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For: Boeva V, Popova T, Lienard M, Toffoli S, Kamal M, Le Tourneau C, Gentien D, Servant N, Gestraud P, Rio Frio T, Hupé P, Barillot E, Laes JF. Multi-factor data normalization enables the detection of copy number aberrations in amplicon sequencing data. ACTA ACUST UNITED AC 2014;30:3443-50. [PMID: 25016581 PMCID: PMC4253825 DOI: 10.1093/bioinformatics/btu436] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Number Cited by Other Article(s)
51
Hou TC, Wu PS, Huang WY, Yang YT, Tan KT, Liu SH, Chen YJ, Chen SJ, Su YW. Over expression of CDK4 and MDM2 in a patient with recurrent ALK-negative mediastinal inflammatory myofibroblastic tumor: A case report. Medicine (Baltimore) 2020;99:e19577. [PMID: 32195970 PMCID: PMC7220190 DOI: 10.1097/md.0000000000019577] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]  Open
52
Derouault P, Chauzeix J, Rizzo D, Miressi F, Magdelaine C, Bourthoumieu S, Durand K, Dzugan H, Feuillard J, Sturtz F, Mérillou S, Lia AS. CovCopCan: An efficient tool to detect Copy Number Variation from amplicon sequencing data in inherited diseases and cancer. PLoS Comput Biol 2020;16:e1007503. [PMID: 32049956 PMCID: PMC7041855 DOI: 10.1371/journal.pcbi.1007503] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 02/25/2020] [Accepted: 10/23/2019] [Indexed: 02/07/2023]  Open
53
Olbryt M, Pigłowski W, Rajczykowski M, Pfeifer A, Student S, Fiszer-Kierzkowska A. Genetic Profiling of Advanced Melanoma: Candidate Mutations for Predicting Sensitivity and Resistance to Targeted Therapy. Target Oncol 2020;15:101-113. [PMID: 31980996 PMCID: PMC7028806 DOI: 10.1007/s11523-020-00695-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
54
Tan TZ, Ye J, Yee CV, Lim D, Ngoi NYL, Tan DSP, Huang RYJ. Analysis of gene expression signatures identifies prognostic and functionally distinct ovarian clear cell carcinoma subtypes. EBioMedicine 2019;50:203-210. [PMID: 31761620 PMCID: PMC6921362 DOI: 10.1016/j.ebiom.2019.11.017] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 11/06/2019] [Accepted: 11/08/2019] [Indexed: 12/17/2022]  Open
55
Sheen Y, Tan K, Tse K, Liao Y, Lin M, Chen J, Liau J, Tseng Y, Lee C, Hong C, Liao J, Chang H, Chu C. Genetic alterations in primary melanoma in Taiwan. Br J Dermatol 2019;182:1205-1213. [DOI: 10.1111/bjd.18425] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2019] [Indexed: 12/27/2022]
56
Simbolo M, Barbi S, Fassan M, Mafficini A, Ali G, Vicentini C, Sperandio N, Corbo V, Rusev B, Mastracci L, Grillo F, Pilotto S, Pelosi G, Pelliccioni S, Lawlor RT, Tortora G, Fontanini G, Volante M, Scarpa A, Bria E. Gene Expression Profiling of Lung Atypical Carcinoids and Large Cell Neuroendocrine Carcinomas Identifies Three Transcriptomic Subtypes with Specific Genomic Alterations. J Thorac Oncol 2019;14:1651-1661. [PMID: 31085341 DOI: 10.1016/j.jtho.2019.05.003] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 03/25/2019] [Accepted: 05/06/2019] [Indexed: 12/12/2022]
57
Barresi V, Simbolo M, Mafficini A, Piredda ML, Caffo M, Cardali SM, Germanò A, Cingarlini S, Ghimenton C, Scarpa A. Ultra-Mutation in IDH Wild-Type Glioblastomas of Patients Younger than 55 Years is Associated with Defective Mismatch Repair, Microsatellite Instability, and Giant Cell Enrichment. Cancers (Basel) 2019;11:cancers11091279. [PMID: 31480372 PMCID: PMC6770353 DOI: 10.3390/cancers11091279] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 08/27/2019] [Accepted: 08/27/2019] [Indexed: 12/16/2022]  Open
58
Datta KK, Patil S, Patel K, Babu N, Raja R, Nanjappa V, Mangalaparthi KK, Dhaka B, Rajagopalan P, Deolankar SC, Kannan R, Kumar P, Prasad TSK, Mathur PP, Kumari A, Manoharan M, Coral K, Murugan S, Sidransky D, Gupta R, Gupta R, Khanna-Gupta A, Chatterjee A, Gowda H. Chronic Exposure to Chewing Tobacco Induces Metabolic Reprogramming and Cancer Stem Cell-Like Properties in Esophageal Epithelial Cells. Cells 2019;8:cells8090949. [PMID: 31438645 PMCID: PMC6770059 DOI: 10.3390/cells8090949] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 08/10/2019] [Accepted: 08/17/2019] [Indexed: 12/14/2022]  Open
59
Chang SC, Lai YC, Chang CY, Huang LK, Chen SJ, Tan KT, Yu PN, Lai JI. Concomitant Genetic Alterations are Associated with Worse Clinical Outcome in EGFR Mutant NSCLC Patients Treated with Tyrosine Kinase Inhibitors. Transl Oncol 2019;12:1425-1431. [PMID: 31401335 PMCID: PMC6700434 DOI: 10.1016/j.tranon.2019.07.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/08/2019] [Accepted: 07/10/2019] [Indexed: 01/17/2023]  Open
60
Liao Y, Ma Z, Zhang Y, Li D, Lv D, Chen Z, Li P, Ai-Dherasi A, Zheng F, Tian J, Zou K, Wang Y, Wang D, Cordova M, Zhou H, Li X, Liu D, Yu R, Zhang Q, Zhang X, Zhang J, Zhang X, Zhang X, Li Y, Shao Y, Song L, Liu R, Wang Y, Sufiyan S, Liu Q, Owen GI, Li Z, Chen J. Targeted deep sequencing from multiple sources demonstrates increased NOTCH1 alterations in lung cancer patient plasma. Cancer Med 2019;8:5673-5686. [PMID: 31369215 PMCID: PMC6745866 DOI: 10.1002/cam4.2458] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 07/13/2019] [Accepted: 07/18/2019] [Indexed: 12/19/2022]  Open
61
Chung AK, OuYang CN, Liu H, Chao M, Luo JD, Lee CY, Lu YJ, Chung IC, Chen LC, Wu SM, Tsang NM, Chang KP, Hsu CL, Li HP, Chang YS. Targeted sequencing of cancer-related genes in nasopharyngeal carcinoma identifies mutations in the TGF-β pathway. Cancer Med 2019;8:5116-5127. [PMID: 31328403 PMCID: PMC6718742 DOI: 10.1002/cam4.2429] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/28/2019] [Accepted: 07/03/2019] [Indexed: 12/18/2022]  Open
62
Nie D, Cao P, Wang F, Zhang J, Liu M, Zhang W, Liu L, Zhao H, Teng W, Tian W, Chen X, Zhang Y, Nan H, Wei Z, Wang T, Liu H. Analysis of overlapping heterozygous novel submicroscopic CNVs and FANCA-VPS9D1 fusion transcripts in a Fanconi anemia patient. J Hum Genet 2019;64:899-909. [PMID: 31239491 DOI: 10.1038/s10038-019-0629-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/28/2019] [Accepted: 06/03/2019] [Indexed: 12/19/2022]
63
Bellini A, Bessoltane-Bentahar N, Bhalshankar J, Clement N, Raynal V, Baulande S, Bernard V, Danzon A, Chicard M, Colmet-Daage L, Pierron G, Le Roux L, Planchon JM, Combaret V, Lapouble E, Corradini N, Thebaud E, Gambart M, Valteau-Couanet D, Michon J, Louis-Brennetot C, Janoueix-Lerosey I, Defachelles AS, Bourdeaut F, Delattre O, Schleiermacher G. Study of chromatin remodeling genes implicates SMARCA4 as a putative player in oncogenesis in neuroblastoma. Int J Cancer 2019;145:2781-2791. [PMID: 31018240 PMCID: PMC6771805 DOI: 10.1002/ijc.32361] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 02/21/2019] [Accepted: 03/14/2019] [Indexed: 12/21/2022]
64
Ducharme O, Beylot-Barry M, Pham-Ledard A, Bohers E, Viailly PJ, Bandres T, Faur N, Frison E, Vergier B, Jardin F, Merlio JP, Gros A. Mutations of the B-Cell Receptor Pathway Confer Chemoresistance in Primary Cutaneous Diffuse Large B-Cell Lymphoma Leg Type. J Invest Dermatol 2019;139:2334-2342.e8. [PMID: 31150604 DOI: 10.1016/j.jid.2019.05.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/16/2019] [Accepted: 05/10/2019] [Indexed: 11/25/2022]
65
Petridis C, Arora I, Shah V, Megalios A, Moss C, Mera A, Clifford A, Gillett C, Pinder SE, Tomlinson I, Roylance R, Simpson MA, Sawyer EJ. Frequency of pathogenic germline variants in BRCA1, BRCA2, PALB2, CHEK2 and TP53 in ductal carcinoma in situ diagnosed in women under the age of 50 years. Breast Cancer Res 2019;21:58. [PMID: 31060593 PMCID: PMC6501320 DOI: 10.1186/s13058-019-1143-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 04/17/2019] [Indexed: 11/10/2022]  Open
66
Cho WCS, Tan KT, Ma VWS, Li JYC, Ngan RKC, Cheuk W, Yip TTC, Yang YT, Chen SJ. Targeted next-generation sequencing reveals recurrence-associated genomic alterations in early-stage non-small cell lung cancer. Oncotarget 2018;9:36344-36357. [PMID: 30555633 PMCID: PMC6284742 DOI: 10.18632/oncotarget.26349] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 11/01/2018] [Indexed: 12/14/2022]  Open
67
O'Leary B, Cutts RJ, Liu Y, Hrebien S, Huang X, Fenwick K, André F, Loibl S, Loi S, Garcia-Murillas I, Cristofanilli M, Huang Bartlett C, Turner NC. The Genetic Landscape and Clonal Evolution of Breast Cancer Resistance to Palbociclib plus Fulvestrant in the PALOMA-3 Trial. Cancer Discov 2018;8:1390-1403. [PMID: 30206110 PMCID: PMC6368247 DOI: 10.1158/2159-8290.cd-18-0264] [Citation(s) in RCA: 435] [Impact Index Per Article: 62.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 07/09/2018] [Accepted: 09/06/2018] [Indexed: 12/20/2022]
68
Kang Y, Nam SH, Park KS, Kim Y, Kim JW, Lee E, Ko JM, Lee KA, Park I. DeviCNV: detection and visualization of exon-level copy number variants in targeted next-generation sequencing data. BMC Bioinformatics 2018;19:381. [PMID: 30326846 PMCID: PMC6192323 DOI: 10.1186/s12859-018-2409-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 10/04/2018] [Indexed: 12/30/2022]  Open
69
Hsu CL, Lui KW, Chi LM, Kuo YC, Chao YK, Yeh CN, Lee LY, Huang Y, Lin TL, Huang MY, Lai YR, Yeh YM, Fan HC, Lin AC, Lu YJ, Hsieh CH, Chang KP, Tsang NM, Wang HM, Chang AY, Chang YS, Li HP. Integrated genomic analyses in PDX model reveal a cyclin-dependent kinase inhibitor Palbociclib as a novel candidate drug for nasopharyngeal carcinoma. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2018;37:233. [PMID: 30236142 PMCID: PMC6149192 DOI: 10.1186/s13046-018-0873-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 08/13/2018] [Indexed: 02/07/2023]
70
Hsu HC, Lapke N, Chen SJ, Lu YJ, Jhou RS, Yeh CY, Tsai WS, Hung HY, Hsieh JCH, Yang TS, Thiam TK, You JF. PTPRT and PTPRD Deleterious Mutations and Deletion Predict Bevacizumab Resistance in Metastatic Colorectal Cancer Patients. Cancers (Basel) 2018;10:cancers10090314. [PMID: 30200630 PMCID: PMC6162606 DOI: 10.3390/cancers10090314] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 08/25/2018] [Accepted: 09/03/2018] [Indexed: 12/22/2022]  Open
71
Liang X, Vacher S, Boulai A, Bernard V, Baulande S, Bohec M, Bièche I, Lerebours F, Callens C. Targeted next-generation sequencing identifies clinically relevant somatic mutations in a large cohort of inflammatory breast cancer. Breast Cancer Res 2018;20:88. [PMID: 30086764 PMCID: PMC6081877 DOI: 10.1186/s13058-018-1007-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 06/18/2018] [Indexed: 11/10/2022]  Open
72
Bohers E, Viailly PJ, Becker S, Marchand V, Ruminy P, Maingonnat C, Bertrand P, Etancelin P, Picquenot JM, Camus V, Menard AL, Lemasle E, Contentin N, Leprêtre S, Lenain P, Stamatoullas A, Lanic H, Libraire J, Vaudaux S, Pepin LF, Vera P, Tilly H, Jardin F. Non-invasive monitoring of diffuse large B-cell lymphoma by cell-free DNA high-throughput targeted sequencing: analysis of a prospective cohort. Blood Cancer J 2018;8:74. [PMID: 30069017 PMCID: PMC6070497 DOI: 10.1038/s41408-018-0111-6] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 05/28/2018] [Accepted: 06/08/2018] [Indexed: 12/15/2022]  Open
73
Her NG, Oh JW, Oh YJ, Han S, Cho HJ, Lee Y, Ryu GH, Nam DH. Potent effect of the MDM2 inhibitor AMG232 on suppression of glioblastoma stem cells. Cell Death Dis 2018;9:792. [PMID: 30022047 PMCID: PMC6052082 DOI: 10.1038/s41419-018-0825-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 06/08/2018] [Accepted: 06/20/2018] [Indexed: 02/07/2023]
74
Maitre E, Bertrand P, Maingonnat C, Viailly PJ, Wiber M, Naguib D, Salaün V, Cornet E, Damaj G, Sola B, Jardin F, Troussard X. New generation sequencing of targeted genes in the classical and the variant form of hairy cell leukemia highlights mutations in epigenetic regulation genes. Oncotarget 2018;9:28866-28876. [PMID: 29989027 PMCID: PMC6034755 DOI: 10.18632/oncotarget.25601] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 05/24/2018] [Indexed: 11/25/2022]  Open
75
Rieber N, Bohnert R, Ziehm U, Jansen G. Reliability of algorithmic somatic copy number alteration detection from targeted capture data. Bioinformatics 2018;33:2791-2798. [PMID: 28472276 PMCID: PMC5870863 DOI: 10.1093/bioinformatics/btx284] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 05/03/2017] [Indexed: 01/11/2023]  Open
76
Fontanilles M, Marguet F, Bohers É, Viailly PJ, Dubois S, Bertrand P, Camus V, Mareschal S, Ruminy P, Maingonnat C, Lepretre S, Veresezan EL, Derrey S, Tilly H, Picquenot JM, Laquerrière A, Jardin F. Non-invasive detection of somatic mutations using next-generation sequencing in primary central nervous system lymphoma. Oncotarget 2018. [PMID: 28636991 PMCID: PMC5564634 DOI: 10.18632/oncotarget.18325] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]  Open
77
Nishio S, Moteki H, Usami S. Simple and efficient germline copy number variant visualization method for the Ion AmpliSeq™ custom panel. Mol Genet Genomic Med 2018;6:678-686. [PMID: 29633566 PMCID: PMC6081219 DOI: 10.1002/mgg3.399] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 03/02/2018] [Accepted: 03/06/2018] [Indexed: 12/18/2022]  Open
78
Wang YA, Jian JW, Hung CF, Peng HP, Yang CF, Cheng HCS, Yang AS. Germline breast cancer susceptibility gene mutations and breast cancer outcomes. BMC Cancer 2018;18:315. [PMID: 29566657 PMCID: PMC5863855 DOI: 10.1186/s12885-018-4229-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 03/15/2018] [Indexed: 01/07/2023]  Open
79
Lesueur P, Chevalier F, El-Habr EA, Junier MP, Chneiweiss H, Castera L, Müller E, Stefan D, Saintigny Y. Radiosensitization Effect of Talazoparib, a Parp Inhibitor, on Glioblastoma Stem Cells Exposed to Low and High Linear Energy Transfer Radiation. Sci Rep 2018;8:3664. [PMID: 29483558 PMCID: PMC5826933 DOI: 10.1038/s41598-018-22022-4] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 02/15/2018] [Indexed: 11/09/2022]  Open
80
Luo Z, Fan X, Su Y, Huang YS. Accurity: accurate tumor purity and ploidy inference from tumor-normal WGS data by jointly modelling somatic copy number alterations and heterozygous germline single-nucleotide-variants. Bioinformatics 2018;34:2004-2011. [PMID: 29385401 PMCID: PMC9881684 DOI: 10.1093/bioinformatics/bty043] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 01/26/2018] [Indexed: 02/02/2023]  Open
81
Dubot C, Bernard V, Sablin MP, Vacher S, Chemlali W, Schnitzler A, Pierron G, Ait Rais K, Bessoltane N, Jeannot E, Klijanienko J, Mariani O, Jouffroy T, Calugaru V, Hoffmann C, Lesnik M, Badois N, Berger F, Le Tourneau C, Kamal M, Bieche I. Comprehensive genomic profiling of head and neck squamous cell carcinoma reveals FGFR1 amplifications and tumour genomic alterations burden as prognostic biomarkers of survival. Eur J Cancer 2018;91:47-55. [PMID: 29331751 DOI: 10.1016/j.ejca.2017.12.016] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 11/25/2017] [Accepted: 12/09/2017] [Indexed: 12/20/2022]
82
van Riet J, Krol NMG, Atmodimedjo PN, Brosens E, van IJcken WFJ, Jansen MPHM, Martens JWM, Looijenga LH, Jenster G, Dubbink HJ, Dinjens WNM, van de Werken HJG. SNPitty: An Intuitive Web Application for Interactive B-Allele Frequency and Copy Number Visualization of Next-Generation Sequencing Data. J Mol Diagn 2018;20:166-176. [PMID: 29305224 DOI: 10.1016/j.jmoldx.2017.11.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 11/16/2017] [Accepted: 11/27/2017] [Indexed: 01/19/2023]  Open
83
Calling Chromosome Alterations, DNA Methylation Statuses, and Mutations in Tumors by Simple Targeted Next-Generation Sequencing. J Mol Diagn 2017;19:776-787. [DOI: 10.1016/j.jmoldx.2017.06.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 06/01/2017] [Indexed: 12/16/2022]  Open
84
Russo M, Broach J, Sheldon K, Houser KR, Liu DJ, Kesterson J, Phaeton R, Hossler C, Hempel N, Baker M, Newell JM, Zaino R, Warrick JI. Clonal evolution in paired endometrial intraepithelial neoplasia/atypical hyperplasia and endometrioid adenocarcinoma. Hum Pathol 2017;67:69-77. [PMID: 28712776 DOI: 10.1016/j.humpath.2017.07.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 06/18/2017] [Accepted: 07/05/2017] [Indexed: 12/01/2022]
85
The AURORA pilot study for molecular screening of patients with advanced breast cancer-a study of the breast international group. NPJ Breast Cancer 2017;3:23. [PMID: 28685159 PMCID: PMC5491498 DOI: 10.1038/s41523-017-0026-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 05/04/2017] [Accepted: 06/01/2017] [Indexed: 12/24/2022]  Open
86
Goldenberg D, Russo M, Houser K, Crist H, Derr JB, Walter V, Warrick JI, Sheldon KE, Broach J, Bann DV. Altered molecular profile in thyroid cancers from patients affected by the Three Mile Island nuclear accident. Laryngoscope 2017;127 Suppl 3:S1-S9. [PMID: 28555940 DOI: 10.1002/lary.26687] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2017] [Indexed: 01/02/2023]
87
Page K, Guttery DS, Fernandez-Garcia D, Hills A, Hastings RK, Luo J, Goddard K, Shahin V, Woodley-Barker L, Rosales BM, Coombes RC, Stebbing J, Shaw JA. Next Generation Sequencing of Circulating Cell-Free DNA for Evaluating Mutations and Gene Amplification in Metastatic Breast Cancer. Clin Chem 2017;63:532-541. [PMID: 27940449 PMCID: PMC6241835 DOI: 10.1373/clinchem.2016.261834] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 09/19/2016] [Indexed: 12/21/2022]
88
Rizzo D, Viailly PJ, Mareschal S, Bohers E, Picquenot JM, Penther D, Dubois S, Marchand V, Bertrand P, Maingonnat C, Etancelin P, Feuillard J, Bastard C, Tilly H, Jardin F, Ruminy P. Oncogenic events rather than antigen selection pressure may be the main driving forces for relapse in diffuse large B-cell lymphomas. Am J Hematol 2017;92:68-76. [PMID: 27737507 DOI: 10.1002/ajh.24584] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 09/29/2016] [Accepted: 10/11/2016] [Indexed: 01/07/2023]
89
Dubois S, Viailly PJ, Bohers E, Bertrand P, Ruminy P, Marchand V, Maingonnat C, Mareschal S, Picquenot JM, Penther D, Jais JP, Tesson B, Peyrouze P, Figeac M, Desmots F, Fest T, Haioun C, Lamy T, Copie-Bergman C, Fabiani B, Delarue R, Peyrade F, André M, Ketterer N, Leroy K, Salles G, Molina TJ, Tilly H, Jardin F. Biological and Clinical Relevance of Associated Genomic Alterations in MYD88 L265P and non-L265P-Mutated Diffuse Large B-Cell Lymphoma: Analysis of 361 Cases. Clin Cancer Res 2016;23:2232-2244. [PMID: 27923841 DOI: 10.1158/1078-0432.ccr-16-1922] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 11/01/2016] [Accepted: 11/17/2016] [Indexed: 01/01/2023]
90
Demidov G, Simakova T, Vnuchkova J, Bragin A. A statistical approach to detection of copy number variations in PCR-enriched targeted sequencing data. BMC Bioinformatics 2016;17:429. [PMID: 27770783 PMCID: PMC5075217 DOI: 10.1186/s12859-016-1272-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 09/21/2016] [Indexed: 12/24/2022]  Open
91
Macintyre G, Ylstra B, Brenton JD. Sequencing Structural Variants in Cancer for Precision Therapeutics. Trends Genet 2016;32:530-542. [PMID: 27478068 DOI: 10.1016/j.tig.2016.07.002] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 07/11/2016] [Accepted: 07/12/2016] [Indexed: 12/18/2022]
92
Dubbink HJ, Atmodimedjo PN, van Marion R, Krol NMG, Riegman PHJ, Kros JM, van den Bent MJ, Dinjens WNM. Diagnostic Detection of Allelic Losses and Imbalances by Next-Generation Sequencing: 1p/19q Co-Deletion Analysis of Gliomas. J Mol Diagn 2016;18:775-786. [PMID: 27461031 DOI: 10.1016/j.jmoldx.2016.06.002] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Revised: 05/06/2016] [Accepted: 06/01/2016] [Indexed: 02/05/2023]  Open
93
Mason-Suares H, Landry L, S. Lebo M. Detecting Copy Number Variation via Next Generation Technology. CURRENT GENETIC MEDICINE REPORTS 2016. [DOI: 10.1007/s40142-016-0091-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
94
Peng CH, Liao CT, Ng KP, Tai AS, Peng SC, Yeh JP, Chen SJ, Tsao KC, Yen TC, Hsieh WP. Somatic copy number alterations detected by ultra-deep targeted sequencing predict prognosis in oral cavity squamous cell carcinoma. Oncotarget 2016;6:19891-906. [PMID: 26087196 PMCID: PMC4637328 DOI: 10.18632/oncotarget.4336] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 05/23/2015] [Indexed: 12/20/2022]  Open
95
Talevich E, Shain AH, Botton T, Bastian BC. CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing. PLoS Comput Biol 2016;12:e1004873. [PMID: 27100738 PMCID: PMC4839673 DOI: 10.1371/journal.pcbi.1004873] [Citation(s) in RCA: 1341] [Impact Index Per Article: 149.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 03/16/2016] [Indexed: 01/19/2023]  Open
96
Dubois S, Jardin F. The role of next-generation sequencing in understanding the genomic basis of diffuse large B cell lymphoma and advancing targeted therapies. Expert Rev Hematol 2016;9:255-69. [PMID: 26652775 DOI: 10.1586/17474086.2016.1130616] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
97
Le Tourneau C, Kamal M, Tsimberidou AM, Bedard P, Pierron G, Callens C, Rouleau E, Vincent-Salomon A, Servant N, Alt M, Rouzier R, Paoletti X, Delattre O, Bièche I. Treatment Algorithms Based on Tumor Molecular Profiling: The Essence of Precision Medicine Trials. J Natl Cancer Inst 2015;108:djv362. [PMID: 26598514 PMCID: PMC4830395 DOI: 10.1093/jnci/djv362] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 10/26/2015] [Indexed: 12/13/2022]  Open
98
Genomic landscapes of breast fibroepithelial tumors. Nat Genet 2015;47:1341-5. [PMID: 26437033 DOI: 10.1038/ng.3409] [Citation(s) in RCA: 165] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 08/31/2015] [Indexed: 12/13/2022]
99
Walker CJ, Miranda MA, O'Hern MJ, McElroy JP, Coombes KR, Bundschuh R, Cohn DE, Mutch DG, Goodfellow PJ. Patterns of CTCF and ZFHX3 Mutation and Associated Outcomes in Endometrial Cancer. J Natl Cancer Inst 2015;107:djv249. [PMID: 26330387 DOI: 10.1093/jnci/djv249] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 08/05/2015] [Indexed: 12/11/2022]  Open
100
Tattini L, D'Aurizio R, Magi A. Detection of Genomic Structural Variants from Next-Generation Sequencing Data. Front Bioeng Biotechnol 2015;3:92. [PMID: 26161383 PMCID: PMC4479793 DOI: 10.3389/fbioe.2015.00092] [Citation(s) in RCA: 169] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 06/10/2015] [Indexed: 01/16/2023]  Open
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