Clinical whole-genome sequencing from routine formalin-fixed, paraffin-embedded specimens: pilot study for the 100,000 Genomes Project.

ABSTRACT:

Purpose

Fresh-frozen (FF) tissue is the optimal source of DNA for whole-genome sequencing (WGS) of cancer patients. However, it is not always available, limiting the widespread application of WGS in clinical practice. We explored the viability of using formalin-fixed, paraffin-embedded (FFPE) tissues, available routinely for cancer patients, as a source of DNA for clinical WGS.

Methods

We conducted a prospective study using DNAs from matched FF, FFPE, and peripheral blood germ-line specimens collected from 52 cancer patients (156 samples) following routine diagnostic protocols. We compared somatic variants detected in FFPE and matching FF samples.

Results

We found the single-nucleotide variant agreement reached 71% across the genome and somatic copy-number alterations

SUBMITTER: Robbe P 

PROVIDER: S-EPMC6520241 | biostudies-literature | 2018 Oct

REPOSITORIES: biostudies-literature