{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,3]],"date-time":"2026-08-03T19:43:29Z","timestamp":1785786209779,"version":"3.56.0"},"reference-count":38,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2026,2,2]],"date-time":"2026-02-02T00:00:00Z","timestamp":1769990400000},"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":["JP23ek0510040"],"award-info":[{"award-number":["JP23ek0510040"]}],"id":[{"id":"10.13039\/100009619","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS One"],"abstract":"<jats:p>\n                    Measurement of donor-derived cell-free DNA (dd-cfDNA) enables early, non-invasive monitoring of transplanted organs, including rejection detection. We developed a method to estimate dd-cfDNA ratios using capture hybridization of 300 SNPs, next-generation sequencing (NGS), and clustering analysis. Validation was conducted using simulated mixtures of fragmented genomic DNA from two individuals (0\u2013100%). dd-cfDNA ratios were estimated via clustering, with and without 0% mixture samples to simulate the presence or absence of pre-transplant recipient plasma. When 0% samples were included, estimation achieved an\n                    <jats:italic>r\u00b2<\/jats:italic>\n                    of 0.9987 across the full 0\u2013100% range; without them,\n                    <jats:italic>r\u00b2<\/jats:italic>\n                    remained high (0.9973) in the clinically relevant 0\u201310% range. The robustness of the method was further demonstrated by\n                    <jats:italic>in silico<\/jats:italic>\n                    downsampling. MAEs with 0% samples were 0.823%, 0.766%, and 0.702% at full, 50%, and 25% read depths, respectively (0\u2013100% range). For the 0\u201310% range, MAEs were 0.333%, 0.300%, and 0.467% with 0% samples, and 0.413%, 0.367%, and 0.503% without them. These results indicate that the method maintains high accuracy even under reduced input and when pre-transplant data are unavailable. We also compared clustering-based estimates with direct calculations from kidney transplant recipients, where donor and recipient SNP genotypes were known. The concordance correlation coefficient (CCC) from day 0 to day 28 post-transplantation was 0.9887 and 0.9316 for unrelated pairs with and without pre-transplant data, respectively. For sibling pairs, CCCs were 0.9923 and 0.9675; for parent\u2013child pairs, the CCC was 0.9831 with pre-transplant data. CCC was not calculated for parent\u2013child pairs without pre-transplant data due to limited samples (&lt;10%, n\u2009=\u20093). These findings demonstrate high concordance, accuracy, and robustness of our clustering-based dd-cfDNA estimation method and support its potential utility in clinical transplantation settings.\n                  <\/jats:p>","DOI":"10.1371\/journal.pone.0342082","type":"journal-article","created":{"date-parts":[[2026,2,2]],"date-time":"2026-02-02T18:39:26Z","timestamp":1770057566000},"page":"e0342082","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["A SNP-based capture and clustering workflow to assess donor-derived cell-free DNA in transplantation"],"prefix":"10.1371","volume":"21","author":[{"given":"Shigeki","family":"Mitsunaga","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6059-7660","authenticated-orcid":true,"given":"Yohei","family":"Yamada","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Phuong Thanh","family":"Nguyen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Naoko","family":"Fujito","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hirofumi","family":"Nakaoka","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hiromichi","family":"Aoyama","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hiroshi","family":"Kitamura","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kenichi","family":"Saigo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ituro","family":"Inoue","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Akihiro","family":"Fujino","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Masahiro","family":"Shinoda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kazumasa","family":"Fukuda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuko","family":"Kitagawa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,2,2]]},"reference":[{"issue":"21","key":"pone.0342082.ref001","doi-asserted-by":"crossref","first-page":"8062","DOI":"10.3390\/ijms21218062","article-title":"Putative origins of cell-free DNA in humans: a review of active and passive nucleic acid release mechanisms","volume":"21","author":"S Grabuschnig","year":"2020","journal-title":"Int J Mol Sci"},{"issue":"9","key":"pone.0342082.ref002","doi-asserted-by":"crossref","first-page":"110742","DOI":"10.1016\/j.isci.2024.110742","article-title":"Comparison of cell-free and small extracellular-vesicle-associated DNA by sequencing plasma of lung cancer patients","volume":"27","author":"N Moldovan","year":"2024","journal-title":"iScience"},{"issue":"3","key":"pone.0342082.ref003","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1097\/TP.0000000000003393","article-title":"The Monitoring of donor-derived cell-free DNA in kidney transplantation","volume":"105","author":"EJ Filippone","year":"2020","journal-title":"Transplantation"},{"issue":"8","key":"pone.0342082.ref004","doi-asserted-by":"crossref","first-page":"2320","DOI":"10.1038\/s41591-024-03087-3","article-title":"Cell-free DNA for the detection of kidney allograft rejection","volume":"30","author":"O Aubert","year":"2024","journal-title":"Nat Med"},{"key":"pone.0342082.ref005","author":"PT Nguyen","year":"2025","journal-title":"Applications of donor-derived cell-free DNA in kidney transplantation healthcare: view from a prospective single-center study. 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