Accuracy and reproducibility of somatic point mutation calling in clinical-type targeted sequencing data.

ABSTRACT:

Background

Treating cancer depends in part on identifying the mutations driving each patient's disease. Many clinical laboratories are adopting high-throughput sequencing for assaying patients' tumours, applying targeted panels to formalin-fixed paraffin-embedded tumour tissues to detect clinically-relevant mutations. While there have been some benchmarking and best practices studies of this scenario, much variant calling work focuses on whole-genome or whole-exome studies, with fresh or fresh-frozen tissue. Thus, definitive guidance on best choices for sequencing platforms, sequencing strategies, and variant calling for clinical variant detection is still being developed.

Methods

Because ground truth for clinical specimens is rarely known, we used the well-characterized Cor

SUBMITTER: Karimnezhad A 

PROVIDER: S-EPMC7560075 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature