{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"dataset_type":["Illumina HiSeq 2000;ILLUMINA, Illumina HiSeq 2500;ILLUMINA"],"full_dataset_link":["https://ega-archive.org/datasets/EGAD00001003829"],"sample_count":["96"],"description":["EGA dataset EGAD00001003829"],"repository":["EGA"],"title":["Exome sequencing data for LMS tumor and control samples"],"pubmed_abstract":["Leiomyosarcoma (LMS) is an aggressive mesenchymal malignancy with few therapeutic options. The mechanisms underlying LMS development, including clinically actionable genetic vulnerabilities, are largely unknown. Here we show, using whole-exome and transcriptome sequencing, that LMS tumors are characterized by substantial mutational heterogeneity, near-universal inactivation of TP53 and RB1, widespread DNA copy number alterations including chromothripsis, and frequent whole-genome duplication. Furthermore, we detect alternative telomere lengthening in 78% of cases and identify recurrent alterations in telomere maintenance genes such as ATRX, RBL2, and SP100, providing insight into the genetic basis of this mechanism. Finally, most tumors display hallmarks of \"BRCAness\", including alterations in homologous recombination DNA repair genes, multiple structural rearrangements, and enrichment of specific mutational signatures, and cultured LMS cells are sensitive towards olaparib and cisplatin. This comprehensive study of LMS genomics has uncovered key biological features that may inform future experimental research and enable the design of novel therapies."],"pubmed_title":["Integrative genomic and transcriptomic analysis of leiomyosarcoma."],"pubmed_authors":["Chudasama Priya P, Mughal Sadaf S SS, Sanders Mathijs A MA, Hübschmann Daniel D, Chung Inn I, Deeg Katharina I KI, Wong Siao-Han SH, Rabe Sophie S, Hlevnjak Mario M, Zapatka Marc M, Ernst Aurélie A, Kleinheinz Kortine K, Schlesner Matthias M, Sieverling Lina L, Klink Barbara B, Schröck Evelin E, Hoogenboezem Remco M RM, Kasper Bernd B, Heilig Christoph E CE, Egerer Gerlinde G, Wolf Stephan S, von Kalle Christof C, Eils Roland R, Stenzinger Albrecht A, Weichert Wilko W, Glimm Hanno H, Gröschel Stefan S, Kopp Hans-Georg HG, Omlor Georg G, Lehner Burkhard B, Bauer Sebastian S, Schimmack Simon S, Ulrich Alexis A, Mechtersheimer Gunhild G, Rippe Karsten K, Brors Benedikt B, Hutter Barbara B, Renner Marcus M, Hohenberger Peter P, Scholl Claudia C, Fröhling Stefan S"],"description_synonyms":["data, Controlling, preventive therapy, Complete Exome Sequencings, Malignant Neoplasm, Data Set, Edg, Complete Exome, malignant, Neoplasms, Exome, leiomyosarcoma, Benign Neoplasm, Tumor, Malignant, Myxoid Leiomyosarcomas, Exome Sequencing, Benign, Myxoid Leiomyosarcoma, Neoplasm, Epithelioid Leiomyosarcoma, Whole Transcriptome, Transcriptome Sequencing, Leiomyosarcoma, END, prevention and control, Epithelioid, WES, Complete Transcriptome, Complete, Complete Transcriptome Sequencing, Exome Sequencings, reference sample, Malignancy, Leiomyosarcomas, prophylaxis, Complete Exome Sequencing, Whole Transcriptome Sequencing, Benign Neoplasms, prevention., Cancers, Myxoid, leiomyosarcoma (excluding uterine leiomyosarcoma), Sequencing, Malignant Neoplasms, Neoplasias, preventive measures, Epithelioid Leiomyosarcomas, Whole Exome, control, Whole, leiomyosarcoma - not uterine, Whole Exome Sequencing, Malignancies, ORW1, other neoplasm, Transcriptome Sequencings, HHT1, Neoplasia, Controlled, Cancer, Tumors"],"pubmed_title_synonyms":["Epithelioid Leiomyosarcomas, Myxoid Leiomyosarcoma, determination, Leiomyosarcomas, leiomyosarcoma - not uterine, malignant, chemical analysis, leiomyosarcoma, Epithelioid Leiomyosarcoma, assay, Leiomyosarcoma, Myxoid, leiomyosarcoma (excluding uterine leiomyosarcoma), Epithelioid., Myxoid Leiomyosarcomas, Epithelioid"],"name_synonyms":["Vasp, VASP, Data Set., DmelCG15112, ENHANCER OF ATNSI ACTIVITY, MENA, NDPP1, l(2)02029, Enb, enb, ENA, Ena, CG15112, ENA/VASP"],"pubmed_abstract_synonyms":["RB1, chromosomal crossover, telomere, Materials, Platinol, cis-Diamminedichloroplatinum(II), cis-Dichlorodiammineplatinum(II), Activity, Laboratory, Randa, postnatal development, AZD 2281, Gene Expression Profile, (SP-4-2)-, growth and development, Profiles, RBF, ALPHA-thalassemia/mental retardation syndrome, Tumor, Xnp, XNP, Tp53, RBR, Recombinations, XLMR hypotonic face syndrome, B(p51B), bbl, TP73L, RB, rb, Peyrone's chloride, nuclear chromosome, RETINOBLASTOMA PROTEIN, rbf, Research Activity, Alpha-thalassemia-X-linked intellectual disability syndrome, Laboratory Research, KET, Peyrone's salt, Priorities, thymus nucleic acid, OFC8, BCC7, Genomes, pp110, Homologous, B(p51A), cis-diamminedichloridoplatinum(II), Comparative Genomics, p73H, cis-DDP, Rb, Myxoid, Briplatin, Signatures, genetic, allergic reaction, high frequency, Expression Signature, leiomyosarcoma - not uterine, Cisplatin, Transcriptomes, Shattering, (SP-4-2)-diamminedichloroplatinum, Malignancies, CG7413, Double-Stranded DNA, lysp100b, deoxyribonucleic acids, Research Priority, DNAn, INSDC_feature:telomere, somatic mutation, Hp1bp38, Tumors, ATR, Lynparza, retinoblastoma-related 1, Genomics, LNMS, DP, rbf1, NSC-119875, Comparative, Expression Profiles, familial, Research Priorities, retinoblastoma, Alpha thalassemia mental retardation syndrome, Alpha thalassemia intellectual disability syndrome, Double-Stranded, Functional Genomics, cis Platinum, telomeric sequence, RETINOBLASTOMA 1, diamminedichloro-, hereditary retinoblastoma, SHS, (Deoxyribonucleotide)n+m, Gene Expression, Benign, ectrodactyly, Expression Signatures, MRXS3, Alpha-thalassemia/mental retardation syndrome, Epithelioid Leiomyosarcoma, ATRBR1, Genetic Materials, CDDP, p73L, bfy, Chromosome Shattering, desoxyribose nucleic acid, ATRX syndrome, Expression Profile, Genetic Material, Transcriptome Profiles, Research and Development, pRb, Recombination, DmelCG7413, EEC3, MRXHF1, Dichlorodiammineplatinum, Exomes, [PtCl2(NH3)2], Platinum Diamminodichloride, Benign Neoplasms, ZNF-HX, whole genome, RAD54L, RHS, Malignant Neoplasms, experimental procedures, Activities, Epithelioid Leiomyosarcomas, p105-Rb, ALPHA-thalassemia/intellectual disability syndrome, familial retinoblastoma, Chromosome, Material, p40, Platidiam, ds DNA, P53, telomeric DNA, Laurence-Moon-Biedl syndrome, p44, bhy, Lms, LMS, Cistron, inherited genetic, cisplatinum, DNA, EG:34F3.3, Rbf1, RBF1, whole exome, telomeric region, DNS, X-linked, (Deoxyribonucleotide)n, experimental, Transcriptome Profile, FBF, p51, Neoplasms, p53, leiomyosarcoma, Benign Neoplasm, number, Gene, AZD221, Malignant, LFS1, autosomal dominant, dRBF, presence, Myxoid Leiomyosarcomas, NBP, Deoxyribonucleic acids, 4833408C14Rik, AZD-2281, LMNS, eye cancer, Structural, Deoxyribonucleic Acid, nondeletion type, HP1-BP38, AIS, sensitive, p63, RHOMBOID-like 2, OSRC, DNA Damage Response, Functional, SFM1, mammary hypoplasia, Leiomyosarcoma, AZD2281, sensitivity, Laurence-MOON syndrome, study, XH2, methods, telomeres, Genetic, cis-Diamminedichloroplatinum, Malignancy, Research, experimental section, Profile, Chromothripses, cis-Platinum, Double Stranded, Deoxyribonucleic acid, leiomyosarcoma (excluding uterine leiomyosarcoma), Lederplatin, Research Activities., Platamine, Neoplasias, AI447451, Trp53, SHFM4, Chromosome Shatterings, heterogeneity, JMS, (Deoxyribonucleotide)m, Development and Research, TRP53, constitutitional genetic, Cancer, F16M19_4, Transcriptome, Malignant Neoplasm, Cismaplat, malignant, ATR2, Homologous Recombinations, DNAn+1, and other hand/foot anomalies, PRB2, Cistrons, Cell, Xp53, whole transcriptome, Alpha-thalassemia/intellectual disability syndrome, development, count in organism, Priority, MT, ATRX, Myxoid Leiomyosarcoma, F16M19.4, Gene Expression Signatures, (SP-4-2)-diamminedichloridoplatinum, Neoplasm, PPP1R130, Telomeres, Gene Expression Signature, TP53L, ds-DNA, p53CP, Epithelioid, cis-diammineplatinum(II) dichloride, cis-diamminedichloroplatinum, regulation of telomere length, cis-platin, Nondeletion type, cis-[PtCl2(NH3)2], frequent, cis-diamminedichloroplatinum(II), cis-dichlorodiammineplatinum(II), Leiomyosarcomas, Neoplatin, reciprocal DNA recombination, TP53CP, Diamminodichloride, postnatal growth, Rb-1, cis Diamminedichloroplatinum, Platinum, cisplatine, Cancers, P130, cisplatin, cisplatino, Rb1, DXHXS6677E, Rb2, Hp1bp2, Rad54, RBR-2, Gene Expression Profiles, Alpha-thalassemia X-linked intellectual disability syndrome, A430075G10Rik, p130, cardinality, Biocisplatinum, RETINOBLASTOMA-RELATED PROTEIN 1, RETINOBLASTOMA-RELATED, Desoxyribonukleinsaeure, Platino, Structural Genomics, RAD54, Signature, RbF, trilateral, ATRBL2, growth, hereditary, Neoplasia, Platinex"],"additional_accession":[]},"is_claimable":false,"name":"ena-DATASET-DKFZ-HIPO-01-12-2017-13:14:23:391-67 - samples","description":"The data set contains paired end fastq files for whole exome sequencing data for Leiomyosarcoma tumor and control samples","dates":{"updated":"2018-03-15 14:50:56"},"accession":"EGAD00001003829","cross_references":{"TAXONOMY":["9606"],"pubmed":["29321523"],"EGA":["EGAC00001000452","EGAS00001002437"]}}