{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:39Z","timestamp":1740185139864,"version":"3.37.3"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2022,2,17]],"date-time":"2022-02-17T00:00:00Z","timestamp":1645056000000},"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\/501100000024","name":"Canadian Institutes of Health Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Gulf Coast Consortia"},{"name":"Computational Cancer Biology Training Program","award":["RP170593"],"award-info":[{"award-number":["RP170593"]}]},{"DOI":"10.13039\/100000005","name":"Department of Defense","doi-asserted-by":"publisher","award":["W81XWH-18-1-0357"],"award-info":[{"award-number":["W81XWH-18-1-0357"]}],"id":[{"id":"10.13039\/100000005","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["R01CA227156"],"award-info":[{"award-number":["R01CA227156"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Cancer Prevention and Research Institute of Texas grant","award":["RP170668"],"award-info":[{"award-number":["RP170668"]}]},{"name":"NIH\/NCATS","award":["1 UL1 TR003167 01"],"award-info":[{"award-number":["1 UL1 TR003167 01"]}]},{"DOI":"10.13039\/100000054","name":"NCI","doi-asserted-by":"publisher","award":["P30 CA016672"],"award-info":[{"award-number":["P30 CA016672"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["UL1TR003167","5R01GM122775"],"award-info":[{"award-number":["UL1TR003167","5R01GM122775"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,4,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Cross-sectional analyses of primary cancer genomes have identified regions of recurrent somatic copy-number alteration, many of which result from positive selection during cancer formation and contain driver genes. However, no effective approach exists for identifying genomic loci under significantly different degrees of selection in cancers of different subtypes, anatomic sites or disease stages.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>CNGPLD is a new tool for performing case\u2013control somatic copy-number analysis that facilitates the discovery of differentially amplified or deleted copy-number aberrations in a case group of cancer compared with a control group of cancer. This tool uses a Gaussian process statistical framework in order to account for the covariance structure of copy-number data along genomic coordinates and to control the false discovery rate at the region level.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>CNGPLD is freely available at https:\/\/bitbucket.org\/djhshih\/cngpld as an R package.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac096","type":"journal-article","created":{"date-parts":[[2022,2,15]],"date-time":"2022-02-15T13:42:44Z","timestamp":1644932564000},"page":"2096-2101","source":"Crossref","is-referenced-by-count":1,"title":["CNGPLD: case\u2013control copy-number analysis using Gaussian process latent difference"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9802-4937","authenticated-orcid":false,"given":"David J H","family":"Shih","sequence":"first","affiliation":[{"name":"Broad Institute of Massachusetts Institute of Technology and Harvard , Cambridge, MA 02142, USA"},{"name":"Department of Systems Biology, University of Texas MD Anderson Cancer Center , Houston, TX 77030, USA"},{"name":"School of Biomedical Informatics, University of Texas Health Science Center at Houston , Houston, TX 77030, USA"}]},{"given":"Ruoxing","family":"Li","sequence":"additional","affiliation":[{"name":"School of Biomedical Informatics, University of Texas Health Science Center at Houston , Houston, TX 77030, USA"}]},{"given":"Peter","family":"M\u00fcller","sequence":"additional","affiliation":[{"name":"Department of Mathematics, University of Texas at Austin , Houston, TX 78712, USA"},{"name":"Department of Statistics & Data Science, University of Texas at Austin , Houston, TX 78712, USA"},{"name":"Department of Biostatistics, University of Texas MD Anderson Cancer Center , Houston, TX 77030, USA"}]},{"given":"W Jim","family":"Zheng","sequence":"additional","affiliation":[{"name":"School of Biomedical Informatics, University of Texas Health Science Center at Houston , Houston, TX 77030, USA"}]},{"given":"Kim-Anh","family":"Do","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, University of Texas MD Anderson Cancer Center , Houston, TX 77030, USA"}]},{"given":"Shiaw-Yih","family":"Lin","sequence":"additional","affiliation":[{"name":"Department of Systems Biology, University of Texas MD Anderson Cancer Center , Houston, TX 77030, USA"}]},{"given":"Scott L","family":"Carter","sequence":"additional","affiliation":[{"name":"Broad Institute of Massachusetts Institute of Technology and Harvard , Cambridge, MA 02142, USA"},{"name":"Department of Biostatistics, Harvard T.H. Chan School of Public Health , Boston, MA 02115, USA"},{"name":"Department of Data Sciences, Dana-Farber Cancer Institute , Boston, MA 02115, USA"}]}],"member":"286","published-online":{"date-parts":[[2022,2,17]]},"reference":[{"key":"2023021701090847600_","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1038\/ng.3564","article-title":"Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas","volume":"48","author":"Campbell","year":"2016","journal-title":"Nat. Genet"},{"key":"2023021701090847600_","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1038\/nbt.2203","article-title":"Absolute quantification of somatic DNA alterations in human cancer","volume":"30","author":"Carter","year":"2012","journal-title":"Nat. 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