Functional comparison of exome capture-based methods for transcriptomic profiling of formalin-fixed paraffin-embedded tumors.

ABSTRACT: The availability of fresh frozen (FF) tissue is a barrier for implementing RNA sequencing (RNA-seq) in the clinic. The majority of clinical samples are stored as formalin-fixed, paraffin-embedded (FFPE) tissues. Exome capture platforms have been developed for RNA-seq from FFPE samples. However, these methods have not been systematically compared. We performed transcriptomic analysis of 32 FFPE tumor samples from 11 patients using three exome capture-based methods: Agilent SureSelect V6, TWIST NGS Exome, and IDT XGen Exome Research Panel. We compared these methods to the TruSeq RNA-seq of fresh frozen (FF-TruSeq) tumor samples from the same patients. We assessed the recovery of clinically relevant biological features. The Spearman's correlation coefficients between the global expression pro

SUBMITTER: Shohdy KS 

PROVIDER: S-EPMC8360986 | biostudies-literature | 2021 Aug

REPOSITORIES: biostudies-literature