{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,8]],"date-time":"2025-12-08T22:24:29Z","timestamp":1765232669308,"version":"3.37.3"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"16","license":[{"start":{"date-parts":[[2019,1,5]],"date-time":"2019-01-05T00:00:00Z","timestamp":1546646400000},"content-version":"vor","delay-in-days":1,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"University of Leeds PhD scholarship","award":["11061191"],"award-info":[{"award-number":["11061191"]}]},{"name":"UK Research and Innovation Rutherford Fund Fellowship","award":["MR\/ S00386X\/1"],"award-info":[{"award-number":["MR\/ S00386X\/1"]}]},{"name":"University of Leeds Academic Fellowship","award":["11061187"],"award-info":[{"award-number":["11061187"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Tumour evolution results in progressive cancer phenotypes such as metastatic spread and treatment resistance. To better treat cancers, we must characterize tumour evolution and the genetic events that confer progressive phenotypes. This is facilitated by high coverage genome or exome sequencing. However, the best approach by which, or indeed whether, these data can be used to accurately model and interpret underlying evolutionary dynamics is yet to be confirmed. Establishing this requires sequencing data from appropriately heterogeneous tumours in which the exact trajectory and combination of events occurring throughout its evolution are known. We therefore developed HeteroGenesis: a tool to generate realistically evolved tumour genomes, which can be sequenced using weighted-Wessim (w-Wessim), an in silico exome sequencing tool that we have adapted from previous methods. HeteroGenesis simulates more complex and realistic heterogeneous tumour genomes than existing methods, can model different evolutionary dynamics, and enables the creation of multi-region and longitudinal data.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>HeteroGenesis and w-Wessim are freely available under the GNU General Public Licence from https:\/\/github.com\/GeorgetteTanner, implemented in Python and supported on linux and MS Windows.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty1063","type":"journal-article","created":{"date-parts":[[2019,1,2]],"date-time":"2019-01-02T12:09:08Z","timestamp":1546430948000},"page":"2850-2852","source":"Crossref","is-referenced-by-count":7,"title":["Simulation of heterogeneous tumour genomes with HeteroGenesis and <i>in silico<\/i> whole exome sequencing"],"prefix":"10.1093","volume":"35","author":[{"given":"Georgette","family":"Tanner","sequence":"first","affiliation":[{"name":"Leeds Institute of Medical Research at St James\u2019s, St James\u2019s University Hospital, Leeds, UK"}]},{"given":"David R","family":"Westhead","sequence":"additional","affiliation":[{"name":"School of Molecular and Cellular Biology, University of Leeds, Leeds, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7695-7480","authenticated-orcid":false,"given":"Alastair","family":"Droop","sequence":"additional","affiliation":[{"name":"Leeds Institute of Data Analytics, University of Leeds, Leeds, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9550-4150","authenticated-orcid":false,"given":"Lucy F","family":"Stead","sequence":"additional","affiliation":[{"name":"Leeds Institute of Medical Research at St James\u2019s, St James\u2019s University Hospital, Leeds, UK"}]}],"member":"286","published-online":{"date-parts":[[2019,1,4]]},"reference":[{"key":"2023062708580850600_bty1063-B1","doi-asserted-by":"crossref","first-page":"805","DOI":"10.1158\/2159-8290.CD-17-0343","article-title":"Tumor evolution as a therapeutic target","volume":"7","author":"Amirouchene-Angelozzi","year":"2017","journal-title":"Cancer Discov"},{"key":"2023062708580850600_bty1063-B3","first-page":"656","article-title":"BLAT\u2013the BLAST-like alignment tool","volume":"12","author":"Kent","year":"2002","journal-title":"Genome Res"},{"key":"2023062708580850600_bty1063-B4","doi-asserted-by":"crossref","first-page":"1076","DOI":"10.1093\/bioinformatics\/btt074","article-title":"Wessim: a whole-exome sequencing simulator based on in silico exome capture","volume":"29","author":"Kim","year":"2013","journal-title":"Bioinformatics"},{"key":"2023062708580850600_bty1063-B5","doi-asserted-by":"crossref","first-page":"74.","DOI":"10.1186\/1471-2164-13-74","article-title":"GemSIM: general, error-model based simulator of next-generation sequencing data","volume":"13","author":"McElroy","year":"2012","journal-title":"BMC Genomics"},{"key":"2023062708580850600_bty1063-B6","doi-asserted-by":"crossref","first-page":"1015","DOI":"10.1038\/ng.3891","article-title":"Between-region genetic divergence reflects the mode and tempo of tumor evolution","volume":"49","author":"Sun","year":"2017","journal-title":"Nat. Genet"},{"key":"2023062708580850600_bty1063-B7","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1038\/ng.3489","article-title":"Identification of neutral tumor evolution across cancer types","volume":"48","author":"Williams","year":"2016","journal-title":"Nat. Genet"},{"key":"2023062708580850600_bty1063-B8","doi-asserted-by":"crossref","first-page":"895","DOI":"10.1038\/s41588-018-0128-6","article-title":"Quantification of subclonal selection in cancer from bulk sequencing data","volume":"50","author":"Williams","year":"2018","journal-title":"Nat. Genet"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/16\/2850\/50719251\/bty1063.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/16\/2850\/50719251\/bty1063.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,27]],"date-time":"2023-06-27T08:58:59Z","timestamp":1687856339000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/16\/2850\/5273483"}},"subtitle":[],"editor":[{"given":"John","family":"Hancock","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2019,1,4]]},"references-count":7,"journal-issue":{"issue":"16","published-print":{"date-parts":[[2019,8,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty1063","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2019,8,15]]},"published":{"date-parts":[[2019,1,4]]}}}