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For: Rubanova Y, Shi R, Harrigan CF, Li R, Wintersinger J, Sahin N, Deshwar AG, Morris QD. Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig. Nat Commun 2020;11:731. [PMID: 32024834 PMCID: PMC7002414 DOI: 10.1038/s41467-020-14352-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 12/23/2019] [Indexed: 12/14/2022]  Open
Number Cited by Other Article(s)
1
Salcedo A, Tarabichi M, Buchanan A, Espiritu SMG, Zhang H, Zhu K, Ou Yang TH, Leshchiner I, Anastassiou D, Guan Y, Jang GH, Mootor MFE, Haase K, Deshwar AG, Zou W, Umar I, Dentro S, Wintersinger JA, Chiotti K, Demeulemeester J, Jolly C, Sycza L, Ko M, Wedge DC, Morris QD, Ellrott K, Van Loo P, Boutros PC. Crowd-sourced benchmarking of single-sample tumor subclonal reconstruction. Nat Biotechnol 2025;43:581-592. [PMID: 38862616 PMCID: PMC11994449 DOI: 10.1038/s41587-024-02250-y] [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: 04/11/2022] [Accepted: 04/17/2024] [Indexed: 06/13/2024]
2
Morrill Gavarró L, Couturier DL, Markowetz F. A Dirichlet-multinomial mixed model for determining differential abundance of mutational signatures. BMC Bioinformatics 2025;26:59. [PMID: 39966709 PMCID: PMC11837616 DOI: 10.1186/s12859-025-06055-x] [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: 07/07/2024] [Accepted: 01/16/2025] [Indexed: 02/20/2025]  Open
3
Jakobsdottir GM, Dentro SC, Bristow RG, Wedge DC. AmplificationTimeR: an R package for timing sequential amplification events. Bioinformatics 2024;40:btae281. [PMID: 38656989 PMCID: PMC11153944 DOI: 10.1093/bioinformatics/btae281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 02/23/2024] [Accepted: 04/23/2024] [Indexed: 04/26/2024]  Open
4
Dayton TL, Alcala N, Moonen L, den Hartigh L, Geurts V, Mangiante L, Lap L, Dost AFM, Beumer J, Levy S, van Leeuwaarde RS, Hackeng WM, Samsom K, Voegele C, Sexton-Oates A, Begthel H, Korving J, Hillen L, Brosens LAA, Lantuejoul S, Jaksani S, Kok NFM, Hartemink KJ, Klomp HM, Borel Rinkes IHM, Dingemans AM, Valk GD, Vriens MR, Buikhuisen W, van den Berg J, Tesselaar M, Derks J, Speel EJ, Foll M, Fernández-Cuesta L, Clevers H. Druggable growth dependencies and tumor evolution analysis in patient-derived organoids of neuroendocrine neoplasms from multiple body sites. Cancer Cell 2023;41:2083-2099.e9. [PMID: 38086335 DOI: 10.1016/j.ccell.2023.11.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/06/2023] [Accepted: 11/08/2023] [Indexed: 12/18/2023]
5
Legrand C, Andriantsoa R, Lichter P, Raddatz G, Lyko F. Time-resolved, integrated analysis of clonally evolving genomes. PLoS Genet 2023;19:e1011085. [PMID: 38096267 PMCID: PMC10754456 DOI: 10.1371/journal.pgen.1011085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 12/28/2023] [Accepted: 11/27/2023] [Indexed: 12/29/2023]  Open
6
Rodriguez-Fos E, Planas-Fèlix M, Burkert M, Puiggròs M, Toedling J, Thiessen N, Blanc E, Szymansky A, Hertwig F, Ishaque N, Beule D, Torrents D, Eggert A, Koche RP, Schwarz RF, Haase K, Schulte JH, Henssen AG. Mutational topography reflects clinical neuroblastoma heterogeneity. CELL GENOMICS 2023;3:100402. [PMID: 37868040 PMCID: PMC10589636 DOI: 10.1016/j.xgen.2023.100402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/13/2023] [Accepted: 08/11/2023] [Indexed: 10/24/2023]
7
Abbas S, Pich O, Devonshire G, Zamani SA, Katz-Summercorn A, Killcoyne S, Cheah C, Nutzinger B, Grehan N, Lopez-Bigas N, Fitzgerald RC, Secrier M. Mutational signature dynamics shaping the evolution of oesophageal adenocarcinoma. Nat Commun 2023;14:4239. [PMID: 37454136 PMCID: PMC10349863 DOI: 10.1038/s41467-023-39957-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 07/03/2023] [Indexed: 07/18/2023]  Open
8
Long X, Lu H, Cai MC, Zang J, Zhang Z, Wu J, Liu X, Cheng L, Cheng J, Cheung LWT, Shen Z, Zhou Y, Di W, Zhuang G, Yin X. APOBEC3B stratifies ovarian clear cell carcinoma with distinct immunophenotype and prognosis. Br J Cancer 2023;128:2054-2062. [PMID: 36997661 PMCID: PMC10206171 DOI: 10.1038/s41416-023-02239-5] [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: 04/18/2022] [Revised: 03/07/2023] [Accepted: 03/16/2023] [Indexed: 04/01/2023]  Open
9
Timmons C, Morris Q, Harrigan CF. Regional mutational signature activities in cancer genomes. PLoS Comput Biol 2022;18:e1010733. [PMID: 36469539 PMCID: PMC9754594 DOI: 10.1371/journal.pcbi.1010733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 12/15/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022]  Open
10
Lee ND, Bozic I. Inferring parameters of cancer evolution in chronic lymphocytic leukemia. PLoS Comput Biol 2022;18:e1010677. [PMID: 36331987 PMCID: PMC9668150 DOI: 10.1371/journal.pcbi.1010677] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 11/16/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022]  Open
11
The shaping of cancer genomes with the regional impact of mutation processes. EXPERIMENTAL & MOLECULAR MEDICINE 2022;54:1049-1060. [PMID: 35902761 PMCID: PMC9355972 DOI: 10.1038/s12276-022-00808-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/03/2022] [Accepted: 04/28/2022] [Indexed: 11/09/2022]
12
Angaroni F, Guidi A, Ascolani G, d'Onofrio A, Antoniotti M, Graudenzi A. J-SPACE: a Julia package for the simulation of spatial models of cancer evolution and of sequencing experiments. BMC Bioinformatics 2022;23:269. [PMID: 35804300 PMCID: PMC9270769 DOI: 10.1186/s12859-022-04779-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 06/09/2022] [Indexed: 11/15/2022]  Open
13
Stella GM, Scialò F, Bortolotto C, Agustoni F, Sanci V, Saddi J, Casali L, Corsico AG, Bianco A. Pragmatic Expectancy on Microbiota and Non-Small Cell Lung Cancer: A Narrative Review. Cancers (Basel) 2022;14:cancers14133131. [PMID: 35804901 PMCID: PMC9264919 DOI: 10.3390/cancers14133131] [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: 05/05/2022] [Revised: 06/08/2022] [Accepted: 06/21/2022] [Indexed: 11/16/2022]  Open
14
A phylogenetic approach to study the evolution of somatic mutational processes in cancer. Commun Biol 2022;5:617. [PMID: 35732905 PMCID: PMC9217972 DOI: 10.1038/s42003-022-03560-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 06/07/2022] [Indexed: 11/09/2022]  Open
15
Georgeson P, Harrison TA, Pope BJ, Zaidi SH, Qu C, Steinfelder RS, Lin Y, Joo JE, Mahmood K, Clendenning M, Walker R, Amitay EL, Berndt SI, Brenner H, Campbell PT, Cao Y, Chan AT, Chang-Claude J, Doheny KF, Drew DA, Figueiredo JC, French AJ, Gallinger S, Giannakis M, Giles GG, Gsur A, Gunter MJ, Hoffmeister M, Hsu L, Huang WY, Limburg P, Manson JE, Moreno V, Nassir R, Nowak JA, Obón-Santacana M, Ogino S, Phipps AI, Potter JD, Schoen RE, Sun W, Toland AE, Trinh QM, Ugai T, Macrae FA, Rosty C, Hudson TJ, Jenkins MA, Thibodeau SN, Winship IM, Peters U, Buchanan DD. Identifying colorectal cancer caused by biallelic MUTYH pathogenic variants using tumor mutational signatures. Nat Commun 2022;13:3254. [PMID: 35668106 PMCID: PMC9170691 DOI: 10.1038/s41467-022-30916-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 05/24/2022] [Indexed: 01/11/2023]  Open
16
Mutational signatures and processes in hepatobiliary cancers. Nat Rev Gastroenterol Hepatol 2022;19:367-382. [PMID: 35273358 DOI: 10.1038/s41575-022-00587-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/01/2022] [Indexed: 12/08/2022]
17
Li Z, Spoelstra NS, Sikora MJ, Sams SB, Elias A, Richer JK, Lee AV, Oesterreich S. Mutual exclusivity of ESR1 and TP53 mutations in endocrine resistant metastatic breast cancer. NPJ Breast Cancer 2022;8:62. [PMID: 35538119 PMCID: PMC9090919 DOI: 10.1038/s41523-022-00426-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 03/31/2022] [Indexed: 12/12/2022]  Open
18
Matsutani T, Hamada M. Clone decomposition based on mutation signatures provides novel insights into mutational processes. NAR Genom Bioinform 2021;3:lqab093. [PMID: 34734181 PMCID: PMC8559167 DOI: 10.1093/nargab/lqab093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 09/17/2021] [Accepted: 10/19/2021] [Indexed: 11/24/2022]  Open
19
Satas G, Zaccaria S, El-Kebir M, Raphael BJ. DeCiFering the elusive cancer cell fraction in tumor heterogeneity and evolution. Cell Syst 2021;12:1004-1018.e10. [PMID: 34416171 DOI: 10.1016/j.cels.2021.07.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/09/2021] [Accepted: 07/21/2021] [Indexed: 12/22/2022]
20
Koh G, Degasperi A, Zou X, Momen S, Nik-Zainal S. Mutational signatures: emerging concepts, caveats and clinical applications. Nat Rev Cancer 2021;21:619-637. [PMID: 34316057 DOI: 10.1038/s41568-021-00377-7] [Citation(s) in RCA: 147] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/08/2021] [Indexed: 02/05/2023]
21
Abécassis J, Reyal F, Vert JP. CloneSig can jointly infer intra-tumor heterogeneity and mutational signature activity in bulk tumor sequencing data. Nat Commun 2021;12:5352. [PMID: 34504064 PMCID: PMC8429716 DOI: 10.1038/s41467-021-24992-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 07/12/2021] [Indexed: 02/07/2023]  Open
22
Giunta S. Decoding human cancer with whole genome sequencing: a review of PCAWG Project studies published in February 2020. Cancer Metastasis Rev 2021;40:909-924. [PMID: 34097189 PMCID: PMC8180541 DOI: 10.1007/s10555-021-09969-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/21/2021] [Indexed: 12/15/2022]
23
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]
24
Vavoulis DV, Cutts A, Taylor JC, Schuh A. A statistical approach for tracking clonal dynamics in cancer using longitudinal next-generation sequencing data. Bioinformatics 2021;37:147-154. [PMID: 32722772 PMCID: PMC8055230 DOI: 10.1093/bioinformatics/btaa672] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 05/13/2020] [Accepted: 07/20/2020] [Indexed: 01/22/2023]  Open
25
Dentro SC, Leshchiner I, Haase K, Tarabichi M, Wintersinger J, Deshwar AG, Yu K, Rubanova Y, Macintyre G, Demeulemeester J, Vázquez-García I, Kleinheinz K, Livitz DG, Malikic S, Donmez N, Sengupta S, Anur P, Jolly C, Cmero M, Rosebrock D, Schumacher SE, Fan Y, Fittall M, Drews RM, Yao X, Watkins TBK, Lee J, Schlesner M, Zhu H, Adams DJ, McGranahan N, Swanton C, Getz G, Boutros PC, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Martincorena I, Markowetz F, Mustonen V, Yuan K, Gerstung M, Spellman PT, Wang W, Morris QD, Wedge DC, Van Loo P. Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes. Cell 2021;184:2239-2254.e39. [PMID: 33831375 PMCID: PMC8054914 DOI: 10.1016/j.cell.2021.03.009] [Citation(s) in RCA: 311] [Impact Index Per Article: 77.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 09/21/2020] [Accepted: 03/03/2021] [Indexed: 02/07/2023]
26
Zhang C, El-Kebir M, Ochoa I. Moss enables high sensitivity single-nucleotide variant calling from multiple bulk DNA tumor samples. Nat Commun 2021;12:2204. [PMID: 33850139 PMCID: PMC8044184 DOI: 10.1038/s41467-021-22466-9] [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: 06/07/2020] [Accepted: 03/05/2021] [Indexed: 11/17/2022]  Open
27
Hübschmann D, Jopp-Saile L, Andresen C, Krämer S, Gu Z, Heilig CE, Kreutzfeldt S, Teleanu V, Fröhling S, Eils R, Schlesner M. Analysis of mutational signatures with yet another package for signature analysis. Genes Chromosomes Cancer 2020;60:314-331. [PMID: 33222322 DOI: 10.1002/gcc.22918] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 11/06/2020] [Accepted: 11/06/2020] [Indexed: 12/11/2022]  Open
28
Hu X, Xu Z, De S. Characteristics of mutational signatures of unknown etiology. NAR Cancer 2020;2:zcaa026. [PMID: 33015626 PMCID: PMC7520824 DOI: 10.1093/narcan/zcaa026] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 09/01/2020] [Accepted: 09/23/2020] [Indexed: 12/25/2022]  Open
29
Emerging Precision Oncology Applications of Liquid Biopsy using Circulating Tumour DNA and Methylome Profiling. Clin Oncol (R Coll Radiol) 2020;32:626-631. [PMID: 32586654 DOI: 10.1016/j.clon.2020.05.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 05/13/2020] [Accepted: 05/29/2020] [Indexed: 01/13/2023]
30
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
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