{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,1,26]],"date-time":"2023-01-26T05:19:58Z","timestamp":1674710398820},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"9","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The careful normalization of array-based comparative genomic hybridization (aCGH) data is of critical importance for the accurate detection of copy number changes. The difference in labelling affinity between the two fluorophores used in aCGH\u2014usually Cy5 and Cy3\u2014can be observed as a bias within the intensity distributions. If left unchecked, this bias is likely to skew data interpretation during downstream analysis and lead to an increased number of false discoveries.<\/jats:p>\n               <jats:p>Results: In this study, we have developed aCGH.Spline, a natural cubic spline interpolation method followed by linear interpolation of outlier values, which is able to remove a large portion of the dye bias from large aCGH datasets in a quick and efficient manner.<\/jats:p>\n               <jats:p>Conclusions: We have shown that removing this bias and reducing the experimental noise has a strong positive impact on the ability to detect accurately both copy number variation (CNV) and copy number alterations (CNA).<\/jats:p>\n               <jats:p>Contact: \u00a0l.larcombe@cranfield.ac.uk; tf2@sanger.ac.uk<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr107","type":"journal-article","created":{"date-parts":[[2011,2,27]],"date-time":"2011-02-27T01:13:12Z","timestamp":1298769192000},"page":"1195-1200","source":"Crossref","is-referenced-by-count":3,"title":["aCGH.Spline\u2014an R package for aCGH dye bias normalization"],"prefix":"10.1093","volume":"27","author":[{"given":"Tomas W.","family":"Fitzgerald","sequence":"first","affiliation":[{"name":"1 Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, 2Bioinformatics Group, Cranfield University, Cranfield, Bedfordshire MK43 0AL, UK and 3Inserm UMR915, l'Institut du Thorax and Centre Hospitalier Universitaire (CHU), Nantes, France"}]},{"given":"Lee D.","family":"Larcombe","sequence":"additional","affiliation":[{"name":"1 Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, 2Bioinformatics Group, Cranfield University, Cranfield, Bedfordshire MK43 0AL, UK and 3Inserm UMR915, l'Institut du Thorax and Centre Hospitalier Universitaire (CHU), Nantes, France"}]},{"given":"Solena","family":"Le Scouarnec","sequence":"additional","affiliation":[{"name":"1 Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, 2Bioinformatics Group, Cranfield University, Cranfield, Bedfordshire MK43 0AL, UK and 3Inserm UMR915, l'Institut du Thorax and Centre Hospitalier Universitaire (CHU), Nantes, France"}]},{"given":"Stephen","family":"Clayton","sequence":"additional","affiliation":[{"name":"1 Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, 2Bioinformatics Group, Cranfield University, Cranfield, Bedfordshire MK43 0AL, UK and 3Inserm UMR915, l'Institut du Thorax and Centre Hospitalier Universitaire (CHU), Nantes, France"}]},{"given":"Diana","family":"Rajan","sequence":"additional","affiliation":[{"name":"1 Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, 2Bioinformatics Group, Cranfield University, Cranfield, Bedfordshire MK43 0AL, UK and 3Inserm UMR915, l'Institut du Thorax and Centre Hospitalier Universitaire (CHU), Nantes, France"}]},{"given":"Nigel P.","family":"Carter","sequence":"additional","affiliation":[{"name":"1 Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, 2Bioinformatics Group, Cranfield University, Cranfield, Bedfordshire MK43 0AL, UK and 3Inserm UMR915, l'Institut du Thorax and Centre Hospitalier Universitaire (CHU), Nantes, France"}]},{"given":"Richard","family":"Redon","sequence":"additional","affiliation":[{"name":"1 Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, 2Bioinformatics Group, Cranfield University, Cranfield, Bedfordshire MK43 0AL, UK and 3Inserm UMR915, l'Institut du Thorax and Centre Hospitalier Universitaire (CHU), Nantes, France"}]}],"member":"286","published-online":{"date-parts":[[2011,2,25]]},"reference":[{"key":"2023012512170963700_B1","doi-asserted-by":"crossref","first-page":"194","DOI":"10.1186\/1471-2105-5-194","article-title":"Optimized LOWESS normalization parameter selection for DNA microarray data","volume":"5","author":"Berger","year":"2004","journal-title":"BMC bioinformatics"},{"key":"2023012512170963700_B2","first-page":"48","article-title":"Computational methods for the analysis of array comparative genomic hybridization","volume":"2","author":"Chari","year":"2007","journal-title":"Cancer Inform."},{"key":"2023012512170963700_B3","doi-asserted-by":"crossref","first-page":"704","DOI":"10.1038\/nature08516","article-title":"Origins and functional impact of copy number variation in the human genome","volume":"464","author":"Conrad","year":"2010","journal-title":"Nature"},{"key":"2023012512170963700_B4","doi-asserted-by":"crossref","first-page":"1566","DOI":"10.1101\/gr.5630906","article-title":"Accurate and reliable high-throughput detection of copy number variation in the human genome","volume":"16","author":"Fiegler","year":"2006","journal-title":"Genome Res."},{"key":"2023012512170963700_B5","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1186\/1755-8417-1-4","article-title":"Mechanisms for human genomic rearrangements","volume":"1","author":"Gu","year":"2008","journal-title":"PathoGenetics"},{"key":"2023012512170963700_B6","doi-asserted-by":"crossref","first-page":"R228.1","DOI":"10.1186\/gb-2007-8-10-r228","article-title":"Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization","volume":"8","author":"Marioni","year":"2007","journal-title":"Genome Biol."},{"key":"2023012512170963700_B7","article-title":"Curve fitting","volume-title":"Numerical Methods for Mathematics, Science and Engineering.","author":"Mathews","year":"1992","edition":"2"},{"key":"2023012512170963700_B8","doi-asserted-by":"crossref","first-page":"264","DOI":"10.1186\/1471-2105-7-264","article-title":"Spatial normalization of array-CGH data","volume":"7","author":"Neuvial","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023012512170963700_B9","doi-asserted-by":"crossref","first-page":"R2.1","DOI":"10.1186\/gb-2007-8-1-r2","article-title":"Normalization of boutique two-color microarrays with a high proportion of differentially expressed probes","volume":"8","author":"Oshlack","year":"2007","journal-title":"Genome Biol."},{"key":"2023012512170963700_B10","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1093\/bioinformatics\/btm601","article-title":"Sparse representation and Bayesian detection of genome copy number alterations from microarray data","volume":"24","author":"Pique-Regi","year":"2008","journal-title":"Bioinformatics"},{"key":"2023012512170963700_B11","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1186\/1471-2105-8-203","article-title":"Using expression arrays for copy number detection: an example from E. coli","volume":"8","author":"Skvortsov","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"2023012512170963700_B12","doi-asserted-by":"crossref","first-page":"e1000734","DOI":"10.1371\/journal.pgen.1000734","article-title":"Maize inbreds exhibit high levels of copy number variation (CNV) and presence\/absence variation (PAV) in genome content","volume":"5","author":"Springer","year":"2009","journal-title":"PLoS Genet."},{"key":"2023012512170963700_B13","doi-asserted-by":"crossref","first-page":"382","DOI":"10.1186\/1471-2164-8-382","article-title":"Normalization of array-CGH data: influence of copy number imbalances","volume":"8","author":"Staaf","year":"2007","journal-title":"BMC Genomics"},{"key":"2023012512170963700_B14","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1186\/1471-2164-10-401","article-title":"CGHnormaliter: an iterative strategy to enhance normalization of array CGH data with imbalanced aberrations","volume":"10","author":"van Houte","year":"2009","journal-title":"BMC Genomics"},{"key":"2023012512170963700_B15","doi-asserted-by":"crossref","first-page":"892","DOI":"10.1093\/bioinformatics\/btm030","article-title":"CGHcall: calling aberrations for array CGH tumor profiles","volume":"23","author":"van de Wiel","year":"2007","journal-title":"Bioinformatics"},{"key":"2023012512170963700_B16","doi-asserted-by":"crossref","first-page":"783","DOI":"10.2174\/1386207043328274","article-title":"Normalization of cDNA microarray data using wavelet regressions","volume":"7","author":"Wang","year":"2004","journal-title":"Comb. Chem. High Throughput Screen."},{"key":"2023012512170963700_B17","doi-asserted-by":"crossref","first-page":"0048.1","DOI":"10.1186\/gb-2002-3-9-research0048","article-title":"A new non-linear normalization method for reducing variability in DNA microarray experiments","volume":"3","author":"Workman","year":"2002","journal-title":"Genome Biol."},{"key":"2023012512170963700_B18","doi-asserted-by":"crossref","first-page":"e15","DOI":"10.1093\/nar\/30.4.e15","article-title":"Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation","volume":"30","author":"Yang","year":"2002","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/9\/1195\/48866914\/bioinformatics_27_9_1195.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/9\/1195\/48866914\/bioinformatics_27_9_1195.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T14:49:35Z","timestamp":1674658175000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/9\/1195\/241886"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,2,25]]},"references-count":18,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2011,5,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr107","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2011,5,1]]},"published":{"date-parts":[[2011,2,25]]}}}