REPURPOSING GERMLINE EXOMES OF THE CANCER GENOME ATLAS DEMANDS A CAUTIOUS APPROACH AND SAMPLE-SPECIFIC VARIANT FILTERING.

ABSTRACT: When seeking to reproduce results derived from whole-exome or genome sequencing data that could advance precision medicine, the time and expense required to produce a patient cohort make data repurposing an attractive option. The first step in repurposing is setting some quality baseline for the data so that conclusions are not spurious. This is difficult because there can be variations in quality from center to center, clinic to clinic and even patient to patient. Here, we assessed the quality of the whole-exome germline mutations of TCGA cancer patients using patterns of nucleotide substitution and negative selection against impactful mutations. We estimated the fraction of false positive variant calls for each exome with respect to two gold standard germline exomes, and found large vari

SUBMITTER: Koire A 

PROVIDER: S-EPMC4720392 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature