Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig
DC Field | Value | Language |
---|---|---|
dc.contributor.author | Rubanova, Y. | - |
dc.contributor.author | Shi, R. | - |
dc.contributor.author | Harrigan, C.F. | - |
dc.contributor.author | Li, R. | - |
dc.contributor.author | Wintersinger, J. | - |
dc.contributor.author | Sahin, N. | - |
dc.contributor.author | Deshwar, A. | - |
dc.contributor.author | Dentro, S.C. | - |
dc.contributor.author | Leshchiner, I. | - |
dc.contributor.author | Gerstung, M. | - |
dc.contributor.author | Jolly, C. | - |
dc.contributor.author | Haase, K. | - |
dc.contributor.author | Tarabichi, M. | - |
dc.contributor.author | Wintersinger, J. | - |
dc.contributor.author | Deshwar, A.G. | - |
dc.contributor.author | Yu, K. | - |
dc.contributor.author | Gonzalez, S. | - |
dc.contributor.author | Rubanova, Y. | - |
dc.contributor.author | Macintyre, G. | - |
dc.contributor.author | Adams, D.J. | - |
dc.contributor.author | Anur, P. | - |
dc.contributor.author | Beroukhim, R. | - |
dc.contributor.author | Boutros, P.C. | - |
dc.contributor.author | Bowtell, D.D. | - |
dc.contributor.author | Campbell, P.J. | - |
dc.contributor.author | Cao, S. | - |
dc.contributor.author | Christie, E.L. | - |
dc.contributor.author | Cmero, M. | - |
dc.contributor.author | Cun, Y. | - |
dc.contributor.author | Dawson, K.J. | - |
dc.contributor.author | Demeulemeester, J. | - |
dc.contributor.author | Donmez, N. | - |
dc.contributor.author | Drews, R.M. | - |
dc.contributor.author | Eils, R. | - |
dc.contributor.author | Fan, Y. | - |
dc.contributor.author | Fittall, M. | - |
dc.contributor.author | Garsed, D.W. | - |
dc.contributor.author | Getz, G. | - |
dc.contributor.author | Ha, G. | - |
dc.contributor.author | Imielinski, M. | - |
dc.contributor.author | Jerman, L. | - |
dc.contributor.author | Ji, Y. | - |
dc.contributor.author | Kleinheinz, K. | - |
dc.contributor.author | Lee, J. | - |
dc.contributor.author | Lee-Six, H. | - |
dc.contributor.author | Livitz, D.G. | - |
dc.contributor.author | Malikic, S. | - |
dc.contributor.author | Markowetz, F. | - |
dc.contributor.author | Martincorena, I. | - |
dc.contributor.author | Mitchell, T.J. | - |
dc.contributor.author | Mustonen, V. | - |
dc.contributor.author | Oesper, L. | - |
dc.contributor.author | Peifer, M. | - |
dc.contributor.author | Peto, M. | - |
dc.contributor.author | Raphael, B.J. | - |
dc.contributor.author | Rosebrock, D. | - |
dc.contributor.author | Sahinalp, S.C. | - |
dc.contributor.author | Salcedo, A. | - |
dc.contributor.author | Schlesner, M. | - |
dc.contributor.author | Schumacher, S. | - |
dc.contributor.author | Sengupta, S. | - |
dc.contributor.author | Shi, R. | - |
dc.contributor.author | Shin, S.J. | - |
dc.contributor.author | Spiro, O. | - |
dc.contributor.author | Stein, L.D. | - |
dc.contributor.author | Vázquez-García, I. | - |
dc.contributor.author | Vembu, S. | - |
dc.contributor.author | Wheeler, D.A. | - |
dc.contributor.author | Yang, T.-P. | - |
dc.contributor.author | Yao, X. | - |
dc.contributor.author | Yuan, K. | - |
dc.contributor.author | Zhu, H. | - |
dc.contributor.author | Wang, W. | - |
dc.contributor.author | Morris, Q.D. | - |
dc.contributor.author | Spellman, P.T. | - |
dc.contributor.author | Wedge, D.C. | - |
dc.contributor.author | Van, Loo P. | - |
dc.contributor.author | Morris, Q. | - |
dc.contributor.author | PCAWG Evolution and Heterogeneity Working Group | - |
dc.contributor.author | PCAWG Consortium | - |
dc.date.accessioned | 2021-08-31T19:29:03Z | - |
dc.date.available | 2021-08-31T19:29:03Z | - |
dc.date.created | 2021-06-17 | - |
dc.date.issued | 2020 | - |
dc.identifier.issn | 2041-1723 | - |
dc.identifier.uri | https://scholar.korea.ac.kr/handle/2021.sw.korea/60800 | - |
dc.description.abstract | The type and genomic context of cancer mutations depend on their causes. These causes have been characterized using signatures that represent mutation types that co-occur in the same tumours. However, it remains unclear how mutation processes change during cancer evolution due to the lack of reliable methods to reconstruct evolutionary trajectories of mutational signature activity. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole-genome sequencing data from 2658 cancers across 38 tumour types, we present TrackSig, a new method that reconstructs these trajectories using optimal, joint segmentation and deconvolution of mutation type and allele frequencies from a single tumour sample. In simulations, we find TrackSig has a 3–5% activity reconstruction error, and 12% false detection rate. It outperforms an aggressive baseline in situations with branching evolution, CNA gain, and neutral mutations. Applied to data from 2658 tumours and 38 cancer types, TrackSig permits pan-cancer insight into evolutionary changes in mutational processes. © 2020, The Author(s). | - |
dc.language | English | - |
dc.language.iso | en | - |
dc.publisher | Nature Research | - |
dc.subject | cancer | - |
dc.subject | genomics | - |
dc.subject | mutation | - |
dc.subject | reconstruction | - |
dc.subject | trajectory | - |
dc.subject | allele | - |
dc.subject | analytical error | - |
dc.subject | Article | - |
dc.subject | cancer classification | - |
dc.subject | cancer genetics | - |
dc.subject | cancer tissue | - |
dc.subject | controlled study | - |
dc.subject | data analysis | - |
dc.subject | false positive result | - |
dc.subject | gene frequency | - |
dc.subject | gene mutation | - |
dc.subject | genome analysis | - |
dc.subject | human | - |
dc.subject | malignant neoplasm | - |
dc.subject | simulation | - |
dc.subject | whole genome sequencing | - |
dc.subject | biology | - |
dc.subject | computer simulation | - |
dc.subject | genetics | - |
dc.subject | human genome | - |
dc.subject | molecular evolution | - |
dc.subject | mutation | - |
dc.subject | neoplasm | - |
dc.subject | pathology | - |
dc.subject | procedures | - |
dc.subject | single nucleotide polymorphism | - |
dc.subject | Computational Biology | - |
dc.subject | Computer Simulation | - |
dc.subject | Evolution, Molecular | - |
dc.subject | Gene Frequency | - |
dc.subject | Genome, Human | - |
dc.subject | Humans | - |
dc.subject | Mutation | - |
dc.subject | Neoplasms | - |
dc.subject | Polymorphism, Single Nucleotide | - |
dc.subject | Whole Genome Sequencing | - |
dc.title | Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig | - |
dc.type | Article | - |
dc.contributor.affiliatedAuthor | Shin, S.J. | - |
dc.identifier.doi | 10.1038/s41467-020-14352-7 | - |
dc.identifier.scopusid | 2-s2.0-85079071600 | - |
dc.identifier.bibliographicCitation | Nature Communications, v.11, no.1 | - |
dc.relation.isPartOf | Nature Communications | - |
dc.citation.title | Nature Communications | - |
dc.citation.volume | 11 | - |
dc.citation.number | 1 | - |
dc.type.rims | ART | - |
dc.type.docType | Article | - |
dc.description.journalClass | 1 | - |
dc.description.journalRegisteredClass | scie | - |
dc.description.journalRegisteredClass | scopus | - |
dc.subject.keywordPlus | cancer | - |
dc.subject.keywordPlus | genomics | - |
dc.subject.keywordPlus | mutation | - |
dc.subject.keywordPlus | reconstruction | - |
dc.subject.keywordPlus | trajectory | - |
dc.subject.keywordPlus | allele | - |
dc.subject.keywordPlus | analytical error | - |
dc.subject.keywordPlus | Article | - |
dc.subject.keywordPlus | cancer classification | - |
dc.subject.keywordPlus | cancer genetics | - |
dc.subject.keywordPlus | cancer tissue | - |
dc.subject.keywordPlus | controlled study | - |
dc.subject.keywordPlus | data analysis | - |
dc.subject.keywordPlus | false positive result | - |
dc.subject.keywordPlus | gene frequency | - |
dc.subject.keywordPlus | gene mutation | - |
dc.subject.keywordPlus | genome analysis | - |
dc.subject.keywordPlus | human | - |
dc.subject.keywordPlus | malignant neoplasm | - |
dc.subject.keywordPlus | simulation | - |
dc.subject.keywordPlus | whole genome sequencing | - |
dc.subject.keywordPlus | biology | - |
dc.subject.keywordPlus | computer simulation | - |
dc.subject.keywordPlus | genetics | - |
dc.subject.keywordPlus | human genome | - |
dc.subject.keywordPlus | molecular evolution | - |
dc.subject.keywordPlus | mutation | - |
dc.subject.keywordPlus | neoplasm | - |
dc.subject.keywordPlus | pathology | - |
dc.subject.keywordPlus | procedures | - |
dc.subject.keywordPlus | single nucleotide polymorphism | - |
dc.subject.keywordPlus | Computational Biology | - |
dc.subject.keywordPlus | Computer Simulation | - |
dc.subject.keywordPlus | Evolution, Molecular | - |
dc.subject.keywordPlus | Gene Frequency | - |
dc.subject.keywordPlus | Genome, Human | - |
dc.subject.keywordPlus | Humans | - |
dc.subject.keywordPlus | Mutation | - |
dc.subject.keywordPlus | Neoplasms | - |
dc.subject.keywordPlus | Polymorphism, Single Nucleotide | - |
dc.subject.keywordPlus | Whole Genome Sequencing | - |
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