Personalized genome assembly for accurate cancer somatic mutation discovery using tumor-normal paired reference samples.

ABSTRACT:

Background

The use of a personalized haplotype-specific genome assembly, rather than an unrelated, mosaic genome like GRCh38, as a reference for detecting the full spectrum of somatic events from cancers has long been advocated but has never been explored in tumor-normal paired samples. Here, we provide the first demonstrated use of de novo assembled personalized genome as a reference for cancer mutation detection and quantifying the effects of the reference genomes on the accuracy of somatic mutation detection.

Results

We generate de novo assemblies of the first tumor-normal paired genomes, both nuclear and mitochondrial, derived from the same individual with triple negative breast cancer. The personalized genome was chromosomal scale, haplotype phased, and annotated. We de

SUBMITTER: Xiao C 

PROVIDER: S-EPMC9648002 | biostudies-literature | 2022 Nov

REPOSITORIES: biostudies-literature