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Number Cited by Other Article(s)
51
Samur MK, Aktas Samur A, Fulciniti M, Szalat R, Han T, Shammas M, Richardson P, Magrangeas F, Minvielle S, Corre J, Moreau P, Thakurta A, Anderson KC, Parmigiani G, Avet-Loiseau H, Munshi NC. Genome-Wide Somatic Alterations in Multiple Myeloma Reveal a Superior Outcome Group. J Clin Oncol 2020;38:3107-3118. [PMID: 32687451 PMCID: PMC7499613 DOI: 10.1200/jco.20.00461] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/05/2020] [Indexed: 02/06/2023]  Open
52
Huang B, Trujillo MA, Fujikura K, Qiu M, Chen F, Felsenstein M, Zhou C, Skaro M, Gauthier C, Macgregor-Das A, Hutchings D, Hong SM, Hruban RH, Eshleman JR, Thompson ED, Klein AP, Goggins M, Wood LD, Roberts NJ. Molecular characterization of organoids derived from pancreatic intraductal papillary mucinous neoplasms. J Pathol 2020;252:252-262. [PMID: 32696980 DOI: 10.1002/path.5515] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 06/12/2020] [Accepted: 07/17/2020] [Indexed: 12/15/2022]
53
Yang L. A Practical Guide for Structural Variation Detection in the Human Genome. CURRENT PROTOCOLS IN HUMAN GENETICS 2020;107:e103. [PMID: 32813322 PMCID: PMC7738216 DOI: 10.1002/cphg.103] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
54
Wei R, Li P, He F, Wei G, Zhou Z, Su Z, Ni T. Comprehensive analysis reveals distinct mutational signature and its mechanistic insights of alcohol consumption in human cancers. Brief Bioinform 2020;22:5841903. [PMID: 32480415 DOI: 10.1093/bib/bbaa066] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/24/2020] [Accepted: 03/31/2020] [Indexed: 12/20/2022]  Open
55
Aguiar TFM, Rivas MP, Costa S, Maschietto M, Rodrigues T, Sobral de Barros J, Barbosa AC, Valieris R, Fernandes GR, Bertola DR, Cypriano M, Caminada de Toledo SR, Major A, Tojal I, Apezzato MLDP, Carraro DM, Rosenberg C, Lima da Costa CM, Cunha IW, Sarabia SF, Terrada DL, Krepischi ACV. Insights Into the Somatic Mutation Burden of Hepatoblastomas From Brazilian Patients. Front Oncol 2020;10:556. [PMID: 32432034 PMCID: PMC7214543 DOI: 10.3389/fonc.2020.00556] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 03/27/2020] [Indexed: 12/23/2022]  Open
56
Sason I, Wojtowicz D, Robinson W, Leiserson MDM, Przytycka TM, Sharan R. A Sticky Multinomial Mixture Model of Strand-Coordinated Mutational Processes in Cancer. iScience 2020;23:100900. [PMID: 32088392 PMCID: PMC7038582 DOI: 10.1016/j.isci.2020.100900] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/23/2020] [Accepted: 02/05/2020] [Indexed: 01/09/2023]  Open
57
Alexandrov LB, Kim J, Haradhvala NJ, Huang MN, Tian Ng AW, Wu Y, Boot A, Covington KR, Gordenin DA, Bergstrom EN, Islam SMA, Lopez-Bigas N, Klimczak LJ, McPherson JR, Morganella S, Sabarinathan R, Wheeler DA, Mustonen V, Getz G, Rozen SG, Stratton MR. The repertoire of mutational signatures in human cancer. Nature 2020;578:94-101. [PMID: 32025018 PMCID: PMC7054213 DOI: 10.1038/s41586-020-1943-3] [Citation(s) in RCA: 2166] [Impact Index Per Article: 433.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 11/18/2019] [Indexed: 01/27/2023]
58
CANCERSIGN: a user-friendly and robust tool for identification and classification of mutational signatures and patterns in cancer genomes. Sci Rep 2020;10:1286. [PMID: 31992766 PMCID: PMC6987109 DOI: 10.1038/s41598-020-58107-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 01/06/2020] [Indexed: 11/20/2022]  Open
59
Bobrovnitchaia I, Valieris R, Drummond RD, Lima JP, Freitas HC, Bartelli TF, de Amorim MG, Nunes DN, Dias-Neto E, da Silva IT. APOBEC-mediated DNA alterations: A possible new mechanism of carcinogenesis in EBV-positive gastric cancer. Int J Cancer 2020;146:181-191. [PMID: 31090066 DOI: 10.1002/ijc.32411] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 04/22/2019] [Accepted: 04/30/2019] [Indexed: 12/17/2023]
60
Su SC, Chang LC, Lin CW, Chen MK, Yu CP, Chung WH, Yang SF. Mutational signatures and mutagenic impacts associated with betel quid chewing in oral squamous cell carcinoma. Hum Genet 2019;138:1379-1389. [DOI: 10.1007/s00439-019-02083-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 10/26/2019] [Indexed: 12/12/2022]
61
Matsutani T, Ueno Y, Fukunaga T, Hamada M. Discovering novel mutation signatures by latent Dirichlet allocation with variational Bayes inference. Bioinformatics 2019;35:4543-4552. [PMID: 30993319 PMCID: PMC6853711 DOI: 10.1093/bioinformatics/btz266] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 04/03/2019] [Accepted: 04/10/2019] [Indexed: 12/18/2022]  Open
62
Omichessan H, Severi G, Perduca V. Computational tools to detect signatures of mutational processes in DNA from tumours: A review and empirical comparison of performance. PLoS One 2019;14:e0221235. [PMID: 31513583 PMCID: PMC6741849 DOI: 10.1371/journal.pone.0221235] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/01/2019] [Indexed: 12/03/2022]  Open
63
Bergstrom EN, Huang MN, Mahto U, Barnes M, Stratton MR, Rozen SG, Alexandrov LB. SigProfilerMatrixGenerator: a tool for visualizing and exploring patterns of small mutational events. BMC Genomics 2019;20:685. [PMID: 31470794 PMCID: PMC6717374 DOI: 10.1186/s12864-019-6041-2] [Citation(s) in RCA: 171] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 08/19/2019] [Indexed: 12/15/2022]  Open
64
Yang Z, Pandey P, Shibata D, Conti DV, Marjoram P, Siegmund KD. HiLDA: a statistical approach to investigate differences in mutational signatures. PeerJ 2019;7:e7557. [PMID: 31523512 PMCID: PMC6717498 DOI: 10.7717/peerj.7557] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 07/25/2019] [Indexed: 12/30/2022]  Open
65
Wojtowicz D, Sason I, Huang X, Kim YA, Leiserson MDM, Przytycka TM, Sharan R. Hidden Markov models lead to higher resolution maps of mutation signature activity in cancer. Genome Med 2019;11:49. [PMID: 31349863 PMCID: PMC6660659 DOI: 10.1186/s13073-019-0659-1] [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: 01/17/2019] [Accepted: 07/12/2019] [Indexed: 12/19/2022]  Open
66
Baez-Ortega A, Gori K. Computational approaches for discovery of mutational signatures in cancer. Brief Bioinform 2019;20:77-88. [PMID: 28968631 DOI: 10.1093/bib/bbx082] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Indexed: 01/07/2023]  Open
67
Robinson W, Sharan R, Leiserson MDM. Modeling clinical and molecular covariates of mutational process activity in cancer. Bioinformatics 2019;35:i492-i500. [PMID: 31510643 PMCID: PMC6612886 DOI: 10.1093/bioinformatics/btz340] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
68
Maura F, Degasperi A, Nadeu F, Leongamornlert D, Davies H, Moore L, Royo R, Ziccheddu B, Puente XS, Avet-Loiseau H, Campbell PJ, Nik-Zainal S, Campo E, Munshi N, Bolli N. A practical guide for mutational signature analysis in hematological malignancies. Nat Commun 2019;10:2969. [PMID: 31278357 PMCID: PMC6611883 DOI: 10.1038/s41467-019-11037-8] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 06/10/2019] [Indexed: 02/08/2023]  Open
69
Grolleman JE, Díaz-Gay M, Franch-Expósito S, Castellví-Bel S, de Voer RM. Somatic mutational signatures in polyposis and colorectal cancer. Mol Aspects Med 2019;69:62-72. [PMID: 31108140 DOI: 10.1016/j.mam.2019.05.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 05/13/2019] [Accepted: 05/16/2019] [Indexed: 02/04/2023]
70
Van Hoeck A, Tjoonk NH, van Boxtel R, Cuppen E. Portrait of a cancer: mutational signature analyses for cancer diagnostics. BMC Cancer 2019;19:457. [PMID: 31092228 PMCID: PMC6521503 DOI: 10.1186/s12885-019-5677-2] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 05/03/2019] [Indexed: 01/10/2023]  Open
71
Funnell T, Zhang AW, Grewal D, McKinney S, Bashashati A, Wang YK, Shah SP. Integrated structural variation and point mutation signatures in cancer genomes using correlated topic models. PLoS Comput Biol 2019;15:e1006799. [PMID: 30794536 PMCID: PMC6402697 DOI: 10.1371/journal.pcbi.1006799] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 03/06/2019] [Accepted: 01/14/2019] [Indexed: 11/18/2022]  Open
72
Fullard JF, Charney AW, Voloudakis G, Uzilov AV, Haroutunian V, Roussos P. Assessment of somatic single-nucleotide variation in brain tissue of cases with schizophrenia. Transl Psychiatry 2019;9:21. [PMID: 30655504 PMCID: PMC6336839 DOI: 10.1038/s41398-018-0342-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/15/2018] [Accepted: 11/13/2018] [Indexed: 12/20/2022]  Open
73
Carlson J, Li JZ, Zöllner S. Helmsman: fast and efficient mutation signature analysis for massive sequencing datasets. BMC Genomics 2018;19:845. [PMID: 30486787 PMCID: PMC6263557 DOI: 10.1186/s12864-018-5264-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 11/19/2018] [Indexed: 12/14/2022]  Open
74
Wong HL, Zhao EY, Jones MR, Reisle CR, Eirew P, Pleasance E, Grande BM, Karasinska JM, Kalloger SE, Lim HJ, Shen Y, Yip S, Morin RD, Laskin J, Marra MA, Jones SJ, Schrader KA, Schaeffer DF, Renouf DJ. Temporal Dynamics of Genomic Alterations in a BRCA1 Germline-Mutated Pancreatic Cancer With Low Genomic Instability Burden but Exceptional Response to Fluorouracil, Oxaliplatin, Leucovorin, and Irinotecan. JCO Precis Oncol 2018;2:PO.18.00057. [PMID: 32913994 PMCID: PMC7446469 DOI: 10.1200/po.18.00057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]  Open
75
Ng AWT, Poon SL, Huang MN, Lim JQ, Boot A, Yu W, Suzuki Y, Thangaraju S, Ng CCY, Tan P, Pang ST, Huang HY, Yu MC, Lee PH, Hsieh SY, Chang AY, Teh BT, Rozen SG. Aristolochic acids and their derivatives are widely implicated in liver cancers in Taiwan and throughout Asia. Sci Transl Med 2018;9:9/412/eaan6446. [PMID: 29046434 DOI: 10.1126/scitranslmed.aan6446] [Citation(s) in RCA: 256] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 07/31/2017] [Accepted: 09/25/2017] [Indexed: 12/21/2022]
76
MutationalPatterns: comprehensive genome-wide analysis of mutational processes. Genome Med 2018;10:33. [PMID: 29695279 PMCID: PMC5922316 DOI: 10.1186/s13073-018-0539-0] [Citation(s) in RCA: 451] [Impact Index Per Article: 64.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 04/04/2018] [Indexed: 12/23/2022]  Open
77
Raj N, Shah R, Stadler Z, Mukherjee S, Chou J, Untch B, Li J, Kelly V, Saltz LB, Mandelker D, Ladanyi M, Berger MF, Klimstra DS, Reidy-Lagunes D, Osoba M. Real-Time Genomic Characterization of Metastatic Pancreatic Neuroendocrine Tumors Has Prognostic Implications and Identifies Potential Germline Actionability. JCO Precis Oncol 2018;2018. [PMID: 30687805 DOI: 10.1200/po.17.00267] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]  Open
78
Mutational and epigenetic signatures in cancer tissue linked to environmental exposures and lifestyle. Curr Opin Oncol 2018;30:61-67. [DOI: 10.1097/cco.0000000000000418] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
79
Bianconi D, Heller G, Spies D, Herac M, Gleiss A, Liebmann-Reindl S, Unseld M, Kieler M, Scheithauer W, Streubel B, Zielinski CC, Prager GW. Biochemical and genetic predictors of overall survival in patients with metastatic pancreatic cancer treated with capecitabine and nab-paclitaxel. Sci Rep 2017;7:4851. [PMID: 28687745 PMCID: PMC5501799 DOI: 10.1038/s41598-017-04743-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 05/30/2017] [Indexed: 12/18/2022]  Open
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