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For: 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] [What about the content of this article? (0)] [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
Number Cited by Other Article(s)
1
Wang YW, Allen I, Funingana G, Tischkowitz M, Joko-Fru YW. Predictive biomarkers for the efficacy of PARP inhibitors in ovarian cancer: an updated systematic review. BJC REPORTS 2025;3:14. [PMID: 40069561 PMCID: PMC11897386 DOI: 10.1038/s44276-025-00122-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Revised: 12/06/2024] [Accepted: 01/09/2025] [Indexed: 03/15/2025]
2
Nittas V, Ormond KE, Vayena E, Blasimme A. Realizing the promise of machine learning in precision oncology: expert perspectives on opportunities and challenges. BMC Cancer 2025;25:276. [PMID: 39962436 PMCID: PMC11834663 DOI: 10.1186/s12885-025-13621-2] [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: 04/17/2024] [Accepted: 01/31/2025] [Indexed: 02/20/2025]  Open
3
Chakraborty S, Guan Z, Kostrzewa CE, Shen R, Begg CB. Identifying somatic fingerprints of cancers defined by germline and environmental risk factors. Genet Epidemiol 2024;48:455-467. [PMID: 38686586 PMCID: PMC11522022 DOI: 10.1002/gepi.22565] [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: 07/27/2023] [Revised: 01/18/2024] [Accepted: 04/16/2024] [Indexed: 05/02/2024]
4
Kefas J, Flynn M. Unlocking the potential of immunotherapy in platinum-resistant ovarian cancer: rationale, challenges, and novel strategies. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2024;7:39. [PMID: 39534871 PMCID: PMC11555186 DOI: 10.20517/cdr.2024.67] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 10/07/2024] [Accepted: 10/09/2024] [Indexed: 11/16/2024]
5
Weiner AC, Williams MJ, Shi H, Vázquez-García I, Salehi S, Rusk N, Aparicio S, Shah SP, McPherson A. Inferring replication timing and proliferation dynamics from single-cell DNA sequencing data. Nat Commun 2024;15:8512. [PMID: 39353885 PMCID: PMC11445576 DOI: 10.1038/s41467-024-52544-7] [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: 01/29/2024] [Accepted: 09/11/2024] [Indexed: 10/03/2024]  Open
6
Thapa B, De Sarkar N, Giri S, Sharma K, Kim M, Kilari D. Integrating PARP Inhibitors in mCRPC Therapy: Current Strategies and Emerging Trends. Cancer Manag Res 2024;16:1267-1283. [PMID: 39308935 PMCID: PMC11416116 DOI: 10.2147/cmar.s411023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Accepted: 08/16/2024] [Indexed: 09/25/2024]  Open
7
Williams MJ, Vázquez-García I, Tam G, Wu M, Varice N, Havasov E, Shi H, Satas G, Lees HJ, Lee JJK, Myers MA, Zatzman M, Rusk N, Ali E, Shah RH, Berger MF, Mohibullah N, Lakhman Y, Chi DS, Abu-Rustum NR, Aghajanian C, McPherson A, Zamarin D, Loomis B, Weigelt B, Friedman CF, Shah SP. Tracking clonal evolution of drug resistance in ovarian cancer patients by exploiting structural variants in cfDNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.21.609031. [PMID: 39229105 PMCID: PMC11370573 DOI: 10.1101/2024.08.21.609031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
8
McPherson A, Vázquez-García I, Myers MA, Zatzman M, Al-Rawi D, Weiner A, Freeman S, Mohibullah N, Satas G, Williams MJ, Ceglia N, Zhang AW, Li J, Lim JLP, Wu M, Choi S, Havasov E, Grewal D, Shi H, Kim M, Schwarz R, Kaufmann T, Dinh KN, Uhlitz F, Tran J, Wu Y, Patel R, Ramakrishnan S, Kim D, Clarke J, Green H, Ali E, DiBona M, Varice N, Kundra R, Broach V, Gardner GJ, Roche KL, Sonoda Y, Zivanovic O, Kim SH, Grisham RN, Liu YL, Viale A, Rusk N, Lakhman Y, Ellenson LH, Tavaré S, Aparicio S, Chi DS, Aghajanian C, Abu-Rustum NR, Friedman CF, Zamarin D, Weigelt B, Bakhoum SF, Shah SP. Ongoing genome doubling promotes evolvability and immune dysregulation in ovarian cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.11.602772. [PMID: 39071261 PMCID: PMC11275742 DOI: 10.1101/2024.07.11.602772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
9
Shah AM, Lee KY, Hidayat A, Falchook A, Muhammad W. A text analytics approach for mining public discussions in online cancer forum: Analysis of multi-intent lung cancer treatment dataset. Int J Med Inform 2024;184:105375. [PMID: 38367390 DOI: 10.1016/j.ijmedinf.2024.105375] [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: 06/05/2023] [Revised: 01/25/2024] [Accepted: 02/07/2024] [Indexed: 02/19/2024]
10
Chakraborty S, Guan Z, Begg CB, Shen R. Topical hidden genome: discovering latent cancer mutational topics using a Bayesian multilevel context-learning approach. Biometrics 2024;80:ujae030. [PMID: 38682463 PMCID: PMC11056772 DOI: 10.1093/biomtc/ujae030] [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: 12/29/2022] [Revised: 03/18/2024] [Accepted: 04/04/2024] [Indexed: 05/01/2024]
11
Bateman NW, Abulez T, Soltis AR, McPherson A, Choi S, Garsed DW, Pandey A, Tian C, Hood BL, Conrads KA, Teng PN, Oliver J, Gist G, Mitchell D, Litzi TJ, Tarney CM, Crothers BA, Mhawech-Fauceglia P, Dalgard CL, Wilkerson MD, Pierobon M, Petricoin EF, Yan C, Meerzaman D, Bodelon C, Wentzensen N, Lee JSH, Huntsman DG, Shah S, Shriver CD, Phippen NT, Darcy KM, Bowtell DDL, Conrads TP, Maxwell GL. Proteogenomic analysis of enriched HGSOC tumor epithelium identifies prognostic signatures and therapeutic vulnerabilities. NPJ Precis Oncol 2024;8:68. [PMID: 38480868 PMCID: PMC10937683 DOI: 10.1038/s41698-024-00519-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 01/15/2024] [Indexed: 03/17/2024]  Open
12
Jin H, Gulhan DC, Geiger B, Ben-Isvy D, Geng D, Ljungström V, Park PJ. Accurate and sensitive mutational signature analysis with MuSiCal. Nat Genet 2024;56:541-552. [PMID: 38361034 PMCID: PMC10937379 DOI: 10.1038/s41588-024-01659-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 01/08/2024] [Indexed: 02/17/2024]
13
Neijzen D, Lunter G. Unsupervised learning for medical data: A review of probabilistic factorization methods. Stat Med 2023;42:5541-5554. [PMID: 37850249 DOI: 10.1002/sim.9924] [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: 06/19/2023] [Accepted: 09/13/2023] [Indexed: 10/19/2023]
14
Peng X, Lee J, Adamow M, Maher C, Postow MA, Callahan MK, Panageas KS, Shen R. A topic modeling approach reveals the dynamic T cell composition of peripheral blood during cancer immunotherapy. CELL REPORTS METHODS 2023;3:100546. [PMID: 37671017 PMCID: PMC10475788 DOI: 10.1016/j.crmeth.2023.100546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 02/15/2023] [Accepted: 07/10/2023] [Indexed: 09/07/2023]
15
Kahane I, Leiserson MDM, Sharan R. A mutation-level covariate model for mutational signatures. PLoS Comput Biol 2023;19:e1011195. [PMID: 37276234 DOI: 10.1371/journal.pcbi.1011195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 05/17/2023] [Indexed: 06/07/2023]  Open
16
Peng X, Lee J, Adamow M, Maher C, Postow MA, Callahan MK, Panageas KS, Shen R. Uncovering the hidden structure of dynamic T cell composition in peripheral blood during cancer immunotherapy: a topic modeling approach. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.24.538095. [PMID: 37162890 PMCID: PMC10168231 DOI: 10.1101/2023.04.24.538095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
17
Ostroverkhova D, Przytycka TM, Panchenko AR. Cancer driver mutations: predictions and reality. Trends Mol Med 2023:S1471-4914(23)00067-9. [PMID: 37076339 DOI: 10.1016/j.molmed.2023.03.007] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/17/2023] [Accepted: 03/23/2023] [Indexed: 04/21/2023]
18
Ritch EJ, Herberts C, Warner EW, Ng SWS, Kwan EM, Bacon JVW, Bernales CQ, Schönlau E, Fonseca NM, Giri VN, Maurice-Dror C, Vandekerkhove G, Jones SJM, Chi KN, Wyatt AW. A generalizable machine learning framework for classifying DNA repair defects using ctDNA exomes. NPJ Precis Oncol 2023;7:27. [PMID: 36914848 PMCID: PMC10011564 DOI: 10.1038/s41698-023-00366-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 02/27/2023] [Indexed: 03/16/2023]  Open
19
Liu M, Wu Y, Jiang N, Boot A, Rozen S. mSigHdp: hierarchical Dirichlet process mixture modeling for mutational signature discovery. NAR Genom Bioinform 2023;5:lqad005. [PMID: 36694663 PMCID: PMC9869330 DOI: 10.1093/nargab/lqad005] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 01/19/2023] [Indexed: 01/24/2023]  Open
20
Vázquez-García I, Uhlitz F, Ceglia N, Lim JLP, Wu M, Mohibullah N, Niyazov J, Ruiz AEB, Boehm KM, Bojilova V, Fong CJ, Funnell T, Grewal D, Havasov E, Leung S, Pasha A, Patel DM, Pourmaleki M, Rusk N, Shi H, Vanguri R, Williams MJ, Zhang AW, Broach V, Chi DS, Da Cruz Paula A, Gardner GJ, Kim SH, Lennon M, Long Roche K, Sonoda Y, Zivanovic O, Kundra R, Viale A, Derakhshan FN, Geneslaw L, Issa Bhaloo S, Maroldi A, Nunez R, Pareja F, Stylianou A, Vahdatinia M, Bykov Y, Grisham RN, Liu YL, Lakhman Y, Nikolovski I, Kelly D, Gao J, Schietinger A, Hollmann TJ, Bakhoum SF, Soslow RA, Ellenson LH, Abu-Rustum NR, Aghajanian C, Friedman CF, McPherson A, Weigelt B, Zamarin D, Shah SP. Ovarian cancer mutational processes drive site-specific immune evasion. Nature 2022;612:778-786. [PMID: 36517593 PMCID: PMC9771812 DOI: 10.1038/s41586-022-05496-1] [Citation(s) in RCA: 129] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 10/28/2022] [Indexed: 12/15/2022]
21
Garsed DW, Pandey A, Fereday S, Kennedy CJ, Takahashi K, Alsop K, Hamilton PT, Hendley J, Chiew YE, Traficante N, Provan P, Ariyaratne D, Au-Yeung G, Bateman NW, Bowes L, Brand A, Christie EL, Cunningham JM, Friedlander M, Grout B, Harnett P, Hung J, McCauley B, McNally O, Piskorz AM, Saner FAM, Vierkant RA, Wang C, Winham SJ, Pharoah PDP, Brenton JD, Conrads TP, Maxwell GL, Ramus SJ, Pearce CL, Pike MC, Nelson BH, Goode EL, DeFazio A, Bowtell DDL. The genomic and immune landscape of long-term survivors of high-grade serous ovarian cancer. Nat Genet 2022;54:1853-1864. [PMID: 36456881 PMCID: PMC10478425 DOI: 10.1038/s41588-022-01230-9] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 10/17/2022] [Indexed: 12/03/2022]
22
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]
23
Proteogenomic analysis of lung adenocarcinoma reveals tumor heterogeneity, survival determinants, and therapeutically relevant pathways. Cell Rep Med 2022;3:100819. [PMID: 36384096 PMCID: PMC9729884 DOI: 10.1016/j.xcrm.2022.100819] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/09/2022] [Accepted: 10/18/2022] [Indexed: 11/17/2022]
24
Gasper W, Rossi F, Ligorio M, Ghersi D. Variant calling enhances the identification of cancer cells in single-cell RNA sequencing data. PLoS Comput Biol 2022;18:e1010576. [PMID: 36191033 PMCID: PMC9560611 DOI: 10.1371/journal.pcbi.1010576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 10/13/2022] [Accepted: 09/15/2022] [Indexed: 12/14/2022]  Open
25
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
26
Kumar R, Ningombam SS, Kumar R, Goel H, Gogia A, Khurana S, Deo SVS, Mathur S, Tanwar P. Comprehensive mutations analyses of FTO (fat mass and obesity-associated gene) and their effects on FTO’s substrate binding implicated in obesity. Front Nutr 2022;9:852944. [PMID: 35923209 PMCID: PMC9339907 DOI: 10.3389/fnut.2022.852944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022]  Open
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Boehm KM, Aherne EA, Ellenson L, Nikolovski I, Alghamdi M, Vázquez-García I, Zamarin D, Long Roche K, Liu Y, Patel D, Aukerman A, Pasha A, Rose D, Selenica P, Causa Andrieu PI, Fong C, Capanu M, Reis-Filho JS, Vanguri R, Veeraraghavan H, Gangai N, Sosa R, Leung S, McPherson A, Gao J, Lakhman Y, Shah SP. Multimodal data integration using machine learning improves risk stratification of high-grade serous ovarian cancer. NATURE CANCER 2022;3:723-733. [PMID: 35764743 PMCID: PMC9239907 DOI: 10.1038/s43018-022-00388-9] [Citation(s) in RCA: 142] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 04/27/2022] [Indexed: 04/25/2023]
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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]
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Mas-Ponte D, McCullough M, Supek F. Spectrum of DNA mismatch repair failures viewed through the lens of cancer genomics and implications for therapy. Clin Sci (Lond) 2022;136:383-404. [PMID: 35274136 PMCID: PMC8919091 DOI: 10.1042/cs20210682] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/02/2022] [Accepted: 02/28/2022] [Indexed: 12/15/2022]
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Boehm KM, Khosravi P, Vanguri R, Gao J, Shah SP. Harnessing multimodal data integration to advance precision oncology. Nat Rev Cancer 2022;22:114-126. [PMID: 34663944 PMCID: PMC8810682 DOI: 10.1038/s41568-021-00408-3] [Citation(s) in RCA: 229] [Impact Index Per Article: 76.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/08/2021] [Indexed: 02/07/2023]
31
Wu Y, Chua EHZ, Ng AWT, Boot A, Rozen SG. Accuracy of mutational signature software on correlated signatures. Sci Rep 2022;12:390. [PMID: 35013428 PMCID: PMC8748538 DOI: 10.1038/s41598-021-04207-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/17/2021] [Indexed: 11/09/2022]  Open
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Mei Y, Liang D, Wang T, Yu D. Gaining insights into relevance across cancers based on mutation features of TP53 gene. Biochem Biophys Rep 2021;28:101165. [PMID: 34786492 PMCID: PMC8579115 DOI: 10.1016/j.bbrep.2021.101165] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 11/26/2022]  Open
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Chiang YC, Lin PH, Cheng WF. Homologous Recombination Deficiency Assays in Epithelial Ovarian Cancer: Current Status and Future Direction. Front Oncol 2021;11:675972. [PMID: 34722237 PMCID: PMC8551835 DOI: 10.3389/fonc.2021.675972] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 09/17/2021] [Indexed: 01/02/2023]  Open
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Sason I, Chen Y, Leiserson MDM, Sharan R. A mixture model for signature discovery from sparse mutation data. Genome Med 2021;13:173. [PMID: 34724984 PMCID: PMC8559697 DOI: 10.1186/s13073-021-00988-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 10/12/2021] [Indexed: 12/15/2022]  Open
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Kim YA, Leiserson MDM, Moorjani P, Sharan R, Wojtowicz D, Przytycka TM. Mutational Signatures: From Methods to Mechanisms. Annu Rev Biomed Data Sci 2021;4:189-206. [PMID: 34465178 DOI: 10.1146/annurev-biodatasci-122320-120920] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Vöhringer H, Hoeck AV, Cuppen E, Gerstung M. Learning mutational signatures and their multidimensional genomic properties with TensorSignatures. Nat Commun 2021;12:3628. [PMID: 34131135 PMCID: PMC8206343 DOI: 10.1038/s41467-021-23551-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 04/15/2021] [Indexed: 01/09/2023]  Open
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Miller RE, Leary A, Scott CL, Serra V, Lord CJ, Bowtell D, Chang DK, Garsed DW, Jonkers J, Ledermann JA, Nik-Zainal S, Ray-Coquard I, Shah SP, Matias-Guiu X, Swisher EM, Yates LR. ESMO recommendations on predictive biomarker testing for homologous recombination deficiency and PARP inhibitor benefit in ovarian cancer. Ann Oncol 2020;31:1606-1622. [PMID: 33004253 DOI: 10.1016/j.annonc.2020.08.2102] [Citation(s) in RCA: 287] [Impact Index Per Article: 57.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 12/20/2022]  Open
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Li BZ, Putnam CD, Kolodner RD. Mechanisms underlying genome instability mediated by formation of foldback inversions in Saccharomyces cerevisiae. eLife 2020;9:58223. [PMID: 32762846 PMCID: PMC7467729 DOI: 10.7554/elife.58223] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/04/2020] [Indexed: 01/09/2023]  Open
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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]
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Nussinov R, Tsai CJ, Jang H. Why Are Some Driver Mutations Rare? Trends Pharmacol Sci 2019;40:919-929. [PMID: 31699406 DOI: 10.1016/j.tips.2019.10.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/09/2019] [Accepted: 10/10/2019] [Indexed: 12/13/2022]
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Himoto Y, Veeraraghavan H, Zheng J, Zamarin D, Snyder A, Capanu M, Nougaret S, Vargas HA, Shitano F, Callahan M, Wang W, Sala E, Lakhman Y. Computed Tomography-Derived Radiomic Metrics Can Identify Responders to Immunotherapy in Ovarian Cancer. JCO Precis Oncol 2019;3:1900038. [PMID: 32914033 DOI: 10.1200/po.19.00038] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2019] [Indexed: 12/11/2022]  Open
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