Detecting mutations and ploidy in chromosomal segments

Abstract

To provide methods, systems and computer-readable media for detecting ploidy of chromosome segments or entire chromosomes, on the basis of phase determination of an allele and determination of individual and joint probabilities and of a best fit model.SOLUTION: According to some aspects, the invention provides methods, systems and computer readable media for detecting cancer or a chromosomal abnormality in a gestating fetus. The invention also provides methods for detecting circulating tumor nucleic acids on the basis of allelic imbalance ratios of polymorphic loci found by ploidy determination. The invention further provides methods for detecting single nucleotide variants on the basis of estimates of the amplification efficiency and the error rate, and methods for detecting single nucleotide variants on the basis of a median variant allele frequency for control samples derived from a plurality of individuals.SELECTED DRAWING: Figure 20A-20B

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