Inferring structural variant cancer cell fraction
| Autor: | Cmero, Marek, Yuan, Ke, Ong, Cheng Soon, Schröder, Jan, Corcoran, Niall M., Papenfuss, Tony, Hovens, Christopher M., Markowetz, Florian, Macintyre, Geoff, Adams, David J., Anur, Pavana, Beroukhim, Rameen, Boutros, Paul C., Bowtell, David D. L., Campbell, Peter J., Cao, Shaolong, Christie, Elizabeth L., Cun, Yupeng, Dawson, Kevin J., Demeulemeester, Jonas, Dentro, Stefan C., Deshwar, Amit G., Donmez, Nilgun, Drews, Ruben M., Eils, Roland, Fan, Yu, Fittall, Matthew W., Garsed, Dale W., Gerstung, Moritz, Getz, Gad, Gonzalez, Santiago, Ha, Gavin, Haase, Kerstin, Imielinski, Marcin, Jerman, Lara, Ji, Yuan, Jolly, Clemency, Kleinheinz, Kortine, Lee, Juhee, Lee-Six, Henry, Leshchiner, Ignaty, Livitz, Dimitri, Malikic, Salem, Martincorena, Iñigo, Mitchell, Thomas J., Morris, Quaid D., Mustonen, Ville, Oesper, Layla, Peifer, Martin, Peto, Myron, Raphael, Benjamin J., Rosebrock, Daniel, Rubanova, Yulia, Sahinalp, S. Cenk, Salcedo, Adriana, Schlesner, Matthias, Schumacher, Steven E., Sengupta, Subhajit, Shi, Ruian, Shin, Seung Jun, Spellman, Paul T., Spiro, Oliver, Stein, Lincoln D., Tarabichi, Maxime, Van Loo, Peter, Vembu, Shankar, Vázquez-García, Ignacio, Wang, Wenyi, Wedge, David C., Wheeler, David A., Wintersinger, Jeffrey A., Yang, Tsun-Po, Yao, Xiaotong, Yu, Kaixian, Zhu, Hongtu |
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| Přispěvatelé: | Cmero, Marek [0000-0001-7783-5530], Yuan, Ke [0000-0002-2318-1460], Ong, Cheng Soon [0000-0002-2302-9733], Papenfuss, Tony [0000-0002-1102-8506], Markowetz, Florian [0000-0002-2784-5308], Macintyre, Geoff [0000-0003-3906-467X], Apollo - University of Cambridge Repository, Dentro, SC, Wedge, DC, Yang, T-P, Organismal and Evolutionary Biology Research Programme, Institute of Biotechnology, Bioinformatics, Department of Computer Science |
| Rok vydání: | 2020 |
| Předmět: |
Male
0301 basic medicine Medizin General Physics and Astronomy Somatic evolution in cancer Genome 0302 clinical medicine Gene Frequency Neoplasms 129 lcsh:Science Cancer Ovarian Neoplasms Women's cancers Radboud Institute for Molecular Life Sciences [Radboudumc 17] Multidisciplinary Manchester Cancer Research Centre Prostatic Neoplasms/genetics Liver Neoplasms 1184 Genetics developmental biology physiology Neoplasms/genetics Women's cancers Radboud Institute for Health Sciences [Radboudumc 17] Ovarian Cancer 3. Good health 030220 oncology & carcinogenesis 1181 Ecology evolutionary biology 139 Female Algorithms Human 631/67 DNA Copy Number Variations Science In silico Computational biology Biology Sensitivity and Specificity Article General Biochemistry Genetics and Molecular Biology Ovarian Neoplasms/genetics 03 medical and health sciences Rare Diseases Machine learning Genetics PCAWG Evolution and Heterogeneity Working Group medicine Humans Computer Simulation ddc:610 Liver Neoplasms/genetics Allele frequency Whole genome sequencing 45 Whole Genome Sequencing Genome Human ResearchInstitutes_Networks_Beacons/mcrc Human Genome Breakpoint Computational Biology Prostatic Neoplasms PCAWG Consortium General Chemistry Computational Biology/methods 631/114/1305 113 Computer and information sciences Pancreatic Neoplasms/genetics medicine.disease Computational biology and bioinformatics Pancreatic Neoplasms 030104 developmental biology lcsh:Q Human genome 631/114 119 Digestive Diseases |
| Zdroj: | Nature communications, vol 11, iss 1 Nature Communications Nature Communications, Vol 11, Iss 1, Pp 1-15 (2020) Nature Communications, 11 Nature Communications, 11, 1 Cmero, M, Yuan, K, Ong, C S, Schröder, J, Adams, D J, Anur, P, Beroukhim, R, Boutros, P C, Bowtell, D D L, Campbell, P J, Cao, S, Christie, E L, Cun, Y, Dawson, K J, Demeulemeester, J, Dentro, S C, Deshwar, A G, Donmez, N, Drews, R M, Eils, R, Fan, Y, Fittall, M W, Garsed, D W, Gerstung, M, Getz, G, Gonzalez, S, Ha, G, Haase, K, Imielinski, M, Jerman, L, Ji, Y, Jolly, C, Kleinheinz, K, Lee, J, Lee-Six, H, Leshchiner, I, Livitz, D, Malikic, S, Martincorena, I, Mitchell, T J, Morris, Q D, Mustonen, V, Oesper, L, Peifer, M, Peto, M, Raphael, B J, Rosebrock, D, Rubanova, Y, Sahinalp, S C, Salcedo, A, Schlesner, M, Schumacher, S E, Sengupta, S, Shi, R, Shin, S J, Spellman, P T, Spiro, O, Stein, L D, Tarabichi, M, Van Loo, P, Vembu, S, Vázquez-García, I, Wang, W, Wedge, D C, Wheeler, D A, Wintersinger, J A, Yang, T-P, Yao, X, Yu, K, Zhu, H, Corcoran, N M, Papenfuss, T, Hovens, C M, Markowetz, F & Macintyre, G 2020, ' Inferring structural variant cancer cell fraction ', Nature Communications, vol. 11, no. 1 . https://doi.org/10.1038/s41467-020-14351-8 |
| ISSN: | 2041-1723 |
| DOI: | 10.1038/s41467-020-14351-8 |
| Popis: | We present SVclone, a computational method for inferring the cancer cell fraction of structural variant (SV) breakpoints from whole-genome sequencing data. SVclone accurately determines the variant allele frequencies of both SV breakends, then simultaneously estimates the cancer cell fraction and SV copy number. We assess performance using in silico mixtures of real samples, at known proportions, created from two clonal metastases from the same patient. We find that SVclone’s performance is comparable to single-nucleotide variant-based methods, despite having an order of magnitude fewer data points. As part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) consortium, which aggregated whole-genome sequencing data from 2658 cancers across 38 tumour types, we use SVclone to reveal a subset of liver, ovarian and pancreatic cancers with subclonally enriched copy-number neutral rearrangements that show decreased overall survival. SVclone enables improved characterisation of SV intra-tumour heterogeneity. The authors present SVclone, a computational method for inferring the cancer cell fraction of structural variants from whole-genome sequencing data. |
| Databáze: | OpenAIRE |
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