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

PloS One
Vinu JoseChristos Sotiriou

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 expression analysis was investigated by developing de-novo ER/HER2 pathway gene-modules from the matched datasets and validating them on external FF/FFPE gene expression datasets using ROC analysis. Spearman's rank correlation coefficient of module scores between matched FFPE/frozen datasets was used to measure the reliability of gene-modules derived from external datasets in FFPE expression profiles. Independent of the array/amplification-kit/sam...Continue Reading

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Datasets Mentioned

BETA
GSE93338
GSE20713

Methods Mentioned

BETA
RNAseq

Software Mentioned

R affy
MAS
plotROC
grid
Affymetrix
reshape2
gridExtra
PVAC
NetAffx
nCounter

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