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

Publikováno v: 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

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 simult

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0101d219e26fc7313f20519ac4e4dfc2
https://doi.org/10.1038/s41467-020-14351-8

Self-sustaining long-term 3D epithelioid cultures reveal drivers of clonal expansion in esophageal epithelium.

Autor: Herms A; Wellcome Sanger Institute, Hinxton, UK.; Department of Biomedical Sciences, Universitat de Barcelona, Barcelona, Spain.; Lipid Trafficking and Disease Group, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain., Fernandez-Antoran D; Wellcome Sanger Institute, Hinxton, UK.; Wellcome/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK.; ARAID Foundation, Aragón Health Research Institute (IIS Aragón), Zaragoza, Spain., Alcolea MP; Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK., Kalogeropoulou A; Wellcome Sanger Institute, Hinxton, UK., Banerjee U; Wellcome Sanger Institute, Hinxton, UK., Piedrafita G; Wellcome Sanger Institute, Hinxton, UK.; Department of Biochemistry and Molecular Biology, Complutense University of Madrid, Madrid, Spain.; Spanish National Cancer Research Centre (CNIO), Madrid, Spain., Abby E; Wellcome Sanger Institute, Hinxton, UK., Valverde-Lopez JA; Wellcome/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK., Ferreira IS; Wellcome/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK., Caseda I; Department of Biomedical Sciences, Universitat de Barcelona, Barcelona, Spain.; Lipid Trafficking and Disease Group, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain., Bejar MT; Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK., Dentro SC; Wellcome Sanger Institute, Hinxton, UK.; European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK.; Artificial Intelligence in Oncology (B450), Deutsches Krebsforschungszentrum, Heidelberg, Germany., Vidal-Notari S; Department of Biochemistry and Molecular Biology, Complutense University of Madrid, Madrid, Spain.; Spanish National Cancer Research Centre (CNIO), Madrid, Spain., Ong SH; Wellcome Sanger Institute, Hinxton, UK., Colom B; Wellcome Sanger Institute, Hinxton, UK.; Cambridge Institute of Science, Altos Labs, Cambridge, UK., Murai K; Wellcome Sanger Institute, Hinxton, UK., King C; Wellcome Sanger Institute, Hinxton, UK., Mahbubani K; Department of Surgery, University of Cambridge, Cambridge, UK.; Collaborative Biorepository for Translational Medicine (CBTM), Cambridge NIHR Biomedical Research Centre, Cambridge, UK., Saeb-Parsy K; Department of Surgery, University of Cambridge, Cambridge, UK.; Collaborative Biorepository for Translational Medicine (CBTM), Cambridge NIHR Biomedical Research Centre, Cambridge, UK., Lowe AR; Institute for Structural and Molecular Biology, University College London, London, UK.; Institute for the Physics of Living Systems, University College London, London, UK.; Department of Physics and Astronomy, University College London, London, UK., Gerstung M; European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK.; Artificial Intelligence in Oncology (B450), Deutsches Krebsforschungszentrum, Heidelberg, Germany., Jones PH; Wellcome Sanger Institute, Hinxton, UK. pj3@sanger.ac.uk.; Department of Oncology, Hutchison Research Centre, University of Cambridge, Cambridge, UK. pj3@sanger.ac.uk.

Publikováno v: Nature genetics [Nat Genet] 2024 Oct; Vol. 56 (10), pp. 2158-2173. Date of Electronic Publication: 2024 Sep 23.

Single-cell and spatial transcriptomics analysis of non-small cell lung cancer.

Autor: De Zuani M; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.; OpenTargets, Wellcome Genome Campus, Hinxton, UK.; Department of Haematology, University of Cambridge, Cambridge, UK.; Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK., Xue H; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.; OpenTargets, Wellcome Genome Campus, Hinxton, UK.; Department of Haematology, University of Cambridge, Cambridge, UK.; Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK., Park JS; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.; OpenTargets, Wellcome Genome Campus, Hinxton, UK.; European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Genome Campus, Hinxton, UK., Dentro SC; European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Genome Campus, Hinxton, UK.; Division of Artificial Intelligence in Oncology, DKFZ, Heidelberg, Germany., Seferbekova Z; European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Genome Campus, Hinxton, UK., Tessier J; Precision Medicine and Computational Biology, Sanofi, Cambridge, MA, USA., Curras-Alonso S; Precision Medicine and Computational Biology, Sanofi, Paris, France., Hadjipanayis A; Precision Medicine and Computational Biology, Sanofi, Cambridge, MA, USA., Athanasiadis EI; OpenTargets, Wellcome Genome Campus, Hinxton, UK.; Medical Image and Signal Processing Laboratory (MEDISP), Department of Biomedical Engineering, University of West Attica, Athens, Greece., Gerstung M; OpenTargets, Wellcome Genome Campus, Hinxton, UK.; European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Genome Campus, Hinxton, UK.; Division of Artificial Intelligence in Oncology, DKFZ, Heidelberg, Germany., Bayraktar O; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.; OpenTargets, Wellcome Genome Campus, Hinxton, UK., Cvejic A; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK. ana.cvejic@bric.ku.dk.; OpenTargets, Wellcome Genome Campus, Hinxton, UK. ana.cvejic@bric.ku.dk.; Department of Haematology, University of Cambridge, Cambridge, UK. ana.cvejic@bric.ku.dk.; Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark. ana.cvejic@bric.ku.dk.

Publikováno v: Nature communications [Nat Commun] 2024 May 23; Vol. 15 (1), pp. 4388. Date of Electronic Publication: 2024 May 23.

Author Correction: Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition.

Autor: Rodriguez-Martin B; Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.; Biomedical Research Centre (CINBIO), University of Vigo, Vigo, Spain.; Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain., Alvarez EG; Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.; Biomedical Research Centre (CINBIO), University of Vigo, Vigo, Spain.; Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain., Baez-Ortega A; Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK., Zamora J; Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.; Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain.; The Biomedical Research Centre (CINBIO), Universidade de Vigo, Vigo, Spain.; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK., Supek F; Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.; Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain., Demeulemeester J; The Francis Crick Institute, London, UK.; Department of Human Genetics, University of Leuven, Leuven, Belgium., Santamarina M; Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.; Biomedical Research Centre (CINBIO), University of Vigo, Vigo, Spain.; Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain., Ju YS; Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.; Cancer Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Cambridge, UK., Temes J; Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.; Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain., Garcia-Souto D; Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain., Detering H; Biomedical Research Centre (CINBIO), University of Vigo, Vigo, Spain.; Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain.; Galicia Sur Health Research Institute, Vigo, Spain., Li Y; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK., Rodriguez-Castro J; Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain., Dueso-Barroso A; Faculty of Science and Technology, University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain.; Barcelona Supercomputing Center (BSC), Barcelona, Spain., Bruzos AL; Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.; Biomedical Research Centre (CINBIO), University of Vigo, Vigo, Spain.; Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain., Dentro SC; The Francis Crick Institute, London, UK.; Experimental Cancer Genetics, Wellcome Sanger Institute, Cambridge, UK.; Oxford Big Data Institute, University of Oxford, Oxford, UK., Blanco MG; DNA Repair and Genome Integrity, Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain.; Department of Biochemistry and Molecular Biology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain., Contino G; Medical Research Council (MRC) Cancer Unit, University of Cambridge, Cambridge, UK., Ardeljan D; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Baltimore, MD, USA., Tojo M; The Biomedical Research Centre (CINBIO), Universidade de Vigo, Vigo, Spain.; Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain., Roberts ND; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK., Zumalave S; Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.; Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain., Edwards PA; University of Cambridge, Cambridge, UK.; Li Ka Shing Centre, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK., Weischenfeldt J; European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.; Finsen Laboratory and Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.; Department of Urology, Charité Universitätsmedizin Berlin, Berlin, Germany., Puiggròs M; Barcelona Supercomputing Center (BSC), Barcelona, Spain., Chong Z; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.; Department of Genetics and Informatics Institute, University of Alabama at Birmingham (UAB) School of Medicine, Birmingham, AL, USA., Chen K; University of Texas MD Anderson Cancer Center, Houston, TX, USA., Lee EA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA., Wala JA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA.; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.; Harvard Medical School, Boston, MA, USA., Raine KM; Cancer Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Cambridge, UK., Butler A; Cancer Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Cambridge, UK., Waszak SM; European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany., Navarro FCP; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA.; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.; Department of Computer Science, Yale University, New Haven, CT, USA., Schumacher SE; The Broad Institute of Harvard and MIT, Cambridge, MA, USA.; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA., Monlong J; Department of Human Genetics, McGill University, Montreal, Québec, Canada., Maura F; Cancer Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Cambridge, UK.; Department of Oncology and Onco-Hematology, University of Milan, Milan, Italy.; Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy., Bolli N; Department of Oncology and Onco-Hematology, University of Milan, Milan, Italy.; Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy., Bourque G; Canadian Center for Computational Genomics, McGill University, Montreal, Quebec, Canada., Gerstein M; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA.; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.; Department of Computer Science, Yale University, New Haven, CT, USA., Park PJ; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.; Ludwig Center at Harvard, Boston, MA, USA., Wedge DC; Cancer Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Cambridge, UK.; Experimental Cancer Genetics, Wellcome Sanger Institute, Cambridge, UK.; Oxford NIHR Biomedical Research Centre, Oxford, UK., Beroukhim R; The Broad Institute of Harvard and MIT, Cambridge, MA, USA.; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.; Harvard Medical School, Boston, MA, USA., Torrents D; Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.; Barcelona Supercomputing Center (BSC), Barcelona, Spain., Korbel JO; European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK., Martincorena I; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK., Fitzgerald RC; Medical Research Council (MRC) Cancer Unit, University of Cambridge, Cambridge, UK., Van Loo P; The Francis Crick Institute, London, UK.; Department of Human Genetics, University of Leuven, Leuven, Belgium., Kazazian HH; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Baltimore, MD, USA., Burns KH; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Baltimore, MD, USA.; McKusick-Nathans Institute of Genetic Medicine, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University School of Medicine, Baltimore, MD, USA., Campbell PJ; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK. pc8@sanger.ac.uk.; Department of Haematology, University of Cambridge, Cambridge, UK. pc8@sanger.ac.uk., Tubio JMC; Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain. jose.mc.tubio@usc.es.; Biomedical Research Centre (CINBIO), University of Vigo, Vigo, Spain. jose.mc.tubio@usc.es.; Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain. jose.mc.tubio@usc.es.; Cancer Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Cambridge, UK. jose.mc.tubio@usc.es.

Publikováno v: Nature genetics [Nat Genet] 2023 Jun; Vol. 55 (6), pp. 1080.

Notch1 mutations drive clonal expansion in normal esophageal epithelium but impair tumor growth.

Autor: Abby E; Wellcome Sanger Institute, Hinxton, UK., Dentro SC; Wellcome Sanger Institute, Hinxton, UK.; European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK.; Artificial Intelligence in Oncology (B450), Deutsches Krebsforschungszentrum, Heidelberg, Germany., Hall MWJ; Wellcome Sanger Institute, Hinxton, UK.; Department of Oncology, University of Cambridge, Cambridge, UK., Fowler JC; Wellcome Sanger Institute, Hinxton, UK., Ong SH; Wellcome Sanger Institute, Hinxton, UK., Sood R; Wellcome Sanger Institute, Hinxton, UK., Herms A; Wellcome Sanger Institute, Hinxton, UK.; Department of Biomedical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain., Piedrafita G; Department of Biochemistry and Molecular Biology, Complutense University, Madrid, Spain.; Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain., Abnizova I; Wellcome Sanger Institute, Hinxton, UK., Siebel CW; Department of Discovery Oncology, Genentech, South San Francisco, CA, USA., Gerstung M; European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK.; Artificial Intelligence in Oncology (B450), Deutsches Krebsforschungszentrum, Heidelberg, Germany., Hall BA; Department of Medical Physics and Biomedical Engineering, University College London, London, UK., Jones PH; Wellcome Sanger Institute, Hinxton, UK. pj3@sanger.ac.uk.; Department of Oncology, University of Cambridge, Cambridge, UK. pj3@sanger.ac.uk.

Publikováno v: Nature genetics [Nat Genet] 2023 Feb; Vol. 55 (2), pp. 232-245. Date of Electronic Publication: 2023 Jan 19.