Methods for detecting biallelic loss of function in next-generation sequencing genomic data

Abstract

A genomic data analyzer maybe configured to detect and characterize biallelic genomic alterations for at least one gene in next generation sequencing variant calling information for patient tumor samples characterized by different purity ratios of somatic genomic material. The variant analysis module may compare the observed variant fraction distributions of putative heterozygous germline mutations to the theoretical distributions corresponding to different chromosomal aberration events to detect a combination of genomic alteration events. The variant analysis module maybe used in next-generation-sequencing oncogenomics testing to identify biallelic loss of function on tumor suppressor genes to facilitate the biological understanding and choice of a personalized oncology treatment targeting the analyzed patient tumor solely from next generation sequencing data variant information, without requiring complementary germline analysis or biological assays. The proposed genomic data analyzed may help determine whether PARP inhibitors such as Olaparib are a recommended chemotherapy treatment to target ovarian or breast cancers.