Mutational signatures of colorectal cancers according to distinct computational workflows

Abstract Tumor mutational signatures have gained prominence in cancer research, yet the lack of standardized methods hinders reproducibility and robustness. Leveraging colorectal cancer (CRC) as a model, we explored the influence of computational parameters on mutational signature analyses across 23...

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Published in:	Briefings in bioinformatics Vol. 25; no. 4
Main Authors:	Battuello, Paolo, Corti, Giorgio, Bartolini, Alice, Lorenzato, Annalisa, Sogari, Alberto, Russo, Mariangela, Di Nicolantonio, Federica, Bardelli, Alberto, Crisafulli, Giovanni
Format:	Journal Article
Language:	English
Published:	England Oxford University Press 23.05.2024 Oxford Publishing Limited (England)
Subjects:	Algorithms Cancer Cell Line, Tumor Colorectal cancer Colorectal carcinoma Colorectal Neoplasms - genetics Colorectal Neoplasms - pathology Computational Biology - methods Computer applications Datasets Endometrial cancer Exome Sequencing - methods Female Gene sequencing Genomic analysis Humans Impact analysis Lung cancer Mismatch repair Mutation Organoids Precision medicine Signature analysis Signatures Software Statistical analysis Uterine cancer Whole genome sequencing Workflow computational biology precision oncology colorectal cancer benchmarking mutational signatures bioinformatics genomics
ISSN:	1467-5463, 1477-4054, 1477-4054
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Abstract	Abstract Tumor mutational signatures have gained prominence in cancer research, yet the lack of standardized methods hinders reproducibility and robustness. Leveraging colorectal cancer (CRC) as a model, we explored the influence of computational parameters on mutational signature analyses across 230 CRC cell lines and 152 CRC patients. Results were validated in three independent datasets: 483 endometrial cancer patients stratified by mismatch repair (MMR) status, 35 lung cancer patients by smoking status and 12 patient-derived organoids (PDOs) annotated for colibactin exposure. Assessing various bioinformatic tools, reference datasets and input data sizes including whole genome sequencing, whole exome sequencing and a pan-cancer gene panel, we demonstrated significant variability in the results. We report that the use of distinct algorithms and references led to statistically different results, highlighting how arbitrary choices may induce variability in the mutational signature contributions. Furthermore, we found a differential contribution of mutational signatures between coding and intergenic regions and defined the minimum number of somatic variants required for reliable mutational signature assignment. To facilitate the identification of the most suitable workflows, we developed Comparative Mutational Signature analysis on Coding and Extragenic Regions (CoMSCER), a bioinformatic tool which allows researchers to easily perform comparative mutational signature analysis by coupling the results from several tools and public reference datasets and to assess mutational signature contributions in coding and non-coding genomic regions. In conclusion, our study provides a comparative framework to elucidate the impact of distinct computational workflows on mutational signatures.
AbstractList	Abstract Tumor mutational signatures have gained prominence in cancer research, yet the lack of standardized methods hinders reproducibility and robustness. Leveraging colorectal cancer (CRC) as a model, we explored the influence of computational parameters on mutational signature analyses across 230 CRC cell lines and 152 CRC patients. Results were validated in three independent datasets: 483 endometrial cancer patients stratified by mismatch repair (MMR) status, 35 lung cancer patients by smoking status and 12 patient-derived organoids (PDOs) annotated for colibactin exposure. Assessing various bioinformatic tools, reference datasets and input data sizes including whole genome sequencing, whole exome sequencing and a pan-cancer gene panel, we demonstrated significant variability in the results. We report that the use of distinct algorithms and references led to statistically different results, highlighting how arbitrary choices may induce variability in the mutational signature contributions. Furthermore, we found a differential contribution of mutational signatures between coding and intergenic regions and defined the minimum number of somatic variants required for reliable mutational signature assignment. To facilitate the identification of the most suitable workflows, we developed Comparative Mutational Signature analysis on Coding and Extragenic Regions (CoMSCER), a bioinformatic tool which allows researchers to easily perform comparative mutational signature analysis by coupling the results from several tools and public reference datasets and to assess mutational signature contributions in coding and non-coding genomic regions. In conclusion, our study provides a comparative framework to elucidate the impact of distinct computational workflows on mutational signatures. Tumor mutational signatures have gained prominence in cancer research, yet the lack of standardized methods hinders reproducibility and robustness. Leveraging colorectal cancer (CRC) as a model, we explored the influence of computational parameters on mutational signature analyses across 230 CRC cell lines and 152 CRC patients. Results were validated in three independent datasets: 483 endometrial cancer patients stratified by mismatch repair (MMR) status, 35 lung cancer patients by smoking status and 12 patient-derived organoids (PDOs) annotated for colibactin exposure. Assessing various bioinformatic tools, reference datasets and input data sizes including whole genome sequencing, whole exome sequencing and a pan-cancer gene panel, we demonstrated significant variability in the results. We report that the use of distinct algorithms and references led to statistically different results, highlighting how arbitrary choices may induce variability in the mutational signature contributions. Furthermore, we found a differential contribution of mutational signatures between coding and intergenic regions and defined the minimum number of somatic variants required for reliable mutational signature assignment. To facilitate the identification of the most suitable workflows, we developed Comparative Mutational Signature analysis on Coding and Extragenic Regions (CoMSCER), a bioinformatic tool which allows researchers to easily perform comparative mutational signature analysis by coupling the results from several tools and public reference datasets and to assess mutational signature contributions in coding and non-coding genomic regions. In conclusion, our study provides a comparative framework to elucidate the impact of distinct computational workflows on mutational signatures. Tumor mutational signatures have gained prominence in cancer research, yet the lack of standardized methods hinders reproducibility and robustness. Leveraging colorectal cancer (CRC) as a model, we explored the influence of computational parameters on mutational signature analyses across 230 CRC cell lines and 152 CRC patients. Results were validated in three independent datasets: 483 endometrial cancer patients stratified by mismatch repair (MMR) status, 35 lung cancer patients by smoking status and 12 patient-derived organoids (PDOs) annotated for colibactin exposure. Assessing various bioinformatic tools, reference datasets and input data sizes including whole genome sequencing, whole exome sequencing and a pan-cancer gene panel, we demonstrated significant variability in the results. We report that the use of distinct algorithms and references led to statistically different results, highlighting how arbitrary choices may induce variability in the mutational signature contributions. Furthermore, we found a differential contribution of mutational signatures between coding and intergenic regions and defined the minimum number of somatic variants required for reliable mutational signature assignment. To facilitate the identification of the most suitable workflows, we developed Comparative Mutational Signature analysis on Coding and Extragenic Regions (CoMSCER), a bioinformatic tool which allows researchers to easily perform comparative mutational signature analysis by coupling the results from several tools and public reference datasets and to assess mutational signature contributions in coding and non-coding genomic regions. In conclusion, our study provides a comparative framework to elucidate the impact of distinct computational workflows on mutational signatures.Tumor mutational signatures have gained prominence in cancer research, yet the lack of standardized methods hinders reproducibility and robustness. Leveraging colorectal cancer (CRC) as a model, we explored the influence of computational parameters on mutational signature analyses across 230 CRC cell lines and 152 CRC patients. Results were validated in three independent datasets: 483 endometrial cancer patients stratified by mismatch repair (MMR) status, 35 lung cancer patients by smoking status and 12 patient-derived organoids (PDOs) annotated for colibactin exposure. Assessing various bioinformatic tools, reference datasets and input data sizes including whole genome sequencing, whole exome sequencing and a pan-cancer gene panel, we demonstrated significant variability in the results. We report that the use of distinct algorithms and references led to statistically different results, highlighting how arbitrary choices may induce variability in the mutational signature contributions. Furthermore, we found a differential contribution of mutational signatures between coding and intergenic regions and defined the minimum number of somatic variants required for reliable mutational signature assignment. To facilitate the identification of the most suitable workflows, we developed Comparative Mutational Signature analysis on Coding and Extragenic Regions (CoMSCER), a bioinformatic tool which allows researchers to easily perform comparative mutational signature analysis by coupling the results from several tools and public reference datasets and to assess mutational signature contributions in coding and non-coding genomic regions. In conclusion, our study provides a comparative framework to elucidate the impact of distinct computational workflows on mutational signatures.
Author	Corti, Giorgio Di Nicolantonio, Federica Bardelli, Alberto Sogari, Alberto Russo, Mariangela Battuello, Paolo Lorenzato, Annalisa Crisafulli, Giovanni Bartolini, Alice
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Cites_doi	10.1093/bioinformatics/btad756 10.1371/journal.pone.0221235 10.1016/j.gde.2013.11.014 10.1038/s41586-020-1943-3 10.1038/s41586-022-04738-6 10.1200/JCO.21.01015 10.1158/1078-0432.CCR-22-0875 10.1016/S1470-2045(22)00197-8 10.1002/ijc.31878 10.1038/s41586-020-2080-8 10.1038/s41408-019-0221-9 10.1038/s41467-019-11037-8 10.1038/s41575-019-0126-x 10.1038/s43018-020-0027-5 10.1016/j.clcc.2019.02.008 10.1126/sciadv.abg4398 10.1186/s13059-016-0893-4 10.1056/NEJMc2031965 10.1056/NEJMoa2017699 10.1038/ncomms8002 10.1038/ng.2764 10.1038/s41559-021-01470-8 10.1093/nar/gky1015 10.1186/s13073-019-0654-6 10.1016/j.cell.2019.03.001 10.1158/2159-8290.CD-21-1434 10.1038/s43018-021-00230-8 10.1158/1078-0432.CCR-18-3440 10.1093/bioinformatics/btp324 10.1038/nrc.2016.126 10.1186/s13073-018-0539-0 10.1016/j.cell.2012.04.024 10.1136/gutjnl-2019-320462 10.1136/esmoopen-2019-000572 10.1016/j.xgen.2022.100179 10.1093/bioinformatics/btp352 10.1038/ng.2503 10.3389/fgene.2022.987205 10.1038/nrm1907 10.1016/j.dnarep.2020.102827 10.1038/s41568-021-00377-7 10.1038/nature12477 10.1016/j.semcancer.2021.04.007 10.1038/nm.4292 10.1016/j.cell.2019.02.012 10.1158/1078-0432.CCR-11-1469
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References	Cancer Genome Atlas Research N (2024052406004550700_ref32) 2013; 45 Maura (2024052406004550700_ref10) 2019; 10 Diaz-Gay (2024052406004550700_ref41) 2023; 39 Steele (2024052406004550700_ref9) 2022; 606 Woolston (2024052406004550700_ref26) 2021; 5 Palles (2024052406004550700_ref20) 2013; 45 Nik-Zainal (2024052406004550700_ref6) 2012; 149 Petljak (2024052406004550700_ref11) 2019; 176 Dienstmann (2024052406004550700_ref21) 2017; 17 Yang (2024052406004550700_ref24) 2021; 2 Lazzari (2024052406004550700_ref28) 2019; 25 Koh (2024052406004550700_ref2) 2021; 21 Nemeth (2024052406004550700_ref44) 2020; 89 Diaz (2024052406004550700_ref18) 2022; 23 Kim (2024052406004550700_ref43) 2022; 13 Jiricny (2024052406004550700_ref12) 2006; 7 Medico (2024052406004550700_ref29) 2015; 6 Corti (2024052406004550700_ref34) 2019; 18 Sinicrope (2024052406004550700_ref13) 2012; 18 Li (2024052406004550700_ref37) 2009; 25 Kucab (2024052406004550700_ref3) 2019; 177 Buchhalter (2024052406004550700_ref27) 2019; 144 Fang (2024052406004550700_ref45) 2021; 7 Crisafulli (2024052406004550700_ref35) 2019; 4 Blokzijl (2024052406004550700_ref38) 2018; 10 Andre (2024052406004550700_ref17) 2020; 383 Georgeson (2024052406004550700_ref46) 2021; 70 Ganesh (2024052406004550700_ref15) 2019; 16 Crisafulli (2024052406004550700_ref22) 2022; 12 Davies (2024052406004550700_ref25) 2017; 23 Tate (2024052406004550700_ref7) 2019; 47 Alexandrov (2024052406004550700_ref4) 2014; 24 Islam (2024052406004550700_ref42) 2022; 2 Pleguezuelos-Manzano (2024052406004550700_ref33) 2020; 580 Durinikova (2024052406004550700_ref30) 2022; 28 Hoang (2024052406004550700_ref23) 2019; 9 Lenz (2024052406004550700_ref19) 2022; 40 Alexandrov (2024052406004550700_ref1) 2013; 500 Andrei (2024052406004550700_ref14) 2022; 84 Rosenthal (2024052406004550700_ref39) 2016; 17 Omichessan (2024052406004550700_ref5) 2019; 14 Rousseau (2024052406004550700_ref16) 2021; 384 Li (2024052406004550700_ref36) 2009; 25 Degasperi (2024052406004550700_ref40) 2020; 1 Alexandrov (2024052406004550700_ref8) 2020; 578 Rospo (2024052406004550700_ref31) 2019; 11
References_xml	– volume: 39 issue: 12 year: 2023 ident: 2024052406004550700_ref41 article-title: Assigning mutational signatures to individual samples and individual somatic mutations with SigProfilerAssignment publication-title: Bioinformatics doi: 10.1093/bioinformatics/btad756 – volume: 14 issue: 9 year: 2019 ident: 2024052406004550700_ref5 article-title: Computational tools to detect signatures of mutational processes in DNA from tumours: a review and empirical comparison of performance publication-title: PloS One doi: 10.1371/journal.pone.0221235 – volume: 24 start-page: 52 issue: 100 year: 2014 ident: 2024052406004550700_ref4 article-title: Mutational signatures: the patterns of somatic mutations hidden in cancer genomes publication-title: Curr Opin Genet Dev doi: 10.1016/j.gde.2013.11.014 – volume: 578 start-page: 94 issue: 7793 year: 2020 ident: 2024052406004550700_ref8 article-title: The repertoire of mutational signatures in human cancer publication-title: Nature doi: 10.1038/s41586-020-1943-3 – volume: 606 start-page: 984 issue: 7916 year: 2022 ident: 2024052406004550700_ref9 article-title: Signatures of copy number alterations in human cancer publication-title: Nature doi: 10.1038/s41586-022-04738-6 – volume: 40 start-page: 161 issue: 2 year: 2022 ident: 2024052406004550700_ref19 article-title: First-line Nivolumab plus low-dose Ipilimumab for microsatellite instability-high/mismatch repair-deficient metastatic colorectal cancer: the phase II CheckMate 142 study publication-title: J Clin Oncol doi: 10.1200/JCO.21.01015 – volume: 28 start-page: 3874 issue: 17 year: 2022 ident: 2024052406004550700_ref30 article-title: Targeting the DNA damage response pathways and replication stress in colorectal cancer publication-title: Clin Cancer Res doi: 10.1158/1078-0432.CCR-22-0875 – volume: 23 start-page: 659 issue: 5 year: 2022 ident: 2024052406004550700_ref18 article-title: Pembrolizumab versus chemotherapy for microsatellite instability-high or mismatch repair-deficient metastatic colorectal cancer (KEYNOTE-177): final analysis of a randomised, open-label, phase 3 study publication-title: Lancet Oncol doi: 10.1016/S1470-2045(22)00197-8 – volume: 144 start-page: 848 issue: 4 year: 2019 ident: 2024052406004550700_ref27 article-title: Size matters: dissecting key parameters for panel-based tumor mutational burden analysis publication-title: Int J Cancer doi: 10.1002/ijc.31878 – volume: 580 start-page: 269 issue: 7802 year: 2020 ident: 2024052406004550700_ref33 article-title: Mutational signature in colorectal cancer caused by genotoxic pks(+) E. Coli publication-title: Nature doi: 10.1038/s41586-020-2080-8 – volume: 9 start-page: 60 issue: 8 year: 2019 ident: 2024052406004550700_ref23 article-title: Mutational processes contributing to the development of multiple myeloma publication-title: Blood Cancer J doi: 10.1038/s41408-019-0221-9 – volume: 10 start-page: 2969 issue: 1 year: 2019 ident: 2024052406004550700_ref10 article-title: A practical guide for mutational signature analysis in hematological malignancies publication-title: Nat Commun doi: 10.1038/s41467-019-11037-8 – volume: 16 start-page: 361 issue: 6 year: 2019 ident: 2024052406004550700_ref15 article-title: Immunotherapy in colorectal cancer: rationale, challenges and potential publication-title: Nat Rev Gastroenterol Hepatol doi: 10.1038/s41575-019-0126-x – volume: 1 start-page: 249 issue: 2 year: 2020 ident: 2024052406004550700_ref40 article-title: A practical framework and online tool for mutational signature analyses show inter-tissue variation and driver dependencies publication-title: Nat Cancer doi: 10.1038/s43018-020-0027-5 – volume: 18 start-page: 91 issue: 2 year: 2019 ident: 2024052406004550700_ref34 article-title: A genomic analysis workflow for colorectal cancer precision oncology publication-title: Clin Colorectal Cancer doi: 10.1016/j.clcc.2019.02.008 – volume: 7 start-page: eabg4398 issue: 45 year: 2021 ident: 2024052406004550700_ref45 article-title: Deficiency of replication-independent DNA mismatch repair drives a 5-methylcytosine deamination mutational signature in cancer publication-title: Sci Adv doi: 10.1126/sciadv.abg4398 – volume: 17 start-page: 31 year: 2016 ident: 2024052406004550700_ref39 article-title: DeconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution publication-title: Genome Biol doi: 10.1186/s13059-016-0893-4 – volume: 384 start-page: 1168 issue: 12 year: 2021 ident: 2024052406004550700_ref16 article-title: The Spectrum of benefit from checkpoint blockade in Hypermutated Tumors publication-title: N Engl J Med doi: 10.1056/NEJMc2031965 – volume: 383 start-page: 2207 issue: 23 year: 2020 ident: 2024052406004550700_ref17 article-title: Pembrolizumab in microsatellite-instability-high advanced colorectal cancer publication-title: N Engl J Med doi: 10.1056/NEJMoa2017699 – volume: 6 start-page: 7002 year: 2015 ident: 2024052406004550700_ref29 article-title: The molecular landscape of colorectal cancer cell lines unveils clinically actionable kinase targets publication-title: Nat Commun doi: 10.1038/ncomms8002 – volume: 45 start-page: 1113 issue: 10 year: 2013 ident: 2024052406004550700_ref32 article-title: The cancer genome atlas Pan-cancer analysis project publication-title: Nat Genet doi: 10.1038/ng.2764 – volume: 5 start-page: 1024 issue: 7 year: 2021 ident: 2024052406004550700_ref26 article-title: Mutational signatures impact the evolution of anti-EGFR antibody resistance in colorectal cancer publication-title: Nat Ecol Evol doi: 10.1038/s41559-021-01470-8 – volume: 47 start-page: D941 issue: D1 year: 2019 ident: 2024052406004550700_ref7 article-title: COSMIC: the catalogue of somatic mutations In cancer publication-title: Nucleic Acids Res doi: 10.1093/nar/gky1015 – volume: 11 start-page: 42 issue: 1 year: 2019 ident: 2024052406004550700_ref31 article-title: Evolving neoantigen profiles in colorectal cancers with DNA repair defects publication-title: Genome Med doi: 10.1186/s13073-019-0654-6 – volume: 177 start-page: 821 issue: 4 year: 2019 ident: 2024052406004550700_ref3 article-title: A compendium of mutational signatures of environmental agents publication-title: Cell doi: 10.1016/j.cell.2019.03.001 – volume: 12 start-page: 1656 issue: 7 year: 2022 ident: 2024052406004550700_ref22 article-title: Temozolomide treatment alters mismatch repair and boosts mutational burden in tumor and blood of colorectal cancer patients publication-title: Cancer Discov doi: 10.1158/2159-8290.CD-21-1434 – volume: 2 start-page: 819 issue: 8 year: 2021 ident: 2024052406004550700_ref24 article-title: Chemotherapy and mismatch repair deficiency cooperate to fuel TP53 mutagenesis and ALL relapse publication-title: Nat Cancer doi: 10.1038/s43018-021-00230-8 – volume: 25 start-page: 6243 issue: 20 year: 2019 ident: 2024052406004550700_ref28 article-title: Patient-derived xenografts and matched cell lines identify Pharmacogenomic vulnerabilities in colorectal cancer publication-title: Clin Cancer Res doi: 10.1158/1078-0432.CCR-18-3440 – volume: 25 start-page: 1754 issue: 14 year: 2009 ident: 2024052406004550700_ref36 article-title: Fast and accurate short read alignment with burrows-wheeler transform publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp324 – volume: 17 start-page: 79 issue: 2 year: 2017 ident: 2024052406004550700_ref21 article-title: Consensus molecular subtypes and the evolution of precision medicine in colorectal cancer publication-title: Nat Rev Cancer doi: 10.1038/nrc.2016.126 – volume: 10 start-page: 33 issue: 1 year: 2018 ident: 2024052406004550700_ref38 article-title: MutationalPatterns: comprehensive genome-wide analysis of mutational processes publication-title: Genome Med doi: 10.1186/s13073-018-0539-0 – volume: 149 start-page: 979 issue: 5 year: 2012 ident: 2024052406004550700_ref6 article-title: Mutational processes molding the genomes of 21 breast cancers publication-title: Cell doi: 10.1016/j.cell.2012.04.024 – volume: 70 start-page: 2138 issue: 11 year: 2021 ident: 2024052406004550700_ref46 article-title: Evaluating the utility of tumour mutational signatures for identifying hereditary colorectal cancer and polyposis syndrome carriers publication-title: Gut doi: 10.1136/gutjnl-2019-320462 – volume: 4 start-page: e000572 year: 2019 ident: 2024052406004550700_ref35 article-title: Whole exome sequencing analysis of urine trans-renal tumour DNA in metastatic colorectal cancer patients publication-title: ESMO Open doi: 10.1136/esmoopen-2019-000572 – volume: 2 start-page: 100179 issue: 11 year: 2022 ident: 2024052406004550700_ref42 article-title: Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor publication-title: Cell Genom doi: 10.1016/j.xgen.2022.100179 – volume: 25 start-page: 2078 issue: 16 year: 2009 ident: 2024052406004550700_ref37 article-title: The sequence alignment/map format and SAMtools publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp352 – volume: 45 start-page: 136 issue: 2 year: 2013 ident: 2024052406004550700_ref20 article-title: Germline mutations affecting the proofreading domains of POLE and POLD1 predispose to colorectal adenomas and carcinomas publication-title: Nat Genet doi: 10.1038/ng.2503 – volume: 13 start-page: 987205 year: 2022 ident: 2024052406004550700_ref43 article-title: Two subtypes of cutaneous melanoma with distinct mutational signatures and clinico-genomic characteristics publication-title: Front Genet doi: 10.3389/fgene.2022.987205 – volume: 7 start-page: 335 issue: 5 year: 2006 ident: 2024052406004550700_ref12 article-title: The multifaceted mismatch-repair system publication-title: Nat Rev Mol Cell Biol doi: 10.1038/nrm1907 – volume: 89 start-page: 102827 year: 2020 ident: 2024052406004550700_ref44 article-title: Two main mutational processes operate in the absence of DNA mismatch repair publication-title: DNA Repair (Amst) doi: 10.1016/j.dnarep.2020.102827 – volume: 21 start-page: 619 issue: 10 year: 2021 ident: 2024052406004550700_ref2 article-title: Mutational signatures: emerging concepts, caveats and clinical applications publication-title: Nat Rev Cancer doi: 10.1038/s41568-021-00377-7 – volume: 500 start-page: 415 issue: 7463 year: 2013 ident: 2024052406004550700_ref1 article-title: Signatures of mutational processes in human cancer publication-title: Nature doi: 10.1038/nature12477 – volume: 84 start-page: 199 year: 2022 ident: 2024052406004550700_ref14 article-title: Integrated approaches for precision oncology in colorectal cancer: the more you know, the better publication-title: Semin Cancer Biol doi: 10.1016/j.semcancer.2021.04.007 – volume: 23 start-page: 517 issue: 4 year: 2017 ident: 2024052406004550700_ref25 article-title: HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures publication-title: Nat Med doi: 10.1038/nm.4292 – volume: 176 start-page: 1282 issue: 6 year: 2019 ident: 2024052406004550700_ref11 article-title: Characterizing mutational signatures in human cancer cell lines reveals episodic APOBEC mutagenesis publication-title: Cell doi: 10.1016/j.cell.2019.02.012 – volume: 18 start-page: 1506 issue: 6 year: 2012 ident: 2024052406004550700_ref13 article-title: Molecular pathways: microsatellite instability in colorectal cancer: prognostic, predictive, and therapeutic implications publication-title: Clin Cancer Res doi: 10.1158/1078-0432.CCR-11-1469
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Snippet	Abstract Tumor mutational signatures have gained prominence in cancer research, yet the lack of standardized methods hinders reproducibility and robustness.... Tumor mutational signatures have gained prominence in cancer research, yet the lack of standardized methods hinders reproducibility and robustness. Leveraging...
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SubjectTerms	Algorithms Cancer Cell Line, Tumor Colorectal cancer Colorectal carcinoma Colorectal Neoplasms - genetics Colorectal Neoplasms - pathology Computational Biology - methods Computer applications Datasets Endometrial cancer Exome Sequencing - methods Female Gene sequencing Genomic analysis Humans Impact analysis Lung cancer Mismatch repair Mutation Organoids Precision medicine Signature analysis Signatures Software Statistical analysis Uterine cancer Whole genome sequencing Workflow
Title	Mutational signatures of colorectal cancers according to distinct computational workflows
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