EGAGenomicsChristos Sotiriouhttps://ega-archive.org/dacs/EGAC00001000120EGAEGA DAC EGAC00001000120EGAchristos.sotiriou@bordet.be<h4>Background</h4>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.<h4>Results</h4>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).<h4>Conclusions</h4>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.Transfer of clinically relevant gene expression signatures in breast cancer: from Affymetrix microarray to Illumina RNA-Sequencing technology.Fumagalli Debora D, Blanchet-Cohen Alexis A, Brown David D, Desmedt Christine C, Gacquer David D, Michiels Stefan S, Rothé Françoise F, Majjaj Samira S, Salgado Roberto R, Larsimont Denis D, Ignatiadis Michail M, Maetens Marion M, Piccart Martine M, Detours Vincent V, Sotiriou Christos C, Haibe-Kains Benjamin BBreast Carcinoma, Human Mammary Neoplasm, primary breast cancer, Carcinoma, malignant tumor of the breast, RNA, Ribonucleic, Breast Carcinomas, "breast neoplasm" EXACT [MTH:120], ribose nucleic acid, Neoplasms, Arts, ribonucleic acids, mammary neoplasm, Gene, Mammary Cancers, Human Mammary Neoplasms, RNS, Tumor, "breast tumor" EXACT [NCI2004_11_17:C2910], Human, Breast Malignant Neoplasm, Breast Malignant Tumor, "neoplasm of breast (disorder)" EXACT [SNOMEDCT_2005_07_31:126926005], Mammary Carcinomas, Breast Tumor, yeast nucleic acid, Ribonukleinsaeure, Neoplasm, Gene Products, Human Mammary Carcinoma, "mammary tumor" EXACT [CSP2005:2016-0671], pentosenucleic acids, NOS, breast tumor, cancer of the breast, Ribonucleic acids, Malignant Neoplasm of Breast, Non Polyadenylated, RNA Gene Products, Carcinomas, BC, Mammary Neoplasms, malignant neoplasm of breast, ribonucleic acid, Acid, Human Mammary, Breast Neoplasm, Gene Expressions, Industrial Arts, Mammary Neoplasm, Non Polyadenylated RNA, Mammary Carcinoma, Human Mammary Carcinomas, Non-Polyadenylated, Cancers, Ribonucleic Acid, "mammary neoplasm" RELATED [], Expressions, Cancer of the Breast, Non-Polyadenylated RNA, breast cancer, cancer of breast, Malignant Tumor of Breast, Mammary, Mammary Cancer, Breast Tumors, Breast Cancer, Breast Malignant Tumors, microarray, Cancer of Breast, Expression, Industrial., Breast, mammary cancer, cancer, mammary tumor, Breast Malignant Neoplasms, breast, Tumors, CancerErbb-2, PR, malignant tumor of the breast, scale tissue, Ribonucleic, IPP2A2, Biological Markers, Viral Marker, Materials, Surrogate Endpoints, Activity, determination, Laboratory, ectodin, selection process, FLNMS, Receptors, Biochemical, mammary neoplasm, Gene Expression Profile, Hs.6719, Estrogen Receptor Type II, Endpoint, Human Mammary Neoplasms, Profiles, Estra, Progress Reports, Nuclear Receptor, Tumor, Serum, Technic, HiSeq 2000, BCS1, 5730420M11Rik, CD340, Techniques, Laboratory Markers, Kiaa3023, Immunogold-Silver Techniques, "neoplasm of breast (disorder)" EXACT [SNOMEDCT_2005_07_31:126926005], Biological, Summary Report, Immunogold-Silver Technique, BCS, cancer of the breast, Research Activity, ENSMUSG00000074510, Laboratory Research, Non Polyadenylated, Summary Reports, HER2delta16 protein, RNA Gene Products, Priorities, HER-2 protein, BC, Mammary Neoplasms, malignant neoplasm of breast, SET, Luminal A subtype of breast carcinoma, Gene Expressions, Luminal B breast cancer, Progress Report, TAF-I, Progesterone receptor, plant peltate hair, Human Mammary Carcinomas, BCs, USAG-1, Signatures, epidermal growth factor receptor 2, DmelCG4299, Progress, IGAAD, set, isoform CRA_e, Immunogold-Silver Technic, Immune, Field Reports, Markers, DmelCG10574, cancer of breast, Expression Signature, Viral Markers, HG-U133 Plus 2 array, Immunolabeling Technique, Transcriptomes, Progesterone Receptor, BB114106, Research Priority, mammary cancer, HER2 protein, Breast Malignant Neoplasms, REM, Immunogold Technics, Tumors, 0610006G05Rik, phapii, Luminal A breast carcinoma, h-BCS, Carcinoma, Viral, "breast neoplasm" EXACT [MTH:120], wide/broad, Surrogate Endpoint, ribose nucleic acid, Arts, Expression Profiles, ribonucleic acids, Immunogold Technique, StF-IT-1, Research Priorities, RNA-seq, Biochemical Markers, MLN19, Luminal B oestrogen receptor positive subtype of breast carcinoma, Biologic Marker, results, Gene Expression, Immunogold, Immunogold Techniques, Immunolabeling Technic, Investigative Report, Marker, Expression Signatures, Ribonukleinsaeure, Immunolabeling Technics, pentosenucleic acids, Genetic Materials, NOS, Ribonucleic acids, Technics, Malignant Neoplasm of Breast, Expression Profile, Genetic Material, Luminal B, c-neu, Transcriptome Profiles, Luminal A, Carcinomas, Research and Development, PTD, Acid, Estrogen Receptor Type I, GD - REM, Epistemology, HLA-DR-associated protein II, Industrial Arts, End Points, DI-2, Affymetrix HT Human Genome U133 Plus 2 Array Plate Set, I-2Dm, Field, common, Immunogold Silver Techniques, INSDC_feature:gene, CG4299, Immunologic, "mammary neoplasm" RELATED [], Laboratory Marker, Estrogen Receptors, EGFR2 protein, human, Activities, I-2PP1, MLN 19, wide, Report, TAF-IBETA, breast cancer, Material, Sostl, Biochemical Marker, human epidermal growth factor receptor 2, Breast Tumors, Wise, Breast Malignant Tumors, TKR1, microarray, Cistron, TAF-Ibeta, Progestin, v-erb-b2 erythroblastic leukemia viral oncogene homolog 2 protein, cancer, i2pp2a, Estrogen Receptors Type I, primary breast cancer, Immunogold-Silver, Estrogen Receptor, BJS, Transcriptome Profile, Clinical Markers, Clinical Marker, Neoplasms, Luminal A oestrogen receptor positive subtype of breast carcinoma, NR3C3, peltate hair, PR-B, PR-A, Mammary Cancers, Gene, broad, PHAPII, Human, Surrogate End Points, Surrogate Markers, Breast Malignant Tumor, Investigative, RRG6, Estrogen Nuclear Receptor, Breast Tumor, Estrogen Receptors Type II, Gene Products, "mammary tumor" EXACT [CSP2005:2016-0671], Whole Transcriptome Shotgun Sequencing, breast tumor, GES, Type I, HER-2/neu, Technique, Immunogold Silver Technics, study, Biomarker, Human Mammary, MC3DN1, Genetic, Neu protein, Clinical, Research, Mammary Neoplasm, HER-2, Estrogen Nuclear, Profile, NR3A1, Mammary Carcinoma, Biological Marker, ipp2a2, xpr-2, 2pp2a, pgr, Expressions, GD:REM, CG10574, Cancer of the Breast, Non-Polyadenylated RNA, Luminal A estrogen receptor positive subtype of breast carcinoma, GEP6, ESR, Immunologic Markers, 2PP2A, taf-ibeta, Malignant Tumor of Breast, Mammary, Mammary Cancer, Luminal A breast cancer, GRACILE, dSET, dSet, Development and Research, Expression, Luminal B subtype of breast carcinoma, Breast, Investigative Reports, Progesterone Receptors, mammary tumor, Immunologic Marker, Biologic, Cancer, Neu, NEU, Breast Carcinoma, Human Mammary Neoplasm, XPR-1, RNA, Breast Carcinomas, Transcriptome, Immunogold Technic, HER-2|neu, mKIAA3023, Serum Markers, igaad, Immunohistocytochemistry, End Point, RNS, "breast tumor" EXACT [NCI2004_11_17:C2910], Progestin Receptor, Cistrons, group, Luminal B estrogen receptor positive subtype of breast carcinoma, isoform CRA_a, Immune Marker, Breast Malignant Neoplasm, HG-U133 Plus 2, Priority, Mammary Carcinomas, I-2PP2A, Surrogate End Point, yeast nucleic acid, Gene Expression Signatures, Dm I-2, chemical analysis, Research Reports, Research Activities, I2PP2A, Neoplasm, Human Mammary Carcinoma, NGL, Gene Expression Signature, background, scales, 9930019P03Rik, Immunolabeling, Biologic Markers, ribonucleic acid, Breast Neoplasm, Immunocytochemistry, Serum Marker, Estrogen, scale, ensemble, c-erbB2, Surrogate, Non Polyadenylated RNA, Endpoints, Non-Polyadenylated, Cancers, Ribonucleic Acid, Progestin Receptors, Surrogate Marker, introduction, dSET/TAF-Ibeta, BPs, 2610030F17Rik, Reports, Gene Expression Profiles, Breast Cancer, Estr, Immunogold-Silver Technics, Immunolabeling Techniques, Cancer of Breast, assay, Receptor, Industrial., Signature, Type II, AA407739, Summary, Progesterone, HER2, breast, stromal connective tissue, Field Report, Luminal B breast carcinoma, Immune MarkersfalseDATA ACCESS COMMITTEE BCTL-IRIBHMData Access Committee EGAC00001000120EGAC00001000120960625412710EGAS00001000495EGAD00001000626EGAD00001000627EGAD00001000708EGAD00010000847