{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:09Z","timestamp":1772138049966,"version":"3.50.1"},"reference-count":28,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2021,12,9]],"date-time":"2021-12-09T00:00:00Z","timestamp":1639008000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["HRD-1901258"],"award-info":[{"award-number":["HRD-1901258"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006545","name":"National Institute on Minority Health and Health Disparities","doi-asserted-by":"publisher","award":["5G12MD007595"],"award-info":[{"award-number":["5G12MD007595"]}],"id":[{"id":"10.13039\/100006545","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["8UL1GM118967"],"award-info":[{"award-number":["8UL1GM118967"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["TL4GM118968"],"award-info":[{"award-number":["TL4GM118968"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100020367","name":"Louisiana Cancer Research Consortium","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100020367","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,2,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Double minute (DM) chromosomes are acentric extrachromosomal DNA artifacts that are frequently observed in the cells of numerous cancers. They are highly amplified and contain oncogenes and drug-resistance genes, making their presence a challenge for effective cancer treatment. Algorithmic discovery of DM can potentially improve bench-derived therapies for cancer treatment. A hindrance to this task is that DMs evolve, yielding circular chromatin that shares segments from progenitor DMs. This creates DMs with overlapping amplicon coordinates. Existing DM discovery algorithms use whole genome shotgun sequencing (WGS) in isolation, which can potentially incorrectly classify DMs that share overlapping coordinates.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>In this study, we describe an algorithm called \u2018HolistIC\u2019 that can predict DMs in tumor genomes by integrating WGS and Hi\u2013C sequencing data. The consolidation of these sources of information resolves ambiguity in DM amplicon prediction that exists in DM prediction with WGS data used in isolation. We implemented and tested our algorithm on the tandem Hi\u2013C and WGS datasets of three cancer datasets and a simulated dataset. Results on the cancer datasets demonstrated HolistIC\u2019s ability to predict DMs from Hi\u2013C and WGS data in tandem. The results on the simulated data showed the HolistIC can accurately distinguish DMs that have overlapping amplicon coordinates, an advance over methods that predict extrachromosomal amplification using WGS data in isolation.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Our software, named \u2018HolistIC\u2019, is available at http:\/\/www.github.com\/mhayes20\/HolistIC.<\/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\/btab816","type":"journal-article","created":{"date-parts":[[2021,12,4]],"date-time":"2021-12-04T07:09:11Z","timestamp":1638601751000},"page":"1208-1215","source":"Crossref","is-referenced-by-count":11,"title":["HolistIC: leveraging Hi\u2013C and whole genome shotgun sequencing for double minute chromosome discovery"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0457-8550","authenticated-orcid":false,"given":"Matthew","family":"Hayes","sequence":"first","affiliation":[{"name":"Department of Physics and Computer Science, Xavier University of Louisiana , New Orleans, LA 70125, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Angela","family":"Nguyen","sequence":"additional","affiliation":[{"name":"Department of Biology, Xavier University of Louisiana , New Orleans, LA 70125, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rahib","family":"Islam","sequence":"additional","affiliation":[{"name":"Department of Biology, Xavier University of Louisiana , New Orleans, LA 70125, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Caryn","family":"Butler","sequence":"additional","affiliation":[{"name":"Department of Public Health Sciences, Xavier University of Louisiana , New Orleans, LA 70125, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ethan","family":"Tran","sequence":"additional","affiliation":[{"name":"Department of Biology, Xavier University of Louisiana , New Orleans, LA 70125, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Derrick","family":"Mullins","sequence":"additional","affiliation":[{"name":"Department of Physics and Computer Science, Xavier University of Louisiana , New Orleans, LA 70125, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chindo","family":"Hicks","sequence":"additional","affiliation":[{"name":"Department of Genetics, Louisiana State University Health Sciences Center New Orleans , New Orleans, LA 70112, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,12,9]]},"reference":[{"key":"2023030901055411700_","doi-asserted-by":"crossref","first-page":"999","DOI":"10.1101\/gr.160374.113","article-title":"Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts","volume":"24","author":"Ay","year":"2014","journal-title":"Genome Res"},{"key":"2023030901055411700_","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1016\/0165-4608(82)90043-7","article-title":"Double minutes in human tumor cells","volume":"5","author":"Barker","year":"1982","journal-title":"Cancer Genet. 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