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We sought to incorporate a third, previously developed bisulfite conversion quality check prior to processing 255 FFPE tissue derived DNA samples.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>FFPE tissue-derived DNAs were prepared for 255 prostate tumour specimens and four controls. Checkpoint 1 assessed all samples to have 500ng DNA available for analysis except for two samples that yielded 483 and 486ng. All DNA samples passed both the quality checkpoint 2 and the bisulfite conversion quality assessment checkpoint 3. Assessment of array performance showed one of the 259 (0.4%) DNA samples had less than 90% of probes detected at <jats:italic>p<\/jats:italic>\u2009=\u20090.05. Controls and replicate showed reliable reproducibility with correlations of 0.981 and 0.994. High quantity and quality measures of the FFPE tissue-derived DNAs (assessed by checkpoint 1 and 2) were likely responsible for 99.6% of DNAs producing high quality EPIC array data. This report suggests that checkpoint 3 has limited value in a setting where the FFPE tissue derived DNA has high quantity and quality measures.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/s13104-025-07221-3","type":"journal-article","created":{"date-parts":[[2025,7,10]],"date-time":"2025-07-10T08:43:48Z","timestamp":1752137028000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Quality control checkpoints for high throughput DNA methylation measurement using the human MethylationEPICv1 array: application to formalin-fixed paraffin embedded prostate tissue"],"prefix":"10.1186","volume":"18","author":[{"given":"Robert L.","family":"O\u2019Reilly","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fleur","family":"Hammet","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Neil","family":"O\u2019Callaghan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Robert J.","family":"MacInnis","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Damien","family":"Bolton","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Graham G.","family":"Giles","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pierre-Antoine","family":"Dugu\u00e9","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Melissa C.","family":"Southey","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2025,7,9]]},"reference":[{"issue":"1","key":"7221_CR1","doi-asserted-by":"publisher","first-page":"16381","DOI":"10.1038\/s41598-023-43788-2","volume":"13","author":"ME Dupont","year":"2023","unstructured":"Dupont ME, Jacobsen SB, Christiansen SNN, Tfelt-Hansen J, Smerup MH, Andersen JD, et al. Fresh and frozen cardiac tissue are comparable in DNA methylation array \u03b2-values, but formalin-fixed, paraffin-embedded tissue May overestimate DNA methylation levels. Sci Rep. 2023;13(1):16381.","journal-title":"Sci Rep"},{"issue":"11","key":"7221_CR2","doi-asserted-by":"publisher","first-page":"3212","DOI":"10.1007\/s43032-021-00589-0","volume":"28","author":"D Oliveira","year":"2021","unstructured":"Oliveira D, Hentze J, O\u2019Rourke CJ, Andersen JB, H\u00f8gdall C, H\u00f8gdall EV. DNA methylation in ovarian Tumors-a comparison between fresh tissue and FFPE samples. Reprod Sci. 2021;28(11):3212\u20138.","journal-title":"Reprod Sci"},{"issue":"1","key":"7221_CR3","doi-asserted-by":"publisher","first-page":"3","DOI":"10.3390\/biology5010003","volume":"5","author":"S Kurdyukov","year":"2016","unstructured":"Kurdyukov S, Bullock M. DNA methylation analysis: choosing the right method. 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This study was registered with the Human Ethics Research Committee at Monash University (registration # 20523).","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"The authors declare no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}},{"value":"Not applicable.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}}],"article-number":"280"}}