Transfer of clinically relevant gene expression signatures in breast cancer: from Affymetrix microarray to Illumina RNA-Sequencing technology

Microarrays have revolutionized breast cancer (BC) research by enabling studies of gene expression on a transcriptome-wide scale. Recently, RNA-Sequencing (RNA-Seq) has emerged as an alternative for precise readouts of the transcriptome. To date, no study has compared the ability of the two technologies to quantify clinically relevant individual genes and microarray-derived gene expression signatures (GES) in a set of BC samples encompassing the known molecular BC's subtypes. To accomplish this, the RNA from 57 BCs representing the four main molecular subtypes (triple negative, HER2 positive, luminal A, luminal B), was profiled with Affymetrix HG-U133 Plus 2.0 chips and sequenced using the Illumina HiSeq 2000 platform. The correlations of three clinically relevant BC genes, six molecular subtype classifiers, and a selection of 21 GES were evaluated. 58 tumors representing the different molecular subtypes [triple negative (ER-/PgR-/HER2-); HER2 positive (HER2+); luminal A (ER+/HER2-/histological grade 1), luminal B (ER+/HER2-/histological grade 3)] were obtained from patients recruited between 2007 and 2011 at the Institut Jules Bordet. RNA was profiled using the Affymetrix HG-U133 Plus 2.0 chips and sequenced on the Illumina platform, producing ~30 million 50 bp paired-end reads per sample. The reads alignment and expression quantification were performed using the Tophat/Cufflinks pipeline and the Ensembl genome version hg19. The Affymetrix microarray data were normalized using fRMA and probesets were selected based on the JetSet reannotation package. This submission represents the gene expression component of the study only.