{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:42:36Z","timestamp":1772138556893,"version":"3.50.1"},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2019,5,3]],"date-time":"2019-05-03T00:00:00Z","timestamp":1556841600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000266","name":"Engineering and Physical Sciences Research Council","doi-asserted-by":"publisher","award":["EP\/N510129\/1"],"award-info":[{"award-number":["EP\/N510129\/1"]}],"id":[{"id":"10.13039\/501100000266","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","award":["MC_UU_00002\/7"],"award-info":[{"award-number":["MC_UU_00002\/7"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000288","name":"Royal Society","doi-asserted-by":"publisher","award":["204623\/Z\/16\/Z"],"award-info":[{"award-number":["204623\/Z\/16\/Z"]}],"id":[{"id":"10.13039\/501100000288","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,8,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Bisulfite amplicon sequencing has become the primary choice for single-base methylation quantification of multiple targets in parallel. The main limitation of this technology is a preferential amplification of an allele and strand in the PCR due to methylation state. This effect, known as \u2018PCR bias', causes inaccurate estimation of the methylation levels and calibration methods based on standard controls have been proposed to correct for it. Here, we present a Bayesian calibration tool, MethylCal, which can analyse jointly all CpGs within a CpG island (CGI) or a Differentially Methylated Region (DMR), avoiding \u2018one-at-a-time' CpG calibration. This enables more precise modeling of the methylation levels observed in the standard controls. It also provides accurate predictions of the methylation levels not considered in the controlled experiment, a feature that is paramount in the derivation of the corrected methylation degree. We tested the proposed method on eight independent assays (two CpG islands and six imprinting DMRs) and demonstrated its benefits, including the ability to detect outliers. We also evaluated MethylCal\u2019s calibration in two practical cases, a clinical diagnostic test on 18 patients potentially affected by Beckwith\u2013Wiedemann syndrome, and 17 individuals with celiac disease. The calibration of the methylation levels obtained by MethylCal allows a clearer identification of patients undergoing loss or gain of methylation in borderline cases and could influence further clinical or treatment decisions.<\/jats:p>","DOI":"10.1093\/nar\/gkz325","type":"journal-article","created":{"date-parts":[[2019,4,20]],"date-time":"2019-04-20T07:10:52Z","timestamp":1555744252000},"page":"e81-e81","source":"Crossref","is-referenced-by-count":6,"title":["MethylCal: Bayesian calibration of methylation levels"],"prefix":"10.1093","volume":"47","author":[{"given":"Eguzkine","family":"Ochoa","sequence":"first","affiliation":[{"name":"Department of Medical Genetics, University of Cambridge, Cambridge CB2 0QQ, UK"},{"name":"Cambridge NIHR Biomedical Research Centre, Cambridge CB2 0QQ, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Verena","family":"Zuber","sequence":"additional","affiliation":[{"name":"Department of Epidemiology and Biostatistics, Imperial College London, London W2 1PG, UK"},{"name":"MRC Biostatistics Unit, University of Cambridge, Cambridge CB2 0SR, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nora","family":"Fernandez-Jimenez","sequence":"additional","affiliation":[{"name":"Department of Genetics, Physical Anthropology and Animal Physiology, Biocruces-Bizkaia Health Research Institute, University of the Basque Country (UPV\/EHU), Leioa, Bizkaia, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3176-501X","authenticated-orcid":false,"given":"Jose Ramon","family":"Bilbao","sequence":"additional","affiliation":[{"name":"Department of Genetics, Physical Anthropology and Animal Physiology, Biocruces-Bizkaia Health Research Institute, University of the Basque Country (UPV\/EHU), Leioa, Bizkaia, Spain"},{"name":"CIBERDEM Diabetes and Associated Metabolic Diseases, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Graeme R","family":"Clark","sequence":"additional","affiliation":[{"name":"Department of Medical Genetics, University of Cambridge, Cambridge CB2 0QQ, UK"},{"name":"Cambridge NIHR Biomedical Research Centre, Cambridge CB2 0QQ, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eamonn R","family":"Maher","sequence":"additional","affiliation":[{"name":"Department of Medical Genetics, University of Cambridge, Cambridge CB2 0QQ, UK"},{"name":"Cambridge NIHR Biomedical Research Centre, Cambridge CB2 0QQ, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6381-2327","authenticated-orcid":false,"given":"Leonardo","family":"Bottolo","sequence":"additional","affiliation":[{"name":"Department of Medical Genetics, University of Cambridge, Cambridge CB2 0QQ, UK"},{"name":"MRC Biostatistics Unit, University of Cambridge, Cambridge CB2 0SR, UK"},{"name":"The Alan Turing Institute, London NW1 2DB, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,5,3]]},"reference":[{"key":"2019081902250985600_B1","doi-asserted-by":"crossref","first-page":"1055","DOI":"10.1126\/science.6844925","article-title":"DNA methylation decreases in a ging but not in immortal cells","volume":"220","author":"Wilson","year":"1983","journal-title":"Science"},{"key":"2019081902250985600_B2","doi-asserted-by":"crossref","first-page":"1665","DOI":"10.1002\/art.1780331109","article-title":"Evidence for impaired T cell DNA methylation in systemic lupus erythematosus and rheumatoid arthritis","volume":"33","author":"Richardson","year":"1990","journal-title":"Arthritis Rheumatol."},{"key":"2019081902250985600_B3","doi-asserted-by":"crossref","first-page":"362","DOI":"10.1038\/366362a0","article-title":"Role for DNA methylation in genomic imprinting","volume":"366","author":"Li","year":"1993","journal-title":"Nature"},{"key":"2019081902250985600_B4","first-page":"5274","article-title":"Hypomethylation of DNA in pathological conditions of the human prostate","volume":"47","author":"Bedford","year":"1987","journal-title":"Cancer Res."},{"key":"2019081902250985600_B5","doi-asserted-by":"crossref","first-page":"1350","DOI":"10.1126\/science.6262918","article-title":"5-Methylcytosine in eukaryotic DNA","volume":"212","author":"Ehrlich","year":"1981","journal-title":"Science"},{"key":"2019081902250985600_B6","doi-asserted-by":"crossref","DOI":"10.1155\/2016\/2192853","article-title":"Discovery and validation of hypermethylated markers for colorectal cancer","volume":"2016","author":"Wei","year":"2016","journal-title":"Dis. 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Clin. Invest."},{"key":"2019081902250985600_B18","doi-asserted-by":"crossref","first-page":"1298","DOI":"10.1093\/hmg\/ddt520","article-title":"Coregulation and modulation of NF\u03baB-related genes in celiac disease: uncovered aspects of gut mucosal inflammation","volume":"23","author":"Fernandez-Jimenez","year":"2013","journal-title":"Hum. Mol. Genet."},{"key":"2019081902250985600_B19","doi-asserted-by":"crossref","first-page":"e0137006","DOI":"10.1371\/journal.pone.0137006","article-title":"Reference materials for calibration of analytical biases in quantification of DNA methylation","volume":"10","author":"Yu","year":"2015","journal-title":"PLoS One"},{"key":"2019081902250985600_B20","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1186\/1756-8935-6-33","article-title":"Focused, high accuracy 5-methylcytosine quantitation with base resolution by benchtop next-generation sequencing","volume":"6","author":"Masser","year":"2013","journal-title":"Epigenet. 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