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For: Ortiz-Estevez M, Aramburu A, Bengtsson H, Neuvial P, Rubio A. CalMaTe: a method and software to improve allele-specific copy number of SNP arrays for downstream segmentation. ACTA ACUST UNITED AC 2012;28:1793-4. [PMID: 22576175 DOI: 10.1093/bioinformatics/bts248] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Number Cited by Other Article(s)
1
Sangaralingam A, Dayem Ullah AZ, Marzec J, Gadaleta E, Nagano A, Ross-Adams H, Wang J, Lemoine NR, Chelala C. 'Multi-omic' data analysis using O-miner. Brief Bioinform 2019;20:130-143. [PMID: 28981577 PMCID: PMC6357557 DOI: 10.1093/bib/bbx080] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Indexed: 12/19/2022]  Open
2
Tokutomi N, Moyret‐Lalle C, Puisieux A, Sugano S, Martinez P. Quantifying local malignant adaptation in tissue-specific evolutionary trajectories by harnessing cancer's repeatability at the genetic level. Evol Appl 2019;12:1062-1075. [PMID: 31080515 PMCID: PMC6503823 DOI: 10.1111/eva.12781] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 12/03/2018] [Accepted: 02/07/2019] [Indexed: 02/06/2023]  Open
3
Martinez P, Kimberley C, BirkBak NJ, Marquard A, Szallasi Z, Graham TA. Quantification of within-sample genetic heterogeneity from SNP-array data. Sci Rep 2017;7:3248. [PMID: 28607403 PMCID: PMC5468233 DOI: 10.1038/s41598-017-03496-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 05/03/2017] [Indexed: 01/17/2023]  Open
4
Kanu N, Grönroos E, Martinez P, Burrell RA, Yi Goh X, Bartkova J, Maya-Mendoza A, Mistrík M, Rowan AJ, Patel H, Rabinowitz A, East P, Wilson G, Santos CR, McGranahan N, Gulati S, Gerlinger M, Birkbak NJ, Joshi T, Alexandrov LB, Stratton MR, Powles T, Matthews N, Bates PA, Stewart A, Szallasi Z, Larkin J, Bartek J, Swanton C. SETD2 loss-of-function promotes renal cancer branched evolution through replication stress and impaired DNA repair. Oncogene 2015;34:5699-708. [PMID: 25728682 PMCID: PMC4660036 DOI: 10.1038/onc.2015.24] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 12/29/2014] [Accepted: 01/06/2015] [Indexed: 12/13/2022]
5
Alentorn A, Dehais C, Ducray F, Carpentier C, Mokhtari K, Figarella-Branger D, Chinot O, Cohen-Moyal E, Ramirez C, Loiseau H, Elouahdani-Hamdi S, Beauchesne P, Langlois O, Desenclos C, Guillamo JS, Dam-Hieu P, Ghiringhelli F, Colin P, Godard J, Parker F, Dhermain F, Carpentier AF, Frenel JS, Menei P, Bauchet L, Faillot T, Fesneau M, Fontaine D, Motuo-Fotso MJ, Vauleon E, Gaultier C, Le Guerinel C, Gueye EM, Noel G, Desse N, Durando X, Barrascout E, Wager M, Ricard D, Carpiuc I, Delattre JY, Idbaih A. Allelic loss of 9p21.3 is a prognostic factor in 1p/19q codeleted anaplastic gliomas. Neurology 2015;85:1325-31. [PMID: 26385879 DOI: 10.1212/wnl.0000000000002014] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Accepted: 06/17/2015] [Indexed: 12/18/2022]  Open
6
Marquard AM, Eklund AC, Joshi T, Krzystanek M, Favero F, Wang ZC, Richardson AL, Silver DP, Szallasi Z, Birkbak NJ. Pan-cancer analysis of genomic scar signatures associated with homologous recombination deficiency suggests novel indications for existing cancer drugs. Biomark Res 2015;3:9. [PMID: 26015868 PMCID: PMC4443545 DOI: 10.1186/s40364-015-0033-4] [Citation(s) in RCA: 210] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 03/25/2015] [Indexed: 02/08/2023]  Open
7
McGranahan N, Favero F, de Bruin EC, Birkbak NJ, Szallasi Z, Swanton C. Clonal status of actionable driver events and the timing of mutational processes in cancer evolution. Sci Transl Med 2015;7:283ra54. [PMID: 25877892 PMCID: PMC4636056 DOI: 10.1126/scitranslmed.aaa1408] [Citation(s) in RCA: 534] [Impact Index Per Article: 53.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
8
de Bruin EC, McGranahan N, Mitter R, Salm M, Wedge DC, Yates L, Jamal-Hanjani M, Shafi S, Murugaesu N, Rowan AJ, Grönroos E, Muhammad MA, Horswell S, Gerlinger M, Varela I, Jones D, Marshall J, Voet T, Van Loo P, Rassl DM, Rintoul RC, Janes SM, Lee SM, Forster M, Ahmad T, Lawrence D, Falzon M, Capitanio A, Harkins TT, Lee CC, Tom W, Teefe E, Chen SC, Begum S, Rabinowitz A, Phillimore B, Spencer-Dene B, Stamp G, Szallasi Z, Matthews N, Stewart A, Campbell P, Swanton C. Spatial and temporal diversity in genomic instability processes defines lung cancer evolution. Science 2014;346:251-6. [PMID: 25301630 PMCID: PMC4636050 DOI: 10.1126/science.1253462] [Citation(s) in RCA: 871] [Impact Index Per Article: 79.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
9
Lönnstedt IM, Caramia F, Li J, Fumagalli D, Salgado R, Rowan A, Salm M, Kanu N, Savas P, Horswell S, Gade S, Loibl S, Neven P, Sotiriou C, Swanton C, Loi S, Speed TP. Deciphering clonality in aneuploid breast tumors using SNP array and sequencing data. Genome Biol 2014;15:470. [PMID: 25270265 PMCID: PMC4220069 DOI: 10.1186/s13059-014-0470-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 09/15/2014] [Indexed: 12/30/2022]  Open
10
Liu Y, Wang M, Feng H, Li A. Comprehensive study of tumour single nucleotide polymorphism array data reveals significant driver aberrations and disrupted signalling pathways in human hepatocellular cancer. IET Syst Biol 2014;8:24-32. [PMID: 25014222 DOI: 10.1049/iet-syb.2013.0027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]  Open
11
Genome-wide identification of somatic aberrations from paired normal-tumor samples. PLoS One 2014;9:e87212. [PMID: 24498045 PMCID: PMC3907544 DOI: 10.1371/journal.pone.0087212] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 12/26/2013] [Indexed: 12/13/2022]  Open
12
Tumor mutation burden forecasts outcome in ovarian cancer with BRCA1 or BRCA2 mutations. PLoS One 2013;8:e80023. [PMID: 24265793 PMCID: PMC3827141 DOI: 10.1371/journal.pone.0080023] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 09/27/2013] [Indexed: 12/16/2022]  Open
13
Martinez P, Birkbak NJ, Gerlinger M, McGranahan N, Burrell RA, Rowan AJ, Joshi T, Fisher R, Larkin J, Szallasi Z, Swanton C. Parallel evolution of tumour subclones mimics diversity between tumours. J Pathol 2013;230:356-64. [PMID: 23716380 DOI: 10.1002/path.4214] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 05/17/2013] [Accepted: 05/22/2013] [Indexed: 01/17/2023]
14
Ortiz-Estevez M, Aramburu A, Rubio A. Getting DNA copy numbers without control samples. Algorithms Mol Biol 2012;7:19. [PMID: 22898240 PMCID: PMC3512512 DOI: 10.1186/1748-7188-7-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 06/15/2012] [Indexed: 01/30/2023]  Open
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