{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,25]],"date-time":"2026-01-25T05:38:58Z","timestamp":1769319538844,"version":"3.49.0"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The advent of high-throughput sequencing technologies is revolutionizing our ability in discovering and genotyping DNA copy number variants (CNVs). Read count-based approaches are able to detect CNV regions with an unprecedented resolution. Although this computational strategy has been recently introduced in literature, much work has been already done for the preparation, normalization and analysis of this kind of data.<\/jats:p>\n               <jats:p>Results: Here we face the many aspects that cover the detection of CNVs by using read count approach. We first study the characteristics and systematic biases of read count distributions, focusing on the normalization methods designed for removing these biases. Subsequently, we compare the algorithms designed to detect the boundaries of CNVs and we investigate the ability of read count data to predict the exact number of DNA copy. Finally, we review the tools publicly available for analysing read count data. To better understand the state of the art of read count approaches, we compare the performance of the three most widely used sequencing technologies (Illumina Genome Analyzer, Roche 454 and Life Technologies SOLiD) in all the analyses that we perform.<\/jats:p>\n               <jats:p>Contact: \u00a0albertomagi@gmail.com<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr707","type":"journal-article","created":{"date-parts":[[2011,12,25]],"date-time":"2011-12-25T01:23:15Z","timestamp":1324776195000},"page":"470-478","source":"Crossref","is-referenced-by-count":68,"title":["Read count approach for DNA copy number variants detection"],"prefix":"10.1093","volume":"28","author":[{"given":"Alberto","family":"Magi","sequence":"first","affiliation":[{"name":"1 Faculty of Medicine, 2Center for the Study of Complex Dynamics (CSDC), University of Florence, Florence 50019, 3Department of Gyneacological, Obstetric and Paediatric Sciences, Medical Genetics Unit, University of Bologna, Bologna 40138 and 4Laboratory Department, Diagnostic Genetic Unit, Careggi Hospital, Florence 5014 and\\newline 5I.N.F.N, Sezione di Firenze, Florence 50100, Italy"}]},{"given":"Lorenzo","family":"Tattini","sequence":"additional","affiliation":[{"name":"1 Faculty of Medicine, 2Center for the Study of Complex Dynamics (CSDC), University of Florence, Florence 50019, 3Department of Gyneacological, Obstetric and Paediatric Sciences, Medical Genetics Unit, University of Bologna, Bologna 40138 and 4Laboratory Department, Diagnostic Genetic Unit, Careggi Hospital, Florence 5014 and\\newline 5I.N.F.N, Sezione di Firenze, Florence 50100, Italy"}]},{"given":"Tommaso","family":"Pippucci","sequence":"additional","affiliation":[{"name":"1 Faculty of Medicine, 2Center for the Study of Complex Dynamics (CSDC), University of Florence, Florence 50019, 3Department of Gyneacological, Obstetric and Paediatric Sciences, Medical Genetics Unit, University of Bologna, Bologna 40138 and 4Laboratory Department, Diagnostic Genetic Unit, Careggi Hospital, Florence 5014 and\\newline 5I.N.F.N, Sezione di Firenze, Florence 50100, Italy"}]},{"given":"Francesca","family":"Torricelli","sequence":"additional","affiliation":[{"name":"1 Faculty of Medicine, 2Center for the Study of Complex Dynamics (CSDC), University of Florence, Florence 50019, 3Department of Gyneacological, Obstetric and Paediatric Sciences, Medical Genetics Unit, University of Bologna, Bologna 40138 and 4Laboratory Department, Diagnostic Genetic Unit, Careggi Hospital, Florence 5014 and\\newline 5I.N.F.N, Sezione di Firenze, Florence 50100, Italy"}]},{"given":"Matteo","family":"Benelli","sequence":"additional","affiliation":[{"name":"1 Faculty of Medicine, 2Center for the Study of Complex Dynamics (CSDC), University of Florence, Florence 50019, 3Department of Gyneacological, Obstetric and Paediatric Sciences, Medical Genetics Unit, University of Bologna, Bologna 40138 and 4Laboratory Department, Diagnostic Genetic Unit, Careggi Hospital, Florence 5014 and\\newline 5I.N.F.N, Sezione di Firenze, Florence 50100, Italy"},{"name":"1 Faculty of Medicine, 2Center for the Study of Complex Dynamics (CSDC), University of Florence, Florence 50019, 3Department of Gyneacological, Obstetric and Paediatric Sciences, Medical Genetics Unit, University of Bologna, Bologna 40138 and 4Laboratory Department, Diagnostic Genetic Unit, Careggi Hospital, Florence 5014 and\\newline 5I.N.F.N, Sezione di Firenze, Florence 50100, Italy"},{"name":"1 Faculty of Medicine, 2Center for the Study of Complex Dynamics (CSDC), University of Florence, Florence 50019, 3Department of Gyneacological, Obstetric and Paediatric Sciences, Medical Genetics Unit, University of Bologna, Bologna 40138 and 4Laboratory Department, Diagnostic Genetic Unit, Careggi Hospital, Florence 5014 and\\newline 5I.N.F.N, Sezione di Firenze, Florence 50100, Italy"}]}],"member":"286","published-online":{"date-parts":[[2011,12,23]]},"reference":[{"key":"2023012512182963700_B1","doi-asserted-by":"crossref","first-page":"974","DOI":"10.1101\/gr.114876.110","article-title":"CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing","volume":"21","author":"Abyzov","year":"2011","journal-title":"Genome Res."},{"key":"2023012512182963700_B2","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1038\/nrg2958","article-title":"Genome structural variation discovery and genotyping","volume":"12","author":"Alkan","year":"2011","journal-title":"Nat. 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