleotides that are 5′ to X and 3′ to Y. The flanking polynucleotides are different at one or more nucleotide positions between mitochondrial and genomic polynucleotides. The regions upstream and downstream of X and Y should have enough differences to allow for design of amplification primer pairs that are specific for mitochondrial polynucleotides or genomic polynucleotides. The mitochondrial polynucleotide amplification primers will not bind the genomic polynucleotide and vice versa. In some embodiments, methods employing amplification primers specific for mitochondrial polynucleotides can be used to reduce the amplification of the abundant mitochondrial polynucleotide relative to the amplification of the less abundant genomic polynucleotide. In some embodiments, the amplification primer that is specific for the mitochondrial polynucleotide is designed not to hybridize as well to amplification primer binding site (e.g., binding site contains nucleotide mismatches and/or nucleotides that have reduced hydrogen binding) as does the amplification primer that is specific for the genomic polynucleotide in a set. The amplicons corresponding to the mitochondrial polynucleotide are reduced with respect to the amplicons corresponding to the genomic polynucleotide in each set.
In some embodiments, the amplification primers that specifically hybridize to the mitochondrial polynucleotide are provided at a lower concentration than the concentration of the amplification primers that specifically hybridize to the genomic polynucleotide. The amplicons corresponding to the mitochondrial polynucleotide are reduced with respect to the amplicons corresponding to the genomic polynucleotide in each set. In some embodiments, the concentration of the amplification primers that specifically hybridize to the mitochondrial polynucleotide is about 2 times to about 30 times lower than the concentration of amplification primers that specifically hybridize to the genomic polynucleotide in a set. The concentration of the amplification primer for the mitochondrial polynucleotide relative to the concentration of the amplification primer for the genomic polynucleotide can be optimized to try to achieve equal signal strength based on the following scheme, for example.
In some embodiments, the two approaches can be used together.
In some embodiments, amplification primers are designed to amplify a paralog 5′X—V—Y3′ in which the mitochondrial polynucleotide and the genomic polynucleotide of such a set are amplified by an amplification primer that hybridizes to a polynucleotide within X and two different amplification primers that hybridize to flanking polynucleotides that are 3′ to Y. The amplification primers that hybridize to X are the same for the mitochondrial and genomic polynucleotide, as X is identical for the mitochondrial and genomic polynucleotide. The amplification primers that hybridize to flanking polynucleotides 3′ to Y are different for the mitochondrial and genomic polynucleotide. In some embodiments, amplification primers are designed to amplify a paralog 5′X—V—Y3′ in which the mitochondrial polynucleotide and the genomic polynucleotide of such a set are amplified by an amplification primer that hybridizes to a polynucleotide within Y and two different amplification primers that hybridize to flanking polynucleotides that are 5′ to X. The amplification primers that hybridize to Y are the same for the mitochondrial and genomic polynucleotide, as Y is identical for the mitochondrial and genomic polynucleotide. The amplification primers that hybridize to flanking polynucleotides 5′ to X are different for the mitochondrial and genomic polynucleotide. Having at least one amplification primer for the mitochondrial and genomic polynucleotides that is different allows for an assay to be designed so the amplification of the mitochondrial polynucleotide of a set is reduced relative to the amplification of the genomic polynucleotide of the set. The concentration of the amplification primer specific for the mitochondrial polynucleotide can be made lower than the concentration of the amplification primer specific for the genomic polynucleotide. In some embodiments, the forward amplification primers specifically hybridize to and amplify either mitochondrial or genomic polynucleotides are at different concentrations relative to each other (e.g., 0.1 (mitochondrial) and 1.0 (genomic)) and the reverse amplification primer is universal and hybridizes and amplifies both species of polynucleotides (mitochondrial and genomic) is at the same relative concentration as the genomic specific forward amplification primer (e.g., 1.0). In some embodiments, the reverse amplification primers specifically hybridize to and amplify either mitochondrial or genomic polynucleotides are at different concentrations relative to each other (e.g., 0.1 (mitochondrial) and 1.0 (genomic)) and the forward amplification primer is universal and hybridizes and amplifies both species of polynucleotides (mitochondrial and genomic) is present at the same relative concentration as the genomic specific reverse amplification primer (e.g., 1.0). In some embodiments, the concentration of the amplification primer that specifically hybridizes to the mitochondrial polynucleotide is about 2 times to about 30 times lower than the concentration of the amplification primer that specifically hybridizes to the genomic polynucleotide in a set. Optimization of concentration of amplification primers is as described above. Forward and reverse amplification primers and their relative concentrations can be chosen based on the sequence of the polynucleotides that are to be amplified using known principles of PCR.
Alternatively, a primer binding site for the amplification primer specific for the mitochondrial polynucleotide can be selected so that the amplification primer for the mitochondrial polynucleotide does not hybridize to its primer binding site as well (e.g., binding site contains nucleotide mismatches and/or nucleotides that have reduced hydrogen binding) as the amplification primer specific for the genomic polynucleotide.
In some embodiments, the two approaches can be used together.
In some embodiments, amplification primers are designed so a paralog 5′J-V—K3′ of the mitochondrial polynucleotides of a set or a paralog 5′J-V—K3′ of the nuclear polynucleotides of a set are reproducibly amplified relative to each other by a single pair of amplification primers that hybridize to an internal polynucleotide within J and K. One primer in the pair hybridizes to a polynucleotide within J and the other primer in the pair hybridizes to another polynucleotide within K. The mitochondrial polynucleotides of a set are co-amplified using a single primer pair that binds to regions upstream and downstream of V. The nuclear polynucleotides of a set are co-amplified using a single primer pair that binds to regions upstream and downstream of V. In some embodiments, mitochondrial polynucleotides of a set are amplified under conditions that amplify each polynucleotide at a “substantially reproducible level”. In some embodiments, nuclear polynucleotides of a set are amplified under conditions that amplify each polynucleotide at a “substantially reproducible level.” In certain embodiments, a “substantially reproducible level” varies by about 1% or less. In some embodiments, a substantially reproducible level varies by 10%, 5%, 4%, 3%, 2%, 1.5%, 1%, 0.5%, 0.1%, 0.05%, 0.01%, 0.005% or 0.001%. Unbiased amplification of the mitochondrial polynucleotides of a set allow for a direct comparison of the amplicons in a single reaction. Unbiased amplification of nuclear polynucleotides of a set allow for a direct comparison of the amplicons in a single reaction. In some embodiments, determining the identity and quantity of the nucleotide at V is a good marker for relative copy number quantification.
Quantitation of Amplicons
In some embodiments, amplicons corresponding to the mitochondrial polynucleotide of a set and amplicons corresponding to the genomic polynucleotide of a set are quantified. In some embodiments amplicons are quantified by determining the amount of a nucleotide at V in the amplicons corresponding to the mitochondrial polynucleotide of a set and the amount of the nucleotide at V in the amplicons corresponding to the genomic polynucleotide of a set is determined. Based on the amount of a nucleotide at V in the amplicons corresponding to the mitochondrial polynucleotide of a set and the amount of the nucleotide at V in the amplicons corresponding to the genomic polynucleotide of a set a ratio of the amount of a mitochondrial polynucleotide relative to the amount of a genomic polynucleotide can be obtained and used to determine the dosage of mitochondrial nucleic acid relative to genomic nucleic acid.
In some embodiments, amplicons corresponding to the mitochondrial polynucleotides of a set are quantified and amplicons corresponding to the nuclear polynucleotides of a set are quantified. In some embodiments amplicons are quantified by determining the amount of a nucleotide at V in the amplicons corresponding to each of the mitochondrial polynucleotides of a set (e.g., first and second species, human and chimpanzee). In some embodiments amplicons are quantified by determining the amount of a nucleotide at V in the amplicons corresponding to each of the nuclear polynucleotides of a set (e.g., first and second species, human and chimpanzee).
Any suitable technology can be used to detect and/or quantify amplicons. Non-limiting examples of technologies that can be utilized to detect and/or quantify amplicons include primer extension assays, amplification (e.g., digital PCR, quantitative polymerase chain reaction (qPCR)), sequencing (e.g., nanopore sequencing, massive parallel sequencing), mass spectrometry, array hybridization (e.g., microarray hybridization; gene-chip analysis), flow cytometry, gel electrophoresis (e.g., capillary electrophoresis), cytofluorimetric analysis, fluorescence microscopy, confocal laser scanning microscopy, laser scanning cytometry, affinity chromatography, manual batch mode separation, electric field suspension, the like and combinations of the foregoing. Further detail is provided hereafter for certain amplicon detection and/or quantification technologies.
Primer Extension Reactions
In some embodiments, determining the amount of a nucleotide at V in the amplicons corresponding to the mitochondrial polynucleotide of a set and the amount of the nucleotide at V in the amplicons corresponding to the genomic polynucleotide of a set is by a primer extension reaction process. In some embodiments, determining the amount of a nucleotide at V in the amplicons corresponding to each of the mitochondrial polynucleotides of a set and the amount of the nucleotide at V in the amplicons corresponding to each of the nuclear polynucleotides of a set is by a primer extension reaction process. An extension reaction is conducted under extension conditions, and a variety of such conditions are known and selected for a particular application. Extension conditions can include certain reagents, including without limitation, one or more oligonucleotides, extension nucleotides (e.g., nucleotide triphosphates (dNTPs)), chain terminating reagents or nucleotides (e.g., one or more dideoxynucleotide triphosphates (ddNTPs) or acyclic terminators), one or more salts (e.g., magnesium-containing salt), one or more buffers (e.g., with beta-NAD, Triton X-100), and one or more polymerizing agents (e.g., DNA polymerase, RNA polymerase).
Extension can be conducted under isothermal conditions or under non-isothermal conditions (e.g., thermocycled conditions), in certain embodiments. One or more nucleic acid species can be extended in an extension reaction and one or more molecules of each nucleic acid species can be extended. A nucleic acid can be extended by one or more nucleotides, and in some embodiments, the extension product is about 10 nucleotides to about 10,000 nucleotides in length, about 10 to about 1000 nucleotides in length, about 10 to about 500 nucleotides in length, 10 to about 100 nucleotides in length, and sometimes about 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 80, 85, 90, 95, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, 600, 700, 800, 900 or 1000 nucleotides in length. Incorporation of a terminating nucleotide (e.g., ddNTP), the hybridization location, or other factors, can determine the length to which the oligonucleotide is extended. In certain embodiments, amplification and extension processes are carried out in the same detection procedure.
In some embodiments an extension reaction includes multiple temperature cycles repeated to amplify the amount of extension product in the reaction. In some embodiments the extension reaction is cycled 2 or more times. In some embodiments the extension reaction is cycled 10 or more times. In some embodiments the extension reaction is cycled about 10, 15, 20, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 200, 300, 400, 500 or 600 or more times. In some embodiments the extension reaction is cycled 20 to 50 times. In some embodiments the extension reaction is cycled 20 to 100 times. In some embodiments the extension reaction is cycled 20 to 300 times. In some embodiments the extension reaction is cycled 200 to 300 times. In certain embodiments, the extension reaction is cycled at least 50, 55, 60, 65, 70, 75, 80, 85, 90, 95 or 100 times.
Primer extension processes include methods such as iPLEX™ or homogeneous MassExtend® (hME) (see, for example, U.S. Published Patent Application No. 2013/0237428 A1, U.S. Pat. Nos. 8,349,566, and 8,003,317, the contents of which are incorporated in their entirety by reference herein), in which a mixture of minor nucleic acid species (e.g., mutant alleles) and major nucleic acid species (e.g., wild type alleles) are subjected to a polymerase chain reaction (PCR) amplification using a set of amplification primers, a polymerase and deoxynucleotides (dNTPs), thereby generating amplicons of the wild type and mutant species. After treatment with shrimp alkaline phosphatase (SAP) to dephosphorylate unincorporated dNTPs, the amplicon mixture is extended using extension primers (unextended primers or UEPs), a polymerase and a termination mix that includes chain terminating reagents (e.g., dideoxunucleotides or ddNTPs). The UEPs hybridize to the amplicons and are extended either up to the site of variance between the mutant and wild type species (i.e., extension stops at the mutation site where there is a difference in bases between the mutant and wild type species to generate single base extension products or SBEs, as in iPLEX™) or a few bases (e.g., 2-3 bases) past the site of variance (as in, for example, the hME method). The resulting extension products can then be processed (e.g., by desalting prior to mass spectrometry) and analyzed for the presence of the mutant alleles based on a difference in detection signal (e.g., mass) relative to the wild type allele.
The above-described iPLEX™ and homogeneous MassExtend® (hME) methods use an equimolar mixture of ddNTPs in the extension step for generating extension products corresponding to wild type and mutant species. Thus, in the iPLEX™ and homogeneous MassExtend® (hME) methods, all other factors being equal with the exception of the major nucleic acid species being present in a large excess relative to the minor nucleic acid species, the majority of the UEPs hybridize to the major nucleic acid species and are extended using the chain terminating reagent specific for the major nucleic acid species. Relatively few molecules of UEP are available for hybridization and extension of the minor nucleic acid species. This compromises the magnitude of the detection signal corresponding to the minor nucleic acid species, which is overshadowed by the predominant detection signal from the major nucleic acid species and may be subsumed by background noise.
In certain embodiments, the extension step uses a limiting concentration of chain terminating reagent specific for the mitochondrial polynucleotide, relative to the chain terminating reagent specific for the genomic polynucleotide. Amplicons are contacted with extension primers under extension conditions with chain terminating reagents. The chain terminating reagent that is specific for the amplicons corresponding to the mitochondrial polynucleotide is not specific for the amplicons corresponding to genomic polynucleotide and the chain terminating reagent specific for the amplicons corresponding to the genomic polynucleotide is not specific for the amplicons corresponding to mitochondrial polynucleotide. The extension primers are extended up to V, thereby generating chain terminated extension products corresponding to the mitochondrial polynucleotide or the genomic polynucleotide. The concentration of the chain terminating reagent specific for the mitochondrial polynucleotide is less than the concentration of the chain terminating reagent specific for the genomic polynucleotide.
In some embodiments, the ratio of the amount of extension product corresponding to the mitochondrial polynucleotides relative to the amount of extension product corresponding to the genomic polynucleotide is determined and the amount of mitochondrial nucleic acid relative to the amount of genomic nucleic acid in the sample is determined based on the ratio and based on the concentration of the chain terminating reagent specific for the mitochondrial polynucleotide relative to the concentration of the chain terminating reagent specific for genomic polynucleotide.
In certain embodiments, the concentration of the chain terminating reagent specific for a mitochondrial polynucleotide is between about 1% to about 20% of the concentration of the chain terminating reagent specific for a genomic polynucleotide. The concentration of the chain terminating reagent specific for a mitochondrial polynucleotide generally being between about 0.5% to less than about 20% of the concentration of the chain terminating reagent specific for a genomic polynucleotide, about 0.5% to less than about 15%, about 1% to about 15%, about 1% to about 10%, about 2% to about 10% or about 1%, 1.5%, 2%, 2.5%, 3%, 3.5%, 4%, 4.5%, 5%, 5.5%, 6%, 6.5%, 7%, 7.5%, 8%, 8.5%, 9%, 9.5% or 10% of the concentration of the chain terminating reagent specific for a genomic polynucleotide.
In certain embodiments, the extension step uses an equimolar concentration of chain terminating reagents specific for each of the mitochondrial polynucleotides of a set or an equimolar concentration of chain terminating reagents specific for each of the nuclear polynucleotides of a set. Amplicons are contacted with extension primers under extension conditions with chain terminating reagents. The chain terminating reagent that is specific for the amplicons corresponding to the mitochondrial polynucleotide of the first species is not specific for the amplicons corresponding to the mitochondrial polynucleotide of the second species; and the chain terminating reagent specific for the amplicons corresponding to the nuclear polynucleotide of the first species is not specific for the amplicons corresponding to the nuclear polynucleotide of the second species. The primers are extended up to V, thereby generating chain terminated extension products corresponding to the mitochondrial polynucleotide of the first species, the mitochondrial polynucleotide of the second species, the nuclear polynucleotide of the first species and the nuclear polynucleotide of the second species.
In some embodiments, a ratio of the amount of extension product corresponding to the mitochondrial polynucleotide of the second species to the amount of extension product corresponding to the mitochondrial polynucleotide of the first species is determined. In some embodiments, a ratio of the amount of extension product corresponding to the nuclear polynucleotide of the second species to the amount of extension product corresponding to the nuclear polynucleotide of the first species and the amount of mitochondrial nucleic acid relative to the amount of nuclear nucleic acid in the sample is determined based on the ratios.
The term “up to” as used herein includes nucleotide position V.
In some embodiments, the chain terminating reagents are chain terminating nucleotides. In some embodiments, the chain terminating nucleotides independently are selected from among ddATP, ddGTP, ddCTP, ddTTP and ddUTP. In some embodiments, the chain terminating reagents comprise one or more acyclic terminators. In some embodiments, one or more of the chain terminating reagents comprises a detectable label. In some embodiments, the label is a fluorescent label or dye. In some embodiments, the label is a mass label and detection is by mass spectrometry.
Any suitable extension reaction can be selected and utilized. An extension reaction can be utilized, for example, to discriminate the nucleotide of a mitochondrial polynucleotide from the nucleotide of a genomic polynucleotide at V, to discriminate the nucleotide of a mitochondrial polynucleotide of a first species from the nucleotide of a mitochondrial polynucleotide of a second species at V or to discriminate the nucleotide of a nuclear polynucleotide of a first species from the nucleotide of a nuclear polynucleotide of a second species at V by the incorporation of deoxynucleotides and/or dideoxynucleotides to an extension oligonucleotide that hybridizes to a region adjacent to V in the amplicon. The primer often is extended with a polymerase. In some embodiments, the oligonucleotide is extended by only one deoxynucleotide or dideoxynucleotide complementary to the V site. In some embodiments, an oligonucleotide may be extended by dNTP incorporation and terminated by a ddNTP, or terminated by ddNTP incorporation without dNTP extension in certain embodiments. Extension may be carried out using unmodified extension oligonucleotides and unmodified dideoxynucleotides, unmodified extension oligonucleotides and biotinylated dideoxynucleotides, extension oligonucleotides containing a deoxyinosine and unmodified dideoxynucleotides, extension oligonucleotides containing a deoxyinosine and biotinylated dideoxynucleotides, extension by biotinylated dideoxynucleotides, or extension by biotinylated deoxynucleotide and/or unmodified dideoxynucleotides, in some embodiments.
The extension products corresponding to the mitochondrial polynucleotide and the genomic polynucleotide of a set, the mitochondrial polynucleotide of a first species and the mitochondrial polynucleotide of a second species of a set or the nuclear polynucleotide of a first species and the nuclear polynucleotide of a second species of a set that are obtained by the methods provided herein can be detected by a variety of methods. For example, the extension primers (UEPs) and/or the chain terminating reagents may be labeled with any type of chemical group or moiety that allows for detection of a signal and/or quantification of the signal including, but not limited to, mass labels, radioactive molecules, fluorescent molecules, antibodies, antibody fragments, haptens, carbohydrates, biotin, derivatives of biotin, phosphorescent moieties, luminescent moieties, electrochemiluminescent moieties, moieties that generate an electrochemical signal upon oxidation or reduction, e.g., complexes of iron, ruthenium or osmium (see, for example, eSensor technology used by Genmark Diagnostics, Inc. e.g., as described in Pierce et al., J. Clin. Micribiol., 50(11):3458-3465 (2012)), chromatic moieties, and moieties having a detectable electron spin resonance, electrical capacitance, dielectric constant or electrical conductivity, or any combination of labels thereof.
The labeled extension products corresponding to the mitochondrial polynucleotide and the genomic polynucleotide of a set, the mitochondrial polynucleotide of a first species and the mitochondrial polynucleotide of a second species of a set or the nuclear polynucleotide of a first species and the nuclear polynucleotide of a second species of a set can be analyzed by a variety of methods including, but not limited to, mass spectrometry, MALDI-TOF mass spectrometry, fluorescence detection, DNA sequencing gel, capillary electrophoresis on an automated DNA sequencing machine, microchannel electrophoresis, and other methods of sequencing, mass spectrometry, time of flight mass spectrometry, quadrupole mass spectrometry, magnetic sector mass spectrometry, electric sector mass spectrometry infrared spectrometry, ultraviolet spectrometry, palentiostatic amperometry, measurement of current/electrochemical signal or by DNA hybridization techniques including Southern Blots, Slot Blots, Dot Blots, and DNA microarrays, wherein DNA fragments would be useful as both “probes” and “targets,” ELISA, fluorimetry, Fluorescence Resonance Energy Transfer (FRET), SNP-IT, GeneChips, HuSNP, BeadArray, TaqMan assay, Invader assay, MassExtend®, or MassCleave® method.
In some embodiments, a chain terminating reagent or chain terminating nucleotide includes one detectable label. In some embodiments, a first chain terminating reagent or chain terminating nucleotide includes a detectable label that is different from the detectable label of a second chain terminating reagent or chain terminating nucleotide. In some embodiments, an extension composition includes one or more chain terminating reagents or chain terminating nucleotides where each chain terminating reagent or chain terminating nucleotide includes a different detectable label. In some embodiments, an extension composition includes one or more chain terminating reagents or chain terminating nucleotides where each contains the same detection label. In some embodiments, an extension composition includes a chain terminating reagent or chain terminating nucleotide and an extension nucleotide (e.g., dNTP) and one or more of the nucleotides (e.g. terminating nucleotides and/or extension nucleotides) includes a detection label. In some embodiments, the relative amount (frequency or copy number, e.g.) of a mitochondrial polynucleotide to that of a genomic polynucleotide can be determined by the proportions of their detection signals relative to the ratio of the concentration of the chain terminating reagents specific for the mitochondrial polynucleotide to the concentration of the chain terminating reagents specific for genomic polynucleotide, using a normalization coefficient. In some embodiments the amount (e.g. copy number, concentration, percentage) of mitochondrial polynucleotide is quantified by normalizing the ratio of the signal for the genomic polynucleotide to the signal for the mitochondrial polynucleotide, using a coefficient. This coefficient is inversely proportional to the fraction of concentration of the chain terminating reagent or nucleotide specific for the mitochondrial polynucleotide compared to the concentration of the chain terminating reagent or nucleotide specific for genomic polynucleotide (i.e., the lower the fraction of mitochondrial polynucleotide-specific chain terminating reagent relative to the chain terminating reagent specific for the genomic polynucleotide, the larger the coefficient).
In some embodiments, a normalization coefficient is not required as the ratio for a sample is either compared to a population or to samples obtained from the same subject over a period of time.
Mass Spectrometry
Mass spectrometry methods typically are used to determine the mass of a molecule. In some embodiments, mass spectrometry is used to detect and/or quantify the primer extension product based on its unique mass. The relative signal strength, e.g., mass peak on a spectra, for the nucleic acid nucleic acid can indicate the relative population of the species amongst other nucleic acids in the sample (see e.g., Jurinke et al. (2004) Mol. Biotechnol. 26, 147-164).
Mass spectrometry generally works by ionizing chemical compounds to generate charged molecules or molecule fragments and measuring their mass-to-charge ratios. A typical mass spectrometry procedure involves several steps, including (1) loading a sample onto a mass spectrometry instrument followed by vaporization, (2) ionization of the sample components by any one of a variety of methods (e.g., impacting with an electron beam), resulting in charged particles (ions), (3) separation of ions according to their mass-to-charge ratio in an analyzer by electromagnetic fields, (4) detection of ions (e.g., by a quantitative method), and (5) processing of ion signals into mass spectra.
Mass spectrometry methods are known, and include without limitation quadrupole mass spectrometry, ion trap mass spectrometry, time-of-flight mass spectrometry, gas chromatography mass spectrometry and tandem mass spectrometry can be used with a method described herein. Processes associated with mass spectrometry are generation of gas-phase ions derived from the sample, and measurement of ions. Movement of gas-phase ions can be precisely controlled using electromagnetic fields generated in the mass spectrometer, and movement of ions in these electromagnetic fields is proportional to the mass to charge ratio (m/z) of each ion, which forms the basis of measuring m/z and mass. Movement of ions in these electromagnetic fields allows for containment and focusing of the ions which accounts for high sensitivity of mass spectrometry. During the course of m/z measurement, ions are transmitted with high efficiency to particle detectors that record the arrival of these ions. The quantity of ions at each m/z is demonstrated by peaks on a graph where the x axis is m/z and the y axis is relative abundance. Different mass spectrometers have different levels of resolution (i.e., the ability to resolve peaks between ions closely related in mass). Resolution generally is defined as R=m/delta m, where m is the ion mass and delta m is the difference in mass between two peaks in a mass spectrum. For example, a mass spectrometer with a resolution of 1000 can resolve an ion with a m/z of 100.0 from an ion with a m/z of 100.1.
Certain mass spectrometry methods can utilize various combinations of ion sources and mass analyzers which allows for flexibility in designing customized detection protocols. In some embodiments, mass spectrometers can be programmed to transmit all ions from the ion source into the mass spectrometer either sequentially or at the same time. In some embodiments, a mass spectrometer can be programmed to select ions of a particular mass for transmission into the mass spectrometer while blocking other ions.
Several types of mass spectrometers are available or can be produced with various configurations. In general, a mass spectrometer has the following major components: a sample inlet, an ion source, a mass analyzer, a detector, a vacuum system, and instrument-control system, and a data system. Difference in the sample inlet, ion source, and mass analyzer generally define the type of instrument and its capabilities. For example, an inlet can be a capillary-column liquid chromatography source or can be a direct probe or stage such as used in matrix-assisted laser desorption. Common ion sources are, for example, electrospray, including nanospray and microspray or matrix-assisted laser desorption. Mass analyzers include, for example, a quadrupole mass filter, ion trap mass analyzer and time-of-flight mass analyzer.
An ion formation process generally is a starting point for mass spectrum analysis. Several ionization methods are available and the choice of ionization method depends on the sample used for analysis. For example, for the analysis of polypeptides a relatively gentle ionization procedure such as electrospray ionization (ESI) can be desirable. For ESI, a solution containing the sample is passed through a fine needle at high potential which creates a strong electrical field resulting in a fine spray of highly charged droplets that is directed into the mass spectrometer. Other ionization procedures include, for example, fast-atom bombardment (FAB) which uses a high-energy beam of neutral atoms to strike a solid sample causing desorption and ionization. Matrix-assisted laser desorption ionization (MALDI) is a method in which a laser pulse is used to strike a sample that has been crystallized in an UV-absorbing compound matrix (e.g., 2,5-dihydroxybenzoic acid, alpha-cyano-4-hydroxycinammic acid, 3-hydroxypicolinic acid (3-HPA), di-ammoniumcitrate (DAC) and combinations thereof). Other ionization procedures known in the art include, for example, plasma and glow discharge, plasma desorption ionization, resonance ionization, and secondary ionization.
A variety of mass analyzers are available that can be paired with different ion sources. Different mass analyzers have different advantages as known in the art and as described herein. The mass spectrometer and methods chosen for detection depends on the particular assay, for example, a more sensitive mass analyzer can be used when a small amount of ions are generated for detection. Several types of mass analyzers and mass spectrometry methods are described below. Ion mobility mass (IM) spectrometry is a gas-phase separation method. IM separates gas-phase ions based on their collision cross-section and can be coupled with time-of-flight (TOF) mass spectrometry. IM-MS methods are known in the art.
Quadrupole mass spectrometry utilizes a quadrupole mass filter or analyzer. This type of mass analyzer is composed of four rods arranged as two sets of two electrically connected rods. A combination of rf and dc voltages are applied to each pair of rods which produces fields that cause an oscillating movement of the ions as they move from the beginning of the mass filter to the end. The result of these fields is the production of a high-pass mass filter in one pair of rods and a low-pass filter in the other pair of rods. Overlap between the high-pass and low-pass filter leaves a defined m/z that can pass both filters and traverse the length of the quadrupole. This m/z is selected and remains stable in the quadrupole mass filter while all other m/z have unstable trajectories and do not remain in the mass filter. A mass spectrum results by ramping the applied fields such that an increasing m/z is selected to pass through the mass filter and reach the detector. In addition, quadrupoles can also be set up to contain and transmit ions of all m/z by applying a rf-only field. This allows quadrupoles to function as a lens or focusing system in regions of the mass spectrometer where ion transmission is needed without mass filtering.
A quadrupole mass analyzer, as well as the other mass analyzers described herein, can be programmed to analyze a defined m/z or mass range. Since the desired mass range of nucleic acid fragment is known, in some instances, a mass spectrometer can be programmed to transmit ions of the projected correct mass range while excluding ions of a higher or lower mass range. The ability to select a mass range can decrease the background noise in the assay and thus increase the signal-to-noise ratio. Thus, in some instances, a mass spectrometer can accomplish a separation step as well as detection and identification of certain mass-distinguishable nucleic acid fragments.
Ion trap mass spectrometry utilizes an ion trap mass analyzer. Typically, fields are applied such that ions of all m/z are initially trapped and oscillate in the mass analyzer. Ions enter the ion trap from the ion source through a focusing device such as an octapole lens system. Ion trapping takes place in the trapping region before excitation and ejection through an electrode to the detector. Mass analysis can be accomplished by sequentially applying voltages that increase the amplitude of the oscillations in a way that ejects ions of increasing m/z out of the trap and into the detector. In contrast to quadrupole mass spectrometry, all ions are retained in the fields of the mass analyzer except those with the selected m/z. Control of the number of ions can be accomplished by varying the time over which ions are injected into the trap.
Time-of-flight mass spectrometry utilizes a time-of-flight mass analyzer. Typically, an ion is first given a fixed amount of kinetic energy by acceleration in an electric field (generated by high voltage). Following acceleration, the ion enters a field-free or “drift” region where it travels at a velocity that is inversely proportional to its m/z. Therefore, ions with low m/z travel more rapidly than ions with high m/z. The time required for ions to travel the length of the field-free region is measured and used to calculate the m/z of the ion.
Gas chromatography mass spectrometry often can a target in real-time. The gas chromatography (GC) portion of the system separates the chemical mixture into pulses of analyte and the mass spectrometer (MS) identifies and quantifies the analyte.
Tandem mass spectrometry can utilize combinations of the mass analyzers described above. Tandem mass spectrometers can use a first mass analyzer to separate ions according to their m/z in order to isolate an ion of interest for further analysis. The isolated ion of interest is then broken into fragment ions (called collisionally activated dissociation or collisionally induced dissociation) and the fragment ions are analyzed by the second mass analyzer. These types of tandem mass spectrometer systems are called tandem in space systems because the two mass analyzers are separated in space, usually by a collision cell. Tandem mass spectrometer systems also include tandem in time systems where one mass analyzer is used, however the mass analyzer is used sequentially to isolate an ion, induce fragmentation, and then perform mass analysis.
Mass spectrometers in the tandem in space category have more than one mass analyzer. For example, a tandem quadrupole mass spectrometer system can have a first quadrupole mass filter, followed by a collision cell, followed by a second quadrupole mass filter and then the detector. Another arrangement is to use a quadrupole mass filter for the first mass analyzer and a time-of-flight mass analyzer for the second mass analyzer with a collision cell separating the two mass analyzers. Other tandem systems are known in the art including reflectron-time-of-flight, tandem sector and sector-quadrupole mass spectrometry.
Mass spectrometers in the tandem in time category have one mass analyzer that performs different functions at different times. For example, an ion trap mass spectrometer can be used to trap ions of all m/z. A series of rf scan functions are applied which ejects ions of all m/z from the trap except the m/z of ions of interest. After the m/z of interest has been isolated, an rf pulse is applied to produce collisions with gas molecules in the trap to induce fragmentation of the ions. Then the m/z values of the fragmented ions are measured by the mass analyzer. Ion cyclotron resonance instruments, also known as Fourier transform mass spectrometers, are an example of tandem-in-time systems.
Several types of tandem mass spectrometry experiments can be performed by controlling the ions that are selected in each stage of the experiment. The different types of experiments utilize different modes of operation, sometimes called “scans,” of the mass analyzers. In a first example, called a mass spectrum scan, the first mass analyzer and the collision cell transmit all ions for mass analysis into the second mass analyzer. In a second example, called a product ion scan, the ions of interest are mass-selected in the first mass analyzer and then fragmented in the collision cell. The ions formed are then mass analyzed by scanning the second mass analyzer. In a third example, called a precursor ion scan, the first mass analyzer is scanned to sequentially transmit the mass analyzed ions into the collision cell for fragmentation. The second mass analyzer mass-selects the product ion of interest for transmission to the detector. Therefore, the detector signal is the result of all precursor ions that can be fragmented into a common product ion. Other experimental formats include neutral loss scans where a constant mass difference is accounted for in the mass scans.
For quantification, controls may be used which can provide a signal in relation to the amount of the nucleic acid fragment, for example, that is present or is introduced. A control to allow conversion of relative mass signals into absolute quantities can be accomplished by addition of a known quantity of a mass tag or mass label to each sample before detection of the nucleic acid fragments. Any mass tag that does not interfere with detection of the fragments can be used for normalizing the mass signal. Such standards typically have separation properties that are different from those of any of the molecular tags in the sample, and could have the same or different mass signatures.
A separation step sometimes can be used to remove salts, enzymes, or other buffer components from the nucleic acid sample. Several methods well known in the art, such as chromatography, gel electrophoresis, or precipitation, can be used to clean up the sample. For example, size exclusion chromatography or affinity chromatography can be used to remove salt from a sample. The choice of separation method can depend on the amount of a sample. For example, when small amounts of sample are available or a miniaturized apparatus is used, a micro-affinity chromatography separation step can be used. In addition, whether a separation step is desired, and the choice of separation method, can depend on the detection method used. Salts sometimes can absorb energy from the laser in matrix-assisted laser desorption/ionization and result in lower ionization efficiency. Thus, the efficiency of matrix-assisted laser desorption/ionization and electrospray ionization sometimes can be improved by removing salts from a sample.
Nanopores
In some embodiments, amplicons of mitochondrial and genomic (nuclear) polynucleotides are detected and/or quantified using a nanopore process. In some embodiments, determining the amount of a nucleotide at V in the amplicons corresponding to the mitochondrial polynucleotide of a set and the amount of the nucleotide at V in the amplicons corresponding to the genomic polynucleotide of a set is by using a nanopore process. In some embodiments, determining the amount of a nucleotide at V in the amplicons corresponding to the mitochondrial polynucleotide of the first species and the second species of a set and determining the amount of a nucleotide at V in the amplicons corresponding to the nuclear polynucleotide of the first species and the second species of a set is by a nanopore process.
A nanopore can be used to obtain nucleotide sequencing information for the amplicons. In some embodiments, amplicons are detected and/or quantified using a nanopore without obtaining nucleotide sequences. A nanopore is a small hole or channel, typically of the order of 1 nanometer in diameter. Certain transmembrane cellular proteins can act as nanopores (e.g., alpha-hemolysin). Nanopores can be synthesized (e.g., using a silicon platform). Immersion of a nanopore in a conducting fluid and application of a potential across it results in a slight electrical current due to conduction of ions through the nanopore. The amount of current which flows is sensitive to the size of the nanopore. As a nucleic acid fragment passes through a nanopore, the nucleic acid molecule obstructs the nanopore to a certain degree and generates a change to the current. In some embodiments, the duration of current change as the nucleic acid fragment passes through the nanopore can be measured.
In some embodiments, nanopore technology can be used in a method described herein for obtaining nucleotide sequence information for nucleic acid fragments. Nanopore sequencing is a single-molecule sequencing technology whereby a single nucleic acid molecule (e.g. DNA) is sequenced directly as it passes through a nanopore. As described above, immersion of a nanopore in a conducting fluid and application of a potential across it results in a slight electrical current due to conduction of ions through the nanopore. The amount of current which flows is sensitive to the size of the nanopore. As a DNA molecule passes through a nanopore, each nucleotide on the DNA molecule obstructs the nanopore to a different degree and generates characteristic changes to the current. The amount of current which can pass through the nanopore at any given moment therefore varies depending on whether the nanopore is blocked by an A, a C, a G, a T, or sometimes methyl-C. The change in the current through the nanopore as the DNA molecule passes through the nanopore represents a direct reading of the DNA sequence. In some embodiments, a nanopore can be used to identify individual DNA bases as they pass through the nanopore in the correct order (e.g., International Patent Application No. WO2010/004265).
There are a number of ways that nanopores can be used to sequence nucleic acid molecules. In some embodiments, an exonuclease enzyme, such as a deoxyribonuclease, is used. In this case, the exonuclease enzyme is used to sequentially detach nucleotides from a nucleic acid (e.g. DNA) molecule. The nucleotides are then detected and discriminated by the nanopore in order of their release, thus reading the sequence of the original strand. For such an embodiment, the exonuclease enzyme can be attached to the nanopore such that a proportion of the nucleotides released from the DNA molecule is capable of entering and interacting with the channel of the nanopore. The exonuclease can be attached to the nanopore structure at a site in close proximity to the part of the nanopore that forms the opening of the channel. In some embodiments, the exonuclease enzyme can be attached to the nanopore structure such that its nucleotide exit trajectory site is orientated towards the part of the nanopore that forms part of the opening.
In some embodiments, nanopore sequencing of nucleic acids involves the use of an enzyme that pushes or pulls the nucleic acid (e.g. DNA) molecule through the pore. In this case, the ionic current fluctuates as a nucleotide in the DNA molecule passes through the pore. The fluctuations in the current are indicative of the DNA sequence. For such an embodiment, the enzyme can be attached to the nanopore structure such that it is capable of pushing or pulling the target nucleic acid through the channel of a nanopore without interfering with the flow of ionic current through the pore. The enzyme can be attached to the nanopore structure at a site in close proximity to the part of the structure that forms part of the opening. The enzyme can be attached to the subunit, for example, such that its active site is orientated towards the part of the structure that forms part of the opening.
In some embodiments, nanopore sequencing of nucleic acids involves detection of polymerase bi-products in close proximity to a nanopore detector. In this case, nucleoside phosphates (nucleotides) are labeled so that a phosphate labeled species is released upon the addition of a polymerase to the nucleotide strand and the phosphate labeled species is detected by the pore. Typically, the phosphate species contains a specific label for each nucleotide. As nucleotides are sequentially added to the nucleic acid strand, the bi-products of the base addition are detected. The order that the phosphate labeled species are detected can be used to determine the sequence of the nucleic acid strand.
Probes
In some embodiments, amplicons are detected and/or quantified using one or more probes. In some embodiments, quantification comprises quantifying target nucleic acid (mitochondrial amplicon and/or genomic amplicon, mitochondrial amplicon of a first species, mitochondrial amplicon of a second species, nuclear amplicon of a first species, nuclear amplicon of a second species) specifically hybridized to the probe. In some embodiments, quantification comprises quantifying the probe in the hybridization product. In some embodiments, quantification comprises quantifying target nucleic acid specifically hybridized to the probe and quantifying the probe in the hybridization product. In some embodiments, quantification comprises quantifying the probe after dissociating from the hybridization product. Quantification of hybridization product, probe and/or nucleic acid target can comprise use of, for example, mass spectrometry, MASSARRAY and/or MASSEXTEND technology, as described herein.
In some embodiments, probes are designed such that they each hybridize to a nucleic acid of interest in a sample. For example, a probe may comprise a polynucleotide sequence that is complementary to a nucleic acid of interest or may comprise a series of monomers that can bind to a nucleic acid of interest. Probes may be any length suitable to hybridize (e.g., completely hybridize) to one or more nucleic acid fragments of interest. For example, probes may be of any length which spans or extends beyond the length of a nucleic acid fragment to which it hybridizes. Probes may be about 10 bp or more in length. For example, probes may be at least about 20, 30, 40, 50, 60, 70, 80, 100, 200, 300, 400, 500, 600, 700, 800, 900 or 1000 bp in length. In some embodiments, a detection and/or quantification method is used to detect and/or quantify probe-nucleic acid fragment duplexes.
Probes may be designed and synthesized according to methods known in the art and described herein for oligonucleotides (e.g., capture oligonucleotides). Probes also may include any of the properties known in the art and described herein for oligonucleotides. Probes herein may be designed such that they comprise nucleotides (e.g., adenine (A), thymine (T), cytosine (C), guanine (G) and uracil (U)), modified nucleotides (e.g., mass-modified nucleotides, pseudouridine, dihydrouridine, inosine (I), and 7-methylguanosine), synthetic nucleotides, degenerate bases (e.g., 6H,8H-3,4-dihydropyrimido[4,5-c][1,2]oxazin-7-one (P), 2-amino-6-methoxyaminopurine (K), N6-methoxyadenine (Z), and hypoxanthine (I)), universal bases and/or monomers other than nucleotides, modified nucleotides or synthetic nucleotides, mass tags or combinations thereof.
In some embodiments, probes are dissociated (i.e., separated) from their corresponding nucleic acid fragments. Probes may be separated from their corresponding nucleic acid fragments using any method known in the art, including, but not limited to, heat denaturation. Probes can be distinguished from corresponding nucleic acid fragments by a method known in the art or described herein for labeling and/or isolating a species of molecule in a mixture. For example, a probe and/or nucleic acid fragment may comprise a detectable property such that a probe is distinguishable from the nucleic acid to which it hybridizes. Non-limiting examples of detectable properties include mass properties, optical properties, electrical properties, magnetic properties, chemical properties, and time and/or speed through an opening of known size. In some embodiments, probes and sample nucleic acid fragments are physically separated from each other. Separation can be accomplished, for example, using capture ligands, such as biotin or other affinity ligands, and capture agents, such as avidin, streptavidin, an antibody, or a receptor. A probe or nucleic acid fragment can contain a capture ligand having specific binding activity for a capture agent. For example, fragments from a nucleic acid sample can be biotinylated or attached to an affinity ligand using methods well known in the art and separated away from the probes using a pull-down assay with steptavidin-coated beads, for example. In some embodiments, a capture ligand and capture agent or any other moiety (e.g., mass tag) can be used to add mass to the nucleic acid fragments such that they can be excluded from the mass range of the probes detected in a mass spectrometer. In some embodiments, mass is added to the probes, addition of a mass tag for example, to shift the mass range away from the mass range for the nucleic acid fragments. In some embodiments, a detection and/or quantification method is used to detect and/or quantify dissociated nucleic acid fragments. In some embodiments, detection and/or quantification method is used to detect and/or quantify dissociated probes.
Quantitative PCR
In certain embodiments quantitation of amplicons is by quantitative PCR (qPCR). In some embodiments, determining the amount of a nucleotide at V in the amplicons corresponding to the mitochondrial polynucleotide of a set and the amount of the nucleotide at V in the amplicons corresponding to the genomic polynucleotide of a set is by a process that comprises qPCR using the TAQman biochemistry with two fluorescent probes each specific for either the mitochondrial or genomic nucleotide at V.
In some embodiments, determining the amount of a nucleotide at V in the amplicons corresponding to the mitochondrial polynucleotide of the first species and the second species of a set is by a qPCR process comprising two fluorescent probes specific for the nucleotide at V of the mitochondrial polynucleotide of either the first or second species or a digital PCR process. In some embodiments, determining the amount of a nucleotide at V in the amplicons corresponding to the nuclear polynucleotide of the first species and the second species of a set is by a qPCR process comprising two fluorescent probes specific for the nucleotide at V of the nuclear polynucleotide of either the first or second species or a digital PCR process. In certain embodiments, the qPCR uses TAQman biochemistry.
Digital PCR
In some embodiments, amplicons are detected and/or quantified using digital PCR technology. Digital polymerase chain reaction (digital PCR or dPCR) can be used, for example, to directly identify and quantify nucleic acids in a sample. Digital PCR can be performed in an emulsion, in some embodiments. For example, individual nucleic acids are separated, e.g., in a microfluidic chamber device, and each nucleic acid is individually amplified by PCR. Nucleic acids can be separated such that there is no more than one nucleic acid per well. In some embodiments, different probes can be used to distinguish amplicons corresponding to the mitochondrial polynucleotide of a set and amplicons corresponding to the genomic polynucleotide of a set. In certain embodiments, different probes can be used to distinguish amplicons corresponding to the mitochondrial polynucleotide of the first species and the mitochondrial polynucleotide of the second species of a set or the nuclear polynucleotide of the first species and the nuclear polynucleotide of the second species of a set.
Nucleic acid Sequencing
In certain embodiments quantitation of amplicons is by sequencing amplicons of mitochondrial and genomic (nuclear) polynucleotides. In some embodiments, the sequencing process is massive parallel sequencing. In some embodiments, the amount of a nucleotide at V in the amplicons corresponding to the mitochondrial polynucleotide of a set and the amount of the nucleotide at V in the amplicons corresponding to the genomic polynucleotide of a set is determined by the amount of the nucleotide at V is by a massive parallel sequencing process. In some embodiments, the amount of a nucleotide at V in the amplicons corresponding to the mitochondrial polynucleotide of the first species and the second species of a set and/or the amount of a nucleotide at V in the amplicons corresponding to the nuclear polynucleotide of the first species and the second species of a set is determined by a massive parallel sequencing process. Sometimes the sequencing is by a sequencing by synthesis process. In some embodiments, a sequence tag or barcode is attached to one or more amplification primers in each amplification primer pair. The term “sequence tagging” refers to incorporating a recognizable and distinct sequence into a nucleic acid or population of nucleic acids.
In some embodiments, a full or substantially full sequence is obtained and sometimes a partial sequence is obtained. Sequencing, mapping and related analytical methods are known in the art (e.g., United States Patent Application Publication US2009/0029377, incorporated by reference). Certain aspects of such processes are described hereafter.
Certain sequencing technologies generate nucleotide sequence reads. As used herein, “reads” (i.e., “a read”, “a sequence read”) are short nucleotide sequences produced by any sequencing process described herein or known in the art. Reads can be generated from one end of nucleic acid fragments (“single-end reads”), and sometimes are generated from both ends of nucleic acids (e.g., paired-end reads, double-end reads).
In some embodiments the nominal, average, mean or absolute length of single-end reads sometimes is about 20 contiguous nucleotides to about 50 contiguous nucleotides, sometimes about 30 contiguous nucleotides to about 40 contiguous nucleotides, and sometimes about 35 contiguous nucleotides or about 36 contiguous nucleotides. In some embodiments, the nominal, average, mean or absolute length of single-end reads is about 20 to about 30 bases in length. In some embodiments, the nominal, average, mean or absolute length of single-end reads is about 24 to about 28 bases in length. In some embodiments, the nominal, average, mean or absolute length of single-end reads is about 21, 22, 23, 24, 25, 26, 27, 28 or about 29 bases in length.
In certain embodiments, the nominal, average, mean or absolute length of the paired-end reads sometimes is about 10 contiguous nucleotides to about 50 contiguous nucleotides (e.g., about 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48 or 49 nucleotides in length), sometimes is about 15 contiguous nucleotides to about 25 contiguous nucleotides, and sometimes is about 17 contiguous nucleotides, about 18 contiguous nucleotides, about 20 contiguous nucleotides, about 25 contiguous nucleotides, about 36 contiguous nucleotides or about 45 contiguous nucleotides.
Reads generally are representations of nucleotide sequences in a physical nucleic acid. For example, in a read containing an ATGC depiction of a sequence, “A” represents an adenine nucleotide, “T” represents a thymine nucleotide, “G” represents a guanine nucleotide and “C” represents a cytosine nucleotide, in a physical nucleic acid. Sequence reads obtained from the blood of a pregnant female can be reads from a mixture of fetal and maternal nucleic acid. A mixture of relatively short reads can be transformed by processes described herein into a representation of a genomic nucleic acid present in the pregnant female and/or in the fetus. A mixture of relatively short reads can be transformed into a representation of a copy number variation (e.g., a maternal and/or fetal copy number variation), genetic variation or an aneuploidy, for example. Reads of a mixture of maternal and fetal nucleic acid can be transformed into a representation of a composite chromosome or a segment thereof comprising features of one or both maternal and fetal chromosomes. In certain embodiments, “obtaining” nucleic acid sequence reads of a sample from a subject and/or “obtaining” nucleic acid sequence reads of a biological specimen from one or more reference persons can involve directly sequencing nucleic acid to obtain the sequence information. In some embodiments, “obtaining” can involve receiving sequence information obtained directly from a nucleic acid by another.
Sequence reads can be mapped and the number of reads or sequence tags mapping to a specified nucleic acid region (e.g., a chromosome, a bin, a genomic section) are referred to as counts. In some embodiments, counts can be manipulated or transformed (e.g., normalized, combined, added, filtered, selected, averaged, derived as a mean, the like, or a combination thereof). In some embodiments, counts can be transformed to produce normalized counts.
Normalized counts for multiple genomic sections can be provided in a profile (e.g., a genomic profile, a chromosome profile, a profile of a segment of a chromosome). One or more different elevations in a profile also can be manipulated or transformed (e.g., counts associated with elevations can be normalized) and elevations can be adjusted.
In some embodiments, one nucleic acid sample from one individual is sequenced. In certain embodiments, nucleic acid samples from two or more biological samples, where each biological sample is from one individual or two or more individuals, are pooled and the pool is sequenced. In the latter embodiments, a nucleic acid sample from each biological sample often is identified by one or more unique identification tags.
In some embodiments, a fraction of the genome is sequenced, which sometimes is expressed in the amount of the genome covered by the determined nucleotide sequences (e.g., “fold” coverage less than 1). When a genome is sequenced with about 1-fold coverage, roughly 100% of the nucleotide sequence of the genome is represented by reads. A genome also can be sequenced with redundancy, where a given region of the genome can be covered by two or more reads or overlapping reads (e.g., “fold” coverage greater than 1). In some embodiments, a genome is sequenced with about 0.01-fold to about 100-fold coverage, about 0.2-fold to 20-fold coverage, or about 0.2-fold to about 1-fold coverage (e.g., about 0.02-, 0.03-, 0.04-, 0.05-, 0.06-, 0.07-, 0.08-, 0.09-, 0.1-, 0.2-, 0.3-, 0.4-, 0.5-, 0.6-, 0.7-, 0.8-, 0.9-, 1-, 2-, 3-, 4-, 5-, 6-, 7-, 8-, 9-, 10-, 15-, 20-, 30-, 40-, 50-, 60-, 70-, 80-, 90-fold coverage).
In certain embodiments, a subset of nucleic acid fragments is selected prior to sequencing. In certain embodiments, hybridization-based techniques (e.g., using oligonucleotide arrays) can be used to first select for nucleic acid sequences from certain regions of the mitochondrial and/or nuclear genome. In some embodiments, nucleic acid can be fractionated by size (e.g., by gel electrophoresis, size exclusion chromatography or by microfluidics-based approach). In some embodiments, a portion or subset of a pre-selected set of nucleic acid fragments is sequenced randomly. In some embodiments, the nucleic acid is amplified prior to sequencing. In some embodiments, a portion or subset of the nucleic acid is amplified prior to sequencing.
In some embodiments, a sequencing library is prepared prior to or during a sequencing process. Methods for preparing a sequencing library are known in the art and commercially available platforms may be used for certain applications. Certain commercially available library platforms may be compatible with certain nucleotide sequencing processes described herein. For example, one or more commercially available library platforms may be compatible with a sequencing by synthesis process. In some embodiments, a ligation-based library preparation method is used (e.g., ILLUMINA TRUSEQ, Illumina, San Diego Calif.). Ligation-based library preparation methods typically use a methylated adaptor design which can incorporate an index sequence at the initial ligation step and often can be used to prepare samples for single-read sequencing, paired-end sequencing and multiplexed sequencing. In some embodiments, a transposon-based library preparation method is used (e.g., EPICENTRE NEXTERA, Illumina, Inc., California). Transposon-based methods typically use in vitro transposition to simultaneously fragment and tag DNA in a single-tube reaction (often allowing incorporation of platform-specific tags and optional barcodes), and prepare sequencer-ready libraries.
Any sequencing method suitable for conducting methods described herein can be utilized. In some embodiments, a high-throughput sequencing method is used. High-throughput sequencing methods generally involve clonally amplified DNA templates or single DNA molecules that are sequenced in a massively parallel fashion within a flow cell (e.g. as described in Metzker M Nature Rev 11:31-46 (2010); Volkerding et al. Clin Chem 55:641-658 (2009)). Such sequencing methods also can provide digital quantitative information, where each sequence read is a countable “sequence tag” or “count” representing an individual clonal DNA template, a single DNA molecule, bin or chromosome. Next generation sequencing techniques capable of sequencing DNA in a massively parallel fashion are collectively referred to herein as “massively parallel sequencing” (MPS). Certain MPS techniques include a sequencing-by-synthesis process. High-throughput sequencing technologies include, for example, sequencing-by-synthesis with reversible dye terminators, sequencing by oligonucleotide probe ligation, pyrosequencing and real time sequencing. Non-limiting examples of MPS include Massively Parallel Signature Sequencing (MPSS), Polony sequencing, Pyrosequencing, Illumina (Solexa) sequencing, SOLiD sequencing, Ion semiconductor sequencing, DNA nanoball sequencing, Helioscope single molecule sequencing, single molecule real time (SMRT) sequencing, nanopore sequencing, ION Torrent and RNA polymerase (RNAP) sequencing.
Systems utilized for high-throughput sequencing methods are commercially available and include, for example, the Roche 454 platform, the Applied Biosystems SOLID platform, the Helicos True Single Molecule DNA sequencing technology, the sequencing-by-hybridization platform from Affymetrix Inc., the single molecule, real-time (SMRT) technology of Pacific Biosciences, the sequencing-by-synthesis platforms from 454 Life Sciences, Illumina/Solexa and Helicos Biosciences, and the sequencing-by-ligation platform from Applied Biosystems. The ION TORRENT technology from Life technologies and nanopore sequencing also can be used in high-throughput sequencing approaches.
In some embodiments, first generation technology, such as, for example, Sanger sequencing including the automated Sanger sequencing, can be used in a method provided herein. Additional sequencing technologies that include the use of developing nucleic acid imaging technologies (e.g. transmission electron microscopy (TEM) and atomic force microscopy (AFM)), also are contemplated herein. Examples of various sequencing technologies are described below.
A nucleic acid sequencing technology that may be used in a method described herein is sequencing-by-synthesis and reversible terminator-based sequencing (e.g. Illumina's Genome Analyzer; Genome Analyzer II; HISEQ 2000; HISEQ 2500 (IIlumina, San Diego Calif.)). With this technology, millions of nucleic acid (e.g. DNA) fragments can be sequenced in parallel. In one example of this type of sequencing technology, a flow cell is used which contains an optically transparent slide with 8 individual lanes on the surfaces of which are bound oligonucleotide anchors (e.g., adaptor primers). A flow cell often is a solid support that can be configured to retain and/or allow the orderly passage of reagent solutions over bound analytes. Flow cells frequently are planar in shape, optically transparent, generally in the millimeter or sub-millimeter scale, and often have channels or lanes in which the analyte/reagent interaction occurs.
In certain sequencing by synthesis procedures, for example, template DNA (e.g., circulating cell-free DNA (ccfDNA)) sometimes can be fragmented into lengths of several hundred base pairs in preparation for library generation. In some embodiments, library preparation can be performed without further fragmentation or size selection of the template DNA (e.g., ccfDNA). Sample isolation and library generation may be performed using automated methods and apparatus, in certain embodiments. Briefly, template DNA is end repaired by a fill-in reaction, exonuclease reaction or a combination of a fill-in reaction and exonuclease reaction. The resulting blunt-end repaired template DNA is extended by a single nucleotide, which is complementary to a single nucleotide overhang on the 3′ end of an adapter primer, and often increases ligation efficiency. Any complementary nucleotides can be used for the extension/overhang nucleotides (e.g., A/T, C/G), however adenine frequently is used to extend the end-repaired DNA, and thymine often is used as the 3′ end overhang nucleotide.
In certain sequencing by synthesis procedures, for example, adapter oligonucleotides are complementary to the flow-cell anchors, and sometimes are utilized to associate the modified template DNA (e.g., end-repaired and single nucleotide extended) with a solid support, such as the inside surface of a flow cell, for example. In some embodiments, the adapter also includes identifiers (i.e., indexing nucleotides, or “barcode” nucleotides (e.g., a unique sequence of nucleotides usable as an identifier to allow unambiguous identification of a sample and/or chromosome)), one or more sequencing primer hybridization sites (e.g., sequences complementary to universal sequencing primers, single end sequencing primers, paired end sequencing primers, multiplexed sequencing primers, and the like), or combinations thereof (e.g., adapter/sequencing, adapter/identifier, adapter/identifier/sequencing). Identifiers or nucleotides contained in an adapter often are six or more nucleotides in length, and frequently are positioned in the adaptor such that the identifier nucleotides are the first nucleotides sequenced during the sequencing reaction. In certain embodiments, identifier nucleotides are associated with a sample but are sequenced in a separate sequencing reaction to avoid compromising the quality of sequence reads. Subsequently, the reads from the identifier sequencing and the DNA template sequencing are linked together and the reads de-multiplexed. After linking and de-multiplexing the sequence reads and/or identifiers can be further adjusted or processed as described herein.
In certain sequencing by synthesis procedures, utilization of identifiers allows multiplexing of sequence reactions in a flow cell lane, thereby allowing analysis of multiple samples per flow cell lane. The number of samples that can be analyzed in a given flow cell lane often is dependent on the number of unique identifiers utilized during library preparation and/or probe design. Non limiting examples of commercially available multiplex sequencing kits include Illumina's multiplexing sample preparation oligonucleotide kit and multiplexing sequencing primers and PhiX control kit (e.g., Illumina's catalog numbers PE-400-1001 and PE-400-1002, respectively). A method described herein can be performed using any number of unique identifiers (e.g., 4, 8, 12, 24, 48, 96, or more). The greater the number of unique identifiers, the greater the number of samples and/or chromosomes, for example, that can be multiplexed in a single flow cell lane. Multiplexing using 12 identifiers, for example, allows simultaneous analysis of 96 samples (e.g., equal to the number of wells in a 96 well microwell plate) in an 8 lane flow cell. Similarly, multiplexing using 48 identifiers, for example, allows simultaneous analysis of 384 samples (e.g., equal to the number of wells in a 384 well microwell plate) in an 8 lane flow cell.
In certain sequencing by synthesis procedures, adapter-modified, single-stranded template DNA is added to the flow cell and immobilized by hybridization to the anchors under limiting-dilution conditions. In contrast to emulsion PCR, DNA templates are amplified in the flow cell by “bridge” amplification, which relies on captured DNA strands “arching” over and hybridizing to an adjacent anchor oligonucleotide. Multiple amplification cycles convert the single-molecule DNA template to a clonally amplified arching “cluster,” with each cluster containing approximately 1000 clonal molecules. Approximately 1×10{circumflex over ( )}9 separate clusters can be generated per flow cell. For sequencing, the clusters are denatured, and a subsequent chemical cleavage reaction and wash leave only forward strands for single-end sequencing. Sequencing of the forward strands is initiated by hybridizing a primer complementary to the adapter sequences, which is followed by addition of polymerase and a mixture of four differently colored fluorescent reversible dye terminators. The terminators are incorporated according to sequence complementarity in each strand in a clonal cluster. After incorporation, excess reagents are washed away, the clusters are optically interrogated, and the fluorescence is recorded. With successive chemical steps, the reversible dye terminators are unblocked, the fluorescent labels are cleaved and washed away, and the next sequencing cycle is performed. This iterative, sequencing-by-synthesis process sometimes requires approximately 2.5 days to generate read lengths of 36 bases. With 50×106 clusters per flow cell, the overall sequence output can be greater than 1 billion base pairs (Gb) per analytical run.
Another nucleic acid sequencing technology that may be used with a method described herein is 454 sequencing (Roche). 454 sequencing uses a large-scale parallel pyrosequencing system capable of sequencing about 400-600 megabases of DNA per run. The process typically involves two steps. In the first step, sample nucleic acid (e.g. DNA) is sometimes fractionated into smaller fragments (300-800 base pairs) and polished (made blunt at each end). Short adaptors are then ligated onto the ends of the fragments. These adaptors provide priming sequences for both amplification and sequencing of the sample-library fragments. One adaptor (Adaptor B) contains a 5′-biotin tag for immobilization of the DNA library onto streptavidin-coated beads. After nick repair, the non-biotinylated strand is released and used as a single-stranded template DNA (sstDNA) library. The sstDNA library is assessed for its quality and the optimal amount (DNA copies per bead) needed for emPCR is determined by titration. The sstDNA library is immobilized onto beads. The beads containing a library fragment carry a single sstDNA molecule. The bead-bound library is emulsified with the amplification reagents in a water-in-oil mixture. Each bead is captured within its own microreactor where PCR amplification occurs. This results in bead-immobilized, clonally amplified DNA fragments.
In the second step of 454 sequencing, single-stranded template DNA library beads are added to an incubation mix containing DNA polymerase and are layered with beads containing sulfurylase and luciferase onto a device containing pico-liter sized wells. Pyrosequencing is performed on each DNA fragment in parallel. Addition of one or more nucleotides generates a light signal that is recorded by a CCD camera in a sequencing instrument. The signal strength is proportional to the number of nucleotides incorporated. Pyrosequencing exploits the release of pyrophosphate (PPi) upon nucleotide addition. PPi is converted to ATP by ATP sulfurylase in the presence of adenosine 5′ phosphosulfate. Luciferase uses ATP to convert luciferin to oxyluciferin, and this reaction generates light that is discerned and analyzed (see, for example, Margulies, M. et al. Nature 437:376-380 (2005)).
Another nucleic acid sequencing technology that may be used in a method provided herein is Applied Biosystems' SOLiDTM technology. In SOLiDTM sequencing-by-ligation, a library of nucleic acid fragments is prepared from the sample and is used to prepare clonal bead populations. With this method, one species of nucleic acid fragment will be present on the surface of each bead (e.g. magnetic bead). Sample nucleic acid (e.g. genomic DNA) is sheared into fragments, and adaptors are subsequently attached to the 5′ and 3′ ends of the fragments to generate a fragment library. The adapters are typically universal adapter sequences so that the starting sequence of every fragment is both known and identical. Emulsion PCR takes place in microreactors containing all the necessary reagents for PCR. The resulting PCR products attached to the beads are then covalently bound to a glass slide. Primers then hybridize to the adapter sequence within the library template. A set of four fluorescently labeled di-base probes compete for ligation to the sequencing primer. Specificity of the di-base probe is achieved by interrogating every 1st and 2nd base in each ligation reaction. Multiple cycles of ligation, detection and cleavage are performed with the number of cycles determining the eventual read length. Following a series of ligation cycles, the extension product is removed and the template is reset with a primer complementary to the n−1 position for a second round of ligation cycles. Often, five rounds of primer reset are completed for each sequence tag. Through the primer reset process, each base is interrogated in two independent ligation reactions by two different primers. For example, the base at read position 5 is assayed by primer number 2 in ligation cycle 2 and by primer number 3 in ligation cycle 1.
Another nucleic acid sequencing technology that may be used in a method described herein is Helicos True Single Molecule Sequencing (tSMS). In the tSMS technique, a polyA sequence is added to the 3′ end of each nucleic acid (e.g. DNA) strand from the sample. Each strand is labeled by the addition of a fluorescently labeled adenosine nucleotide. The DNA strands are then hybridized to a flow cell, which contains millions of oligo-T capture sites that are immobilized to the flow cell surface. The templates can be at a density of about 100 million templates/cm2. The flow cell is then loaded into a sequencing apparatus and a laser illuminates the surface of the flow cell, revealing the position of each template. A CCD camera can map the position of the templates on the flow cell surface. The template fluorescent label is then cleaved and washed away. The sequencing reaction begins by introducing a DNA polymerase and a fluorescently labeled nucleotide. The oligo-T nucleic acid serves as a primer. The polymerase incorporates the labeled nucleotides to the primer in a template directed manner. The polymerase and unincorporated nucleotides are removed. The templates that have directed incorporation of the fluorescently labeled nucleotide are detected by imaging the flow cell surface. After imaging, a cleavage step removes the fluorescent label, and the process is repeated with other fluorescently labeled nucleotides until the desired read length is achieved. Sequence information is collected with each nucleotide addition step (see, for example, Harris T. D. et al., Science 320:106-109 (2008)).
Another nucleic acid sequencing technology that may be used in a method provided herein is the single molecule, real-time (SMRTTM) sequencing technology of Pacific Biosciences. With this method, each of the four DNA bases is attached to one of four different fluorescent dyes. These dyes are phospholinked. A single DNA polymerase is immobilized with a single molecule of template single stranded DNA at the bottom of a zero-mode waveguide (ZMW). A ZMW is a confinement structure which enables observation of incorporation of a single nucleotide by DNA polymerase against the background of fluorescent nucleotides that rapidly diffuse in an out of the ZMW (in microseconds). It takes several milliseconds to incorporate a nucleotide into a growing strand. During this time, the fluorescent label is excited and produces a fluorescent signal, and the fluorescent tag is cleaved off. Detection of the corresponding fluorescence of the dye indicates which base was incorporated. The process is then repeated.
Another nucleic acid sequencing technology that may be used in a method described herein is ION TORRENT (Life Technologies) single molecule sequencing which pairs semiconductor technology with a simple sequencing chemistry to directly translate chemically encoded information (A, C, G, T) into digital information (0, 1) on a semiconductor chip. ION TORRENT uses a high-density array of micro-machined wells to perform nucleic acid sequencing in a massively parallel way. Each well holds a different DNA molecule. Beneath the wells is an ion-sensitive layer and beneath that an ion sensor. Typically, when a nucleotide is incorporated into a strand of DNA by a polymerase, a hydrogen ion is released as a byproduct. If a nucleotide, for example a C, is added to a DNA template and is then incorporated into a strand of DNA, a hydrogen ion will be released. The charge from that ion will change the pH of the solution, which can be detected by an ion sensor. A sequencer can call the base, going directly from chemical information to digital information. The sequencer then sequentially floods the chip with one nucleotide after another. If the next nucleotide that floods the chip is not a match, no voltage change will be recorded and no base will be called. If there are two identical bases on the DNA strand, the voltage will be double, and the chip will record two identical bases called. Because this is direct detection (i.e. detection without scanning, cameras or light), each nucleotide incorporation is recorded in seconds.
Another nucleic acid sequencing technology that may be used in a method described herein is the chemical-sensitive field effect transistor (CHEMFET) array. In one example of this sequencing technique, DNA molecules are placed into reaction chambers, and the template molecules can be hybridized to a sequencing primer bound to a polymerase. Incorporation of one or more triphosphates into a new nucleic acid strand at the 3′ end of the sequencing primer can be detected by a change in current by a CHEMFET sensor. An array can have multiple CHEMFET sensors. In another example, single nucleic acids are attached to beads, and the nucleic acids can be amplified on the bead, and the individual beads can be transferred to individual reaction chambers on a CHEMFET array, with each chamber having a CHEMFET sensor, and the nucleic acids can be sequenced (see, for example, U.S. Patent Application Publication No. 2009/0026082).
Another nucleic acid sequencing technology that may be used in a method described herein is electron microscopy. In one example of this sequencing technique, individual nucleic acid (e.g. DNA) molecules are labeled using metallic labels that are distinguishable using an electron microscope. These molecules are then stretched on a flat surface and imaged using an electron microscope to measure sequences (see, for example, Moudrianakis E. N. and Beer M. Proc Natl Acad Sci USA. 1965 March; 53:564-71). In some embodiments, transmission electron microscopy (TEM) is used (e.g. Halcyon Molecular's TEM method). This method, termed Individual Molecule Placement Rapid Nano Transfer (IMPRNT), includes utilizing single atom resolution transmission electron microscope imaging of high-molecular weight (e.g. about 150 kb or greater) DNA selectively labeled with heavy atom markers and arranging these molecules on ultra-thin films in ultra-dense (3 nm strand-to-strand) parallel arrays with consistent base-to-base spacing. The electron microscope is used to image the molecules on the films to determine the position of the heavy atom markers and to extract base sequence information from the DNA (see, for example, International Patent Application No. WO 2009/046445).
Other sequencing methods that may be used to conduct methods herein include digital PCR and sequencing by hybridization. In sequencing by hybridization, the method involves contacting a plurality of polynucleotide sequences with a plurality of polynucleotide probes, where each of the plurality of polynucleotide probes can be optionally tethered to a substrate. The substrate can be a flat surface with an array of known nucleotide sequences, in some embodiments. The pattern of hybridization to the array can be used to determine the polynucleotide sequences present in the sample. In some embodiments, each probe is tethered to a bead, e.g., a magnetic bead or the like. Hybridization to the beads can be identified and used to identify the plurality of polynucleotide sequences within the sample.
In some embodiments, chromosome-specific sequencing is performed. In some embodiments, chromosome-specific sequencing is performed utilizing DANSR (digital analysis of selected regions). Digital analysis of selected regions enables simultaneous quantification of hundreds of loci by cfDNA-dependent catenation of two locus-specific oligonucleotides via an intervening ‘bridge’ oligo to form a PCR template. In some embodiments, chromosome-specific sequencing is performed by generating a library enriched in chromosome-specific sequences. In some embodiments, sequence reads are obtained only for a selected set of chromosomes. In some embodiments, sequence reads are obtained only for chromosomes 21, 18 and 13.
The length of the sequence read often is associated with the particular sequencing technology. High-throughput methods, for example, provide sequence reads that can vary in size from tens to hundreds of base pairs (bp). Nanopore sequencing, for example, can provide sequence reads that can vary in size from tens to hundreds to thousands of base pairs. In some embodiments, the sequence reads are of a mean, median, mode or average length of about 4 bp to 900 bp long (e.g. about 5 bp, about 10 bp, about 15 bp, about 20 bp, about 25 bp, about 30 bp, about 35 bp, about 40 bp, about 45 bp, about 50 bp, about 55 bp, about 60 bp, about 65 bp, about 70 bp, about 75 bp, about 80 bp, about 85 bp, about 90 bp, about 95 bp, about 100 bp, about 110 bp, about 120 bp, about 130, about 140 bp, about 150 bp, about 200 bp, about 250 bp, about 300 bp, about 350 bp, about 400 bp, about 450 bp, or about 500 bp. In some embodiments, the sequence reads are of a mean, median, mode or average length of about 1,000 bp or more.
Distinguishable Labels and Release
As used herein, the terms “distinguishable labels” and “distinguishable tags” refer to types of labels or tags that can be distinguished from one another and used to identify the nucleic acid (e.g., amplicon or primer extension product) to which the tag is attached. A variety of types of labels and tags may be selected and used for multiplex methods provided herein. For example, oligonucleotides, amino acids, small organic molecules, light-emitting molecules, light-absorbing molecules, light-scattering molecules, luminescent molecules, isotopes, enzymes and the like may be used as distinguishable labels or tags. In certain embodiments, oligonucleotides, amino acids, and/or small molecule organic molecules of varying lengths, varying mass-to-charge ratios, varying electrophoretic mobility (e.g., capillary electrophoresis mobility) and/or varying mass also can be used as distinguishable labels or tags. Accordingly, a fluorophore, radioisotope, colormetric agent, light emitting agent, chemiluminescent agent, light scattering agent, and the like, may be used as a label. The choice of label may depend on the sensitivity required, ease of conjugation with a nucleic acid, stability requirements, and available instrumentation. The term “distinguishable feature,” as used herein with respect to distinguishable labels and tags, refers to any feature of one label or tag that can be distinguished from another label or tag (e.g., mass and others described herein). In some embodiments, label composition of the distinguishable labels and tags can be selected and/or designed to result in optimal flight behavior in a mass spectrometer and to allow labels and tags to be distinguished at high multiplexing levels.
For methods used herein, a particular target (mitochondrial or genomic, nuclear)) nucleic acid species, amplicon species and/or extended oligonucleotide species often is paired with a distinguishable detectable label species, such that the detection of a particular label or tag species directly identifies the presence of and/or quantifies a particular target minor or nucleic acid species, amplicon species and/or extended oligonucleotide species in a particular composition. Accordingly, one distinguishable feature of a label species can be used, for example, to identify one target nucleic acid species in a composition, as that particular distinguishable feature corresponds to the particular target nucleic acid. Labels and tags may be attached to a nucleic acid (e.g., oligonucleotide) by any known methods and in any location (e.g., at the 5′ of an oligonucleotide). Thus, reference to each particular label species as “specifically corresponding” to each particular target nucleic acid species, as used herein, refers to one label species being paired with one target species. When the presence of a label species is detected, then the presence of the target nucleic acid species associated with that label species thereby is detected and/or quantified, in certain embodiments.
The term “mass distinguishable label” as used herein refers to a label that is distinguished by mass as a feature. A variety of mass distinguishable labels can be selected and used, such as for example a compomer, amino acid and/or a concatemer. Different lengths and/or compositions of nucleotide strings (e.g., nucleic acids, compomers), amino acid strings (e.g., peptides, polypeptides, compomers) and/or concatemers can be distinguished by mass and be used as labels. Any number of units can be utilized in a mass distinguishable label, and upper and lower limits of such units depends in part on the mass window and resolution of the system used to detect and distinguish such labels. Thus, the length and composition of mass distinguishable labels can be selected based in part on the mass window and resolution of the detector used to detect and distinguish the labels.
The term “compomer” as used herein refers to the composition of a set of monomeric units and not the particular sequence of the monomeric units. For a nucleic acid, the term “compomer” refers to the base composition of the nucleic acid with the monomeric units being bases. The number of each type of base can be denoted by Bn (i.e., AaCcGgTt, with A0C0G0T0 representing an “empty” compomer or a compomer containing no bases). A natural compomer is a compomer for which all component monomeric units (e.g., bases for nucleic acids and amino acids for polypeptides) are greater than or equal to zero. In certain embodiments, at least one of A, C, G or T equals 1 or more (e.g., A0C0G1T0, A1C0G1T0, A2C1G1T2, A3C2G1T5). For purposes of comparing sequences to determine sequence variations, in the methods provided herein, “unnatural” compomers containing negative numbers of monomeric units can be generated by an algorithm utilized to process data. For polypeptides, a compomer refers to the amino acid composition of a polypeptide fragment, with the number of each type of amino acid similarly denoted. A compomer species can correspond to multiple sequences. For example, the compomer A2G3 corresponds to the sequences AGGAG, GGGAA, AAGGG, GGAGA and others. In general, there is a unique compomer corresponding to a sequence, but more than one sequence can correspond to the same compomer. In certain embodiments, one compomer species is paired with (e.g., corresponds to) one target nucleic acid species, amplicon species and/or oligonucleotide species. Different compomer species have different base compositions, and distinguishable masses, in embodiments herein (e.g., A0C0G5T0 and A0C5G0T0 are different and mass-distinguishable compomer species). In some embodiments, a set of compomer species differ by base composition and have the same length. In certain embodiments, a set of compomer species differ by base compositions and length.
A nucleotide compomer used as a mass distinguishable label can be of any length for which all compomer species can be detectably distinguished, for example about 1 to 15, 5 to 20, 1 to 30, 5 to 35, 10 to 30, 15 to 30, 20 to 35, 25 to 35, 30 to 40, 35 to 45, 40 to 50, or 25 to 50, or sometimes about 55, 60, 65, 70, 75, 80, 85, 90, 85 or 100, nucleotides in length. A peptide or polypeptide compomer used as a mass distinguishable label can be of any length for which all compomer species can be detectably distinguished, for example about 1 to 20, 10 to 30, 20 to 40, 30 to 50, 40 to 60, 50 to 70, 60 to 80, 70 to 90, or 80 to 100 amino acids in length. As noted above, the limit to the number of units in a compomer often is limited by the mass window and resolution of the detection method used to distinguish the compomer species.
The terms “concatamer” and “concatemer” are used herein synonymously (collectively “concatemer”), and refer to a molecule that contains two or more units linked to one another (e.g., often linked in series; sometimes branched in certain embodiments). A concatemer sometimes is a nucleic acid and/or an artificial polymer in some embodiments. A concatemer can include the same type of units (e.g., a homoconcatemer) in some embodiments, and sometimes a concatemer can contain different types of units (e.g., a heteroconcatemer). A concatemer can contain any type of unit(s), including nucleotide units, amino acid units, small organic molecule units (e.g., trityl), particular nucleotide sequence units, particular amino acid sequence units, and the like. A homoconcatemer of three particular sequence units ABC is ABCABCABC, in an embodiment. A concatemer can contain any number of units so long as each concatemer species can be detectably distinguished from other species. For example, a trityl concatemer species can contain about 1, 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, 80, 85, 90, 95, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, 600, 700, 800, 900 or 1000 trityl units, in some embodiments.
A distinguishable label can be released from a nucleic acid product (e.g., an extended oligonucleotide) in certain embodiments. The linkage between the distinguishable label and a nucleic acid can be of any type that can be transcribed and cleaved, cleaved and allow for detection of the released label or labels, thereby identifying and/or quantifying the nucleic acid product (e.g., U.S. patent application publication no. US20050287533A1, entitled “Target-Specific Compomers and Methods of Use,” naming Ehrich et al.). Such linkages and methods for cleaving the linkages (“cleaving conditions”) are known. In certain embodiments, a label can be separated from other portions of a molecule to which it is attached. In some embodiments, a label (e.g., a compomer) is cleaved from a larger string of nucleotides (e.g., extended oligonucleotides). Non-limiting examples of linkages include linkages that can be cleaved by a nuclease (e.g., ribonuclease, endonuclease); linkages that can be cleaved by a chemical; linkages that can be cleaved by physical treatment; and photocleavable linkers that can be cleaved by light (e.g., o-nitrobenzyl, 6-nitroveratryloxycarbonyl, 2-nitrobenzyl group). Photocleavable linkers provide an advantage when using a detection system that emits light (e.g., matrix-assisted laser desorption ionization (MALDI) mass spectrometry involves the laser emission of light), as cleavage and detection are combined and occur in a single step.
In certain embodiments, a label can be part of a larger unit, and can be separated from that unit prior to detection. For example, in certain embodiments, a label is a set of contiguous nucleotides in a larger nucleotide sequence, and the label is cleaved from the larger nucleotide sequence. In such embodiments, the label often is located at one terminus of the nucleotide sequence or the nucleic acid in which it resides. In some embodiments, the label, or a precursor thereof, resides in a transcription cassette that includes a promoter sequence operatively linked with the precursor sequence that encodes the label. In the latter embodiments, the promoter sometimes is a RNA polymerase-recruiting promoter that generates an RNA that includes or consists of the label. An RNA that includes a label can be cleaved to release the label prior to detection (e.g., with an RNase).
In certain embodiments, a distinguishable label or tag is not cleaved from an extended oligonucleotide, and in some embodiments, the distinguishable label or tag comprises a capture agent. In certain embodiments, detecting a distinguishable feature includes detecting the presence or absence of an extended oligonucleotide, and in some embodiments an extended oligonucleotide includes a capture agent.
Detection and Degree of Multiplexing
The term “detection” of a label as used herein refers to identification of a label species. Any suitable detection device can be used to distinguish label species in a sample. Detection devices suitable for detecting mass distinguishable labels, include, without limitation, certain mass spectrometers and gel electrophoresis devices. Examples of mass spectrometry formats include, without limitation, Matrix-Assisted Laser Desorption/Ionization Time-of-Flight (MALDI-TOF) Mass Spectrometry (MS), MALDI orthogonal TOF MS (OTOF MS; two dimensional), Laser Desorption Mass Spectrometry (LDMS), Electrospray (ES) MS, Ion Cyclotron Resonance (ICR) MS, and Fourier Transform MS. Methods described herein are readily applicable to mass spectrometry formats in which analyte is volatized and ionized (“ionization MS,” e.g., MALDI-TOF MS, LDMS, ESMS, linear TOF, OTOF). Orthogonal ion extraction MALDI-TOF and axial MALDI-TOF can give rise to relatively high resolution, and thereby, relatively high levels of multiplexing. Detection devices suitable for detecting light-emitting, light absorbing and/or light-scattering labels, include, without limitation, certain light detectors and photodetectors (e.g., for fluorescence, chemiluminescence, absorbtion, and/or light scattering labels).
Multiplex Assay Design
The methods provided herein can be adapted to a multiplexed format to amplify and quantitate polynucleotides of a plurality of sets. Multiplexing can be performed in a single reaction vessel, compartment or container. In some embodiments, paralogs are chosen and assays are designed so that the nucleotide at V for the mitochondrial polynucleotides and genomic polynucleotides for a number of sets can be distinguished and quantified in a single reaction. The following are examples of multiplex reaction schemes and are not meant to be limiting. For example, paralogs with a combination of either C (mitochondrial) and T (genomic) or G (mitochondrial) and A (genomic) are selected. Single base extension reactions to probe C/A would be carried out in the forward direction and reactions to probe G/A in the reverse direction, i.e. at C/T. Thus enabling a plurality of sets to be examined in a single reaction vessel. This approach could be applied to sets of paralogs having C as the nucleotide at V for mitochondrial polynucleotides and A/G/T as the nucleotide at V for genomic polynucleotides. Another possible combination of sets of paralogs that could be plexed in a single reaction vessel has V as C/T, C/A, G/A, G/T, where C and G are mitochondrial and A and T are genomic. An alternative multiplex assay has paralog sets that share a common V nucleotide for the mitochondrial polynucleotides and have any of the other three nucleotides as the V nucleotide for genomic polynucleotides. Additional liberty in design can is obtained for any of the assays by allowing reverse design, i.e., probing a sequence on the opposite stand.
In some embodiments, mitochondrial paralogs are chosen and assays are designed for co-amplification of different sets of mitochondrial paralogs and so that the nucleotide at V for the mitochondrial polynucleotides of a number of sets can be distinguished and quantified in a single reaction. In some embodiments, nuclear paralogs are chosen and assays are designed for co-amplification of different sets of nuclear paralogs and so that the nucleotide at V for the nuclear polynucleotides for a number of sets can be distinguished and quantified in a single reaction. In certain embodiments, assays targeting nuclear paralogs and assays targeting mitochondrial paralogs can be performed in the same reaction. In certain embodiments, assays targeting nuclear paralogs are performed in a separate reaction from assays targeting mitochondrial paralogs (both amplification and single base extension). In some embodiments, amplification of nuclear paralogs and amplification of mitochondrial paralogs are carried out in separate reactions and then combined to carry out single base extension reactions.
Design methods for achieving resolved mass spectra with multiplexed assays can include primer and oligonucleotide design methods, relative concentrations of reagents such as chain terminating reagents, choice of detection labels and other reaction design methods. For primer and oligonucleotide design in multiplexed assays, the same general guidelines for primer design applies for uniplexed reactions, such as avoiding false priming and primer dimers, only more primers are involved for multiplex reactions. In addition, for analysis by mass spectrometry, analyte peaks in the mass spectra for one assay are sufficiently resolved from a product of any assay with which that assay is multiplexed, including pausing peaks and any other by-product peaks. Also, analyte peaks optimally fall within a user-specified mass window, for example, within a range of 5,000-8,500 Da. Extension oligonucleotides can be designed with respect to target sequences of a given V (e.g., SNP) strand, in some embodiments. In such embodiments, the length often is between limits that can be, for example, user-specified (e.g., 17 to 24 bases or 17-26 bases) and often do not contain bases that are uncertain in the target sequence. Hybridization strength sometimes is gauged by calculating the sequence-dependent melting (or hybridization/dissociation) temperature, Tm. A particular primer choice may be disallowed, or penalized relative to other choices of primers, because of its hairpin potential, false priming potential, primer-dimer potential, low complexity regions, and problematic subsequences such as GGGG. Methods and software for designing extension oligonucleotides (e.g., according to these criteria) are known, and include, for example, SpectroDESIGNER™ (Sequenom).
Mitochondrial Dosage
Mitochondrial/Genomic (Nuclear) Paralogs
In certain embodiments, the ratios for a plurality of sets are combined and the relative dosage of mitochondrial nucleic acid to genomic nucleic acid for the sample is determined based on the combined ratio. In some embodiments, the combined ratio is an average ratio or a median ratio. The term “average” as used herein is meant a value that is calculated by adding the value of the ratios for each of a number of sets and then dividing by the total number of sets.
The term “median” as used herein is meant a value for a ratio that is at the midpoint of the frequency distribution of observed values of the ratios for the sets examined, such that there is an equal probability of falling above or below it.
In some embodiments, the ratio of each set is compared to an average or median ratio based on the plurality of sets and an outlier or cluster that deviates from the average or median ratio is an indication of a mitochondrial deletion. In other embodiments, the ratio of a set representing one region of the mitochondrial genome is compared to the ratio of each of the other sets representing different regions of the mitochondrial genome and the presence of one or more deletions in the mitochondrial genome is determined based on a difference in the ratio for the one region compared with the ratios for one or more other regions of the mitochondrial genome.
Mitochondrial/Mitochondrial Paralogs-Nuclear/Nuclear Paralogs
In some embodiments, the ratios for a plurality of sets of mitochondrial polynucleotides are combined and the ratios for a plurality of sets of nuclear polynucleotides are combined and the mitochondrial/nuclear ratio for the sample is determined based on using the combined ratios. In some embodiments, the combined ratio is an average ratio or a median ratio. Variability can be minimized by using the results of multiple independent assays targeting nuclear paralogs and multiple independent assays targeting mitochondrial paralogs to derive Ratio X and Ratio Y.
In some embodiments, the ratio of a set of a mitochondrial paralog representing one region of the mitochondrial genome is compared to an average or median ratio based on the plurality of sets of mitochondrial paralogs and an outlier or cluster that deviates from the average or median ratio is an indication of a mitochondrial deletion.
In certain embodiments, the ratio of a set of a mitochondrial paralog representing one region of the mitochondrial genome is compared to the ratio of each of the other sets of a mitochondrial paralog representing different regions of the mitochondrial genome and the presence of one or more deletions in the mitochondrial genome is determined based on a difference in the ratio of the set representing the one region compared with the ratios for one or more sets representing other regions of the mitochondrial genome.
Baseline Mitochondrial Dosage
The number of mitochondria in a sample can exhibit differences based on the tissue of origin, the genetics of a subject, as well as fitness of the subject. In some embodiments, a baseline mitochondrial dosage is determined for an individual subject and/or population and the dosage determined for the sample is compared to or adjusted relative to the baseline dosage. For example, a baseline mitochondrial dosage for a subject can be based on a sample from the subject obtained at multiple points in time. A baseline mitochondrial dosage for a population can be determined for a sample from individuals that do not have or are not pre-disposed to having a disease, disorder or symptoms associated with an increase or decrease in the dosage of mitochondria nucleic acid or a deletion in the mitochondrial genome. The baseline mitochondrial dosage for a population can be used as the baseline for a subject when the subject and the population share one or more of the following exemplary characteristics: tissue of origin for which the mitochondria are examined, sex, ethnicity, age and activity level. Other relevant characteristics can be utilized depending on the subject and the population. If there are differences, such as tissue of origin, adjusts are made to normalize the samples.
Diseases and Disorders
An increase or decrease in mitochondrial dosage has be associated with a number of diseases, disorder, conditions and symptoms, including, but not limited to the following examples.
Neurodegenerative Disease
Non-limiting examples include: Parkinson's, Alzheimers, Friedreich's Ataxia, Amyotropic lateral sclerosis and Multiple sclerosis (MS).
Diseases Associated with nDNA Mutations that Cause mtDNA Stability
POLG associated diseases are most common (POLG is a gene that codes for the catalytic subunit of the mitochondrial DNA polymerase, called DNA polymerase gamma).
Non-limiting examples include: Opthalmoplegia, Alper's syndrome and Leigh's syndrome.
Diseases Associated with mtDNA Deletions/Mutations
Non-limiting examples include: Kearns-Sayre syndrome (KSS), Leber's heredity optic neuropathy (LHON), Mitochondiral encophalomyopathy, lactic acidosis, stroke like episodes (MELAS) and Myoclonic Epilepsy with Ragged Red Fibers (MERRF).
Cancer
Non-limiting examples include: gastric cancer, hepatocellular carcinoma (HCC), HPV associated cancer, breast cancer and Ewing's Sarcoma, pancreatic cancer, liver cancer, testicular cancer, prostate cancer, renal cell carcinoma (RCC), bladder cancer, and ovarian cancer.
Metabolic Disease
Non-limiting examples include: obesity, diabetes, pre-diabetes and diabetic retinopathy.
Cardiovascular Disease
Non-limiting examples include: diabetic cardiomyopathies and coronary heart disease.
Sepsis
Non-limiting examples include: sepsis caused by bacterial, viral or fungal infection.
In some embodiments, the dosage of mitochondrial nucleic acid relative to genomic nucleic acid for the sample from the subject is used in determining the likelihood the subject has or is pre-disposed to having a disease, disorder or symptoms associated with an increase or decrease in the dosage of mitochondria nucleic acid or a deletion in the mitochondrial genome. In some embodiments, the disease or disorder is a neurodegenerative disease, a cancer, a disease or disorder associated with mitochondrial stability, a disease or disorder associated with a mitochondrial deletion, a metabolic disease or disorder, a cardiovascular disease or disorder, a disease or disorder associated with oxidative stress, a disease or disorder associated with infertility or a disease or disorder associated with sepsis.
In some embodiments, the disease, disorder or condition is Parkinson's disease, Alzheimers disease, Friedreich's Ataxia, Amyotropic lateral sclerosis, Multiple sclerosis (MS), POLG associated diseases, Opthalmoplegia, Alper's syndrome, Leigh's syndrome, Kearns-Sayre syndrome (KSS), Leber's heredity optic neuropathy (LHON), Mitochondiral encophalomyopathy, lactic acidosis, stroke like episodes (MELAS), Myoclonic Epilepsy with Ragged Red Fibers (MERRF), gastric cancer, hepatocellular carcinoma (HCC), HPV associated cancer, breast cancer, Ewing's Sarcoma, pancreatic cancer, liver cancer, testicular cancer, prostate cancer, renal cell carcinoma (RCC), bladder cancer, ovarian cancer, obesity, diabetes, pre-diabetes, diabetic retinopathy, diabetic cardiomyopathies coronary heart disease and sepsis.
In some embodiments, the dosage of mitochondrial nucleic acid relative to genomic nucleic acid for the sample from the subject can be used to monitor the efficacy of treatment of the subject for a disease, disorder or symptoms associated with an increase or decrease in the dosage of mitochondria nucleic acid or a deletion in the mitochondrial genome.
Kits
In some embodiments, provided are kits for carrying out methods described herein. Kits often comprise one or more containers that contain one or more components described herein. A kit comprises one or more components in any number of separate containers, packets, tubes, vials, multiwell plates and the like, or components may be combined in various combinations in such containers. One or more of the following components, for example, may be included in a kit: (i) one or more nucleotides (e.g., terminating nucleotides and/or non-terminating nucleotides); one or more of which can include a detection label; (ii) one or more oligonucleotides, one or more of which can include a detection label (e.g., amplification primers, one or more extension primers (UEPs)); (iii) one or more enzymes (e.g., a polymerase, endonuclease, restriction enzyme, etc.); (iv) one or more buffers and (vii) printed matter (e.g. directions, labels, etc). In some embodiments, a kit comprises amplification primer pairs that comprise polynucleotides chosen from polynucleotides in Table 2 and Table 4, or portions thereof. In some embodiments, a kit also comprises extension primers comprising polynucleotides chosen from polynucleotides in Table 2 and Table 4 or portions thereof.
In some embodiments, a kit comprises amplification primer pairs that comprise polynucleotides chosen from polynucleotides in Table 7, or portions thereof. In some embodiments, a kit also comprises extension primers comprising polynucleotides chosen from polynucleotides in Table 7 or portions thereof.
A kit sometimes is utilized in conjunction with a process, and can include instructions for performing one or more processes and/or a description of one or more compositions. A kit may be utilized to carry out a process described herein. Instructions and/or descriptions may be in tangible form (e.g., paper and the like) or electronic form (e.g., computer readable file on a tangle medium (e.g., compact disc) and the like) and may be included in a kit insert. A kit also may include a written description of an internet location that provides such instructions or descriptions.
The examples set forth below illustrate, and do not limit, the technology.
Mitochondrial/genomic (nuclear) paralogs were identified using a R-based algorithm. Utilizing the Biostrings library from the Bioconductor open source software for bioinformatics matched the sequences to the UCSC hg19 build. Bioconductor contains memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences. When paralog regions were identified these were verified using the BLAST algorithm from NCBI.
An exemplary protocol is as follows:
1) The mitochondrial genome was split into shorter fragments (in the case here 100 bp) and given a name, here Seq-1 is the mitochondrial genome nt 1-100 and Seq-2 is nucleotides 101-200.
2) Each sequence was aligned against the human genome and a certain number of mismatches are allowed in this case 20 mismatches per sequence. Results are displayed in Table 1. Shown are sequence number, chromosome number, start of alignment, end of alignment, regions that are suitable for use as amplicons (potential amplification primer binding regions) and sequence. Dashes indicate matches in the nuclear sequence (genomic) and letter mismatches in the nuclear sequence (genomic).
3) Sequences that do not have a paralog (using the settings in 2) in the nuclear genome will only retrieve the mitochondrial match (Chr=M). Examples here are sequences Seq-3 to Seq-6a.
4) Sequences with multiplex alignments can be identified from sequences with only one or two nuclear alignments.
5) All sequence mismatches can be used for paralog detection (V) as long as the upstream/downstream regions X and Y and regions 5′ to X and regions 3′ to Y fit the strategy for amplification as described below.
6) For Co-amplification of mitochondrial and genomic polynucleotides with a single amplification primer pair—select a region V (denoted by “$” above the sequence) surrounded by regions X and Y (denoted by “*” above the sequence), where X and Y are identical in both the nuclear and mitochondrial genome. Examples are Seq-1 and Seq-41. Another example is sequence Seq-51 where perfect alignment is identified to chromosome 17 with a single mismatch but the alignments to chromosome 2 and 17 are different enough to enable amplification of chromosome 1 and M only. Amplification primers are designed to bind to a region within X and Y, for amplification of both mitochondrial and genomic polynucleotides. Amplicon produced with these amplification primers will include V. The nucleotide at V is analyzed to distinguish an amplicon of a mitochondrial polynucleotide from an amplicon of a genomic polynucleotide.
7) Amplification of mitochondrial polynucleotides with a mitochondrial specific amplification primer pair and amplification of genomic polynucleotides with a genomic specific amplification primer pair—select a region V (denoted by “$” above the sequence) surrounded by regions X and Y, where regions 5′ to X and 3′ to Y (denoted by “+” above the sequence) are not identical in both the genomic and mitochondrial genome. Example is sequence Seq-1. Mitochondrial specific amplification primers are designed to bind to a region outside of X and Y, region 5′ to X and region 3′ to Y. Genomic specific amplification primers are designed to bind to a region outside of X and Y, region 5′ to X and region 3′ to Y. Amplicon produced with these amplification primers will include V. The nucleotide at V is analyzed to distinguish an amplicon of a mitochondrial polynucleotide from an amplicon of a genomic polynucleotide.
8) Amplification with one amplification primer binding to both mitochondrial and genomic paralogs in region X and the other amplification primer being a pair of primers that binds to a region 3′ to Y where one primer is mitochondrial specific and the other is genome specific—select a region V (denoted by “$” above the sequence) surrounded by regions X and Y (denoted by “*” above the sequence), where regions 5′ to X and 3′ to Y (denoted by “+” above the sequence) are not identical in both the genomic and mitochondrial genome. Regions will be selected that are hybrids from 6) and 7). Example is Seq-1 and Seq-95. One amplification primer is designed to bind to a region within X, for use in the amplification of a mitochondrial polynucleotide or a genomic polynucleotide. Two corresponding amplification primers, one specific for a mitochondrial polynucleotide and one specific for a genomic polynucleotide are designed to bind to a region ′3 of Y that has one or more mismatches between mitochondrial and genomic polynucleotides of a set. Amplicon produced with these amplification primers will include V. The nucleotide at V is analyzed to distinguish an amplicon of a mitochondrial polynucleotide from an amplicon of a genomic polynucleotide.
An exemplary protocol used in Examples 3 and 4 is provided.
PCR Amplification
PCR was performed in a 5 μL volume reaction using Agena Bioscience's iPLEX Pro PCR kit, consisting of 2 μL DNA template, 0.5 μL 10×PCR Buffer, 0.4 μL 25 mM MgCl2, 0.1 μL dNTP/dUTP mix, 0.125 μL Uracyl-N-Glycosylase (New England Biolabs®, Ipswich, Mass., USA), 0.2 μL DNA polymerase. For a strategy using the same PCR primer for both mitochondrial and nuclear DNA a concentration of 100 nM was used. For a strategy of template specific primer combinations a set of different combinations was used (Table A). Finally for the hybrid strategy of one universal PCR forward primer and a template specific pair of reverse primers, 100 nM of the universal primer was used and the combinations in Table A was used for the reverse primers. Alternatively, a hybrid strategy can use one universal PCR reverse primer and a template specific pair of forward primers with 100 nM of the universal primer and the combinations in Table A was used for the forward primers. Thermal cycling consisted of an initial incubation at 30° C. for 10 minutes followed by denaturation at 94° C. for 2 minutes; 30 cycles of 94° C. for 30 seconds, 60° C. for 30 seconds, and 72° C. for 1 minute; followed by a final extension of 5 minutes at 72° C. Following PCR, the reactions were treated with a 2 μL SAP mastermix consisting of 0.5 U shrimp alkaline phosphatase (SAP) and 0.17 μL 10×SAP Buffer. Samples were incubated for 20 minutes at 37° C., followed by SAP enzyme denaturation for 10 minutes at 85° C. Thermal cycling and incubation were performed in a GeneAmp® PCR System 9700 (Thermo Fisher). All reagents used were obtained from Agena Bioscience unless otherwise stated.
Single Base Extension
Single base extension was performed by adding 2 μL of a master mix consisting of 0.2×iPLex Buffer, 0.2× Termination Mix, 5-15 μM extension primer mix, and 0.00615 U iPLEX® Pro enzyme. Reaction parameters consisted of an initial incubation at 94° C. for 30 seconds followed by 20 cycles at 94° C. for 5 seconds with five nested cycles of 52° C. for 5 seconds followed by 80° C. for 5 seconds. A final extension was performed at 72° C. for 3 minutes. Thermal cyling was performed in a GeneAmp PCR System 9700.
Maldi-TOF Analysis
After 41 ul of water addition and desalting by the addition of 15 mg Clean Resin, 15 nL of each extend mixture was transferred to a SpectroCHIP® II-G384 and Mass spectra were recorded using a MassARRAY System. Spectra were acquired using SpectroAcquire software (Agena Bioscience, San Diego). The software parameters were set to acquire 20 shots from each of 5 raster positions. The resulting mass spectra were summed and peak detection and intensity analysis performed using Typer 4 software (Agena Bioscience, San Diego).
Table 2: ADF1 Assay design using strategy of species specific PCR primers but same extension primer, please note that each PCR primer has a 10 bp tag to move them out of the MassARRAY window 3500-9000 m/z
Table 3: The alignment showing each primer pair alignment and the sequence of the amplicons (−g=nuclear specific primers, −mt=mitochondrial specific primers)
Table 4: ADF2 Assay design using strategy of universal PCR primers and the same extension primer, please note that each PCR primer has a 10 bp tag to move them out of the MassARRAY window 3500-9000 m/z
Table 5: The alignment showing each primer pair aligning both on nuclear as well as mitochondrial DNA
All samples are set up in 25 uL PCR reactions.
Chimpanzee mitochondrial/human mitochondrial paralogs were identified using a R-based algorithm. Utilizing the Biostrings library from the Bioconductor open source software aligned small fragments (50-100 bps) of the human (Homo sapiens) mitochondrial genome (UCSC hg19 build) against the chimpanzee (Pan troglodytes) mitochondrial genome (P. troglodytes 2013 assembly). Bioconductor contains memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences. Similar nucleotide regions containing at least one mismatch were selected and assays were designed based on these regions. When paralog regions were identified these were verified using the BLAST algorithm from NCBI.
An exemplary protocol is as follows:
The human and chimpanzee nuclear genomes are 99% identical, therefore there are numerous suitable paralog regions. Suitable chimpanzee nuclear/human nuclear paralogs were determined in the same manner as mitochondrial paralogs, e.g., by blasting portions of the human genome against the chimpanzee genome.
All samples were set up in 25 ul PCR reactions.
For circulating cell free DNA three parallel reactions were run using a different amount of chimpanzee DNA in each reaction, as the DNA concentration of the liquid biopsy sample is not known. Reactions were evaluated based on dynamic range. For each sample 3 wells were used. Each well had a different chimpanzee DNA amount (1 ng, 0.5 ng, and 0.125 ng total input).
PCR and single base extension primers are described in Table 7.
Samples were obtained from a single subject over the course of 1 month. Samples were obtained prior to start of a treatment and additional samples were obtained at start, halfway and at the end of treatment. Circulating cell free DNA was extracted and subjected to co-amplification with a known amount of chimpanzee DNA. The DNA was subjected to multiplex amplification in a single reaction using a panel consisting of 7 mitochondrial and 5 nuclear amplicons. PCR and single base extension primers used are shown in Table 8.
Mitochondria copy numbers (
Provided hereafter are non-limiting examples of certain embodiments of the technology.
A1. A multiplex method for determining dosage of mitochondrial nucleic acid relative to genomic nucleic acid for a sample from a subject, comprising:
The entirety of each patent, patent application, publication and document referenced herein hereby is incorporated by reference. Citation of the above patents, patent applications, publications and documents is not an admission that any of the foregoing is pertinent prior art, nor does it constitute any admission as to the contents or date of these publications or documents.
Modifications may be made to the foregoing without departing from the basic aspects of the technology. Although the technology has been described in substantial detail with reference to one or more specific embodiments, those of ordinary skill in the art will recognize that changes may be made to the embodiments specifically disclosed in this application, yet these modifications and improvements are within the scope and spirit of the technology.
The technology illustratively described herein suitably may be practiced in the absence of any element(s) not specifically disclosed herein. Thus, for example, in each instance herein any of the terms “comprising,” “consisting essentially of,” and “consisting of” may be replaced with either of the other two terms. The terms and expressions which have been employed are used as terms of description and not of limitation, and use of such terms and expressions do not exclude any equivalents of the features shown and described or portions thereof, and various modifications are possible within the scope of the technology claimed. The term “a” or “an” can refer to one of or a plurality of the elements it modifies (e.g., “a reagent” can mean one or more reagents) unless it is contextually clear either one of the elements or more than one of the elements is described. The term “about” as used herein refers to a value within 10% of the underlying parameter (i.e., plus or minus 10%), and use of the term “about” at the beginning of a string of values modifies each of the values (i.e., “about 1, 2 and 3” is about 1, about 2 and about 3). For example, a weight of “about 100 grams” can include weights between 90 grams and 110 grams. Thus, it should be understood that although the present technology has been specifically disclosed by representative embodiments and optional features, modification and variation of the concepts herein disclosed may be resorted to by those skilled in the art, and such modifications and variations are considered within the scope of this technology.
Embodiments of the technology are set forth in the claim(s) that follow(s).
This patent application is a divisional of U.S. patent application Ser. No. 15/268,058, filed on Sep. 16, 2016, entitled METHODS AND COMPOSITIONS FOR THE QUANTITATION OF MITOCHONDRIAL NUCLEIC ACID, naming Anders Nygren as inventor and assigned attorney docket no. AGB-7003-UT; which claims the benefit of U.S. Provisional Patent Application No. 62/295,804, filed Feb. 16, 2016, entitled METHODS AND COMPOSITIONS FOR THE QUANTITATION OF MITOCHONDRIAL NUCLEIC ACID, naming Anders Nygren as inventor and assigned attorney docket no. AGB-7003-PV2. U.S. patent application Ser. No. 15/268,058, filed on Sep. 16, 2016, entitled METHODS AND COMPOSITIONS FOR THE QUANTITATION OF MITOCHONDRIAL NUCLEIC ACID, naming Anders Nygren as inventor and assigned attorney docket no. AGB-7003-UT also claims the benefit of U.S. Provisional Application No. 62/220,749, filed Sep. 18, 2015, entitled METHODS AND COMPOSITIONS FOR THE QUANTITATION OF MITOCHONDRIAL NUCLEIC ACID, naming Anders Nygren as inventor and assigned attorney docket no. AGB-7003-PV. The subject matter of each of these applications is incorporated in its entirety by reference thereto, including texts, tables and drawings.
| Number | Date | Country | |
|---|---|---|---|
| 62220749 | Sep 2015 | US | |
| 62295804 | Feb 2016 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | 15268058 | Sep 2016 | US |
| Child | 16983528 | US |
