{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:01Z","timestamp":1772138041346,"version":"3.50.1"},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2020,8,17]],"date-time":"2020-08-17T00:00:00Z","timestamp":1597622400000},"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","id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000121","name":"Division Of Mathematical Sciences","doi-asserted-by":"publisher","award":["DMS1722562"],"award-info":[{"award-number":["DMS1722562"]}],"id":[{"id":"10.13039\/100000121","id-type":"DOI","asserted-by":"publisher"}]},{"name":"University of South Carolina ASPIRE-I award"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,4,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Copy number variation plays important roles in human complex diseases. The detection of copy number variants (CNVs) is identifying mean shift in genetic intensities to locate chromosomal breakpoints, the step of which is referred to as chromosomal segmentation. Many segmentation algorithms have been developed with a strong assumption of independent observations in the genetic loci, and they assume each locus has an equal chance to be a breakpoint (i.e. boundary of CNVs). However, this assumption is violated in the genetics perspective due to the existence of correlation among genomic positions, such as linkage disequilibrium (LD). Our study showed that the LD structure is related to the location distribution of CNVs, which indeed presents a non-random pattern on the genome. To generate more accurate CNVs, we proposed a novel algorithm, LDcnv, that models the CNV data with its biological characteristics relating to genetic dependence structure (i.e. LD).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We theoretically demonstrated the correlation structure of CNV data in SNP array, which further supports the necessity of integrating biological structure in statistical methods for CNV detection. Therefore, we developed the LDcnv that integrated the genomic correlation structure with a local search strategy into statistical modeling of the CNV intensities. To evaluate the performance of LDcnv, we conducted extensive simulations and analyzed large-scale HapMap datasets. We showed that LDcnv presented high accuracy, stability and robustness in CNV detection and higher precision in detecting short CNVs compared to existing methods. This new segmentation algorithm has a wide scope of potential application with data from various high-throughput technology platforms.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>https:\/\/github.com\/FeifeiXiaoUSC\/LDcnv.<\/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\/btaa737","type":"journal-article","created":{"date-parts":[[2020,8,12]],"date-time":"2020-08-12T15:32:50Z","timestamp":1597246370000},"page":"312-317","source":"Crossref","is-referenced-by-count":1,"title":["Integrating genomic correlation structure improves copy number variations detection"],"prefix":"10.1093","volume":"37","author":[{"given":"Xizhi","family":"Luo","sequence":"first","affiliation":[{"name":"Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina , Columbia, SC 29208, USA"}]},{"given":"Fei","family":"Qin","sequence":"additional","affiliation":[{"name":"Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina , Columbia, SC 29208, USA"}]},{"given":"Guoshuai","family":"Cai","sequence":"additional","affiliation":[{"name":"Department of Environmental Health Science, Arnold School of Public Health, University of South Carolina , Columbia, SC 29208, USA"}]},{"given":"Feifei","family":"Xiao","sequence":"additional","affiliation":[{"name":"Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina , Columbia, SC 29208, USA"}]}],"member":"286","published-online":{"date-parts":[[2020,8,17]]},"reference":[{"key":"2023051701213785000_btaa737-B1","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1038\/nature15393","article-title":"A global reference for human genetic variation","volume":"526","year":"2015","journal-title":"Nature"},{"key":"2023051701213785000_btaa737-B2","doi-asserted-by":"crossref","first-page":"1481","DOI":"10.1007\/s00439-012-1183-1","article-title":"Identification of germline genomic copy number variation in familial pancreatic cancer","volume":"131","author":"Al-Sukhni","year":"2012","journal-title":"Hum. 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