EGAGenomicsN/Ahttps://ega-archive.org/datasets/EGAD000010013880EGA dataset EGAD00001001388EGAWe analysed whole-genome sequences of 560 breast cancers to advance understanding of the driver mutations conferring clonal advantage and the mutational processes generating somatic mutations. We found that 93 protein-coding cancer genes carried probable driver mutations. Some non-coding regions exhibited high mutation frequencies, but most have distinctive structural features probably causing elevated mutation rates and do not contain driver mutations. Mutational signature analysis was extended to genome rearrangements and revealed twelve base substitution and six rearrangement signatures. Three rearrangement signatures, characterized by tandem duplications or deletions, appear associated with defective homologous-recombination-based DNA repair: one with deficient BRCA1 function, another with deficient BRCA1 or BRCA2 function, the cause of the third is unknown. This analysis of all classes of somatic mutation across exons, introns and intergenic regions highlights the repertoire of cancer genes and mutational processes operating, and progresses towards a comprehensive account of the somatic genetic basis of breast cancer.Landscape of somatic mutations in 560 breast cancer whole-genome sequences.Nik-Zainal Serena S, Davies Helen H, Staaf Johan J, Ramakrishna Manasa M, Glodzik Dominik D, Zou Xueqing X, Martincorena Inigo I, Alexandrov Ludmil B LB, Martin Sancha S, Wedge David C DC, Van Loo Peter P, Ju Young Seok YS, Smid Marcel M, Brinkman Arie B AB, Morganella Sandro S, Aure Miriam R MR, Lingjærde Ole Christian OC, Langerød Anita A, Ringnér Markus M, Ahn Sung-Min SM, Boyault Sandrine S, Brock Jane E JE, Broeks Annegien A, Butler Adam A, Desmedt Christine C, Dirix Luc L, Dronov Serge S, Fatima Aquila A, Foekens John A JA, Gerstung Moritz M, Hooijer Gerrit K J GK, Jang Se Jin SJ, Jones David R DR, Kim Hyung-Yong HY, King Tari A TA, Krishnamurthy Savitri S, Lee Hee Jin HJ, Lee Jeong-Yeon JY, Li Yilong Y, McLaren Stuart S, Menzies Andrew A, Mustonen Ville V, O'Meara Sarah S, Pauporté Iris I, Pivot Xavier X, Purdie Colin A CA, Raine Keiran K, Ramakrishnan Kamna K, Rodríguez-González F Germán FG, Romieu Gilles G, Sieuwerts Anieta M AM, Simpson Peter T PT, Shepherd Rebecca R, Stebbings Lucy L, Stefansson Olafur A OA, Teague Jon J, Tommasi Stefania S, Treilleux Isabelle I, Van den Eynden Gert G GG, Vermeulen Peter P, Vincent-Salomon Anne A, Yates Lucy L, Caldas Carlos C, van't Veer Laura L, Tutt Andrew A, Knappskog Stian S, Tan Benita Kiat Tee BK, Jonkers Jos J, Borg Åke Å, Ueno Naoto T NT, Sotiriou Christos C, Viari Alain A, Futreal P Andrew PA, Campbell Peter J PJ, Span Paul N PN, Van Laere Steven S, Lakhani Sunil R SR, Eyfjord Jorunn E JE, Thompson Alastair M AM, Birney Ewan E, Stunnenberg Hendrik G HG, van de Vijver Marc J MJ, Martens John W M JW, Børresen-Dale Anne-Lise AL, Richardson Andrea L AL, Kong Gu G, Thomas Gilles G, Stratton Michael R MRVasp, VASP, Data Set., DmelCG15112, ENHANCER OF ATNSI ACTIVITY, MENA, NDPP1, l(2)02029, Enb, enb, ENA, Ena, CG15112, ENA/VASPBreast Carcinoma, Human Mammary Neoplasm, primary breast cancer, Carcinoma, malignant tumor of the breast, Breast Carcinomas, "breast neoplasm" EXACT [MTH:120], Neoplasms, mammary neoplasm, Mammary Cancers, Human Mammary Neoplasms, Tumor, "breast tumor" EXACT [NCI2004_11_17:C2910], Human, Mutations, Breast Malignant Neoplasm, Breast Malignant Tumor, "neoplasm of breast (disorder)" EXACT [SNOMEDCT_2005_07_31:126926005], Mammary Carcinomas, Breast Tumor, Neoplasm, Human Mammary Carcinoma, "mammary tumor" EXACT [CSP2005:2016-0671], NOS, breast tumor, cancer of the breast, Malignant Neoplasm of Breast, Genomes., Carcinomas, BC, Mammary Neoplasms, malignant neoplasm of breast, Human Mammary, Breast Neoplasm, Mammary Neoplasm, Mammary Carcinoma, Human Mammary Carcinomas, Cancers, whole genome, "mammary neoplasm" RELATED [], Cancer of the Breast, breast cancer, cancer of breast, Malignant Tumor of Breast, Mammary, Mammary Cancer, Breast Tumors, Breast Cancer, Breast Malignant Tumors, Cancer of Breast, Breast, mammary cancer, cancer, mammary tumor, Breast Malignant Neoplasms, breast, Tumors, CancerH2S(D2S), Breast Carcinoma, Human Mammary Neoplasm, primary breast cancer, Carcinoma, malignant tumor of the breast, Breast Carcinomas, "breast neoplasm" EXACT [MTH:120], WGBS, hydrosulfite, Neoplasms, mammary neoplasm, Mammary Cancers, Human Mammary Neoplasms, 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, Neoplasm, Human Mammary Carcinoma, "mammary tumor" EXACT [CSP2005:2016-0671], NOS, breast tumor, cancer of the breast, Malignant Neoplasm of Breast, Shotgun bisulfite sequencing, Carcinomas, BC, Mammary Neoplasms, malignant neoplasm of breast, whole genome bisulfite sequencing, Human Mammary, Breast Neoplasm, Genomes, Mammary Neoplasm, Mammary Carcinoma, Human Mammary Carcinomas, bisulfite, whole genome, Cancers, Breast Malignant Neoplasms., "mammary neoplasm" RELATED [], Cancer of the Breast, breast cancer, cancer of breast, Malignant Tumor of Breast, Mammary, Mammary Cancer, Breast Tumors, Breast Cancer, Breast Malignant Tumors, Cancer of Breast, Breast, mammary cancer, cancer, mammary tumor, breast, whole-genome shotgun bisulfite sequencing, WGSBS, Tumors, Cancerrecombination, malignant tumor of the breast, Breasts, Intergenic Region, determination, Junk DNAs, Feature, Intercistronic Regions, DmelCG30169, Lactiferous gland, mammary neoplasm, Mini Exon, Human Mammary Neoplasms, Tumor, PPP1R53, glandula mammaria, Mutation Frequency, Neoplasm Genes, Mutations, Readability, Recombinations, BcDNA:SD25109, Regions, "neoplasm of breast (disorder)" EXACT [SNOMEDCT_2005_07_31:126926005], Familiar breast and Ovarian cancer syndrome, IRIS, Mutation Frequencies, cancer of the breast, BROVCA1, BROVCA2, Spacer DNAs, Genetic Recombination, BC, Mammary Neoplasms, malignant neoplasm of breast, FAD1, BRCC1, Genomes, BRCC2, Junk, bases, Basen, Human Mammary Carcinomas, PNCA4, Genetic Recombinations, Intergenic Sequence, PNCA2, genetic, cancer of breast, Malignancies, mammary cancer, Frequency, RAB163, protein-coding, FACD, DNAs, Tumors, mamma, hereditary breast ovarian cancer, Carcinoma, Intercistronic Sequences, anatomical protrusion, "breast neoplasm" EXACT [MTH:120], aberrant, Nucleobase, BRCA1, BRCA2, Intervening Sequences, familial, BRCAI, CG13583, CG13584, Benign, Frequencies, Lobe of mammary gland, Base2, Base1, NOS, Intergenic, XRCC11, Region, Malignant Neoplasm of Breast, Carcinomas, Recombination, Junk DNA, Benign Neoplasms, whole genome, Cancer Gene, "mammary neoplasm" RELATED [], Features, Intercistronic Sequence, Intervening, brca2, Malignant Neoplasms, Fancd1, AI256696, FAD, Spacer DNA, breast cancer, spine, Breast Tumors, Base, AW045498, Breast Malignant Tumors, inherited genetic, DNA, cancer, base, RNF53, mammary region, atypia, primary breast cancer, GLM3, Neoplasms, Benign Neoplasm, Gene, Mammary Cancers, Coding, Malignant, CG30169, protrusion, Human, Breast Malignant Tumor, Intergenic Regions, Rate, Breast Tumor, Intercistronic, Mini-Exon, DNA Damage Response, "mammary tumor" EXACT [CSP2005:2016-0671], breast tumor, atypical, FANCD1, Medical, Human Mammary, Clinical, Genetic, Malignancy, Mammary Neoplasm, Medical Coding, Mammary Carcinoma, mammary part of chest, Intergenic Sequences, FANCS, Cancer of the Breast, Neoplasias, Cancer Genes, FANCB, Malignant Tumor of Breast, Mammary, Mammary Cancer, FANCD, genetic recombination, Intron, Characteristics, Breast, constitutitional genetic, mammary tumor, Cancer, Breast Carcinoma, Human Mammary Neoplasm, Breast Carcinomas, Malignant Neoplasm, PSCP, defective, function, "breast tumor" EXACT [NCI2004_11_17:C2910], Brustdruese, Breast Malignant Neoplasm, Sequences, Intervening Sequence, MT, Characteristic, Mammary Carcinomas, Sequence, chemical analysis, Mutation Rates, Neoplasm, Human Mammary Carcinoma, Spacer, Intergenic DNAs, Mutation, Rates, Breast Neoplasm, Genes, Intercistronic Region, Mini-Exons, Lobe of breast, 30169, dmbrca2, Exon, Cancers, Understanding, Breast Malignant Neoplasms., Neoplasm Gene, Breast Cancer, Intergenic DNA, Cancer of Breast, assay, nucleobases, hereditary, Neoplasia, breastfalseena-DATASET-SC-01-06-2015-15:56:18:840-199 - samplesWhole-genome bisulfite sequencing (WGBS) on 30 breast cancer cases from the BASIS project.2024-11-04 12:20:36EGAD00001001388960627135926EGAC00001000010EGAS00001001178