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For: 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: 2057] [Impact Index Per Article: 411.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 11/18/2019] [Indexed: 01/27/2023]
Number Cited by Other Article(s)
51
Molefi T, Mabonga L, Hull R, Sebitloane M, Dlamini Z. From Genes to Clinical Practice: Exploring the Genomic Underpinnings of Endometrial Cancer. Cancers (Basel) 2025;17:320. [PMID: 39858102 PMCID: PMC11763595 DOI: 10.3390/cancers17020320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2024] [Revised: 01/08/2025] [Accepted: 01/11/2025] [Indexed: 01/27/2025]  Open
52
Chung T, Oh S, Won J, Park J, Yoo JE, Hwang HK, Choi GH, Kang CM, Han DH, Kim S, Park YN. Genomic and transcriptomic signatures of sequential carcinogenesis from papillary neoplasm to biliary tract cancer. J Hepatol 2025:S0168-8278(25)00013-3. [PMID: 39832657 DOI: 10.1016/j.jhep.2025.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 12/23/2024] [Accepted: 01/01/2025] [Indexed: 01/22/2025]
53
Yang M, Zheng G, Chen F, Tang H, Liu Y, Gao X, Huang Y, Lv Z, Li B, Yang M, Bu Q, Zhu L, Yu P, Huo Z, Wei X, Chen X, Huang Y, He Z, Xia X, Bai J. Molecular characterization of EBV-associated primary pulmonary lymphoepithelial carcinoma by multiomics analysis. BMC Cancer 2025;25:85. [PMID: 39815193 PMCID: PMC11734413 DOI: 10.1186/s12885-024-13410-3] [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: 07/09/2024] [Accepted: 12/30/2024] [Indexed: 01/18/2025]  Open
54
Koch Z, Li A, Evans DS, Cummings S, Ideker T. Somatic mutation as an explanation for epigenetic aging. NATURE AGING 2025:10.1038/s43587-024-00794-x. [PMID: 39806003 DOI: 10.1038/s43587-024-00794-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 12/12/2024] [Indexed: 01/16/2025]
55
Stratton MR, Humphreys L, Alexandrov LB, Balmain A, Brennan P, Campbell PJ, Phillips DH. Implementing Mutational Epidemiology on a Global Scale: Lessons from Mutographs. Cancer Discov 2025;15:22-27. [PMID: 39801236 DOI: 10.1158/2159-8290.cd-24-1687] [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: 11/15/2024] [Accepted: 11/25/2024] [Indexed: 02/11/2025]
56
Kubitschek J, Takhaveev V, Mingard C, Rochlitz M, Reinert P, Keller G, Kloter T, Fernández Cereijo R, Huber S, McKeague M, Sturla S. Single-nucleotide-resolution genomic maps of O6-methylguanine from the glioblastoma drug temozolomide. Nucleic Acids Res 2025;53:gkae1320. [PMID: 39831306 PMCID: PMC11744188 DOI: 10.1093/nar/gkae1320] [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: 01/22/2024] [Revised: 12/20/2024] [Accepted: 01/16/2025] [Indexed: 01/22/2025]  Open
57
Kerle IA, Gross T, Kögler A, Arnold JS, Werner M, Eckardt JN, Möhrmann EE, Arlt M, Hutter B, Hüllein J, Richter D, Schneider MMK, Hlevnjak M, Möhrmann L, Hanf D, Heilig CE, Kreutzfeldt S, Teleanu MV, Schröck E, Hübschmann D, Horak P, Heining C, Fröhling S, Glimm H. Translational and clinical comparison of whole genome and transcriptome to panel sequencing in precision oncology. NPJ Precis Oncol 2025;9:9. [PMID: 39794422 PMCID: PMC11724059 DOI: 10.1038/s41698-024-00788-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Accepted: 12/14/2024] [Indexed: 01/13/2025]  Open
58
Geisenberger C, Chimal E, Jurmeister P, Klauschen F. A cost-effective and scalable approach for DNA extraction from FFPE tissues. Biol Methods Protoc 2025;10:bpaf003. [PMID: 39995602 PMCID: PMC11849955 DOI: 10.1093/biomethods/bpaf003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Revised: 12/17/2024] [Accepted: 01/08/2025] [Indexed: 02/26/2025]  Open
59
Fujii E, Kato MK, Ono H, Yamaguchi M, Higuchi D, Koyama T, Komatsu M, Hamamoto R, Ishikawa M, Kato T, Kohno T, Shiraishi K, Yoshida H. TP53 Mutations and PD-L1 Amplification in Vulvar Adenocarcinoma of the Intestinal Type: Insights From Whole Exome Sequencing of 2 Cases. Int J Gynecol Pathol 2025:00004347-990000000-00218. [PMID: 39868745 DOI: 10.1097/pgp.0000000000001093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2025]
60
Zhang F, Wu X, Jiao T, Dua H, Guo Q, Cui C, Chi Z, Sheng X, Jiang D, Zhang Y, Wu J, Kong Y, Si L. Genomic characterization reveals distinct mutational landscape of acral melanoma in East Asian. J Genet Genomics 2025:S1673-8527(24)00371-0. [PMID: 39798666 DOI: 10.1016/j.jgg.2024.12.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2024] [Revised: 12/24/2024] [Accepted: 12/24/2024] [Indexed: 01/15/2025]
61
Unger M, Loeffler CML, Žigutytė L, Sainath S, Lenz T, Vibert J, Mock A, Fröhling S, Graham TA, Carrero ZI, Kather JN. Deep Learning for Biomarker Discovery in Cancer Genomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.06.631471. [PMID: 39829845 PMCID: PMC11741323 DOI: 10.1101/2025.01.06.631471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2025]
62
Boysen G, Alexandrov L, Rahbari R, Nookaew I, Ussery D, Chao MR, Hu CW, Cooke M. Investigating the origins of the mutational signatures in cancer. Nucleic Acids Res 2025;53:gkae1303. [PMID: 39778866 PMCID: PMC11707540 DOI: 10.1093/nar/gkae1303] [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: 05/30/2024] [Revised: 12/17/2024] [Accepted: 01/05/2025] [Indexed: 01/11/2025]  Open
63
Hwang T, Sitko L, Khoirunnisa R, Navarro-Aguad F, Samuel D, Park H, Cheon B, Mutsnaini L, Lee J, Otlu B, Takeda S, Lee S, Ivanov D, Gartner A. Comprehensive whole-genome sequencing reveals origins of mutational signatures associated with aging, mismatch repair deficiency and temozolomide chemotherapy. Nucleic Acids Res 2025;53:gkae1122. [PMID: 39656916 PMCID: PMC11724276 DOI: 10.1093/nar/gkae1122] [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: 03/12/2024] [Revised: 10/17/2024] [Accepted: 11/07/2024] [Indexed: 12/17/2024]  Open
64
Luzadder MM, Minko IG, Vartanian VL, Davenport M, Fedorov LM, McCullough AK, Stephen Lloyd R. The Distinct Roles of NEIL1 and XPA in Limiting Aflatoxin B1-Induced Mutagenesis in Mice. Mol Cancer Res 2025;23:46-58. [PMID: 39387543 PMCID: PMC11695181 DOI: 10.1158/1541-7786.mcr-24-0577] [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: 06/21/2024] [Revised: 09/17/2024] [Accepted: 10/08/2024] [Indexed: 10/15/2024]
65
Tremmel R, Hübschmann D, Schaeffeler E, Pirmann S, Fröhling S, Schwab M. Innovation in cancer pharmacotherapy through integrative consideration of germline and tumor genomes. Pharmacol Rev 2025;77:100014. [PMID: 39952686 DOI: 10.1124/pharmrev.124.001049] [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: 04/03/2024] [Revised: 10/02/2024] [Accepted: 10/04/2024] [Indexed: 01/22/2025]  Open
66
Lucas O, Ward S, Zaidi R, Bunkum A, Frankell AM, Moore DA, Hill MS, Liu WK, Marinelli D, Lim EL, Hessey S, Naceur-Lombardelli C, Rowan A, Purewal-Mann SK, Zhai H, Dietzen M, Ding B, Royle G, Aparicio S, McGranahan N, Jamal-Hanjani M, Kanu N, Swanton C, Zaccaria S. Characterizing the evolutionary dynamics of cancer proliferation in single-cell clones with SPRINTER. Nat Genet 2025;57:103-114. [PMID: 39614124 PMCID: PMC11735394 DOI: 10.1038/s41588-024-01989-z] [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: 09/11/2023] [Accepted: 10/15/2024] [Indexed: 12/01/2024]
67
Gu L, Zhu Y, Nandi SP, Lee M, Watari K, Bareng B, Ohira M, Liu Y, Sakane S, Carlessi R, Sauceda C, Dhar D, Ganguly S, Hosseini M, Teneche MG, Adams PD, Gonzalez DJ, Kisseleva T, Tirnitz-Parker JEE, Simon MC, Alexandrov LB, Karin M. FBP1 controls liver cancer evolution from senescent MASH hepatocytes. Nature 2025;637:461-469. [PMID: 39743585 DOI: 10.1038/s41586-024-08317-9] [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: 07/22/2023] [Accepted: 10/30/2024] [Indexed: 01/04/2025]
68
Funk JS, Klimovich M, Drangenstein D, Pielhoop O, Hunold P, Borowek A, Noeparast M, Pavlakis E, Neumann M, Balourdas DI, Kochhan K, Merle N, Bullwinkel I, Wanzel M, Elmshäuser S, Teply-Szymanski J, Nist A, Procida T, Bartkuhn M, Humpert K, Mernberger M, Savai R, Soussi T, Joerger AC, Stiewe T. Deep CRISPR mutagenesis characterizes the functional diversity of TP53 mutations. Nat Genet 2025;57:140-153. [PMID: 39774325 PMCID: PMC11735402 DOI: 10.1038/s41588-024-02039-4] [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: 03/17/2024] [Accepted: 11/20/2024] [Indexed: 01/11/2025]
69
Shahbaz W, Greif PA. [(Over-)living with cancer: secondary malignancies (incl. genetics)]. Dtsch Med Wochenschr 2025;150:37-43. [PMID: 39662494 DOI: 10.1055/a-2258-4682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2024]
70
Wang J, Guo C, Wang J, Zhang X, Qi J, Huang X, Hu Z, Wang H, Hong B. Tumor Mutation Signature Reveals the Risk Factors of Lung Adenocarcinoma with EGFR or KRAS Mutation. Cancer Control 2025;32:10732748241307363. [PMID: 39760242 DOI: 10.1177/10732748241307363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2025]  Open
71
Karihtala P, Kilpivaara O, Porvari K. Mutational signatures and their association with cancer survival and gene expression in multiple cancer types. Int J Cancer 2025;156:114-129. [PMID: 39194330 DOI: 10.1002/ijc.35148] [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: 03/21/2024] [Revised: 06/19/2024] [Accepted: 07/15/2024] [Indexed: 08/29/2024]
72
Lu WT, Zalmas LP, Bailey C, Black JRM, Martinez-Ruiz C, Pich O, Gimeno-Valiente F, Usaite I, Magness A, Thol K, Webber TA, Jiang M, Saunders RE, Liu YH, Biswas D, Ige EO, Aerne B, Grönroos E, Venkatesan S, Stavrou G, Karasaki T, Al Bakir M, Renshaw M, Xu H, Schneider-Luftman D, Sharma N, Tovini L, Jamal-Hanjani M, McClelland SE, Litchfield K, Birkbak NJ, Howell M, Tapon N, Fugger K, McGranahan N, Bartek J, Kanu N, Swanton C. TRACERx analysis identifies a role for FAT1 in regulating chromosomal instability and whole-genome doubling via Hippo signalling. Nat Cell Biol 2025;27:154-168. [PMID: 39738653 PMCID: PMC11735399 DOI: 10.1038/s41556-024-01558-w] [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: 07/07/2023] [Accepted: 10/16/2024] [Indexed: 01/02/2025]
73
de Groot D, Spanjaard A, Shah R, Kreft M, Morris B, Lieftink C, Catsman JJI, Ormel S, Ayidah M, Pilzecker B, Buoninfante OA, van den Berk PCM, Beijersbergen RL, Jacobs H. Molecular dependencies and genomic consequences of a global DNA damage tolerance defect. Genome Biol 2024;25:323. [PMID: 39741332 DOI: 10.1186/s13059-024-03451-z] [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: 02/22/2024] [Accepted: 11/29/2024] [Indexed: 01/02/2025]  Open
74
Murat P, Guilbaud G, Sale JE. DNA replication initiation drives focal mutagenesis and rearrangements in human cancers. Nat Commun 2024;15:10850. [PMID: 39738026 DOI: 10.1038/s41467-024-55148-3] [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: 04/10/2024] [Accepted: 12/03/2024] [Indexed: 01/01/2025]  Open
75
Zhuravleva E, Lewinska M, O'Rourke CJ, Pea A, Rashid A, Hsing AW, Taranta A, Chang D, Gao YT, Koshiol J, Oliveira RC, Andersen JB. Mutational signatures define immune and Wnt-associated subtypes of ampullary carcinoma. Gut 2024:gutjnl-2024-333368. [PMID: 39725462 DOI: 10.1136/gutjnl-2024-333368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Accepted: 11/21/2024] [Indexed: 12/28/2024]
76
Ahmed F, Zhong J. Advances in DNA/RNA Sequencing and Their Applications in Acute Myeloid Leukemia (AML). Int J Mol Sci 2024;26:71. [PMID: 39795930 PMCID: PMC11720148 DOI: 10.3390/ijms26010071] [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: 11/04/2024] [Revised: 11/24/2024] [Accepted: 12/19/2024] [Indexed: 01/13/2025]  Open
77
Cordero C, Mehta KPM, Weaver TM, Ling JA, Freudenthal BD, Cortez D, Roberts SA. Contributing factors to the oxidation-induced mutational landscape in human cells. Nat Commun 2024;15:10722. [PMID: 39715760 DOI: 10.1038/s41467-024-55497-z] [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: 05/09/2024] [Accepted: 12/10/2024] [Indexed: 12/25/2024]  Open
78
Mallawaarachchi AC, Hort Y, Wedd L, Lo K, Senum S, Toumari M, Chen W, Utsiwegota M, Mawson J, Leslie S, Laurence J, Anderson L, Snelling P, Salomon R, Rangan GK, Furlong T, Shine J, Cowley MJ. Somatic mutation in autosomal dominant polycystic kidney disease revealed by deep sequencing human kidney cysts. NPJ Genom Med 2024;9:69. [PMID: 39702469 DOI: 10.1038/s41525-024-00452-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 12/02/2024] [Indexed: 12/21/2024]  Open
79
Mitsiades IR, Onozato M, Iafrate AJ, Hicks D, Gülhan DC, Sgroi DC, Rheinbay E. ERBB2/HOXB13 co-amplification with interstitial loss of BRCA1 defines a unique subset of breast cancers. Breast Cancer Res 2024;26:185. [PMID: 39695741 DOI: 10.1186/s13058-024-01943-1] [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: 08/08/2024] [Accepted: 12/03/2024] [Indexed: 12/20/2024]  Open
80
Delgado-de la Mora J, Al Assaad M, Quitian S, Levine MF, Deshpande A, Sigouros M, Manohar J, Medina-Martínez JS, Sboner A, Elemento O, Jessurun J, Hissong E, Mosquera JM. Novel structural variants that impact cell cycle genes are elucidated in metastatic gastrointestinal stromal tumors. Pathol Res Pract 2024;266:155782. [PMID: 39708519 DOI: 10.1016/j.prp.2024.155782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2024] [Accepted: 12/17/2024] [Indexed: 12/23/2024]
81
Shelley CS, Galiègue-Zouitina S, Andritsos LA, Epperla N, Troussard X. The role of the JunD-RhoH axis in the pathogenesis of hairy cell leukemia and its ability to identify existing therapeutics that could be repurposed to treat relapsed or refractory disease. Leuk Lymphoma 2024:1-19. [PMID: 39689307 DOI: 10.1080/10428194.2024.2438800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Revised: 11/19/2024] [Accepted: 12/01/2024] [Indexed: 12/19/2024]
82
Zhang L, Deng T, Liufu Z, Liu X, Chen B, Hu Z, Liu C, Tracy ME, Lu X, Wen HJ, Wu CI. The theory of massively repeated evolution and full identifications of cancer-driving nucleotides (CDNs). eLife 2024;13:RP99340. [PMID: 39688960 DOI: 10.7554/elife.99340] [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] [Indexed: 12/19/2024]  Open
83
Fixman B, Díaz-Gay M, Qiu C, Margaryan T, Lee B, Chen XS. Validation of the APOBEC3A-Mediated RNA Single Base Substitution Signature and Proposal of Novel APOBEC1, APOBEC3B, and APOBEC3G RNA Signatures. J Mol Biol 2024;436:168854. [PMID: 39510348 PMCID: PMC11637894 DOI: 10.1016/j.jmb.2024.168854] [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: 09/05/2024] [Revised: 10/30/2024] [Accepted: 10/31/2024] [Indexed: 11/15/2024]
84
Oelschläger L, Künstner A, Frey F, Leitner T, Leypoldt L, Reimer N, Gebauer N, Bastian L, Weisel K, Sailer VW, Röcken C, Klapper W, Konukiewitz B, Murga Penas EM, Forster M, Schub N, Ahmed HMM, Kirfel J, von Bubnoff NCC, Busch H, Khandanpour C. Whole-Exome Sequencing, Mutational Signature Analysis, and Outcome in Multiple Myeloma-A Pilot Study. Int J Mol Sci 2024;25:13418. [PMID: 39769182 PMCID: PMC11680055 DOI: 10.3390/ijms252413418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2024] [Revised: 12/02/2024] [Accepted: 12/09/2024] [Indexed: 01/11/2025]  Open
85
Avsievich E, Salimgereeva D, Maluchenko A, Antysheva Z, Voloshin M, Feidorov I, Glazova O, Abramov I, Maksimov D, Kaziakhmedova S, Bodunova N, Karnaukhov N, Volchkov P, Krupinova J. Pancreatic Neuroendocrine Tumor: The Case Report of a Patient with Germline FANCD2 Mutation and Tumor Analysis Using Single-Cell RNA Sequencing. J Clin Med 2024;13:7621. [PMID: 39768544 PMCID: PMC11728285 DOI: 10.3390/jcm13247621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2024] [Revised: 11/18/2024] [Accepted: 11/21/2024] [Indexed: 01/16/2025]  Open
86
Teodoro L, Carreira ACO, Sogayar MC. Exploring the Complexity of Pan-Cancer: Gene Convergences and in silico Analyses. BREAST CANCER (DOVE MEDICAL PRESS) 2024;16:913-934. [PMID: 39691553 PMCID: PMC11651076 DOI: 10.2147/bctt.s489246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2024] [Accepted: 11/06/2024] [Indexed: 12/19/2024]
87
Braza MKE, Demir Ö, Ahn SH, Morris CK, Calvó-Tusell C, McGuire KL, de la Peña Avalos B, Carpenter MA, Chen Y, Casalino L, Aihara H, Herzik MA, Harris RS, Amaro RE. Regulatory interactions between APOBEC3B N- and C-terminal domains. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.11.628032. [PMID: 39713448 PMCID: PMC11661193 DOI: 10.1101/2024.12.11.628032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/24/2024]
88
Kadam A, Shilo S, Naor H, Wainstein A, Brilon Y, Feldman T, Minden M, Kaushansky N, Chapal-Ilani N, Shlush L. Utilizing insights of DNA repair machinery to discover MMEJ deletions and novel mechanisms. Nucleic Acids Res 2024;52:e106. [PMID: 39607705 DOI: 10.1093/nar/gkae1132] [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: 09/12/2023] [Revised: 10/17/2024] [Accepted: 10/30/2024] [Indexed: 11/29/2024]  Open
89
Schuster D, LeBlanc DPM, Zhou G, Meier MJ, Dodge AE, White PA, Long AS, Williams A, Hobbs C, Diesing A, Smith-Roe SL, Salk JJ, Marchetti F, Yauk CL. Dose-Related Mutagenic and Clastogenic Effects of Benzo[b]fluoranthene in Mouse Somatic Tissues Detected by Duplex Sequencing and the Micronucleus Assay. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024;58:21450-21463. [PMID: 39602390 PMCID: PMC11636207 DOI: 10.1021/acs.est.4c07236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 10/06/2024] [Accepted: 11/09/2024] [Indexed: 11/29/2024]
90
Yi Z, Feng K, Lv D, Guan Y, Shao Y, Ma F, Xu B. Genomic landscape of circulating tumor DNA in HER2-low metastatic breast cancer. Signal Transduct Target Ther 2024;9:345. [PMID: 39648226 PMCID: PMC11625825 DOI: 10.1038/s41392-024-02047-0] [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: 02/26/2024] [Revised: 10/30/2024] [Accepted: 11/04/2024] [Indexed: 12/10/2024]  Open
91
Seed G, Beije N, Yuan W, Bertan C, Goodall J, Lundberg A, Tyler M, Figueiredo I, Pereira R, Baker C, Bogdan D, Gallagher L, Cieslik JP, Greening S, Lambros M, Neves R, Magraner-Pardo L, Fowler G, Ebbs B, Miranda S, Flohr P, Bianchini D, Rescigno P, Porta N, Hall E, Gurel B, Tunariu N, Sharp A, Pettit S, Stoecklein NH, Sandhu S, Quigley D, Lord CJ, Mateo J, Carreira S, de Bono J. Elucidating acquired PARP inhibitor resistance in advanced prostate cancer. Cancer Cell 2024;42:2113-2123.e4. [PMID: 39577422 DOI: 10.1016/j.ccell.2024.10.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 07/16/2024] [Accepted: 10/28/2024] [Indexed: 11/24/2024]
92
Tandukar B, Deivendran D, Chen L, Cruz-Pacheco N, Sharma H, Xu A, Bandari AK, Chen DB, George C, Marty A, Cho RJ, Cheng J, Saylor D, Gerami P, Arron ST, Bastian BC, Shain AH. Genetic evolution of keratinocytes to cutaneous squamous cell carcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.23.604673. [PMID: 39091884 PMCID: PMC11291049 DOI: 10.1101/2024.07.23.604673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
93
Srivatsa A, Schwartz R. Optimizing design of genomics studies for clonal evolution analysis. BIOINFORMATICS ADVANCES 2024;4:vbae193. [PMID: 39678206 PMCID: PMC11645549 DOI: 10.1093/bioadv/vbae193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2024] [Revised: 11/06/2024] [Accepted: 11/29/2024] [Indexed: 12/17/2024]
94
Kwon SG, Bae GH, Hong JH, Choi JW, Choi JH, Lim NS, Jeon C, Mali NM, Jun MS, Shin J, Kim J, Cho ES, Han MH, Oh JW. Comprehensive analysis of somatic mutations and structural variations in domestic pig. Mamm Genome 2024;35:645-656. [PMID: 39177814 DOI: 10.1007/s00335-024-10058-z] [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: 06/14/2024] [Accepted: 08/01/2024] [Indexed: 08/24/2024]
95
Bedeir A, Ghani H, Oster C, Crymes A, Ibe I, Yamamoto M, Elliott A, Bryant DA, Oberley MJ, Evans MG. Detection of human papillomavirus (HPV) in malignant melanoma. Ann Diagn Pathol 2024;73:152361. [PMID: 39032381 DOI: 10.1016/j.anndiagpath.2024.152361] [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: 06/11/2024] [Revised: 07/12/2024] [Accepted: 07/15/2024] [Indexed: 07/23/2024]
96
van der Werf't Lam AS, Helderman NC, Boot A, Terlouw D, Morreau H, Mei H, Esveldt-van Lange REE, Lakeman IMM, van Asperen CJ, Aten E, Hofland N, de Koning Gans PAM, Rayner E, Tops C, de Wind N, van Wezel T, Nielsen M. Assessing pathogenicity of mismatch repair variants of uncertain significance by molecular tumor analysis. Exp Mol Pathol 2024;140:104940. [PMID: 39437510 DOI: 10.1016/j.yexmp.2024.104940] [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: 04/30/2024] [Revised: 09/27/2024] [Accepted: 10/16/2024] [Indexed: 10/25/2024]
97
Weng Z, Mai Z, Yuan J, Liu Q, Deng F, Yang H, Ling Y, Xie X, Lin X, Lin T, Chen J, Wei X, Luo K, Fu J, Wen J. Evolution of genome and immunogenome in esophageal squamous cell carcinomas driven by neoadjuvant chemoradiotherapy. Int J Cancer 2024;155:2021-2035. [PMID: 39081132 DOI: 10.1002/ijc.35118] [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: 03/25/2024] [Revised: 06/26/2024] [Accepted: 07/05/2024] [Indexed: 10/04/2024]
98
Lukose G, Al Assaad M, Driskill JH, Levine MF, Gundem G, Semaan A, Wilkes DC, Spigland NA, Medina-Martínez JS, Sboner A, Elemento O, Jessurun J, Mosquera JM. Whole genome profiling of rare pediatric thoracic tumors elucidates a YAP1::LEUTX fusion in an unclassified biphasic embryonal neoplasm. Pathol Res Pract 2024;264:155726. [PMID: 39566337 DOI: 10.1016/j.prp.2024.155726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2024] [Accepted: 11/13/2024] [Indexed: 11/22/2024]
99
Deng X, Xiang K, He X, Chen S, Guo Q, Wu H, Liu X, Wen Q, Yang H. Good response of stage IV melanoma to high‑dose radiation therapy combined with immunotherapy: A case report. Oncol Lett 2024;28:598. [PMID: 39493434 PMCID: PMC11529377 DOI: 10.3892/ol.2024.14731] [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: 01/15/2024] [Accepted: 08/22/2024] [Indexed: 11/05/2024]  Open
100
Pfeifer GP, Jin SG. Methods and applications of genome-wide profiling of DNA damage and rare mutations. Nat Rev Genet 2024;25:846-863. [PMID: 38918545 PMCID: PMC11563917 DOI: 10.1038/s41576-024-00748-4] [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] [Accepted: 05/21/2024] [Indexed: 06/27/2024]
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