{"isi":1,"publication_identifier":{"issn":["20411723"]},"volume":8,"date_updated":"2023-09-20T11:55:31Z","has_accepted_license":"1","type":"journal_article","publication_status":"published","publication":"Nature Communications","abstract":[{"text":"Reconstructing the evolutionary history of metastases is critical for understanding their basic biological principles and has profound clinical implications. Genome-wide sequencing data has enabled modern phylogenomic methods to accurately dissect subclones and their phylogenies from noisy and impure bulk tumour samples at unprecedented depth. However, existing methods are not designed to infer metastatic seeding patterns. Here we develop a tool, called Treeomics, to reconstruct the phylogeny of metastases and map subclones to their anatomic locations. Treeomics infers comprehensive seeding patterns for pancreatic, ovarian, and prostate cancers. Moreover, Treeomics correctly disambiguates true seeding patterns from sequencing artifacts; 7% of variants were misclassified by conventional statistical methods. These artifacts can skew phylogenies by creating illusory tumour heterogeneity among distinct samples. In silico benchmarking on simulated tumour phylogenies across a wide range of sample purities (15–95%) and sequencing depths (25-800 × ) demonstrates the accuracy of Treeomics compared with existing methods.","lang":"eng"}],"article_number":"14114","author":[{"last_name":"Reiter","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes","full_name":"Reiter, Johannes","orcid":"0000-0002-0170-7353"},{"first_name":"Alvin","full_name":"Makohon Moore, Alvin","last_name":"Makohon Moore"},{"full_name":"Gerold, Jeffrey","first_name":"Jeffrey","last_name":"Gerold"},{"full_name":"Božić, Ivana","first_name":"Ivana","last_name":"Božić"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"last_name":"Iacobuzio Donahue","first_name":"Christine","full_name":"Iacobuzio Donahue, Christine"},{"last_name":"Vogelstein","first_name":"Bert","full_name":"Vogelstein, Bert"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"doi":"10.1038/ncomms14114","_id":"1080","citation":{"short":"J. Reiter, A. Makohon Moore, J. Gerold, I. Božić, K. Chatterjee, C. Iacobuzio Donahue, B. Vogelstein, M. Nowak, Nature Communications 8 (2017).","mla":"Reiter, Johannes, et al. “Reconstructing Metastatic Seeding Patterns of Human Cancers.” <i>Nature Communications</i>, vol. 8, 14114, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/ncomms14114\">10.1038/ncomms14114</a>.","ama":"Reiter J, Makohon Moore A, Gerold J, et al. Reconstructing metastatic seeding patterns of human cancers. <i>Nature Communications</i>. 2017;8. doi:<a href=\"https://doi.org/10.1038/ncomms14114\">10.1038/ncomms14114</a>","ieee":"J. Reiter <i>et al.</i>, “Reconstructing metastatic seeding patterns of human cancers,” <i>Nature Communications</i>, vol. 8. Nature Publishing Group, 2017.","chicago":"Reiter, Johannes, Alvin Makohon Moore, Jeffrey Gerold, Ivana Božić, Krishnendu Chatterjee, Christine Iacobuzio Donahue, Bert Vogelstein, and Martin Nowak. “Reconstructing Metastatic Seeding Patterns of Human Cancers.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/ncomms14114\">https://doi.org/10.1038/ncomms14114</a>.","ista":"Reiter J, Makohon Moore A, Gerold J, Božić I, Chatterjee K, Iacobuzio Donahue C, Vogelstein B, Nowak M. 2017. Reconstructing metastatic seeding patterns of human cancers. Nature Communications. 8, 14114.","apa":"Reiter, J., Makohon Moore, A., Gerold, J., Božić, I., Chatterjee, K., Iacobuzio Donahue, C., … Nowak, M. (2017). Reconstructing metastatic seeding patterns of human cancers. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms14114\">https://doi.org/10.1038/ncomms14114</a>"},"date_created":"2018-12-11T11:50:02Z","month":"01","article_processing_charge":"No","department":[{"_id":"KrCh"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["004","006"],"file_date_updated":"2018-12-12T10:15:15Z","oa":1,"project":[{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"}],"status":"public","external_id":{"isi":["000393096600001"]},"intvolume":"         8","pubrep_id":"786","file":[{"date_updated":"2018-12-12T10:15:15Z","file_id":"5133","creator":"system","file_name":"IST-2017-786-v1+1_ncomms14114.pdf","relation":"main_file","access_level":"open_access","date_created":"2018-12-12T10:15:15Z","file_size":897050,"content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publist_id":"6301","oa_version":"Published Version","title":"Reconstructing metastatic seeding patterns of human cancers","quality_controlled":"1","scopus_import":"1","date_published":"2017-01-31T00:00:00Z","ec_funded":1,"publisher":"Nature Publishing Group","year":"2017","day":"31","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}}