{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,6]],"date-time":"2026-05-06T16:02:21Z","timestamp":1778083341890,"version":"3.51.4"},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Genomic instability in cancer leads to abnormal genome copy number alterations (CNA) that are associated with the development and behavior of tumors. Advances in microarray technology have allowed for greater resolution in detection of DNA copy number changes (amplifications or deletions) across the genome. However, the increase in number of measured signals and accompanying noise from the array probes present a challenge in accurate and fast identification of breakpoints that define CNA. This article proposes a novel detection technique that exploits the use of piece wise constant (PWC) vectors to represent genome copy number and sparse Bayesian learning (SBL) to detect CNA breakpoints.<\/jats:p>\n               <jats:p>Methods: First, a compact linear algebra representation for the genome copy number is developed from normalized probe intensities. Second, SBL is applied and optimized to infer locations where copy number changes occur. Third, a backward elimination (BE) procedure is used to rank the inferred breakpoints; and a cut-off point can be efficiently adjusted in this procedure to control for the false discovery rate (FDR).<\/jats:p>\n               <jats:p>Results: The performance of our algorithm is evaluated using simulated and real genome datasets and compared to other existing techniques. Our approach achieves the highest accuracy and lowest FDR while improving computational speed by several orders of magnitude. The proposed algorithm has been developed into a free standing software application (GADA, Genome Alteration Detection Algorithm).<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/biron.usc.edu\/~piquereg\/GADA<\/jats:p>\n               <jats:p>Contact: \u00a0shahab@chla.usc.edu and rpique@ieee.org<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm601","type":"journal-article","created":{"date-parts":[[2008,1,19]],"date-time":"2008-01-19T01:34:46Z","timestamp":1200706486000},"page":"309-318","source":"Crossref","is-referenced-by-count":105,"title":["Sparse representation and Bayesian detection of genome copy number alterations from microarray data"],"prefix":"10.1093","volume":"24","author":[{"given":"Roger","family":"Pique-Regi","sequence":"first","affiliation":[{"name":"1 Signal and Image Processing Institute, Ming Hsieh Department of Electrical Engineering, Viterbi School of Engineering, University of Southern California, EEB 400, 3740 McClintock Ave, Los Angeles, CA 90089-2564 and 2Departments of Pediatrics and Pathology, Saban Research Institute, Childrens Hospital Los Angeles, Keck School of Medicine, University of Southern California, USA"},{"name":"1 Signal and Image Processing Institute, Ming Hsieh Department of Electrical Engineering, Viterbi School of Engineering, University of Southern California, EEB 400, 3740 McClintock Ave, Los Angeles, CA 90089-2564 and 2Departments of Pediatrics and Pathology, Saban Research Institute, Childrens Hospital Los Angeles, Keck School of Medicine, University of Southern California, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jordi","family":"Monso-Varona","sequence":"additional","affiliation":[{"name":"1 Signal and Image Processing Institute, Ming Hsieh Department of Electrical Engineering, Viterbi School of Engineering, University of Southern California, EEB 400, 3740 McClintock Ave, Los Angeles, CA 90089-2564 and 2Departments of Pediatrics and Pathology, Saban Research Institute, Childrens Hospital Los Angeles, Keck School of Medicine, University of Southern California, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Antonio","family":"Ortega","sequence":"additional","affiliation":[{"name":"1 Signal and Image Processing Institute, Ming Hsieh Department of Electrical Engineering, Viterbi School of Engineering, University of Southern California, EEB 400, 3740 McClintock Ave, Los Angeles, CA 90089-2564 and 2Departments of Pediatrics and Pathology, Saban Research Institute, Childrens Hospital Los Angeles, Keck School of Medicine, University of Southern California, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Robert C.","family":"Seeger","sequence":"additional","affiliation":[{"name":"1 Signal and Image Processing Institute, Ming Hsieh Department of Electrical Engineering, Viterbi School of Engineering, University of Southern California, EEB 400, 3740 McClintock Ave, Los Angeles, CA 90089-2564 and 2Departments of Pediatrics and Pathology, Saban Research Institute, Childrens Hospital Los Angeles, Keck School of Medicine, University of Southern California, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Timothy J.","family":"Triche","sequence":"additional","affiliation":[{"name":"1 Signal and Image Processing Institute, Ming Hsieh Department of Electrical Engineering, Viterbi School of Engineering, University of Southern California, EEB 400, 3740 McClintock Ave, Los Angeles, CA 90089-2564 and 2Departments of Pediatrics and Pathology, Saban Research Institute, Childrens Hospital Los Angeles, Keck School of Medicine, University of Southern California, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shahab","family":"Asgharzadeh","sequence":"additional","affiliation":[{"name":"1 Signal and Image Processing Institute, Ming Hsieh Department of Electrical Engineering, Viterbi School of Engineering, University of Southern California, EEB 400, 3740 McClintock Ave, Los Angeles, CA 90089-2564 and 2Departments of Pediatrics and Pathology, Saban Research Institute, Childrens Hospital Los Angeles, Keck School of Medicine, University of Southern California, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2008,2,1]]},"reference":[{"key":"2023061011440322400_B1","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1038\/ng1215","article-title":"Chromosome aberrations in solid tumors","volume":"34","author":"Albertson","year":"2003","journal-title":"Nat. Genet"},{"key":"2023061011440322400_B2","doi-asserted-by":"crossref","first-page":"911","DOI":"10.1093\/bioinformatics\/btl035","article-title":"Detection of gene copy number changes in CGH microarrays using a spatially correlated mixture model","volume":"22","author":"Broet","year":"2006","journal-title":"Bioinformatics"},{"key":"2023061011440322400_B3","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1137\/S1064827596304010","article-title":"Atomic decomposition by basis pursuit","volume":"20","author":"Chen","year":"1998","journal-title":"SIAM J. Sci. Comput"},{"key":"2023061011440322400_B4","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1109\/TIT.2005.860430","article-title":"Stable recovery of sparse overcomplete representations in the presence of noise","volume":"52","author":"Donoho","year":"2006","journal-title":"IEEE T. Inform. Theory"},{"key":"2023061011440322400_B5","doi-asserted-by":"crossref","first-page":"1306","DOI":"10.1109\/TSP.2003.810296","article-title":"Wavelet footprints: Theory, algorithms, and applications","volume":"51","author":"Dragotti","year":"2002","journal-title":"IEEE T. Signal Proces"},{"key":"2023061011440322400_B6","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1093\/biostatistics\/kxj015","article-title":"A pseudolikelihood approach for simultaneous analysis of array comparative genomic hybridizations","volume":"7","author":"Engler","year":"2006","journal-title":"Biostatistics"},{"key":"2023061011440322400_B7","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. Multivariate Anal"},{"key":"2023061011440322400_B8","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1038\/nature03664","article-title":"Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma","volume":"436","author":"Garraway","year":"2005","journal-title":"Nature"},{"key":"2023061011440322400_B9","doi-asserted-by":"crossref","DOI":"10.1007\/978-0-387-21606-5","volume-title":"The Elements of Statistical Learning.","author":"Hastie","year":"2001"},{"key":"2023061011440322400_B10","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1093\/biostatistics\/kxi004","article-title":"Denoising array-based comparative genomic hybridization data using wavelets","volume":"6","author":"Hsu","year":"2005","journal-title":"Biostatistics"},{"key":"2023061011440322400_B11","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1186\/1479-7364-1-4-287","article-title":"Whole genome DNA copy number changes identified by high density oligonucleotide arrays","volume":"1","author":"Huang","year":"2004","journal-title":"Hum. Genomics"},{"key":"2023061011440322400_B12","doi-asserted-by":"crossref","first-page":"3811","DOI":"10.1093\/bioinformatics\/bti646","article-title":"Detection of DNA copy number alterations using penalized least squares regression","volume":"21","author":"Huang","year":"2005","journal-title":"Bioinformatics"},{"key":"2023061011440322400_B13","doi-asserted-by":"crossref","first-page":"3413","DOI":"10.1093\/bioinformatics\/bth418","article-title":"Analysis of array cgh data: from signal ratio to gain and loss of dna regions","volume":"20","author":"Hupe","year":"2004","journal-title":"Bioinformatics"},{"key":"2023061011440322400_B14","doi-asserted-by":"crossref","first-page":"818","DOI":"10.1126\/science.1359641","article-title":"Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors","volume":"258","author":"Kallioniemi","year":"1992","journal-title":"Science"},{"key":"2023061011440322400_B15","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1016\/S0004-3702(97)00043-X","article-title":"Wrappers for feature subset selection","volume":"97","author":"Kohavi","year":"1997","journal-title":"Artif. Intell"},{"key":"2023061011440322400_B16","doi-asserted-by":"crossref","first-page":"1575","DOI":"10.1101\/gr.5629106","article-title":"Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays","volume":"16","author":"Komura","year":"2006","journal-title":"Genome Res"},{"key":"2023061011440322400_B17","doi-asserted-by":"crossref","first-page":"1151","DOI":"10.1002\/int.20043","article-title":"Probable equivalence, superpower sets, and superconditionals","volume":"19","author":"Kosko","year":"2004","journal-title":"Int. J. Intell. Sys"},{"key":"2023061011440322400_B18","doi-asserted-by":"crossref","first-page":"3763","DOI":"10.1093\/bioinformatics\/bti611","article-title":"Comparative analysis of algorithms for identifying amplifications and deletions in array cgh data","volume":"21","author":"Lai","year":"2005","journal-title":"Bioinformatics"},{"key":"2023061011440322400_B19","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1089\/cmb.2006.13.215","article-title":"Efficient calculation of interval scores for DNA copy number data analysis","volume":"13","author":"Lipson","year":"2006","journal-title":"J. Comput. Biol"},{"key":"2023061011440322400_B20","doi-asserted-by":"crossref","first-page":"3397","DOI":"10.1109\/78.258082","article-title":"Matching pursuits with time-frequency dictionaries","volume":"41","author":"Mallat","year":"1993","journal-title":"IEEE. Trans. Signal proces"},{"key":"2023061011440322400_B21","doi-asserted-by":"crossref","first-page":"1144","DOI":"10.1093\/bioinformatics\/btl089","article-title":"BioHMM: a heterogeneous hidden markov model for segmenting array CGH data","volume":"22","author":"Marioni","year":"2006","journal-title":"Bioinformatics"},{"key":"2023061011440322400_B22","volume-title":"The EM Algorithm and Extensions.","author":"McLachlan","year":"1997"},{"key":"2023061011440322400_B23","doi-asserted-by":"crossref","first-page":"6071","DOI":"10.1158\/0008-5472.CAN-05-0465","article-title":"A robust algorithm for copy number detection using high-density oligonucleotide single nucleotide polymorphism genotyping arrays","volume":"65","author":"Nannya","year":"2005","journal-title":"Cancer Res"},{"key":"2023061011440322400_B24","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1093\/biostatistics\/kxh008","article-title":"Circular binary segmentation for the analysis of array-based DNA copy number data","volume":"5","author":"Olshen","year":"2004","journal-title":"Biostatistics"},{"key":"2023061011440322400_B25","doi-asserted-by":"crossref","DOI":"10.1109\/ACSSC.1993.342465","article-title":"Orthogonal matching pursuit: Recursive function approximation with applications to wavelet decomposition","author":"Pati","year":"1993"},{"key":"2023061011440322400_B26","doi-asserted-by":"crossref","first-page":"1136","DOI":"10.1101\/gr.5402306","article-title":"High-resolution genomic profiling of chromosomal aberrations using infinium whole-genome genotyping","volume":"16","author":"Peiffer","year":"2006","journal-title":"Genome Res"},{"key":"2023061011440322400_B27","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1186\/1471-2105-6-27","article-title":"A statistical approach for array CGH data analysis","volume":"6","author":"Picard","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"2023061011440322400_B28","doi-asserted-by":"crossref","DOI":"10.1109\/ICASSP.2007.366689","article-title":"Wavelet footprints and sparse bayesian learning for DNA copy number change analysis","author":"Pique-Regi","year":"2007"},{"key":"2023061011440322400_B29","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1038\/12640","article-title":"Genome-wide analysis of DNA copy-number changes using cDNA microarrays","volume":"23","author":"Pollack","year":"1999","journal-title":"Nat. Genet"},{"key":"2023061011440322400_B30","doi-asserted-by":"crossref","first-page":"444","DOI":"10.1038\/nature05329","article-title":"Global variation in copy number in the human genome","volume":"444","author":"Redon","year":"2006","journal-title":"Nature"},{"key":"2023061011440322400_B31","doi-asserted-by":"crossref","first-page":"e122","DOI":"10.1371\/journal.pcbi.0030122","article-title":"Flexible and accurate detection of genomic copy-number changes from acgh","volume":"3","author":"Rueda","year":"2007","journal-title":"PLoS Comput. Biol"},{"key":"2023061011440322400_B32","doi-asserted-by":"crossref","DOI":"10.1002\/9780471722199","volume-title":"Linear Regression Analysis.","author":"Seber","year":"2003","edition":"second edition"},{"key":"2023061011440322400_B33","doi-asserted-by":"crossref","first-page":"e431","DOI":"10.1093\/bioinformatics\/btl238","article-title":"Integrating copy number polymorphisms into array cgh analysis using a robust hmm","volume":"22","author":"Shah","year":"2006","journal-title":"Bioinformatics"},{"key":"2023061011440322400_B34","first-page":"211","article-title":"Sparse bayesian learning and the relevance vector machine","volume":"1","author":"Tipping","year":"2001","journal-title":"J. Mach. Learn. Res"},{"key":"2023061011440322400_B35","doi-asserted-by":"crossref","first-page":"657","DOI":"10.1093\/bioinformatics\/btl646","article-title":"A faster circular binary segmentation algorithm for the analysis of array CGH data","volume":"23","author":"Venkatraman","year":"2007","journal-title":"Bioinformatics"},{"key":"2023061011440322400_B36","doi-asserted-by":"crossref","first-page":"4084","DOI":"10.1093\/bioinformatics\/bti677","article-title":"A comparison study: applying segmentation to array CGH data for downstream analyses","volume":"21","author":"Willenbrock","year":"2005","journal-title":"Bioinformatics"},{"key":"2023061011440322400_B37","doi-asserted-by":"crossref","first-page":"2153","DOI":"10.1109\/TSP.2004.831016","article-title":"Sparse Bayesian learning for basis selection","volume":"52","author":"Wipf","year":"2004","journal-title":"IEEE. Trans. Signal Proces"},{"key":"2023061011440322400_B38","doi-asserted-by":"crossref","first-page":"3060","DOI":"10.1158\/0008-5472.CAN-03-3308","article-title":"An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays","volume":"64","author":"Zhao","year":"2004","journal-title":"Cancer Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/3\/309\/50568048\/bioinformatics_24_3_309.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/3\/309\/50568048\/bioinformatics_24_3_309.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,10]],"date-time":"2023-06-10T11:45:23Z","timestamp":1686397523000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/24\/3\/309\/253648"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,2,1]]},"references-count":38,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2008,2,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btm601","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2008,2,1]]},"published":{"date-parts":[[2008,2,1]]}}}