{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:08Z","timestamp":1772138048013,"version":"3.50.1"},"reference-count":71,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2021,8,12]],"date-time":"2021-08-12T00:00:00Z","timestamp":1628726400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Mohn Cancer Research Laboratory and was supported by funding from the K.G. Jebsen foundation"},{"DOI":"10.13039\/501100005416","name":"Norwegian Research Council","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100005416","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100008730","name":"The Norwegian Cancer Society","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100008730","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Norwegian Health Region West"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,12,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>With recent advances in the field of epigenetics, the focus is widening from large and frequent disease- or phenotype-related methylation signatures to rare alterations transmitted mitotically or transgenerationally (constitutional epimutations). Merging evidence indicate that such constitutional alterations, albeit occurring at a low mosaic level, may confer risk of disease later in life. Given their inherently low incidence rate and mosaic nature, there is a need for bioinformatic tools specifically designed to analyze such events.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We have developed a method (ramr) to identify aberrantly methylated DNA regions (AMRs). ramr can be applied to methylation data obtained by array or next-generation sequencing techniques to discover AMRs being associated with elevated risk of cancer as well as other diseases. We assessed accuracy and performance metrics of ramr and confirmed its applicability for analysis of large public datasets. Using ramr we identified aberrantly methylated regions that are known or may potentially be associated with development of colorectal cancer and provided functional annotation of AMRs that arise at early developmental stages.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The R package is freely available at https:\/\/github.com\/BBCG\/ramr and https:\/\/bioconductor.org\/packages\/ramr.<\/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\/btab586","type":"journal-article","created":{"date-parts":[[2021,8,11]],"date-time":"2021-08-11T07:27:30Z","timestamp":1628666850000},"page":"133-140","source":"Crossref","is-referenced-by-count":3,"title":["<i>ramr<\/i>\n                    : an R\/Bioconductor package for detection of rare aberrantly methylated regions"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5910-4934","authenticated-orcid":false,"given":"Oleksii","family":"Nikolaienko","sequence":"first","affiliation":[{"name":"K. G. Jebsen Center for Genome-Directed Cancer Therapy, Department of Clinical Science, University of Bergen , Bergen, Norway"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Per Eystein","family":"L\u00f8nning","sequence":"additional","affiliation":[{"name":"K. G. Jebsen Center for Genome-Directed Cancer Therapy, Department of Clinical Science, University of Bergen , Bergen, Norway"},{"name":"Department of Oncology, Haukeland University Hospital , Bergen, Norway"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stian","family":"Knappskog","sequence":"additional","affiliation":[{"name":"K. G. Jebsen Center for Genome-Directed Cancer Therapy, Department of Clinical Science, University of Bergen , Bergen, Norway"},{"name":"Department of Oncology, Haukeland University Hospital , Bergen, Norway"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,8,12]]},"reference":[{"key":"2023020108391872000_btab586-B1","doi-asserted-by":"crossref","first-page":"1363","DOI":"10.1093\/bioinformatics\/btu049","article-title":"Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays","volume":"30","author":"Aryee","year":"2014","journal-title":"Bioinformatics"},{"key":"2023020108391872000_btab586-B2","doi-asserted-by":"crossref","first-page":"360","DOI":"10.1016\/j.canlet.2016.03.009","article-title":"Epigenetic field cancerization in gastrointestinal cancers","volume":"375","author":"Baba","year":"2016","journal-title":"Cancer Lett"},{"key":"2023020108391872000_btab586-B3","doi-asserted-by":"crossref","first-page":"4758","DOI":"10.3390\/ijms20194758","article-title":"Epigenetic alterations of Heat Shock Proteins (HSPs) in cancer","volume":"20","author":"Ban","year":"2019","journal-title":"Int J. 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