{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T20:30:50Z","timestamp":1775853050508,"version":"3.50.1"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2021,11,12]],"date-time":"2021-11-12T00:00:00Z","timestamp":1636675200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100005416","name":"Research Council of Norway","doi-asserted-by":"publisher","award":["241117"],"award-info":[{"award-number":["241117"]}],"id":[{"id":"10.13039\/501100005416","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005416","name":"Research Council of Norway","doi-asserted-by":"publisher","award":["250362"],"award-info":[{"award-number":["250362"]}],"id":[{"id":"10.13039\/501100005416","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002341","name":"Academy of Finland","doi-asserted-by":"publisher","award":["308248"],"award-info":[{"award-number":["308248"]}],"id":[{"id":"10.13039\/501100002341","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002341","name":"Academy of Finland","doi-asserted-by":"publisher","award":["312073"],"award-info":[{"award-number":["312073"]}],"id":[{"id":"10.13039\/501100002341","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002341","name":"Academy of Finland","doi-asserted-by":"publisher","award":["307339"],"award-info":[{"award-number":["307339"]}],"id":[{"id":"10.13039\/501100002341","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002341","name":"Academy of Finland","doi-asserted-by":"publisher","award":["251316"],"award-info":[{"award-number":["251316"]}],"id":[{"id":"10.13039\/501100002341","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Sigrid Juselius Foundation"},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01GM083084"],"award-info":[{"award-number":["R01GM083084"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>DNA methylation has been shown to be spatially dependent across chromosomes. Previous studies have focused on the influence of genomic context on the dependency structure, while not considering differences in dependency structure between individuals.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We modeled spatial dependency with a flexible framework to quantify the dependency structure, focusing on inter-individual differences by exploring the association between dependency parameters and technical and biological variables. The model was applied to a subset of the Finnish Twin Cohort study (N\u2009=\u20091611 individuals). The estimates of the dependency parameters varied considerably across individuals, but were generally consistent across chromosomes within individuals. The variation in dependency parameters was associated with bisulfite conversion plate, zygosity, sex and age. The age differences presumably reflect accumulated environmental exposures and\/or accumulated small methylation differences caused by stochastic mitotic events, establishing recognizable, individual patterns more strongly seen in older individuals.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The twin dataset used in the current study are located in the Biobank of the National Institute for Health and Welfare, Finland. All the biobanked data are publicly available for use by qualified researchers following a standardized application procedure (https:\/\/thl.fi\/en\/web\/thl-biobank\/for-researchers). A R-script for fitting the dependency structure to publicly available DNA methylation data with the software used in this article is provided in supplementary data.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab774","type":"journal-article","created":{"date-parts":[[2021,11,9]],"date-time":"2021-11-09T20:18:03Z","timestamp":1636489083000},"page":"885-891","source":"Crossref","is-referenced-by-count":4,"title":["Modeling dependency structures in 450k DNA methylation data"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8659-5716","authenticated-orcid":false,"given":"Haakon E","family":"Nustad","sequence":"first","affiliation":[{"name":"Department of Medical Genetics and Norwegian Sequencing Centre, Oslo University Hospital , 0450 Oslo, Norway"},{"name":"Institute of Clinical Medicine, Faculty of Medicine, University of Oslo , 0372 Oslo, Norway"},{"name":"Department of Pharmacy, PharmaTox Strategic Research Initiative, University of Oslo , 0371 Oslo, Norway"},{"name":"Centre for Fertility and Health, Norwegian Institute of Public Health , 0213 Oslo, Norway"}]},{"given":"Ingelin","family":"Steinsland","sequence":"additional","affiliation":[{"name":"Department of Mathematical Sciences, Norwegian University of Science and Technology , 7034 Trondheim, Norway"}]},{"given":"Miina","family":"Ollikainen","sequence":"additional","affiliation":[{"name":"Institute for Molecular Medicine Finland FIMM, , FI-00014 Helsinki, Finland"},{"name":"Helsinki Institute of Life Science, University of Helsinki , FI-00014 Helsinki, Finland"}]},{"given":"Emma","family":"Cazaly","sequence":"additional","affiliation":[{"name":"Institute for Molecular Medicine Finland FIMM, , FI-00014 Helsinki, Finland"},{"name":"Helsinki Institute of Life Science, University of Helsinki , FI-00014 Helsinki, Finland"}]},{"given":"Jaakko","family":"Kaprio","sequence":"additional","affiliation":[{"name":"Institute for Molecular Medicine Finland FIMM, , FI-00014 Helsinki, Finland"},{"name":"Helsinki Institute of Life Science, University of Helsinki , FI-00014 Helsinki, Finland"}]},{"given":"Yuval","family":"Benjamini","sequence":"additional","affiliation":[{"name":"Department of Statistics and Data Science, The Hebrew University , Mount Scopus, Jerusalem 9190501, Israel"}]},{"given":"Kristina","family":"Gervin","sequence":"additional","affiliation":[{"name":"Department of Pharmacy, PharmaTox Strategic Research Initiative, University of Oslo , 0371 Oslo, Norway"},{"name":"Division of Clinical Neuroscience, Department of Research and Innovation, Oslo University Hospital , 0450 Oslo, Norway"},{"name":"Pharmacoepidemiology and Drug Safety Research Group, Department of Pharmacy, Faculty of Mathematics and Natural Sciences, University of Oslo , 0363 Oslo, Norway"}]},{"given":"Robert","family":"Lyle","sequence":"additional","affiliation":[{"name":"Department of Medical Genetics and Norwegian Sequencing Centre, Oslo University Hospital , 0450 Oslo, Norway"},{"name":"Centre for Fertility and Health, Norwegian Institute of Public Health , 0213 Oslo, Norway"}]}],"member":"286","published-online":{"date-parts":[[2021,11,12]]},"reference":[{"key":"2023020108530708900_btab774-B1","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1016\/j.ygeno.2019.05.007","article-title":"\u2018Nucleotide distance influences co-methylation between nearby CpG sites","volume":"112","author":"Affinito","year":"2020","journal-title":"Genomics"},{"key":"2023020108530708900_btab774-B2","doi-asserted-by":"crossref","first-page":"1138","DOI":"10.1038\/nmeth.3115","article-title":"\u2018Comprehensive analysis of DNA methylation data with RnBeads","volume":"11","author":"Assenov","year":"2014","journal-title":"Nat. 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