Abstract: A method of generating a homologous recombination deficiency score includes generating single nucleotide polymorphism (SNP) panel data describing allele abundance at each SNP locus of a plurality of SNP loci, generating double strand break (DSB) feature panel data describing nucleotide sequences at a plurality of DSB feature loci from the nucleic acid sample, generating allele specific copy number data for the plurality of SNP loci based on the SNP panel data, determining an entropy of the allele specific copy number data, comparing the DSB feature panel data to a known genomic sequence to identify a set of DSB mutations, determining a portion of the set of DSB mutations that are repaired by non-homologous end joining, and generating the homologous recombination deficiency score from the entropy of the allele specific copy number data and the portion of DSB mutations repaired by non-homologous end joining.

Abstract: Described herein are methods for determining the number of unique sequence molecules, such as copy number variants and breakpoints, in Anchored Multiplex PCR (AMP) panels using only sequencing data from the sample of interest.