{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,6]],"date-time":"2025-12-06T07:07:13Z","timestamp":1765004833754},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"22","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2005,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Array comparative genomic hybridization (CGH) allows detection and mapping of copy number of DNA segments. A challenge is to make inferences about the copy number structure of the genome. Several statistical methods have been proposed to determine genomic segments with different copy number levels. However, to date, no comprehensive comparison of various characteristics of these methods exists. Moreover, the segmentation results have not been utilized in downstream analyses.<\/jats:p>\n               <jats:p>Results: We describe a comparison of three popular and publicly available methods for the analysis of array CGH data and we demonstrate how segmentation results may be utilized in the downstream analyses such as testing and classification, yielding higher power and prediction accuracy. Since the methods operate on individual chromosomes, we also propose a novel procedure for merging segments across the genome, which results in an interpretable set of copy number levels, and thus facilitate identification of copy number alterations in each genome.<\/jats:p>\n               <jats:p>Availability: \u00a0<\/jats:p>\n               <jats:p>Contact: \u00a0jfridlyand@cc.ucsf.edu<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0<\/jats:p>","DOI":"10.1093\/bioinformatics\/bti677","type":"journal-article","created":{"date-parts":[[2005,9,14]],"date-time":"2005-09-14T03:13:12Z","timestamp":1126667592000},"page":"4084-4091","source":"Crossref","is-referenced-by-count":232,"title":["A comparison study: applying segmentation to array CGH data for downstream analyses"],"prefix":"10.1093","volume":"21","author":[{"given":"Hanni","family":"Willenbrock","sequence":"first","affiliation":[{"name":"Center for Biological Sequence Analysis, Department of Biotechnology 1 \u00a0 1 \u00a0 \u00a0 Building 208, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark"}]},{"given":"Jane","family":"Fridlyand","sequence":"additional","affiliation":[{"name":"Department of Epidemiology and Biostatistics, University of California at San Francisco 2 \u00a0 2 \u00a0 \u00a0 2340 Sutter Street, N224, San Francisco, CA 94143, USA"}]}],"member":"286","published-online":{"date-parts":[[2005,9,13]]},"reference":[{"key":"2023061007105737600_b1","doi-asserted-by":"crossref","first-page":"687","DOI":"10.1080\/01621459.1972.10481279","article-title":"Constructing confidence sets using rank statistics","volume":"67","author":"Bauer","year":"1972","journal-title":"J. Am. Stat. Assoc."},{"key":"2023061007105737600_b2","doi-asserted-by":"crossref","first-page":"16292","DOI":"10.1073\/pnas.0407247101","article-title":"A versatile statistical analysis algorithm to detect genome copy number variation","volume":"101","author":"Daruwala","year":"2004","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023061007105737600_b3","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1198\/016214502753479248","article-title":"Comparison of discrimination methods for the classification of tumors using gene expression data","volume":"97","author":"Dudoit","year":"2002","journal-title":"J. Am. Stat. Assoc."},{"key":"2023061007105737600_b4","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1016\/j.jmva.2004.02.008","article-title":"Hidden Markov models approach to the analysis of array CGH data","volume":"90","author":"Fridlyand","year":"2004","journal-title":"J. Multivar. Anal."},{"key":"2023061007105737600_b5","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1038\/ng771","article-title":"Genome scanning with array CGH delineates regional alterations in mouse islet carcinomas","volume":"29","author":"Hodgson","year":"2001","journal-title":"Nat. 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