Methods for simultaneous amplification of target loci
DC CAFCFirst Claim
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1. A method for measuring an amount of DNA in a biological sample, comprising:
- (a) extracting cell-free DNA of mixed origin from a biological sample of a subject, wherein the cell-free DNA comprises DNA from the subject and DNA from a genetically distinct individual, wherein neither the subject nor the genetically distinct individual is a fetus, and wherein the DNA of mixed origin comprises DNA from a transplant;
(b) performing targeted PCR amplification of the cell-free DNA at more than 100 SNP loci in a single reaction volume using more than 100 PCR primer pairs, wherein the amplified SNP loci comprise SNP loci on at least chromosome 1, 2, or 3;
(c) determining the genotypes of the amplified SNP loci and measuring an amount of one or more alleles at the SNP loci, wherein the genotypes of the amplified SNP loci are determined by high-throughput sequencing; and
(d) measuring an amount of the DNA from the genetically distinct individual present in the biological sample using the amount of one or more alleles at the SNP loci,wherein the method is performed without prior knowledge of genotypes of the genetically distinct individual.
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Abstract
The invention provides methods for simultaneously amplifying multiple nucleic acid regions of interest in one reaction volume as well as methods for selecting a library of primers for use in such amplification methods. The invention also provides library of primers with desirable characteristics, such as minimal formation of amplified primer dimers or other non-target amplicons.
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16 Claims
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1. A method for measuring an amount of DNA in a biological sample, comprising:
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(a) extracting cell-free DNA of mixed origin from a biological sample of a subject, wherein the cell-free DNA comprises DNA from the subject and DNA from a genetically distinct individual, wherein neither the subject nor the genetically distinct individual is a fetus, and wherein the DNA of mixed origin comprises DNA from a transplant; (b) performing targeted PCR amplification of the cell-free DNA at more than 100 SNP loci in a single reaction volume using more than 100 PCR primer pairs, wherein the amplified SNP loci comprise SNP loci on at least chromosome 1, 2, or 3; (c) determining the genotypes of the amplified SNP loci and measuring an amount of one or more alleles at the SNP loci, wherein the genotypes of the amplified SNP loci are determined by high-throughput sequencing; and (d) measuring an amount of the DNA from the genetically distinct individual present in the biological sample using the amount of one or more alleles at the SNP loci, wherein the method is performed without prior knowledge of genotypes of the genetically distinct individual. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13)
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14. A method for measuring an amount of DNA in a biological sample, the method comprising:
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(a) performing a targeted PCR amplification for more than 100 SNP loci on one or more chromosomes expected to be disomic in a single reaction mixture using more than 100 PCR primer pairs, wherein the reaction mixture comprises cell-free DNA extracted from a biological sample of a subject comprising DNA of mixed origin, wherein the DNA of mixed origin comprises DNA from the subject and DNA from a genetically distinct individual, wherein neither the subject nor the genetically distinct individual is a fetus, wherein the DNA of mixed origin comprises DNA from a transplant, and wherein the amplified SNP loci comprise SNP loci on at least chromosome 1, 2, or 3; (b) measuring a quantity of each allele at a plurality of amplified SNP loci that comprise an allele present in the genetically distinct individual but not the subject, wherein the quantity of each allele at a plurality of amplified SNP loci are measured by high-throughput sequencing; (c) measuring an amount of the DNA from the genetically distinct individual in the biological sample using the quantity of each allele at the SNP loci and an expected quantity of each allele at the SNP loci for different DNA fractions, wherein the method is performed without prior knowledge of genotypes of the genetically distinct individual. - View Dependent Claims (15, 16)
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Specification