Germline contamination and leakage in whole genome somatic single nucleotide variant detection.

ABSTRACT:

Background

The clinical sequencing of cancer genomes to personalize therapy is becoming routine across the world. However, concerns over patient re-identification from these data lead to questions about how tightly access should be controlled. It is not thought to be possible to re-identify patients from somatic variant data. However, somatic variant detection pipelines can mistakenly identify germline variants as somatic ones, a process called "germline leakage". The rate of germline leakage across different somatic variant detection pipelines is not well-understood, and it is uncertain whether or not somatic variant calls should be considered re-identifiable. To fill this gap, we quantified germline leakage across 259 sets of whole-genome somatic single nucleotide variant (SNVs)

SUBMITTER: Sendorek DH 

PROVIDER: S-EPMC5793408 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature