Constructing germline research cohorts from the discarded reads of clinical tumor sequences.

ABSTRACT:

Background

Hundreds of thousands of cancer patients have had targeted (panel) tumor sequencing to identify clinically meaningful mutations. In addition to improving patient outcomes, this activity has led to significant discoveries in basic and translational domains. However, the targeted nature of clinical tumor sequencing has a limited scope, especially for germline genetics. In this work, we assess the utility of discarded, off-target reads from tumor-only panel sequencing for the recovery of genome-wide germline genotypes through imputation.

Methods

We developed a framework for inference of germline variants from tumor panel sequencing, including imputation, quality control, inference of genetic ancestry, germline polygenic risk scores, and HLA alleles. We benchmarked ou

SUBMITTER: Gusev A 

PROVIDER: S-EPMC8576948 | biostudies-literature | 2021 Nov

REPOSITORIES: biostudies-literature