{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"dataset_type":["Illumina Genome Analyzer IIx, Illumina Genome Analyzer IIx;"],"full_dataset_link":["https://ega-archive.org/datasets/EGAD00001000113"],"sample_count":["108"],"description":["EGA dataset EGAD00001000113"],"repository":["EGA"],"title":["Mutational landscapes of primary triple negative breast cancers - Exomes"],"pubmed_abstract":["Primary triple-negative breast cancers (TNBCs), a tumour type defined by lack of oestrogen receptor, progesterone receptor and ERBB2 gene amplification, represent approximately 16% of all breast cancers. Here we show in 104 TNBC cases that at the time of diagnosis these cancers exhibit a wide and continuous spectrum of genomic evolution, with some having only a handful of coding somatic aberrations in a few pathways, whereas others contain hundreds of coding somatic mutations. High-throughput RNA sequencing (RNA-seq) revealed that only approximately 36% of mutations are expressed. Using deep re-sequencing measurements of allelic abundance for 2,414 somatic mutations, we determine for the first time-to our knowledge-in an epithelial tumour subtype, the relative abundance of clonal frequencies among cases representative of the population. We show that TNBCs vary widely in their clonal frequencies at the time of diagnosis, with the basal subtype of TNBC showing more variation than non-basal TNBC. Although p53 (also known as TP53), PIK3CA and PTEN somatic mutations seem to be clonally dominant compared to other genes, in some tumours their clonal frequencies are incompatible with founder status. Mutations in cytoskeletal, cell shape and motility proteins occurred at lower clonal frequencies, suggesting that they occurred later during tumour progression. Taken together, our results show that understanding the biology and therapeutic responses of patients with TNBC will require the determination of individual tumour clonal genotypes."],"pubmed_title":["The clonal and mutational evolution spectrum of primary triple-negative breast cancers."],"pubmed_authors":["Shah Sohrab P SP, Roth Andrew A, Goya Rodrigo R, Oloumi Arusha A, Ha Gavin G, Zhao Yongjun Y, Turashvili Gulisa G, Ding Jiarui J, Tse Kane K, Haffari Gholamreza G, Bashashati Ali A, Prentice Leah M LM, Khattra Jaswinder J, Burleigh Angela A, Yap Damian D, Bernard Virginie V, McPherson Andrew A, Shumansky Karey K, Crisan Anamaria A, Giuliany Ryan R, Heravi-Moussavi Alireza A, Rosner Jamie J, Lai Daniel D, Birol Inanc I, Varhol Richard R, Tam Angela A, Dhalla Noreen N, Zeng Thomas T, Ma Kevin K, Chan Simon K SK, Griffith Malachi M, Moradian Annie A, Cheng S-W Grace SW, Morin Gregg B GB, Watson Peter P, Gelmon Karen K, Chia Stephen S, Chin Suet-Feung SF, Curtis Christina C, Rueda Oscar M OM, Pharoah Paul D PD, Damaraju Sambasivarao S, Mackey John J, Hoon Kelly K, Harkins Timothy T, Tadigotla Vasisht V, Sigaroudinia Mahvash M, Gascard Philippe P, Tlsty Thea T, Costello Joseph F JF, Meyer Irmtraud M IM, Eaves Connie J CJ, Wasserman Wyeth W WW, Jones Steven S, Huntsman David D, Hirst Martin M, Caldas Carlos C, Marra Marco A MA, Aparicio Samuel S"],"name_synonyms":["WES, Complete Transcriptome, Exome Sequencing, Whole Exome, Complete, Complete Transcriptome Sequencing, Exome Sequencings, Complete Exome Sequencings, Whole, Complete Exome Sequencing, Whole Transcriptome Sequencing, Whole Exome Sequencing, Exome, Whole Transcriptome, Transcriptome Sequencing, Transcriptome Sequencings, Sequencing, Complete Exome."],"description_synonyms":["mamma, Lobe of breast, mammary part of chest, mammary region, Lactiferous gland, Breasts, Brustdruese, glandula mammaria, Lobe of mammary gland, breast, Exomes."],"pubmed_title_synonyms":["ER Negative PR Negative HER2 Negative Breast Neoplasms, Triple-Negative Breast Neoplasms, Breast Neoplasm, ER Negative PR Negative HER2 Negative Breast Cancer, Triple Negative Breast Cancer, ER-Negative PR-Negative HER2-Negative Breast Neoplasms, Breast Neoplasms, Triple Negative Breast Neoplasm, Breast Cancer, Triple-Negative Breast Neoplasm, Breast Cancers, Triple-Negative Breast Cancer, Triple-Negative Breast Cancers, Triple-Negative, Triple-Negative., ER-Negative PR-Negative HER2-Negative Breast Cancer"],"pubmed_abstract_synonyms":["Erbb-2, MGC130048, PR, dp53, Breasts, Antemortem Diagnosis, Materials, RNA Sequence Determination, Breast Neoplasms, Sequence Determination, neoplasia, RNA Sequence, estrogenes, Receptors, DPTEN, A4, Lactiferous gland, PI3K, Genotypes., Tumor, Diagnosis, betaTub3, glandula mammaria, Tp53, Long Term, CD340, Mutations, p110-alpha, School-Age, Readability, Kiaa3023, DMP53, bbl, symptoms, p110alpha, Dmp53, TEP1, Analysis, ENSMUSG00000074510, Effect, gamma sarcoglycan, 1323/07, shape of cell, Triple Negative Breast Cancer, Analyses, BCC7, Determination, Progesterone receptor, cell process disease, tumor disease, Breast Cancers, neoplasm (disease), beta-Tub6D, dmp53, T, DmP53, 1422/04, Sequence Determinations, MCAP, isoform CRA_e, B3t, DmelCG3401, Dp53, oestrogene, gamma-sarcoglycan, oestrogens, Progesterone Receptor, BB114106, Cell Shapes, tumor, Estrogene, CG17117, MCMTC, Long-Term Effects, Diagnose, p50/tubulin, Tumors, mamma, screening, CG10873, wide/broad, SG-gamma, Oestrogene, Triple-Negative Breast Cancer, Longterm Effect, RNA-seq, neoplastic disease, MLN19, Shapes, tumours, results, Diagnoses, Determinations, 3t, Postmortem, Screenings, PTEN3, epithelial, PTEN1, School Age, Lobe of mammary gland, Examinations and Diagnoses, Triple-Negative, Genetic Materials, sarcoglycan, bfy, Postmortem Diagnosis, Tub60D, Genetic Material, c-neu, HTH, Hth, oestrogen, Diagnoses and Examination, Populations, beta-tub, Postmortem Diagnoses, Epistemology, Triple-Negative Breast Neoplasms, ER Negative PR Negative HER2 Negative Breast Cancer, ER-Negative PR-Negative HER2-Negative Breast Neoplasms, estrogenes Hormon, MMAC1, DmelCG33336, signs, CG3401, beta3Tub, beta3TUB, gamma (35kDa dystrophin-associated glycoprotein), PTENa, MLN 19, DTB3, wide, hth1, DMDA, hth2, Patient, Material, 35kD dystrophin-associated glycoprotein, Triple-Negative Breast Neoplasm, P53, TKR1, p44, bhy, Cistron, Progestin, School-Age Population, other neoplasm, BZS, ER-Negative PR-Negative HER2-Negative Breast Cancer, CG31325, betaTub, 2310035O07Rik, beta[[3]]-Tub, mammary region, DmelCG17117, SGCG_HUMAN, p50, Effects, GLM2, NR3C3, Neoplasms, p53, Triple-Negative Breast Cancers, PR-B, PR-A, Gene, 143391_i_at, beta3 TU, broad, LFS1, TYPE, l(3)05745, NEOPL, DAGA4, MHAM, AI463227, 35DAG, Mass, Gene Products, Screening, Whole Transcriptome Shotgun Sequencing, Antemortem, anon-EST:Liang-2.13, MAM, gamma-SG, HER-2/neu, SCG3, neoplasm, School-Age Populations, Shape, clone 2.13, Genetic, Longterm, HER-2, D.m.BETA-60D, xpr-2, mammary part of chest, tumour, Long-Term, Diagnoses and Examinations, Population, estrogenos, pgr, DmelCG5671, Sequencing, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS), Trp53, RNA Sequence Analyses, Clients, Triple Negative Breast Neoplasm, betaTub60C, B430203M17Rik, RNA Sequencing, beta3-tubulin, Long-Term Effect, beta[[3]]-tubulin, TRP53, MCM, School Age Population, Progesterone Receptors, Neoplastic Growth, Neu, NEU, Sequence Analyses, beta-Tub60D, Antemortem Diagnoses, XPR-1, RNA, Dmbeta3, findings, Dm-HTH, 6330412C24Rik, PTEN, 35 kDa dystrophin-associated glycoprotein, RNA Sequence Determinations, HER-2|neu, BETA 60D, mKIAA3023, prac, Proteins, beta3t, beta3-Tub, p110, estrogene, dPten, pten, Progestin Receptor, Brustdruese, Cistrons, Client, Examination and Diagnoses, Cell, SGCG, LGMD2C, isoform CRA_a, Xp53, dpten, neoplastic growth, estrogens, CWS5, Genogroup, Mass Screenings, estrogeno, p53/tubulin, CWS1, Long Term Effects, Protein, Amplification, Oestrogen, NGL, beta[[3]] tubulin, dPTEN, 9930019P03Rik, epitheliocyte, CG33336, Breast Neoplasm, Mmac, Exhibit, DMDA1, 10q23del, CG5671, c-erbB2, Lobe of breast, D-p53, beta60C, Dm-P53, l(3)86Ca, beta3, Understanding, A130070J02Rik, Progestin Receptors, disease of cellular proliferation, School Age Populations, dtl, Longterm Effects, Tub, Protein Gene Products, ER Negative PR Negative HER2 Negative Breast Neoplasms, Gene Proteins, Meis1, caPI3K, DEC, Genogroups, CLOVE, betatub60D, Breast Cancer, RNA Sequence Analysis, SCARMD2, Receptor, Progesterone, HER2, NEOPLASMS BENIGN, Neoplasia, breast, oestrogenes"],"additional_accession":[]},"is_claimable":false,"name":"Exome sequencing - samples","description":"Mutational landscapes of primary triple negative breast cancers - Exomes","dates":{"updated":"2017-07-26 15:39:24"},"accession":"EGAD00001000113","cross_references":{"TAXONOMY":["9606"],"pubmed":["22495314"],"EGA":["EGAC00000000011","EGAS00001000132"]}}