{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,28]],"date-time":"2026-01-28T05:37:20Z","timestamp":1769578640364,"version":"3.49.0"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2024,10,16]],"date-time":"2024-10-16T00:00:00Z","timestamp":1729036800000},"content-version":"vor","delay-in-days":23,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82172822"],"award-info":[{"award-number":["82172822"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Key Program of Science and Technology of Liaoning Province","award":["2021JH1\/10400051"],"award-info":[{"award-number":["2021JH1\/10400051"]}]},{"name":"High-level Talent Innovation Support Program of Dalian Science and Technology Bureau","award":["2021RD02"],"award-info":[{"award-number":["2021RD02"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,9,23]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The heterogeneity of tumor clones drives the selection and evolution of distinct tumor cell populations, resulting in an intricate and dynamic tumor evolution process. While tumor bulk DNA sequencing helps elucidate intratumor heterogeneity, challenges such as the misidentification of mutation multiplicity due to copy number variations and uncertainties in the reconstruction process hinder the accurate inference of tumor evolution. In this study, we introduce a novel approach, REconstructing Tumor Clonal Heterogeneity and Evolutionary Relationships (RETCHER), which characterizes more realistic cancer cell fractions by accurately identifying mutation multiplicity while considering uncertainty during the reconstruction process and the credibility and reasonableness of subclone clustering. This method comprehensively and accurately infers multiple forms of tumor clonal heterogeneity and phylogenetic relationships. RETCHER outperforms existing methods on simulated data and infers clearer subclone structures and evolutionary relationships in real multisample sequencing data from five tumor types. By precisely analysing the complex clonal heterogeneity within tumors, RETCHER provides a new approach to tumor evolution research and offers scientific evidence for developing precise and personalized treatment strategies. This approach is expected to play a significant role in tumor evolution research, clinical diagnosis, and treatment. RETCHER is available for free at https:\/\/github.com\/zlsys3\/RETCHER.<\/jats:p>","DOI":"10.1093\/bib\/bbae516","type":"journal-article","created":{"date-parts":[[2024,10,16]],"date-time":"2024-10-16T21:56:58Z","timestamp":1729115818000},"source":"Crossref","is-referenced-by-count":14,"title":["Reconstructing tumor clonal heterogeneity and evolutionary relationships based on tumor DNA sequencing data"],"prefix":"10.1093","volume":"25","author":[{"given":"Zhen","family":"Wang","sequence":"first","affiliation":[{"name":"The Key Laboratory of Biomarker High Throughput Screening and Target Translation of Breast and Gastrointestinal Tumor, Affiliated Zhongshan Hospital of Dalian University , No. 6 Jiefang Street, Zhongshan District, Dalian 116001, Liaoning,","place":["China"]},{"name":"College of Information Engineering, Dalian University , Dalian, Liaoning,","place":["China"]}]},{"given":"Yanhua","family":"Fang","sequence":"additional","affiliation":[{"name":"School of Bioengineering, Dalian University of Technology , Dalian 116024,","place":["China"]}]},{"given":"Ruoyu","family":"Wang","sequence":"additional","affiliation":[{"name":"The Key Laboratory of Biomarker High Throughput Screening and Target Translation of Breast and Gastrointestinal Tumor, Affiliated Zhongshan Hospital of Dalian University , No. 6 Jiefang Street, Zhongshan District, Dalian 116001, Liaoning,","place":["China"]}]},{"given":"Liwen","family":"Kong","sequence":"additional","affiliation":[{"name":"College of Information Engineering, Dalian University , Dalian, Liaoning,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1644-4496","authenticated-orcid":false,"given":"Shanshan","family":"Liang","sequence":"additional","affiliation":[{"name":"The Key Laboratory of Biomarker High Throughput Screening and Target Translation of Breast and Gastrointestinal Tumor, Affiliated Zhongshan Hospital of Dalian University , No. 6 Jiefang Street, Zhongshan District, Dalian 116001, Liaoning,","place":["China"]}]},{"given":"Shuai","family":"Tao","sequence":"additional","affiliation":[{"name":"The Key Laboratory of Biomarker High Throughput Screening and Target Translation of Breast and Gastrointestinal Tumor, Affiliated Zhongshan Hospital of Dalian University , No. 6 Jiefang Street, Zhongshan District, Dalian 116001, Liaoning,","place":["China"]},{"name":"College of Information Engineering, Dalian University , Dalian, Liaoning,","place":["China"]}]}],"member":"286","published-online":{"date-parts":[[2024,10,16]]},"reference":[{"key":"2024101621564266700_ref1","doi-asserted-by":"publisher","first-page":"13","DOI":"10.3390\/cancers13164006","article-title":"Stem cell theory of cancer: Origin of tumor heterogeneity and plasticity","volume":"13","author":"Tu","year":"2021","journal-title":"Cancers (Basel)"},{"key":"2024101621564266700_ref2","doi-asserted-by":"publisher","first-page":"710","DOI":"10.1038\/s41568-023-00602-5","article-title":"Cancers make their own 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