Detecting mutations and ploidy in chromosomal segments
First Claim
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1. A method for determining ploidy of a chromosomal segment in a sample of an individual, the method comprising:
- isolating circulating tumor DNA from a blood sample, serum sample, or plasma sample from an individual suspected of having cancer;
amplifying at least 1,000 polymorphic loci relating to cancer-associated copy number variation from the circulating tumor DNA to obtain amplicons;
sequencing the amplicons to obtain allele frequency data generated from the sample, comprising the amount of each allele present in the sample at each loci in a set of polymorphic loci on the chromosomal segment;
generating phased allelic information for the set of polymorphic loci by estimating the phase of the allele frequency data;
generating individual probabilities of allele frequencies for the polymorphic loci for different ploidy states using the allele frequency data, wherein the individual probabilities are generated using a set of models of both different ploidy states and allelic imbalance fractions for the set of polymorphic loci;
generating joint probabilities for the set of polymorphic loci using the individual probabilities and the phased allelic information and considering the linkage between polymorphic loci on the chromosome segment; and
selecting, based on the joint probabilities, a best fit model indicative of chromosomal ploidy, thereby determining ploidy of the chromosomal segment, and the method further comprises determining based on the selecting, whether copy number variation is present in cells of a tumor of the individual.
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Abstract
The invention provides methods, systems, and computer readable medium for detecting ploidy of chromosome segments or entire chromosomes, for detecting single nucleotide variants and for detecting both ploidy of chromosome segments and single nucleotide variants. In some aspects, the invention provides methods, systems, and computer readable medium for detecting cancer or a chromosomal abnormality in a gestating fetus.
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22 Claims
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1. A method for determining ploidy of a chromosomal segment in a sample of an individual, the method comprising:
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isolating circulating tumor DNA from a blood sample, serum sample, or plasma sample from an individual suspected of having cancer; amplifying at least 1,000 polymorphic loci relating to cancer-associated copy number variation from the circulating tumor DNA to obtain amplicons; sequencing the amplicons to obtain allele frequency data generated from the sample, comprising the amount of each allele present in the sample at each loci in a set of polymorphic loci on the chromosomal segment; generating phased allelic information for the set of polymorphic loci by estimating the phase of the allele frequency data; generating individual probabilities of allele frequencies for the polymorphic loci for different ploidy states using the allele frequency data, wherein the individual probabilities are generated using a set of models of both different ploidy states and allelic imbalance fractions for the set of polymorphic loci; generating joint probabilities for the set of polymorphic loci using the individual probabilities and the phased allelic information and considering the linkage between polymorphic loci on the chromosome segment; and selecting, based on the joint probabilities, a best fit model indicative of chromosomal ploidy, thereby determining ploidy of the chromosomal segment, and the method further comprises determining based on the selecting, whether copy number variation is present in cells of a tumor of the individual. - View Dependent Claims (2, 3, 18, 19, 21, 22)
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4. A method for detecting chromosomal ploidy in a sample of an individual, the method comprising:
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isolating circulating tumor DNA from a blood sample, serum sample, or plasma sample from an individual suspected of having cancer; amplifying at least 1,000 polymorphic loci relating to cancer-associated copy number variation from the circulating tumor DNA to obtain amplicons; sequencing the amplicons to obtain nucleic acid sequence data generated from the sample, for alleles at a set of polymorphic loci on a chromosome segment in the individual; detecting allele frequencies at the set of loci using the nucleic acid sequence data; correcting for allele amplification efficiency bias in the detected allele frequencies to generate corrected allele frequencies for the set of polymorphic loci; generating phased allelic information for the set of polymorphic loci by estimating the phase of the nucleic acid sequence data; generating individual probabilities of allele frequencies for the polymorphic loci for different ploidy states by comparing the corrected allele frequencies to a set of models of different ploidy states and allelic imbalance fractions of the set of polymorphic loci; generating joint probabilities for the set of polymorphic loci by combining the individual probabilities considering the linkage between polymorphic loci on the chromosome segment; and selecting, based on the joint probabilities, the best fit model indicative of chromosomal ploidy, and the method further comprises determining based on the selecting, whether copy number variation is present in cells of a tumor of the individual. - View Dependent Claims (5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20)
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Specification