{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"dataset_type":["Illumina_2.5M"],"full_dataset_link":["https://ega-archive.org/datasets/EGAD00010000278"],"sample_count":["51"],"description":["EGA dataset EGAD00010000278"],"repository":["EGA"],"title":["Title not provided"],"pubmed_abstract":["Small-cell lung cancer (SCLC) is an exceptionally aggressive disease with poor prognosis. Here, we obtained exome, transcriptome and copy-number alteration data from approximately 53 samples consisting of 36 primary human SCLC and normal tissue pairs and 17 matched SCLC and lymphoblastoid cell lines. We also obtained data for 4 primary tumors and 23 SCLC cell lines. We identified 22 significantly mutated genes in SCLC, including genes encoding kinases, G protein-coupled receptors and chromatin-modifying proteins. We found that several members of the SOX family of genes were mutated in SCLC. We also found SOX2 amplification in ∼27% of the samples. Suppression of SOX2 using shRNAs blocked proliferation of SOX2-amplified SCLC lines. RNA sequencing identified multiple fusion transcripts and a recurrent RLF-MYCL1 fusion. Silencing of MYCL1 in SCLC cell lines that had the RLF-MYCL1 fusion decreased cell proliferation. These data provide an in-depth view of the spectrum of genomic alterations in SCLC and identify several potential targets for therapeutic intervention."],"pubmed_title":["Comprehensive genomic analysis identifies SOX2 as a frequently amplified gene in small-cell lung cancer."],"pubmed_authors":["Rudin Charles M CM, Durinck Steffen S, Stawiski Eric W EW, Poirier John T JT, Modrusan Zora Z, Shames David S DS, Bergbower Emily A EA, Guan Yinghui Y, Shin James J, Guillory Joseph J, Rivers Celina Sanchez CS, Foo Catherine K CK, Bhatt Deepali D, Stinson Jeremy J, Gnad Florian F, Haverty Peter M PM, Gentleman Robert R, Chaudhuri Subhra S, Janakiraman Vasantharajan V, Jaiswal Bijay S BS, Parikh Chaitali C, Yuan Wenlin W, Zhang Zemin Z, Koeppen Hartmut H, Wu Thomas D TD, Stern Howard M HM, Yauch Robert L RL, Huffman Kenneth E KE, Paskulin Diego D DD, Illei Peter B PB, Varella-Garcia Marileila M, Gazdar Adi F AF, de Sauvage Frederic J FJ, Bourgon Richard R, Minna John D JD, Brock Malcolm V MV, Seshagiri Somasekar S"],"name_synonyms":["average, preventive measures, Controlling, preventive therapy, pulmo, pulmonary, reference sample, control, parenchyma of lung, prophylaxis, lung, lung parenchyma, Lungs, prevention., neoplasm, prevention and control, neoplasms, Controlled"],"pubmed_abstract_synonyms":["Networks, Materials, Kinship, GTP Binding Protein, RNA Sequence Determination, GTP-Regulatory Proteins, Sequence Determination, RNA Sequence, Gene Expression Profile, Profiles, Tumor, Cell Growth in Number, small cell cancer of the lung, dmTAF[[II]]230, diseases, Line, Alleviating interaction, Cell Number Growth, Life Cycle, AW536278, diseases and disorders, GTP-Binding Protein, Kinase, Analysis, UNQ2520/PRO6013, Chromatins, Family Life Cycle, average, Lung Cancer, human disease, Growth, Prognoses, Man (Taxonomy), Kinship Network, TFIID TAF250, Analyses, cel, Determination, alveolar cell carcinoma, Tissue, hypoplasia, Lung Cancers, Xsox-2, Sequence Determinations, Signatures, KE1.5, LMYC, Expression Signature, chromosome scaffold, Transcriptomes, Therapies, Homo sapiens disease, Malignancies, Family Life Cycles, ATP Phosphotransferases, ATP, Tumors, nuclear chromatin, Therapy, GTP Regulatory Protein, dTAF[[II]]230, Lung cancer, GTP Binding Proteins, ysb, Modern, ZNF292L, Expression Profiles, TAF200, Cancer of Lung, TAFII-250, Procedure, TAF250/230, Guanine Nucleotide Coupling Protein, ANOP3, Determinations, Gene Expression, ley-I-L, TAFII250, Benign, Lmyc-1, cancer of lung, Expression Signatures, Diseases, anop3, Genetic Materials, Cellular, NOS, simple tissue, Filiation, Expression Profile, Genetic Material, Transcriptome Profiles, Lines, Transphosphorylases, Factors, sox-2, Prognostic, Exomes, Benign Neoplasms, CG17603, TAF[[II]], Treatments, human, Malignant Neoplasms, Life Cycles, disease, Sox-2, G Proteins, Taf250, lymphoblastoid cell, Material, SR3-5, Proliferation, cancer of the lung, Cell Number, Cistron, lung neoplasm, Cancer of the Lung, TAF230, Prognostic Factor, RGD1565646, AI195322, other disease, whole exome, cytoplasmic chromatin, d230, Lung, human being, Family Member, Transcriptome Profile, Neoplasms, lung cancer, number, Benign Neoplasm, Gene, dTAFII250, Prognostic Factors, Network, 9230110M18Rik, EfW1, Malignant, presence, Rab2l, Human, Intervention or Procedure, reduced, Homo sapiens, dmTAF1, Taf230, Gene Products, disease or disorder, tiny, Number Growth, Pulmonary Cancer, Man, Phosphotransferase, Pulmonary, TAF250, Taf200, Lmyc1, dTAF[[II]]250, Genetic, Malignancy, Research, interventionDescription, cell, MCOPS3, Rlf, RLF, Profile, LNCR, Interventional, Taf1p, QSCN6, Transphosphorylase, suppressive genetic interaction (sensu inequality), Sequencing, RLNL, non-neoplastic, Neoplasias, dTAF250, cell proliferation, GTP-Regulatory Protein, G Protein, Lung Neoplasm, RNA Sequence Analyses, SURGICAL AND MEDICAL PROCEDURES., G-Proteins, disorder, RNA Sequencing, L-myc, Rgt2, Kinship Networks, TAF, bHLHe38, Family, ZN-15L, Sox, Cancer, Sequence Analyses, small, G-Protein, Multiplication, Intervention Strategies, RNA, TAF[[II]]250, Pulmonary Neoplasms, Guanine Nucleotide Regulatory Proteins, Transcriptome, Cellular Proliferation, Malignant Neoplasm, Family Research, RNA Sequence Determinations, Proteins, disorders, Cell Lines, SRY-box2, l(3)84Ab, BG:DS00004.13, medical condition, Factor, Cistrons, Cell, Phosphotransferases, dTAF230, whole transcriptome, Family Members, count in organism, GTP-Regulatory, MommeD8, p230, Gene Expression Signatures, Protein, Neoplasm, Nonsmall cell lung cancer, TAF[[II]]250/230, TFIID, condition, Gene Expression Signature, Rlnl, Intervention, Taf[[II]]250, TAF[[II]]230, underdeveloped, Kinases, Pulmonary Neoplasm, lcc, TAF[II]250, Cancers, GTP-Binding, MYCL1, Protein Gene Products, Gene Proteins, DmelCG17603, Mycl1, Therapeutic, Gene Expression Profiles, Families, Modern Man, RNA Sequence Analysis, cardinality, Cell Multiplication, mcops3, GTP Regulatory Proteins, protection against, Treatment, Pulmonary Cancers, Signature, Relatives, SCLC1, Neoplasia, TAF1"],"pubmed_title_synonyms":["small, RGD1565646, dTAF[[II]]230, TAF[[II]]250, d230, Pulmonary Neoplasms, Lung cancer, Lung, Materials, ysb, determination, Neoplasms, lung cancer, SRY-box2, TAF200, Cancer of Lung, Gene, l(3)84Ab, dTAFII250, BG:DS00004.13, TAFII-250, TAF250/230, Cistrons, EfW1, ANOP3, Cell, dTAF230, dmTAF[[II]]230, TAFII250, reduced, dmTAF1, cancer of lung, Taf230, p230, chemical analysis, anop3, Neoplasm, Nonsmall cell lung cancer, TAF[[II]]250/230, Genetic Materials, TFIID, NOS, tiny, Pulmonary Cancer, Genetic Material, Pulmonary, TAF250, Taf[[II]]250, Lung Cancer, Taf200, dTAF[[II]]250, TAF[[II]]230, Genetic, sox-2, TFIID TAF250, underdeveloped, cel, cell, MCOPS3, lcc, Pulmonary Neoplasm, alveolar cell carcinoma, hypoplasia, LNCR, Taf1p, INSDC_feature:gene, TAF[II]250, Lung Cancers, Cancers, Xsox-2, CG17603, TAF[[II]], dTAF250, Sox-2, DmelCG17603, Lung Neoplasm, Taf250, Material, SR3-5, cancer of the lung, Pulmonary., mcops3, protection against, Cistron, Pulmonary Cancers, assay, lung neoplasm, Cancer of the Lung, TAF, TAF230, TAF1, Cancer"],"description_synonyms":["small cell cancer of the lung, average, Genogroups, Genotypes., Genogroup, SCLC1"],"additional_accession":[]},"is_claimable":false,"name":"Lung normal control - samples","description":"SCLC matched normal genotypes","dates":{"updated":"2019-10-31 12:52:15"},"accession":"EGAD00010000278","cross_references":{"TAXONOMY":["9606"],"pubmed":["22941189"],"EGA":["EGAC00001000055","EGAS00001000334"]}}