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For: Ding J, Bashashati A, Roth A, Oloumi A, Tse K, Zeng T, Haffari G, Hirst M, Marra MA, Condon A, Aparicio S, Shah SP. Feature-based classifiers for somatic mutation detection in tumour-normal paired sequencing data. ACTA ACUST UNITED AC 2011;28:167-75. [PMID: 22084253 PMCID: PMC3259434 DOI: 10.1093/bioinformatics/btr629] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Number Cited by Other Article(s)
1
Kundu P, Beura S, Mondal S, Das AK, Ghosh A. Machine learning for the advancement of genome-scale metabolic modeling. Biotechnol Adv 2024;74:108400. [PMID: 38944218 DOI: 10.1016/j.biotechadv.2024.108400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 05/13/2024] [Accepted: 06/23/2024] [Indexed: 07/01/2024]
2
Darbandsari A, Farahani H, Asadi M, Wiens M, Cochrane D, Khajegili Mirabadi A, Jamieson A, Farnell D, Ahmadvand P, Douglas M, Leung S, Abolmaesumi P, Jones SJM, Talhouk A, Kommoss S, Gilks CB, Huntsman DG, Singh N, McAlpine JN, Bashashati A. AI-based histopathology image analysis reveals a distinct subset of endometrial cancers. Nat Commun 2024;15:4973. [PMID: 38926357 PMCID: PMC11208496 DOI: 10.1038/s41467-024-49017-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 05/21/2024] [Indexed: 06/28/2024]  Open
3
Deyell RJ, Shen Y, Titmuss E, Dixon K, Williamson LM, Pleasance E, Nelson JMT, Abbasi S, Krzywinski M, Armstrong L, Bonakdar M, Ch'ng C, Chuah E, Dunham C, Fok A, Jones M, Lee AF, Ma Y, Moore RA, Mungall AJ, Mungall KL, Rogers PC, Schrader KA, Virani A, Wee K, Young SS, Zhao Y, Jones SJM, Laskin J, Marra MA, Rassekh SR. Whole genome and transcriptome integrated analyses guide clinical care of pediatric poor prognosis cancers. Nat Commun 2024;15:4165. [PMID: 38755180 PMCID: PMC11099106 DOI: 10.1038/s41467-024-48363-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 04/29/2024] [Indexed: 05/18/2024]  Open
4
Titmuss E, Yu IS, Pleasance ED, Williamson LM, Mungall K, Mungall AJ, Renouf DJ, Moore R, Jones SJM, Marra MA, Laskin JJ, Savage KJ. Exploration of Germline Correlates and Risk of Immune-Related Adverse Events in Advanced Cancer Patients Treated with Immune Checkpoint Inhibitors. Curr Oncol 2024;31:1865-1875. [PMID: 38668043 PMCID: PMC11048877 DOI: 10.3390/curroncol31040140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024]  Open
5
Liu Y, Wang S, Wang Y, Li Y, Zhu X, Lai X, Zhang X, Li X, Xiao X, Wang J. What makes TMB an ambivalent biomarker for immunotherapy? A subtle mismatch between the sample-based design of variant callers and real clinical cohort. Front Immunol 2023;14:1151224. [PMID: 37304296 PMCID: PMC10248171 DOI: 10.3389/fimmu.2023.1151224] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 05/15/2023] [Indexed: 06/13/2023]  Open
6
Vaisband M, Schubert M, Gassner FJ, Geisberger R, Greil R, Zaborsky N, Hasenauer J. Validation of genetic variants from NGS data using deep convolutional neural networks. BMC Bioinformatics 2023;24:158. [PMID: 37081386 PMCID: PMC10116675 DOI: 10.1186/s12859-023-05255-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 03/27/2023] [Indexed: 04/22/2023]  Open
7
Titmuss E, Milne K, Jones MR, Ng T, Topham JT, Brown SD, Schaeffer DF, Kalloger S, Wilson D, Corbett RD, Williamson LM, Mungall K, Mungall AJ, Holt RA, Nelson BH, Jones SJM, Laskin J, Lim HJ, Marra MA. Immune Activation following Irbesartan Treatment in a Colorectal Cancer Patient: A Case Study. Int J Mol Sci 2023;24:5869. [PMID: 36982943 PMCID: PMC10051648 DOI: 10.3390/ijms24065869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/14/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023]  Open
8
Funnell T, O’Flanagan CH, Williams MJ, McPherson A, McKinney S, Kabeer F, Lee H, Salehi S, Vázquez-García I, Shi H, Leventhal E, Masud T, Eirew P, Yap D, Zhang AW, Lim JLP, Wang B, Brimhall J, Biele J, Ting J, Au V, Van Vliet M, Liu YF, Beatty S, Lai D, Pham J, Grewal D, Abrams D, Havasov E, Leung S, Bojilova V, Moore RA, Rusk N, Uhlitz F, Ceglia N, Weiner AC, Zaikova E, Douglas JM, Zamarin D, Weigelt B, Kim SH, Da Cruz Paula A, Reis-Filho JS, Martin SD, Li Y, Xu H, de Algara TR, Lee SR, Llanos VC, Huntsman DG, McAlpine JN, IMAXT ConsortiumHannonGregory J.10BattistoniGeorgia10BressanDario10CannellIan G.10CasboltHannah10JausetCristina10KovačevićTatjana10MulveyClaire M.10NugentFiona10RibesMarta Paez10PearsonIsabella10QosajFatime10SawickaKirsty10WildSophia A.10WilliamsElena10LaksEmma3SmithAustin3LaiDaniel3RothAndrew3411BalasubramanianShankar101213LeeMaximilian101213BodenmillerBernd14BurgerMarcel14KuettLaura14TietscherSandra14WindhagerJonas14BoydenEdward S.15AlonShahar15CuiYi15EmenariAmauche15GoodwinDaniel R.15KaragiannisEmmanouil D.15SinhaAnubhav15WassieAsmamaw T.15CaldasCarlos16BrunaAlejandra16CallariMaurizio10GreenwoodWendy10LerdaGiulia10Eyal-LublingYaniv16RuedaOscar M.16SheaAbigail16HarrisOwen17BeckerRobby17GrimaldoFlaminia17HarrisSuvi17VoglSara Lisa17JoyceJohanna A.18WatsonSpencer S.18TavareSimon101920DinhKhanh N.1920FisherEyal10KunesRussell1920WaltonNicholas A.21Al Sa’dMohammed21ChornayNick21DariushAli21González-SolaresEduardo A.21González-FernándezCarlos21YoldaşAybüke Küpcü21MillerNeil21ZhuangXiaowei222324FanJean222324LeeHsuan222324SepúlvedaLeonardo A.222324XiaChenglong222324ZhengPu222324, Shah SP, Aparicio S, Cannell IG, Casbolt H, Jauset C, Kovačević T, Mulvey CM, Nugent F, Ribes MP, Pearson I, Qosaj F, Sawicka K, Wild SA, Williams E, Laks E, Smith A, Lai D, Roth A, Balasubramanian S, Lee M, Bodenmiller B, Burger M, Kuett L, Tietscher S, Windhager J, Boyden ES, Alon S, Cui Y, Emenari A, Goodwin DR, Karagiannis ED, Sinha A, Wassie AT, Caldas C, Bruna A, Callari M, Greenwood W, Lerda G, Eyal-Lubling Y, Rueda OM, Shea A, Harris O, Becker R, Grimaldo F, Harris S, Vogl SL, Joyce JA, Watson SS, et alFunnell T, O’Flanagan CH, Williams MJ, McPherson A, McKinney S, Kabeer F, Lee H, Salehi S, Vázquez-García I, Shi H, Leventhal E, Masud T, Eirew P, Yap D, Zhang AW, Lim JLP, Wang B, Brimhall J, Biele J, Ting J, Au V, Van Vliet M, Liu YF, Beatty S, Lai D, Pham J, Grewal D, Abrams D, Havasov E, Leung S, Bojilova V, Moore RA, Rusk N, Uhlitz F, Ceglia N, Weiner AC, Zaikova E, Douglas JM, Zamarin D, Weigelt B, Kim SH, Da Cruz Paula A, Reis-Filho JS, Martin SD, Li Y, Xu H, de Algara TR, Lee SR, Llanos VC, Huntsman DG, McAlpine JN, IMAXT ConsortiumHannonGregory J.10BattistoniGeorgia10BressanDario10CannellIan G.10CasboltHannah10JausetCristina10KovačevićTatjana10MulveyClaire M.10NugentFiona10RibesMarta Paez10PearsonIsabella10QosajFatime10SawickaKirsty10WildSophia A.10WilliamsElena10LaksEmma3SmithAustin3LaiDaniel3RothAndrew3411BalasubramanianShankar101213LeeMaximilian101213BodenmillerBernd14BurgerMarcel14KuettLaura14TietscherSandra14WindhagerJonas14BoydenEdward S.15AlonShahar15CuiYi15EmenariAmauche15GoodwinDaniel R.15KaragiannisEmmanouil D.15SinhaAnubhav15WassieAsmamaw T.15CaldasCarlos16BrunaAlejandra16CallariMaurizio10GreenwoodWendy10LerdaGiulia10Eyal-LublingYaniv16RuedaOscar M.16SheaAbigail16HarrisOwen17BeckerRobby17GrimaldoFlaminia17HarrisSuvi17VoglSara Lisa17JoyceJohanna A.18WatsonSpencer S.18TavareSimon101920DinhKhanh N.1920FisherEyal10KunesRussell1920WaltonNicholas A.21Al Sa’dMohammed21ChornayNick21DariushAli21González-SolaresEduardo A.21González-FernándezCarlos21YoldaşAybüke Küpcü21MillerNeil21ZhuangXiaowei222324FanJean222324LeeHsuan222324SepúlvedaLeonardo A.222324XiaChenglong222324ZhengPu222324, Shah SP, Aparicio S, Cannell IG, Casbolt H, Jauset C, Kovačević T, Mulvey CM, Nugent F, Ribes MP, Pearson I, Qosaj F, Sawicka K, Wild SA, Williams E, Laks E, Smith A, Lai D, Roth A, Balasubramanian S, Lee M, Bodenmiller B, Burger M, Kuett L, Tietscher S, Windhager J, Boyden ES, Alon S, Cui Y, Emenari A, Goodwin DR, Karagiannis ED, Sinha A, Wassie AT, Caldas C, Bruna A, Callari M, Greenwood W, Lerda G, Eyal-Lubling Y, Rueda OM, Shea A, Harris O, Becker R, Grimaldo F, Harris S, Vogl SL, Joyce JA, Watson SS, Tavare S, Dinh KN, Fisher E, Kunes R, Walton NA, Al Sa’d M, Chornay N, Dariush A, González-Solares EA, González-Fernández C, Yoldaş AK, Miller N, Zhuang X, Fan J, Lee H, Sepúlveda LA, Xia C, Zheng P, Shah SP, Aparicio S, IMAXT Consortium. Single-cell genomic variation induced by mutational processes in cancer. Nature 2022;612:106-115. [PMID: 36289342 PMCID: PMC9712114 DOI: 10.1038/s41586-022-05249-0] [Show More Authors] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/17/2022] [Indexed: 12/15/2022]
9
Randrianarisoa T. Smoothing and adaptation of shifted Pólya tree ensembles. BERNOULLI 2022. [DOI: 10.3150/21-bej1426] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
10
Eirew P, O'Flanagan C, Ting J, Salehi S, Brimhall J, Wang B, Biele J, Algara T, Lee SR, Hoang C, Yap D, McKinney S, Bates C, Kong E, Lai D, Beatty S, Andronescu M, Zaikova E, Funnell T, Ceglia N, Chia S, Gelmon K, Mar C, Shah S, Roth A, Bouchard-Côté A, Aparicio S. Accurate determination of CRISPR-mediated gene fitness in transplantable tumours. Nat Commun 2022;13:4534. [PMID: 35927228 PMCID: PMC9352714 DOI: 10.1038/s41467-022-31830-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/01/2022] [Indexed: 11/09/2022]  Open
11
Tessier-Cloutier B, Grewal JK, Jones MR, Pleasance E, Shen Y, Cai E, Dunham C, Hoang L, Horst B, Huntsman DG, Ionescu D, Karnezis AN, Lee AF, Lee CH, Lee TH, Twa DD, Mungall AJ, Mungall K, Naso JR, Ng T, Schaeffer DF, Sheffield BS, Skinnider B, Smith T, Williamson L, Zhong E, Regier DA, Laskin J, Marra MA, Gilks CB, Jones SJ, Yip S. The impact of whole genome and transcriptome analysis (WGTA) on predictive biomarker discovery and diagnostic accuracy of advanced malignancies. JOURNAL OF PATHOLOGY CLINICAL RESEARCH 2022;8:395-407. [PMID: 35257510 PMCID: PMC9161328 DOI: 10.1002/cjp2.265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 01/15/2022] [Accepted: 02/04/2022] [Indexed: 12/13/2022]
12
Hilton J, Gelmon K, Bedard PL, Tu D, Xu H, Tinker AV, Goodwin R, Laurie SA, Jonker D, Hansen AR, Veitch ZW, Renouf DJ, Hagerman L, Lui H, Chen B, Kellar D, Li I, Lee SE, Kono T, Cheng BYC, Yap D, Lai D, Beatty S, Soong J, Pritchard KI, Soria-Bretones I, Chen E, Feilotter H, Rushton M, Seymour L, Aparicio S, Cescon DW. Results of the phase I CCTG IND.231 trial of CX-5461 in patients with advanced solid tumors enriched for DNA-repair deficiencies. Nat Commun 2022;13:3607. [PMID: 35750695 PMCID: PMC9232501 DOI: 10.1038/s41467-022-31199-2] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 06/07/2022] [Indexed: 12/12/2022]  Open
13
Computational analysis of cancer genome sequencing data. Nat Rev Genet 2022;23:298-314. [PMID: 34880424 DOI: 10.1038/s41576-021-00431-y] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2021] [Indexed: 02/07/2023]
14
Histologic and Genotypic Characterization of Lung Cancer in the Inuit Population of the Eastern Canadian Arctic. Curr Oncol 2022;29:3171-3186. [PMID: 35621648 PMCID: PMC9139845 DOI: 10.3390/curroncol29050258] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 11/18/2022]  Open
15
Reisle C, Williamson LM, Pleasance E, Davies A, Pellegrini B, Bleile DW, Mungall KL, Chuah E, Jones MR, Ma Y, Lewis E, Beckie I, Pham D, Matiello Pletz R, Muhammadzadeh A, Pierce BM, Li J, Stevenson R, Wong H, Bailey L, Reisle A, Douglas M, Bonakdar M, Nelson JMT, Grisdale CJ, Krzywinski M, Fisic A, Mitchell T, Renouf DJ, Yip S, Laskin J, Marra MA, Jones SJM. A platform for oncogenomic reporting and interpretation. Nat Commun 2022;13:756. [PMID: 35140225 PMCID: PMC8828759 DOI: 10.1038/s41467-022-28348-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 01/14/2022] [Indexed: 01/01/2023]  Open
16
Chang TC, Xu K, Cheng Z, Wu G. Somatic and Germline Variant Calling from Next-Generation Sequencing Data. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022;1361:37-54. [DOI: 10.1007/978-3-030-91836-1_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
17
Williamson LM, Rive CM, Di Francesco D, Titmuss E, Chun HJE, Brown SD, Milne K, Pleasance E, Lee AF, Yip S, Rosenbaum DG, Hasselblatt M, Johann PD, Kool M, Harvey M, Dix D, Renouf DJ, Holt RA, Nelson BH, Hirst M, Jones SJM, Laskin J, Rassekh SR, Deyell RJ, Marra MA. Clinical response to nivolumab in an INI1-deficient pediatric chordoma correlates with immunogenic recognition of brachyury. NPJ Precis Oncol 2021;5:103. [PMID: 34931022 PMCID: PMC8688516 DOI: 10.1038/s41698-021-00238-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 10/22/2021] [Indexed: 01/01/2023]  Open
18
Wang X, Zhai M, Ren Z, Ren H, Li M, Quan D, Chen L, Qiu L. Exploratory study on classification of diabetes mellitus through a combined Random Forest Classifier. BMC Med Inform Decis Mak 2021;21:105. [PMID: 33743696 PMCID: PMC7980612 DOI: 10.1186/s12911-021-01471-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 03/11/2021] [Indexed: 12/23/2022]  Open
19
Jäger N. Bioinformatics workflows for clinical applications in precision oncology. Semin Cancer Biol 2021;84:103-112. [PMID: 33476720 DOI: 10.1016/j.semcancer.2020.12.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/15/2020] [Accepted: 12/28/2020] [Indexed: 12/23/2022]
20
An Efficient and Effective Model to Handle Missing Data in Classification. BIOMED RESEARCH INTERNATIONAL 2020;2020:8810143. [PMID: 33299878 PMCID: PMC7710403 DOI: 10.1155/2020/8810143] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 10/20/2020] [Accepted: 11/04/2020] [Indexed: 11/18/2022]
21
Liu LY, Bhandari V, Salcedo A, Espiritu SMG, Morris QD, Kislinger T, Boutros PC. Quantifying the influence of mutation detection on tumour subclonal reconstruction. Nat Commun 2020;11:6247. [PMID: 33288765 PMCID: PMC7721877 DOI: 10.1038/s41467-020-20055-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 11/10/2020] [Indexed: 02/06/2023]  Open
22
Meng J, Victor B, He Z, Liu H, Jiang T. DeepSSV: detecting somatic small variants in paired tumor and normal sequencing data with convolutional neural network. Brief Bioinform 2020;22:5960414. [PMID: 33164053 DOI: 10.1093/bib/bbaa272] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 09/05/2020] [Accepted: 09/19/2020] [Indexed: 01/16/2023]  Open
23
Gagliardi A, Porter VL, Zong Z, Bowlby R, Titmuss E, Namirembe C, Griner NB, Petrello H, Bowen J, Chan SK, Culibrk L, Darragh TM, Stoler MH, Wright TC, Gesuwan P, Dyer MA, Ma Y, Mungall KL, Jones SJM, Nakisige C, Novik K, Orem J, Origa M, Gastier-Foster JM, Yarchoan R, Casper C, Mills GB, Rader JS, Ojesina AI, Gerhard DS, Mungall AJ, Marra MA. Analysis of Ugandan cervical carcinomas identifies human papillomavirus clade-specific epigenome and transcriptome landscapes. Nat Genet 2020;52:800-810. [PMID: 32747824 PMCID: PMC7498180 DOI: 10.1038/s41588-020-0673-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 06/26/2020] [Indexed: 01/18/2023]
24
Wang M, Luo W, Jones K, Bian X, Williams R, Higson H, Wu D, Hicks B, Yeager M, Zhu B. SomaticCombiner: improving the performance of somatic variant calling based on evaluation tests and a consensus approach. Sci Rep 2020;10:12898. [PMID: 32732891 PMCID: PMC7393490 DOI: 10.1038/s41598-020-69772-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 07/16/2020] [Indexed: 02/06/2023]  Open
25
Huang W, Guo YA, Muthukumar K, Baruah P, Chang MM, Jacobsen Skanderup A. SMuRF: portable and accurate ensemble prediction of somatic mutations. Bioinformatics 2020;35:3157-3159. [PMID: 30649191 PMCID: PMC6735703 DOI: 10.1093/bioinformatics/btz018] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 11/26/2018] [Accepted: 01/07/2019] [Indexed: 12/22/2022]  Open
26
Cao C, Mak L, Jin G, Gordon P, Ye K, Long Q. PRESM: personalized reference editor for somatic mutation discovery in cancer genomics. Bioinformatics 2020;35:1445-1452. [PMID: 30247633 DOI: 10.1093/bioinformatics/bty812] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 08/27/2018] [Accepted: 09/19/2018] [Indexed: 12/16/2022]  Open
27
Pleasance E, Titmuss E, Williamson L, Kwan H, Culibrk L, Zhao EY, Dixon K, Fan K, Bowlby R, Jones MR, Shen Y, Grewal JK, Ashkani J, Wee K, Grisdale CJ, Thibodeau ML, Bozoky Z, Pearson H, Majounie E, Vira T, Shenwai R, Mungall KL, Chuah E, Davies A, Warren M, Reisle C, Bonakdar M, Taylor GA, Csizmok V, Chan SK, Zong Z, Bilobram S, Muhammadzadeh A, D’Souza D, Corbett RD, MacMillan D, Carreira M, Choo C, Bleile D, Sadeghi S, Zhang W, Wong T, Cheng D, Brown SD, Holt RA, Moore RA, Mungall AJ, Zhao Y, Nelson J, Fok A, Ma Y, Lee MKC, Lavoie JM, Mendis S, Karasinska JM, Deol B, Fisic A, Schaeffer DF, Yip S, Schrader K, Regier DA, Weymann D, Chia S, Gelmon K, Tinker A, Sun S, Lim H, Renouf DJ, Laskin J, Jones SJM, Marra MA. Pan-cancer analysis of advanced patient tumors reveals interactions between therapy and genomic landscapes. ACTA ACUST UNITED AC 2020;1:452-468. [DOI: 10.1038/s43018-020-0050-6] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 03/05/2020] [Indexed: 02/08/2023]
28
David R. The promise of toxicogenomics for genetic toxicology: past, present and future. Mutagenesis 2020;35:153-159. [PMID: 32087008 DOI: 10.1093/mutage/geaa007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 02/10/2020] [Indexed: 01/10/2023]  Open
29
Mannakee BK, Gutenkunst RN. BATCAVE: calling somatic mutations with a tumor- and site-specific prior. NAR Genom Bioinform 2020;2:lqaa004. [PMID: 32051931 PMCID: PMC7003682 DOI: 10.1093/nargab/lqaa004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/13/2020] [Accepted: 01/23/2020] [Indexed: 02/06/2023]  Open
30
Salcedo A, Tarabichi M, Espiritu SMG, Deshwar AG, David M, Wilson NM, Dentro S, Wintersinger JA, Liu LY, Ko M, Sivanandan S, Zhang H, Zhu K, Ou Yang TH, Chilton JM, Buchanan A, Lalansingh CM, P'ng C, Anghel CV, Umar I, Lo B, Zou W, DREAM SMC-Het Participants, Simpson JT, Stuart JM, Anastassiou D, Guan Y, Ewing AD, Ellrott K, Wedge DC, Morris Q, Van Loo P, Boutros PC. A community effort to create standards for evaluating tumor subclonal reconstruction. Nat Biotechnol 2020;38:97-107. [PMID: 31919445 PMCID: PMC6956735 DOI: 10.1038/s41587-019-0364-z] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Collaborators] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 11/18/2019] [Indexed: 02/03/2023]
31
Chun HJE, Johann PD, Milne K, Zapatka M, Buellesbach A, Ishaque N, Iskar M, Erkek S, Wei L, Tessier-Cloutier B, Lever J, Titmuss E, Topham JT, Bowlby R, Chuah E, Mungall KL, Ma Y, Mungall AJ, Moore RA, Taylor MD, Gerhard DS, Jones SJM, Korshunov A, Gessler M, Kerl K, Hasselblatt M, Frühwald MC, Perlman EJ, Nelson BH, Pfister SM, Marra MA, Kool M. Identification and Analyses of Extra-Cranial and Cranial Rhabdoid Tumor Molecular Subgroups Reveal Tumors with Cytotoxic T Cell Infiltration. Cell Rep 2019;29:2338-2354.e7. [PMID: 31708418 PMCID: PMC6905433 DOI: 10.1016/j.celrep.2019.10.013] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 08/20/2019] [Accepted: 10/02/2019] [Indexed: 11/23/2022]  Open
32
Laks E, McPherson A, Zahn H, Lai D, Steif A, Brimhall J, Biele J, Wang B, Masud T, Ting J, Grewal D, Nielsen C, Leung S, Bojilova V, Smith M, Golovko O, Poon S, Eirew P, Kabeer F, Ruiz de Algara T, Lee SR, Taghiyar MJ, Huebner C, Ngo J, Chan T, Vatrt-Watts S, Walters P, Abrar N, Chan S, Wiens M, Martin L, Scott RW, Underhill TM, Chavez E, Steidl C, Da Costa D, Ma Y, Coope RJN, Corbett R, Pleasance S, Moore R, Mungall AJ, Mar C, Cafferty F, Gelmon K, Chia S, Marra MA, Hansen C, Shah SP, Aparicio S. Clonal Decomposition and DNA Replication States Defined by Scaled Single-Cell Genome Sequencing. Cell 2019;179:1207-1221.e22. [PMID: 31730858 PMCID: PMC6912164 DOI: 10.1016/j.cell.2019.10.026] [Citation(s) in RCA: 156] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 06/14/2019] [Accepted: 10/22/2019] [Indexed: 01/21/2023]
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Tan YV, Roy J. Bayesian additive regression trees and the General BART model. Stat Med 2019;38:5048-5069. [PMID: 31460678 PMCID: PMC6800811 DOI: 10.1002/sim.8347] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 07/05/2019] [Accepted: 07/23/2019] [Indexed: 11/06/2022]
34
Oota S. Somatic mutations - Evolution within the individual. Methods 2019;176:91-98. [PMID: 31711929 DOI: 10.1016/j.ymeth.2019.11.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 10/31/2019] [Accepted: 11/07/2019] [Indexed: 02/08/2023]  Open
35
Bartha Á, Győrffy B. Comprehensive Outline of Whole Exome Sequencing Data Analysis Tools Available in Clinical Oncology. Cancers (Basel) 2019;11:E1725. [PMID: 31690036 PMCID: PMC6895801 DOI: 10.3390/cancers11111725] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/31/2019] [Accepted: 11/01/2019] [Indexed: 12/17/2022]  Open
36
Wood DE, White JR, Georgiadis A, Van Emburgh B, Parpart-Li S, Mitchell J, Anagnostou V, Niknafs N, Karchin R, Papp E, McCord C, LoVerso P, Riley D, Diaz LA, Jones S, Sausen M, Velculescu VE, Angiuoli SV. A machine learning approach for somatic mutation discovery. Sci Transl Med 2019;10:10/457/eaar7939. [PMID: 30185652 DOI: 10.1126/scitranslmed.aar7939] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 05/26/2018] [Accepted: 08/16/2018] [Indexed: 12/19/2022]
37
Comprehensive genomic profiling of glioblastoma tumors, BTICs, and xenografts reveals stability and adaptation to growth environments. Proc Natl Acad Sci U S A 2019;116:19098-19108. [PMID: 31471491 DOI: 10.1073/pnas.1813495116] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
38
Negri GL, Grande BM, Delaidelli A, El-Naggar A, Cochrane D, Lau CC, Triche TJ, Moore RA, Jones SJ, Montpetit A, Marra MA, Malkin D, Morin RD, Sorensen PH. Integrative genomic analysis of matched primary and metastatic pediatric osteosarcoma. J Pathol 2019;249:319-331. [PMID: 31236944 DOI: 10.1002/path.5319] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 05/23/2019] [Accepted: 06/20/2019] [Indexed: 01/14/2023]
39
Genomic characterization of a well-differentiated grade 3 pancreatic neuroendocrine tumor. Cold Spring Harb Mol Case Stud 2019;5:mcs.a003814. [PMID: 31160355 PMCID: PMC6549554 DOI: 10.1101/mcs.a003814] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 03/06/2019] [Indexed: 01/05/2023]  Open
40
Anzar I, Sverchkova A, Stratford R, Clancy T. NeoMutate: an ensemble machine learning framework for the prediction of somatic mutations in cancer. BMC Med Genomics 2019;12:63. [PMID: 31096972 PMCID: PMC6524241 DOI: 10.1186/s12920-019-0508-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 04/22/2019] [Indexed: 12/30/2022]  Open
41
Jones MR, Williamson LM, Topham JT, Lee MKC, Goytain A, Ho J, Denroche RE, Jang G, Pleasance E, Shen Y, Karasinska JM, McGhie JP, Gill S, Lim HJ, Moore MJ, Wong HL, Ng T, Yip S, Zhang W, Sadeghi S, Reisle C, Mungall AJ, Mungall KL, Moore RA, Ma Y, Knox JJ, Gallinger S, Laskin J, Marra MA, Schaeffer DF, Jones SJM, Renouf DJ. NRG1 Gene Fusions Are Recurrent, Clinically Actionable Gene Rearrangements in KRAS Wild-Type Pancreatic Ductal Adenocarcinoma. Clin Cancer Res 2019;25:4674-4681. [PMID: 31068372 DOI: 10.1158/1078-0432.ccr-19-0191] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 03/07/2019] [Accepted: 04/15/2019] [Indexed: 01/28/2023]
42
Calling Variants in the Clinic: Informed Variant Calling Decisions Based on Biological, Clinical, and Laboratory Variables. Comput Struct Biotechnol J 2019;17:561-569. [PMID: 31049166 PMCID: PMC6482431 DOI: 10.1016/j.csbj.2019.04.002] [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: 11/21/2018] [Revised: 03/12/2019] [Accepted: 04/03/2019] [Indexed: 01/10/2023]  Open
43
Risser MD, Calder CA, Berrocal VJ, Berrett C. NONSTATIONARY SPATIAL PREDICTION OF SOIL ORGANIC CARBON: IMPLICATIONS FOR STOCK ASSESSMENT DECISION MAKING. Ann Appl Stat 2019;13:165-188. [PMID: 39220174 PMCID: PMC11364347 DOI: 10.1214/18-aoas1204] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
44
Chan S, Siegel EL. Will machine learning end the viability of radiology as a thriving medical specialty? Br J Radiol 2019;92:20180416. [PMID: 30325645 PMCID: PMC6404816 DOI: 10.1259/bjr.20180416] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 10/05/2018] [Accepted: 10/10/2018] [Indexed: 11/05/2022]  Open
45
Xu J, Yang P, Xue S, Sharma B, Sanchez-Martin M, Wang F, Beaty KA, Dehan E, Parikh B. Translating cancer genomics into precision medicine with artificial intelligence: applications, challenges and future perspectives. Hum Genet 2019;138:109-124. [PMID: 30671672 PMCID: PMC6373233 DOI: 10.1007/s00439-019-01970-5] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 01/02/2019] [Indexed: 02/07/2023]
46
Dorri F, Jewell S, Bouchard-Côté A, Shah SP. Somatic mutation detection and classification through probabilistic integration of clonal population information. Commun Biol 2019;2:44. [PMID: 30729182 PMCID: PMC6355807 DOI: 10.1038/s42003-019-0291-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 12/20/2018] [Indexed: 01/06/2023]  Open
47
Ko JJ, Grewal JK, Ng T, Lavoie JM, Thibodeau ML, Shen Y, Mungall AJ, Taylor G, Schrader KA, Jones SJM, Kollmannsberger C, Laskin J, Marra MA. Whole-genome and transcriptome profiling of a metastatic thyroid-like follicular renal cell carcinoma. Cold Spring Harb Mol Case Stud 2018;4:mcs.a003137. [PMID: 30446580 PMCID: PMC6318773 DOI: 10.1101/mcs.a003137] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 09/12/2018] [Indexed: 12/17/2022]  Open
48
A deep learning approach to automate refinement of somatic variant calling from cancer sequencing data. Nat Genet 2018;50:1735-1743. [PMID: 30397337 DOI: 10.1038/s41588-018-0257-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 09/14/2018] [Indexed: 12/18/2022]
49
A universal SNP and small-indel variant caller using deep neural networks. Nat Biotechnol 2018;36:983-987. [DOI: 10.1038/nbt.4235] [Citation(s) in RCA: 776] [Impact Index Per Article: 110.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 08/02/2018] [Indexed: 02/06/2023]
50
Coudray A, Battenhouse AM, Bucher P, Iyer VR. Detection and benchmarking of somatic mutations in cancer genomes using RNA-seq data. PeerJ 2018;6:e5362. [PMID: 30083469 PMCID: PMC6074801 DOI: 10.7717/peerj.5362] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 07/09/2018] [Indexed: 02/06/2023]  Open
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