Bioinformatics and DNA-extraction strategies to reliably detect genetic variants from FFPE breast tissue samples.

ABSTRACT:

Background

Archived formalin fixed paraffin embedded (FFPE) samples are valuable clinical resources to examine clinically relevant morphology features and also to study genetic changes. However, DNA quality and quantity of FFPE samples are often sub-optimal, and resulting NGS-based genetics variant detections are prone to false positives. Evaluations of wet-lab and bioinformatics approaches are needed to optimize variant detection from FFPE samples.

Results

As a pilot study, we designed within-subject triplicate samples of DNA derived from paired FFPE and fresh frozen breast tissues to highlight FFPE-specific artifacts. For FFPE samples, we tested two FFPE DNA extraction methods to determine impact of wet-lab procedures on variant calling: QIAGEN QIAamp DNA Mini Kit ("QA"),

SUBMITTER: Bhagwate AV 

PROVIDER: S-EPMC6720378 | biostudies-literature | 2019 Sep

REPOSITORIES: biostudies-literature