Feasibility of developing reliable gene expression modules from FFPE derived RNA profiled on Affymetrix arrays.

ABSTRACT: The reliability of differential gene expression analysis on formalin-fixed, paraffin-embedded (FFPE) expression profiles generated using Affymetrix arrays is questionable, due to the high range of percent-present values reported in studies which profiled FFPE samples using this technology. Moreover, the validity of gene-modules derived from external datasets in FFPE microarray expression profiles is unknown. By generating matched gene expression profiles using RNAs derived from fresh-frozen (FF) and FFPE preserved breast tumors with Affymetrix arrays and FF/FFPE RNA specific amplification-and-labeling kits, the reliability of differential expression analysis and the validity of gene modules derived from external datasets were investigated. Specifically, the reliability of differential expr

SUBMITTER: Jose V 

PROVIDER: S-EPMC6118369 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature