Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing.

ABSTRACT: The lack of samples for generating standardized DNA datasets for setting up a sequencing pipeline or benchmarking the performance of different algorithms limits the implementation and uptake of cancer genomics. Here, we describe reference call sets obtained from paired tumor-normal genomic DNA (gDNA) samples derived from a breast cancer cell line-which is highly heterogeneous, with an aneuploid genome, and enriched in somatic alterations-and a matched lymphoblastoid cell line. We partially validated both somatic mutations and germline variants in these call sets via whole-exome sequencing (WES) with different sequencing platforms and targeted sequencing with >2,000-fold coverage, spanning 82% of genomic regions with high confidence. Although the gDNA reference samples are not representativ

SUBMITTER: Fang LT 

PROVIDER: S-EPMC8532138 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature