EP3957749A1 — Detecting tumour specific mutations in biopsies with whole exome sequencing and in cell-free samples

USPTO Abstract

Claimed is a method for detecting tumor-specific mutations, e.g. SNP mutations, by whole exome sequencing from a tumor biopsy cancer sample, multiplex amplification reaction to amplify at least 10 target loci encompassing the tumor-specific mutations; and high-throughput sequencing to determine the sequences of the amplified target loci. Method for determining the presence or absence of one or more tumor-specific mutations by a multiplex amplification reaction to amplify at least 10 target loci from cell-free DNA used in monitoring the progression of cancer. Method for detecting tumor-specific mutations by multiplex amplification of 10 target loci and sequencing at a depth of read of at least 50000. Described further are methods, systems, and computer readable medium for detecting ploidy of chromosome segments or entire chromosomes based on phasing of the alleles and determination of individual and joint probabilities and a best-fit model.