EGAGenomicsRené Custershttps://ega-archive.org/dacs/EGAC00001002939EGAEGA DAC EGAC00001002939EGAdac@vib.beRNA-seq is a promising technology to re-sequence protein coding genes for the identification of single nucleotide variants (SNV), while simultaneously obtaining information on structural variations and gene expression perturbations. We asked whether RNA-seq is suitable for the detection of driver mutations in T-cell acute lymphoblastic leukemia (T-ALL). These leukemias are caused by a combination of gene fusions, over-expression of transcription factors and cooperative point mutations in oncogenes and tumor suppressor genes. We analyzed 31 T-ALL patient samples and 18 T-ALL cell lines by high-coverage paired-end RNA-seq. First, we optimized the detection of SNVs in RNA-seq data by comparing the results with exome re-sequencing data. We identified known driver genes with recurrent protein altering variations, as well as several new candidates including H3F3A, PTK2B, and STAT5B. Next, we determined accurate gene expression levels from the RNA-seq data through normalizations and batch effect removal, and used these to classify patients into T-ALL subtypes. Finally, we detected gene fusions, of which several can explain the over-expression of key driver genes such as TLX1, PLAG1, LMO1, or NKX2-1; and others result in novel fusion transcripts encoding activated kinases (SSBP2-FER and TPM3-JAK2) or involving MLLT10. In conclusion, we present novel analysis pipelines for variant calling, variant filtering, and expression normalization on RNA-seq data, and successfully applied these for the detection of translocations, point mutations, INDELs, exon-skipping events, and expression perturbations in T-ALL.Comprehensive analysis of transcriptome variation uncovers known and novel driver events in T-cell acute lymphoblastic leukemia.Atak Zeynep Kalender ZK, Gianfelici Valentina V, Hulselmans Gert G, De Keersmaecker Kim K, Devasia Arun George AG, Geerdens Ellen E, Mentens Nicole N, Chiaretti Sabina S, Durinck Kaat K, Uyttebroeck Anne A, Vandenberghe Peter P, Wlodarska Iwona I, Cloos Jacqueline J, Foà Robin R, Speleman Frank F, Cools Jan J, Aerts Stein Sl(3)j5A6, fbwd4, l(3)j7A3, l(2)04454, DmelCG1772, dac, l(3)S045002, CIB1, VIb, p21[dacapo], CG14235, 0450/02, 1104/16, dactylin, E130112M23Rik, cdi4, DmelCG14235, dactylyn, l(3)S045002c, p21, CG1772, FBWD4, Cdi4, CDI4, p27, l(3)S110416, CcoVIb, anon-WO0142479.3, l(3)j7C8, gio, shsf3, anon-WO0172774.28, CG5269, shfm3, Decapo., E(Sev-CycE)2B, Fbw4, FBW4, l(3)j4A3, Dach, CDKN2B, SHFM3, DmelCG5269, Dac, DAC, p27[Dap], dacapo/cyclin-dependent kinase interactor 4, AI182278, Vib, anon-WO0172774.16, Dap, CES5A1, anon-WO0172774.12, P15, fbw4, SHSF3T-cell acute lymphocytic leukaemia, acute T cell lymphoblastic leukemia, T-cell acute lymphocytic leukemia, T-cell leukemia, Transcriptome, precursor T-lymphoblastic leukemia (T-cell ALL), T-ALL., determination, Transcriptome Profile, T-cell ALL, Profile, T-cell acute lymphoblastic leukemia, Expression Profiles, Gene Expression Profile, Gene, T acute lymphoblastic leukemia, acute T-cell lymphocytic leukemia, Profiles, T-cell type acute leukemia, Signatures, Gene Expression, precursor T-lymphoblastic lymphoma/leukemia, Expression Signature, Gene Expression Profiles, Expression Signatures, acute T-cell leukemia, chemical analysis, Gene Expression Signatures, T-cell lymphoblastic leukemia/lymphoma, Transcriptomes, T Acute Lymphoblastic Leukemia, acute T cell leukaemia, acute T cell leukemia, Precursor T Lymphoblastic Leukemia, assay, Gene Expression Signature, Signature, acute T-cell lymphoblastic leukemia, precursor T-lymphoblastic leukemia, Expression Profile, acute T cell lymphocytic leukemia, Transcriptome ProfilesAI504024, acute T cell lymphoblastic leukemia, T-cell leukemia, Dfps, NK-2, Materials, FADK2, hTM30nm, TPMsk3, HOX11, determination, Metastasis, Recessive, RAFTK, Hox-11, CFTD, precursor T-cell acute lymphoblastic leukemia/lymphoma, Tumor Suppressing Gene, OK|SW-cl.5, Mini Exon, acute T-cell lymphocytic leukemia, Rbtn1, CG8874, protein, JTK10, Oncogenes, Precursor T Cell Lymphoblastic Lymphoma, Raftk, Acute., Mutations, Anti-Oncogene, Growth Suppressor Genes, BCH, Acute T-Cell Leukemia, CAKB, dfps, T-Lymphocytic Leukemia, Line, Recessive Oncogenes, TCL3, HD-179, Emerogenes, 26Fe, Transforming, Kinase, 2310079I02Rik, protein aggregate, Precursor T Cell Lymphoblastic Leukemia, NKX2.1, Hox11, Tumor Suppressing, IKKg, T-ALL, Fusion, T-Lymphocytic Leukemias, KEY, Key, T-cell acute lymphocytic leukemia, Flk, Growth, precursor T-lymphoblastic leukemia (T-cell ALL), Gene Expressions, T-cell ALL, Anti Oncogenes, Onco-Suppressor, Leucocythemias, OK/SW-cl.5, TEBP, Growth Suppressor, H3.3A, Transforming Genes, RBTN1, CAKbeta, Rbtn-1, acute T-cell leukemia, Tpm-5, Nkx2.1, FERONIA, Bx, Nucleotide, ATP Phosphotransferases, precursor T-cell acute lymphoblastic leukemia, ATP, mKIAA4140, SSDP2, dfer, Acute T-Cell Leukemias, Cancer Suppressor Genes, CG11849, Arts, RNA-seq, JAK2, dfps85D, PSA, soss-b2, dFer, DmIKKgamma, THCYT3, DmelCG8874, batch, JAK-2, T-Cell, TYK3, dIKK, Kenny, Gene Fusions, DFER, DFer, TM30, Genetic Materials, acute T cell leukaemia, acute T cell leukemia, ZNF912, RHOM1, precursor T-lymphoblastic leukemia, END, Genetic Material, BHC, nucleotides, Lines, Lymphoblastic Leukemia, T-cell acute lymphocytic leukaemia, Transphosphorylases, Leucocythemia, Industrial, T Cell Leukemia, PTK, Acute T-Lymphocytic Leukemias, Factors, Industrial Arts, FPS, Iron, Dm FPS, IKK-gamma, lmo1, Pe1Fe6, Exomes, Pe1Fe3, precursor T-cell acute lymphocytic leukemia/lymphoma, lmo3, Acute T-Lymphocytic Leukemia, STAT5, Tumor Suppressor Gene, TM3, TM5, tlx1-a, Tumor Suppressor, Fe, precursor T-cell acute lymphocytic leukemia, Pe1Fe13, Eisen, Pe1Fe10, Oncogene, DmelCG16910, fps, Patient, A830008M03Rik, Material, stat5, XHox11, DmHD-179, hscp30, Dfer, Cistron, T Cell, AV026640, H3F3, iron, Fert2, whole exome, Antioncogenes, Cancer Suppressor Gene, Lymphocytic Leukemia, TTF1, E430023O05Rik, Gene, Coding, Janus kinase 2, protein-containing complex, AF10, Transcription Factor, h3f3a, dIKK-gamma, T-Cell Leukemias, precursor T-lymphoblastic lymphoma/leukemia, Tpm5, Antioncogene, T-Cell Acute Lymphocytic Leukemia, TTF-1, DmIKK-gamma, Mini-Exon, Gene Products, T Acute Lymphoblastic Leukemia, leukaemia NOS, AW558684, Whole Transcriptome Shotgun Sequencing, C81284, fps85D, Cancer Suppressor, PYK2, Precursor T-Cell Lymphoblastic Leukemia, Leucocythaemia, Pyk2, dmIKKgamma, Trop-5, acute T-cell lymphoblastic leukemia, Tumor Suppressing Genes, IKK[[gamma]], Medical, Phosphotransferase, Af10, Ttf-1, h3.3a, Fert, Lymphocytic, h3.3b, Transcription, hierro, Leukemia, Clinical, Genetic, Transforming Gene, Medical Coding, 9330163K02Rik, Precursor T-Cell Lymphoblastic Lymphoma, Emerogene, CADTK, Anti-Oncogenes, Transphosphorylase, Expressions, gamma-TM, Suppressor Gene, NEM1, FerT, FAK2, SGPA, HEL-S-82p, Acute T-Lymphocytic, IKK, Clients, Ttg1, TTG1, T-cell lymphoblastic leukemia/lymphoma, Dan, T|EBP, Fer, FER, Metastasis Suppressor, Expression, CAPM1, Acute T-Cell, TM30nm, HHT1, 1500004K09Rik, Cancer, dfps 85D, hTMnm, Onco-Suppressor Genes, C330004K01Rik, D630001B22Rik, Edg, protein complex, TRK, Flk_retired, T-cell acute lymphoblastic leukemia, Proteins, Cell Lines, fer, Point Mutations, T acute lymphoblastic leukemia, Factor, T-cell type acute leukemia, Cistrons, XHox11L2, Titf1, Client, Leukemias, Cell, Phosphotransferases, T-Cell Leukemia, DmelCG11849, RGD1563655, IKKgamma, NKX2A, Fd17, PKB, native protein, TITF1, Tm5NM, Protein, Hspc116, chemical analysis, sequence, Recessive Oncogene, Mutation, acute T cell lymphocytic leukemia, B130021D15Rik, Acute T Cell, Leucocythaemias, ferrum, Genes, TM-5, AV082135, Growth Suppressor Gene, Dmikkgamma, Kinases, exonic region, SOSS-B2, Mini-Exons, Metastasis Suppressor Genes, Lymphoblastic, Metastasis Suppressor Gene, Exon, patient, HEL-189, CG16910, PPP1R74, hox11, primary structure of sequence macromolecule, T Lymphocytic Leukemia, TMnm, Protein Gene Products, h3.3, Onco Suppressor, Gene Proteins, Onco-Suppressor Gene, Acute, Point, AU067692, Precursor T Cell Lymphoblastic Leukemia Lymphoma, Suppressor Genes, Fusions, HSPC116, Precursor T Lymphoblastic Leukemia, assay, Tumor Suppressor Genes, ORW1falseVIB Institutional DACData Access Committee EGAC00001002939EGAC00001002939960624367274EGAS00001000268EGAS00001000296EGAS00001000536EGAS00001002830EGAS00001006711EGAS00001005029EGAS00001004440EGAD00001009686EGAD00001000291EGAD00001006167EGAD00001000150EGAD00001003951EGAD00001006955EGAD00001000849