{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,20]],"date-time":"2025-07-20T03:33:52Z","timestamp":1752982432815,"version":"3.37.3"},"reference-count":19,"publisher":"Wiley","issue":"2","license":[{"start":{"date-parts":[[2020,12,17]],"date-time":"2020-12-17T00:00:00Z","timestamp":1608163200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100009619","name":"Japan Agency for Medical Research and Development","doi-asserted-by":"publisher","award":["JP17km0105004"],"award-info":[{"award-number":["JP17km0105004"]}],"id":[{"id":"10.13039\/100009619","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Pathology International"],"published-print":{"date-parts":[[2021,2]]},"abstract":"<jats:p>Formalin\u2010fixed paraffin\u2010embedded (FFPE) tissues are promising biological resources for genetic research. Recent improvements in DNA extraction from FFPE samples allowed the use of these tissues for multiple sequencing methods. However, fundamental research addressing the application of FFPE\u2010derived DNA for targeted\u2010bisulfite sequencing (TB\u2010seq) is lacking. Here, we evaluated the suitability of FFPE\u2010derived DNA for TB\u2010seq. We conducted TB\u2010seq using FFPE\u2010derived DNA and corresponding fresh frozen (FF) tissues of patients with kidney cancer and compared the quality of DNA, libraries, and TB\u2010seq statistics between the two preservation methods. The approximately 600\u2010bp average fragment size of the FFPE\u2010derived DNA was significantly shorter than that of the FF\u2010derived DNA. The sequencing libraries constructed using FFPE\u2010derived DNA and the mapping ratio were approximately 10 times and 10% lower, respectively, than those constructed using FF\u2010derived DNA. In the mapped data of FFPE\u2010derived DNA, duplicated reads accounted for &gt; 60% of the obtained sequence reads, with lower mean on\u2010target coverage. Therefore, the standard TB\u2010seq protocol is inadequate for obtaining high\u2010quality data for epigenetic analysis from FFPE\u2010derived DNA, and technical improvements are necessary for enabling the use of archived FFPE resources.<\/jats:p>","DOI":"10.1111\/pin.13054","type":"journal-article","created":{"date-parts":[[2020,12,18]],"date-time":"2020-12-18T14:04:25Z","timestamp":1608300265000},"page":"135-140","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Evaluation of clinical formalin\u2010fixed paraffin\u2010embedded tissue quality for targeted\u2010bisulfite sequencing"],"prefix":"10.1111","volume":"71","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3524-6524","authenticated-orcid":false,"given":"Hideki","family":"Ohmomo","sequence":"first","affiliation":[{"name":"Iwate Tohoku Medical Megabank Organization, Iwate Medical University, 1\u20101\u20101 Idaidori, Yahaba, Shiwa Iwate 028\u20103694 Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shohei","family":"Komaki","sequence":"additional","affiliation":[{"name":"Iwate Tohoku Medical Megabank Organization, Iwate Medical University, 1\u20101\u20101 Idaidori, Yahaba, Shiwa Iwate 028\u20103694 Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kanako","family":"Ono","sequence":"additional","affiliation":[{"name":"Iwate Tohoku Medical Megabank Organization, Iwate Medical University, 1\u20101\u20101 Idaidori, Yahaba, Shiwa Iwate 028\u20103694 Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yoichi","family":"Sutoh","sequence":"additional","affiliation":[{"name":"Iwate Tohoku Medical Megabank Organization, Iwate Medical University, 1\u20101\u20101 Idaidori, Yahaba, Shiwa Iwate 028\u20103694 Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tsuyoshi","family":"Hachiya","sequence":"additional","affiliation":[{"name":"Iwate Tohoku Medical Megabank Organization, Iwate Medical University, 1\u20101\u20101 Idaidori, Yahaba, Shiwa Iwate 028\u20103694 Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eri","family":"Arai","sequence":"additional","affiliation":[{"name":"Department of Pathology Keio University School of Medicine, 35 Shinanomachi, Shinjuku Tokyo 160\u20108582 Japan"},{"name":"Division of Molecular Pathology National Cancer Center Research Institute, 5\u20101\u20101, Tsukiji, Chuo Tokyo 104\u20100045 Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hiroyuki","family":"Fujimoto","sequence":"additional","affiliation":[{"name":"Department of Urology National Cancer Center Hospital, 5\u20101\u20101 Tsukiji, Chuo Tokyo 104\u20100045 Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Teruhiko","family":"Yoshida","sequence":"additional","affiliation":[{"name":"Department of Clinical Genomics National Cancer Center Research Institute, 5\u20101\u20101 Tsukiji, Chuo Tokyo 104\u20100045 Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yae","family":"Kanai","sequence":"additional","affiliation":[{"name":"Department of Pathology Keio University School of Medicine, 35 Shinanomachi, Shinjuku Tokyo 160\u20108582 Japan"},{"name":"Division of Molecular Pathology National Cancer Center Research Institute, 5\u20101\u20101, Tsukiji, Chuo Tokyo 104\u20100045 Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Makoto","family":"Sasaki","sequence":"additional","affiliation":[{"name":"Iwate Tohoku Medical Megabank Organization, Iwate Medical University, 1\u20101\u20101 Idaidori, Yahaba, Shiwa Iwate 028\u20103694 Japan"},{"name":"Division of Ultrahigh Field MRI Institute for Biomedical Sciences, Iwate Medical University, 1\u20101\u20101 Idaidori, Yahaba, Shiwa Iwate 028\u20103694 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