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The molecular characteristics and tumorigenesis of MPT remain unclear due to insufficient approaches. Here, we present MPTevol, a practical computational framework for comprehensively exploring the MPT from multiregion sequencing (MRS) experiments. To verify the utility of MPTevol, we performed whole-exome MRS for 33 samples of a rare patient with triple-primary tumors and three metastatic sites and systematically investigated clonal dynamics and metastatic routines. MPTevol assists in comparing genomic profiles across samples, detecting clonal evolutionary history and metastatic routines and quantifying the metastatic history. All triple-primary tumors were independent origins and their genomic characteristics were consistent with corresponding sporadic tumors, strongly supporting their independent tumorigenesis. We further showed two independent early monoclonal seeding events for the metastases in the ovary and uterus. We revealed that two ovarian metastases were disseminated from the same subclone of the primary tumor through undergoing whole-genome doubling processes, suggesting metastases-to-metastases seeding occurred when tumors had similar microenvironments. Surprisingly, according to the metastasis timing model of MPTevol, we found that primary tumors of about 0.058\u20130.124\u00a0cm diameter have been disseminating to distant organs, which is much earlier than conventional clinical views. We developed MPT-specialized analysis framework MPTevol and demonstrated its utility in explicitly resolving clonal evolutionary history and metastatic seeding routines with a rare MPT case. MPTevol is implemented in R and is available at https:\/\/github.com\/qingjian1991\/MPTevol under the GPL v3 license.<\/jats:p>","DOI":"10.1093\/bib\/bbac175","type":"journal-article","created":{"date-parts":[[2022,4,19]],"date-time":"2022-04-19T11:19:31Z","timestamp":1650367171000},"source":"Crossref","is-referenced-by-count":3,"title":["Deciphering clonal dynamics and metastatic routines in a rare patient of synchronous triple-primary tumors and multiple metastases with MPTevol"],"prefix":"10.1093","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0628-3198","authenticated-orcid":false,"given":"Qingjian","family":"Chen","sequence":"first","affiliation":[{"name":"State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Oncology, Sun Yat-sen University Cancer Center , Guangzhou, Guangdong 510060, P. R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qi-Nian","family":"Wu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Oncology, Sun Yat-sen University Cancer Center , Guangzhou, Guangdong 510060, P. R. China"},{"name":"Department of Pathology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University , Guangzhou 510060, P. R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yu-Ming","family":"Rong","sequence":"additional","affiliation":[{"name":"Department of VIP Region, Sun Yat-Sen University Cancer Center , Guangzhou 510060, P. R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shixiang","family":"Wang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Oncology, Sun Yat-sen University Cancer Center , Guangzhou, Guangdong 510060, P. R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2492-2689","authenticated-orcid":false,"given":"Zhixiang","family":"Zuo","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Oncology, Sun Yat-sen University Cancer Center , Guangzhou, Guangdong 510060, P. R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Long","family":"Bai","sequence":"additional","affiliation":[{"name":"Department of VIP Region, Sun Yat-Sen University Cancer Center , Guangzhou 510060, P. R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bei","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of VIP Region, Sun Yat-Sen University Cancer Center , Guangzhou 510060, P. R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shuqiang","family":"Yuan","sequence":"additional","affiliation":[{"name":"Department of Gastric Surgery, Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine , Guangzhou, P. R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8683-6145","authenticated-orcid":false,"given":"Qi","family":"Zhao","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Oncology, Sun Yat-sen University Cancer Center , Guangzhou, Guangdong 510060, P. R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,5,23]]},"reference":[{"key":"2022092013201946600_ref1","doi-asserted-by":"crossref","first-page":"e000172","DOI":"10.1136\/esmoopen-2017-000172","article-title":"Multiple primary tumours: challenges and approaches, a review","volume":"2","author":"Vogt","year":"2017","journal-title":"ESMO Open"},{"key":"2022092013201946600_ref2","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1007\/s12029-011-9296-7","article-title":"Multiple primary malignancies: analysis of 23 patients with at least three tumors","volume":"43","author":"Salem","year":"2012","journal-title":"J Gastrointest Cancer"},{"key":"2022092013201946600_ref3","doi-asserted-by":"crossref","first-page":"51","DOI":"10.5604\/01.3001.0012.8371","article-title":"Multiple primary cancers in patients treated for squamous cell carcinoma of the 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