Targeted or whole genome sequencing of formalin fixed tissue samples: potential applications in cancer genomics.

ABSTRACT: Current genomic studies are limited by the poor availability of fresh-frozen tissue samples. Although formalin-fixed diagnostic samples are in abundance, they are seldom used in current genomic studies because of the concern of formalin-fixation artifacts. Better characterization of these artifacts will allow the use of archived clinical specimens in translational and clinical research studies. To provide a systematic analysis of formalin-fixation artifacts on Illumina sequencing, we generated 26 DNA sequencing data sets from 13 pairs of matched formalin-fixed paraffin-embedded (FFPE) and fresh-frozen (FF) tissue samples. The results indicate high rate of concordant calls between matched FF/FFPE pairs at reference and variant positions in three commonly used sequencing approaches (whole ge

SUBMITTER: Munchel S 

PROVIDER: S-EPMC4694877 | biostudies-literature | 2015 Sep

REPOSITORIES: biostudies-literature