{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,9]],"date-time":"2026-03-09T22:14:11Z","timestamp":1773094451023,"version":"3.50.1"},"reference-count":52,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2021,5,31]],"date-time":"2021-05-31T00:00:00Z","timestamp":1622419200000},"content-version":"vor","delay-in-days":0,"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":["32071156"],"award-info":[{"award-number":["32071156"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31872237"],"award-info":[{"award-number":["31872237"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Guangzhou and Guangdong Key Project","award":["202007030002"],"award-info":[{"award-number":["202007030002"]}]},{"name":"Guangzhou and Guangdong Key Project","award":["2018B030335001"],"award-info":[{"award-number":["2018B030335001"]}]},{"DOI":"10.13039\/501100011229","name":"State Key Laboratory of Integrated Management of Pest Insects and Rodents","doi-asserted-by":"publisher","award":["IPM1918"],"award-info":[{"award-number":["IPM1918"]}],"id":[{"id":"10.13039\/501100011229","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,11,5]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Genetic and epigenetic contributions to various diseases and biological processes have been well-recognized. However, simultaneous identification of single-nucleotide variants (SNVs) and DNA methylation levels from traditional bisulfite sequencing data is still challenging. Here, we develop double strand bisulfite sequencing (DSBS) for genome-wide accurate identification of SNVs and DNA methylation simultaneously at a single-base resolution by using one dataset. Locking Watson and Crick strand together by hairpin adapter followed by bisulfite treatment and massive parallel sequencing, DSBS simultaneously sequences the bisulfite-converted Watson and Crick strand in one paired-end read, eliminating the strand bias of bisulfite sequencing data. Mutual correction of read1 and read2 can estimate the amplification and sequencing errors, and enables our developed computational pipeline, DSBS Analyzer (https:\/\/github.com\/tianguolangzi\/DSBS), to accurately identify SNV and DNA methylation. Additionally, using DSBS, we provide a genome-wide hemimethylation landscape in the human cells, and reveal that the density of DNA hemimethylation sites in promoter region and CpG island is lower than that in other genomic regions. The cost-effective new approach, which decodes DNA methylome and genomic variants simultaneously, will facilitate more comprehensive studies on numerous diseases and biological processes driven by both genetic and epigenetic variations.<\/jats:p>","DOI":"10.1093\/bib\/bbab201","type":"journal-article","created":{"date-parts":[[2021,5,4]],"date-time":"2021-05-04T21:25:59Z","timestamp":1620163559000},"source":"Crossref","is-referenced-by-count":9,"title":["A new approach to decode DNA methylome and genomic variants simultaneously from double strand bisulfite sequencing"],"prefix":"10.1093","volume":"22","author":[{"given":"Jialong","family":"Liang","sequence":"first","affiliation":[{"name":"Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China"}]},{"given":"Kun","family":"Zhang","sequence":"additional","affiliation":[{"name":"Institute of Genomic Medicine, Wenzhou Medical University, Beijing 100101, China"}]},{"given":"Jie","family":"Yang","sequence":"additional","affiliation":[{"name":"Institute of Genomic Medicine, Wenzhou Medical University, Beijing 100101, China"}]},{"given":"Xianfeng","family":"Li","sequence":"additional","affiliation":[{"name":"Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China"}]},{"given":"Qinglan","family":"Li","sequence":"additional","affiliation":[{"name":"Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China"}]},{"given":"Yan","family":"Wang","sequence":"additional","affiliation":[{"name":"Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China"}]},{"given":"Wanshi","family":"Cai","sequence":"additional","affiliation":[{"name":"Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China"}]},{"given":"Huajing","family":"Teng","sequence":"additional","affiliation":[{"name":"Department of Radiation Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education) at Peking University Cancer Hospital and Institute, Beijing 100101, China"}]},{"given":"Zhongsheng","family":"Sun","sequence":"additional","affiliation":[{"name":"Beijing Institutes of Life Science, Chinese Academy of Sciences, CAS Center for Excellence in Biotic Interactions and State Key Laboratory of Integrated Management of Pest Insects and Rodents, University of Chinese Academy of Sciences, Beijing 100101, China"}]}],"member":"286","published-online":{"date-parts":[[2021,5,31]]},"reference":[{"issue":"2","key":"2021110815064828800_ref1","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1093\/molbev\/msx297","article-title":"Landscape of DNA methylation on the marsupial X","volume":"35","author":"Waters","year":"2018","journal-title":"Mol Biol Evol"},{"issue":"10","key":"2021110815064828800_ref2","doi-asserted-by":"crossref","first-page":"590","DOI":"10.1038\/s41580-019-0159-6","article-title":"The diverse 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