title: Transfer of clinically relevant gene expression signatures in breast cancer: from Affymetrix microarray to Illumina RNA-Sequencing technology.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  16,097 genes common to the two platforms were retained for downstream analysis. Gene-wise comparison of microarray and RNA-Seq data revealed that 52% had a Spearman's correlation coefficient greater than 0.7 with highly correlated genes displaying significantly higher expression levels. We found excellent correlation between microarray and RNA-Seq for the estrogen receptor (ER; rs = 0.973; 95% CI: 0.971-0.975), progesterone receptor (PgR; rs = 0.95; 0.947-0.954), and human epidermal growth factor receptor 2 (HER2; rs = 0.918; 0.912-0.923), while a few discordances between ER and PgR quantified by immunohistochemistry and RNA-Seq/microarray were observed. All the subtype classifiers evaluated agreed well (Cohen's kappa coefficients >0.8) and all the proliferation-based GES showed excellent Spearman correlations between microarray and RNA-Seq (all rs >0.965). Immune-, stroma- and pathway-based GES showed a lower correlation relative to prognostic signatures (all rs >0.6).
  
  
  CONCLUSIONS
  To our knowledge, this is the first study to report a systematic comparison of RNA-Seq to microarray for the evaluation of single genes and GES clinically relevant to BC. According to our results, the vast majority of single gene biomarkers and well-established GES can be reliably evaluated using the RNA-Seq technology.
authors.forename: Debora
authors.initials: D
authors.lastname: Fumagalli
authors.forename: Alexis
authors.initials: A
authors.lastname: Blanchet-Cohen
authors.forename: David
authors.initials: D
authors.lastname: Brown
authors.forename: Christine
authors.initials: C
authors.lastname: Desmedt
authors.forename: David
authors.initials: D
authors.lastname: Gacquer
authors.forename: Stefan
authors.initials: S
authors.lastname: Michiels
authors.forename: Françoise
authors.initials: F
authors.lastname: Rothé
authors.forename: Samira
authors.initials: S
authors.lastname: Majjaj
authors.forename: Roberto
authors.initials: R
authors.lastname: Salgado
authors.forename: Denis
authors.initials: D
authors.lastname: Larsimont
authors.forename: Michail
authors.initials: M
authors.lastname: Ignatiadis
authors.forename: Marion
authors.initials: M
authors.lastname: Maetens
authors.forename: Martine
authors.initials: M
authors.lastname: Piccart
authors.forename: Vincent
authors.initials: V
authors.lastname: Detours
authors.affiliation: Breast Cancer Translational Research Laboratory (BCTL), Institut Jules Bordet, Brussels, Belgium. christos.sotiriou@bordet.be.
authors.forename: Christos
authors.initials: C
authors.lastname: Sotiriou
authors.forename: Benjamin
authors.initials: B
authors.lastname: Haibe-Kains
mesh_terms: D001483:Base Sequence; D047628:Estrogen Receptor alpha / Q000096:biosynthesis; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D009363:Neoplasm Proteins / Q000096:biosynthesis; D020411:Oligonucleotide Array Sequence Analysis; D011379:Prognosis; D018719:Erb-b2 Receptor Tyrosine Kinases / Q000096:biosynthesis; D011980:Receptors, Progesterone / Q000096:biosynthesis; D059467:Transcriptome / Q000235:genetics*; D064726:Triple Negative Breast Neoplasms / Q000235:genetics* / Q000473:pathology
chemical_list: D047628:Estrogen Receptor alpha; D009363:Neoplasm Proteins; D018719:Erb-b2 Receptor Tyrosine Kinases; D011980:Receptors, Progesterone; C506487:ESR1 protein, human; C508053:ERBB2 protein, human