{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:42:13Z","timestamp":1753875733398,"version":"3.41.2"},"reference-count":48,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2022,9,1]],"date-time":"2022-09-01T00:00:00Z","timestamp":1661990400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100002367","name":"Chinese Academy of Sciences","doi-asserted-by":"publisher","award":["XDB38030400"],"award-info":[{"award-number":["XDB38030400"]}],"id":[{"id":"10.13039\/501100002367","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31970634","32170669"],"award-info":[{"award-number":["31970634","32170669"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Key Research Program of China","award":["2020YFA0907001"],"award-info":[{"award-number":["2020YFA0907001"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,9,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Somatic variants act as critical players during cancer occurrence and development. Thus, an accurate and robust method to identify them is the foundation of cutting-edge cancer genome research. However, due to low accessibility and high individual-\/sample-specificity of the somatic variants in tumor samples, the detection is, to date, still crammed with challenges, particularly when lacking paired normal samples as control. To solve this burning issue, we developed a tumor-only somatic and germline variant identification method (TSomVar) using the random forest algorithm established on sample-specific variant datasets derived from genotype imputation, reads-mapping level annotation and functional annotation. We trained TSomVar by using genomic variant datasets of three major cancer types: colorectal cancer, hepatocellular carcinoma and skin cutaneous melanoma. Compared with existing tumor-only somatic variant identification tools, TSomVar shows excellent performances in somatic variant detection with higher accuracy and better capability of recalling for test datasets from colorectal cancer and skin cutaneous melanoma. In addition, TSomVar is equipped with the competence of accurately identifying germline variants in tumor samples. Taken together, TSomVar will undoubtedly facilitate and revolutionize somatic variant explorations in cancer research.<\/jats:p>","DOI":"10.1093\/bib\/bbac381","type":"journal-article","created":{"date-parts":[[2022,9,11]],"date-time":"2022-09-11T08:03:48Z","timestamp":1662883428000},"source":"Crossref","is-referenced-by-count":0,"title":["TSomVar: a tumor-only somatic and germline variant identification method with random forest"],"prefix":"10.1093","volume":"23","author":[{"given":"Shuo","family":"Shi","sequence":"first","affiliation":[{"name":"National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China"},{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China"},{"name":"University of Chinese Academy of Sciences , Beijing 100049, China"},{"name":"Burning Rock Biotech Ltd , Shanghai 201114, China"}]},{"given":"Qi","family":"Wang","sequence":"additional","affiliation":[{"name":"National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China"},{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China"},{"name":"University of Chinese Academy of Sciences , Beijing 100049, China"},{"name":"Qujiang Culture Finance Holding (Group) Co., Ltd , Xian 710061, China"}]},{"given":"Yunfei","family":"Shang","sequence":"additional","affiliation":[{"name":"National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China"},{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China"},{"name":"University of Chinese Academy of Sciences , Beijing 100049, China"}]},{"given":"Congfan","family":"Bu","sequence":"additional","affiliation":[{"name":"National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China"},{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China"}]},{"given":"Mingming","family":"Lu","sequence":"additional","affiliation":[{"name":"National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China"},{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China"},{"name":"University of Chinese Academy of Sciences , Beijing 100049, China"}]},{"given":"Meiye","family":"Jiang","sequence":"additional","affiliation":[{"name":"National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China"},{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China"},{"name":"University of Chinese Academy of Sciences , Beijing 100049, China"}]},{"given":"Hao","family":"Zhang","sequence":"additional","affiliation":[{"name":"National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China"},{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China"},{"name":"University of Chinese Academy of Sciences , Beijing 100049, China"}]},{"given":"Shuhuan","family":"Yu","sequence":"additional","affiliation":[{"name":"National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China"},{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China"},{"name":"University of Chinese Academy of Sciences , Beijing 100049, China"}]},{"given":"Jingyao","family":"Zeng","sequence":"additional","affiliation":[{"name":"National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China"},{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China"}]},{"given":"Zaichao","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Biology, The University of Western Ontario , London, Ontario N6A 5B7, Canada"}]},{"given":"Zhenglin","family":"Du","sequence":"additional","affiliation":[{"name":"National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China"},{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2835-4340","authenticated-orcid":false,"given":"Jingfa","family":"Xiao","sequence":"additional","affiliation":[{"name":"National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences 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