{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,24]],"date-time":"2026-07-24T03:36:00Z","timestamp":1784864160670,"version":"3.55.0"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"17","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Tumors exhibit numerous genomic lesions such as copy number variations, structural variations and sequence variations. It is difficult to determine whether a specific constellation of lesions observed across a cohort of multiple tumors provides statistically significant evidence that the lesions target a set of genes that may be located across different chromosomes but yet are all involved in a single specific biological process or function.<\/jats:p>\n               <jats:p>Results: We introduce the genomic random interval (GRIN) statistical model and analysis method that evaluates the statistical significance of the abundance of genomic lesions that overlap a specific locus or a pre-defined set of biologically related loci. The GRIN model retains certain biologically important properties of genomic lesions that are ignored by other methods. In a simulation study and two example analyses of leukemia genomic lesion data, GRIN more effectively identified important loci as significant than did three methods based on a permutation-of-markers model. GRIN also identified biologically relevant pathways with a significant abundance of lesions in both examples.<\/jats:p>\n               <jats:p>Availability: An R package will be freely available at CRAN and www.stjuderesearch.org\/site\/depts\/biostats\/software.<\/jats:p>\n               <jats:p>Contact: \u00a0stanley.pounds@stjude.org<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt372","type":"journal-article","created":{"date-parts":[[2013,7,11]],"date-time":"2013-07-11T00:34:28Z","timestamp":1373502868000},"page":"2088-2095","source":"Crossref","is-referenced-by-count":20,"title":["A genomic random interval model for statistical analysis of genomic lesion data"],"prefix":"10.1093","volume":"29","author":[{"given":"Stan","family":"Pounds","sequence":"first","affiliation":[{"name":"1 Department of Biostatistics, 2Department of Computational Biology and 3Department of Pathology, St. Jude Children\u2019s Research Hospital, Memphis, TN 38135, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cheng","family":"Cheng","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics, 2Department of Computational Biology and 3Department of Pathology, St. Jude Children\u2019s Research Hospital, Memphis, TN 38135, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shaoyu","family":"Li","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics, 2Department of Computational Biology and 3Department of Pathology, St. Jude Children\u2019s Research Hospital, Memphis, TN 38135, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhifa","family":"Liu","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics, 2Department of Computational Biology and 3Department of Pathology, St. Jude Children\u2019s Research Hospital, Memphis, TN 38135, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinghui","family":"Zhang","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics, 2Department of Computational Biology and 3Department of Pathology, St. Jude Children\u2019s Research Hospital, Memphis, TN 38135, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charles","family":"Mullighan","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics, 2Department of Computational Biology and 3Department of Pathology, St. Jude Children\u2019s Research Hospital, Memphis, TN 38135, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2013,7,10]]},"reference":[{"key":"2023012810463859700_btt372-B1","doi-asserted-by":"crossref","first-page":"20007","DOI":"10.1073\/pnas.0710052104","article-title":"Assessing the significance of chromosomal aberration in cancer: methodology and application to glioma","volume":"104","author":"Beroukhim","year":"2007","journal-title":"Proc. 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