{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,11]],"date-time":"2026-02-11T15:11:27Z","timestamp":1770822687867,"version":"3.50.1"},"reference-count":22,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2005,4,5]],"date-time":"2005-04-05T00:00:00Z","timestamp":1112659200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0\/"},{"start":{"date-parts":[[2005,4,5]],"date-time":"2005-04-05T00:00:00Z","timestamp":1112659200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0\/"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                        <jats:title>Background<\/jats:title>\n                        <jats:p>Array CGH (Comparative Genomic Hybridisation) is a molecular cytogenetic technique for the genome wide detection of chromosomal imbalances. It is based on the co-hybridisation of differentially labelled test and reference DNA onto arrays of genomic BAC clones, cDNAs or oligonucleotides, and after correction for various intervening variables, loss or gain in the test DNA can be indicated from spots showing aberrant signal intensity ratios.<\/jats:p>\n                        <jats:p>Now that this technique is no longer confined to highly specialized laboratories and is entering the realm of clinical application, there is a need for a user-friendly software package that facilitates estimates of DNA dosage from raw signal intensities obtained by array CGH experiments, and which does not depend on a sophisticated computational environment.<\/jats:p>\n                     <\/jats:sec><jats:sec>\n                        <jats:title>Results<\/jats:title>\n                        <jats:p>We have developed a user-friendly and versatile tool for the normalization, visualization, breakpoint detection and comparative analysis of array-CGH data. CGHPRO is a stand-alone JAVA application that guides the user through the whole process of data analysis. The import option for image analysis data covers several data formats, but users can also customize their own data formats. Several graphical representation tools assist in the selection of the appropriate normalization method. Intensity ratios of each clone can be plotted in a size-dependent manner along the chromosome ideograms. The interactive graphical interface offers the chance to explore the characteristics of each clone, such as the involvement of the clones sequence in segmental duplications. Circular Binary Segmentation and unsupervised Hidden Markov Model algorithms facilitate objective detection of chromosomal breakpoints. The storage of all essential data in a back-end database allows the simultaneously comparative analysis of different cases. The various display options facilitate also the definition of shortest regions of overlap and simplify the identification of odd clones.<\/jats:p>\n                     <\/jats:sec><jats:sec>\n                        <jats:title>Conclusion<\/jats:title>\n                        <jats:p>CGHPRO is a comprehensive and easy-to-use data analysis tool for array CGH. Since all of its features are available offline, CGHPRO may be especially suitable in situations where protection of sensitive patient data is an issue. It is distributed under GNU GPL licence and runs on Linux and Windows.<\/jats:p>\n                     <\/jats:sec>","DOI":"10.1186\/1471-2105-6-85","type":"journal-article","created":{"date-parts":[[2005,4,6]],"date-time":"2005-04-06T14:14:14Z","timestamp":1112796854000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":82,"title":["CGHPRO \u2013 A comprehensive data analysis tool for array CGH"],"prefix":"10.1186","volume":"6","author":[{"given":"Wei","family":"Chen","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fikret","family":"Erdogan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"H-Hilger","family":"Ropers","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Steffen","family":"Lenzner","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Reinhard","family":"Ullmann","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2005,4,5]]},"reference":[{"key":"410_CR1","doi-asserted-by":"publisher","first-page":"818","DOI":"10.1126\/science.1359641","volume":"258","author":"A Kallioniemi","year":"1992","unstructured":"Kallioniemi A, Kallioniemi OP, Sudar D, Rutovitz D, Gray JW, Waldman F, Pinkel D: Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 1992, 258: 818\u2013821.","journal-title":"Science"},{"key":"410_CR2","doi-asserted-by":"publisher","first-page":"399","DOI":"10.1002\/(SICI)1098-2264(199712)20:4<399::AID-GCC12>3.0.CO;2-I","volume":"20","author":"S Solinas-Toldo","year":"1997","unstructured":"Solinas-Toldo S, Lampel S, Stilgenbauer S, Nickolenko J, Benner A, Dohner H, Cremer T, Lichter P: Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances. Genes Chromosomes Cancer 1997, 20: 399\u2013407. 10.1002\/(SICI)1098-2264(199712)20:4<399::AID-GCC12>3.0.CO;2-I","journal-title":"Genes Chromosomes Cancer"},{"key":"410_CR3","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1038\/2524","volume":"20","author":"D Pinkel","year":"1998","unstructured":"Pinkel D, Segraves R, Sudar D, Clark S, Poole I, Kowbel D, Collins C, Kuo WL, Chen C, Zhai Y, Dairkee SH, Ljung BM, Gray JW, Albertson DG: High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet 1998, 20: 207\u2013211. 10.1038\/2524","journal-title":"Nat Genet"},{"key":"410_CR4","doi-asserted-by":"publisher","first-page":"299","DOI":"10.1038\/ng1307","volume":"36","author":"AS Ishkanian","year":"2004","unstructured":"Ishkanian AS, Malloff CA, Watson SK, DeLeeuw RJ, Chi B, Coe BP, Snijders A, Albertson DG, Pinkel D, Marra MA, Ling V, MacAulay C, Lam WL: A tiling resolution DNA microarray with complete coverage of the human genome. Nat Genet 2004, 36: 299\u2013303. 10.1038\/ng1307","journal-title":"Nat Genet"},{"key":"410_CR5","doi-asserted-by":"publisher","first-page":"132","DOI":"10.1016\/j.jmva.2004.02.008","volume":"90","author":"J Fridlyand","year":"2004","unstructured":"Fridlyand J, Snijders AM, Pinkel D, Albertson DG, Jain A: Hidden Markov models approach to the analysis of array CGH data. Journal of Multivariate Analysis 2004, 90: 132\u2013153. 10.1016\/j.jmva.2004.02.008","journal-title":"Journal of Multivariate Analysis"},{"key":"410_CR6","doi-asserted-by":"publisher","first-page":"557","DOI":"10.1093\/biostatistics\/kxh008","volume":"5","author":"AB Olshen","year":"2004","unstructured":"Olshen AB, Venkatraman ES, Lucito R, Wigler M: Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 2004, 5: 557\u2013572. 10.1093\/biostatistics\/kxh008","journal-title":"Biostatistics"},{"key":"410_CR7","doi-asserted-by":"publisher","first-page":"1714","DOI":"10.1093\/bioinformatics\/btg230","volume":"19","author":"R Autio","year":"2003","unstructured":"Autio R, Hautaniemi S, Kauraniemi P, Yli-Harja O, Astola J, Wolf M, Kallioniemi A: CGH-Plotter: MATLAB toolbox for CGH-data analysis. Bioinformatics 2003, 19: 1714\u20131715. 10.1093\/bioinformatics\/btg230","journal-title":"Bioinformatics"},{"key":"410_CR8","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1186\/1471-2105-5-13","volume":"5","author":"B Chi","year":"2004","unstructured":"Chi B, DeLeeuw RJ, Coe BP, MacAulay C, Lam WL: SeeGH \u2013 a software tool for visualization of whole genome array comparative genomic hybridization data. BMC Bioinformatics 2004, 5: 13. 10.1186\/1471-2105-5-13","journal-title":"BMC Bioinformatics"},{"key":"410_CR9","unstructured":"BioConductor[http:\/\/www.bioconductor.org]"},{"key":"410_CR10","doi-asserted-by":"publisher","first-page":"365","DOI":"10.1038\/ng1201-365","volume":"29","author":"A Brazma","year":"2001","unstructured":"Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M: Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 2001, 29: 365\u2013371. 10.1038\/ng1201-365","journal-title":"Nat Genet"},{"key":"410_CR11","unstructured":"Human Genome Browser Gateway[http:\/\/genome.ucsc.edu\/cgi-bin\/hgGateway]"},{"key":"410_CR12","doi-asserted-by":"publisher","first-page":"361","DOI":"10.1002\/gcc.10155","volume":"36","author":"H Fiegler","year":"2003","unstructured":"Fiegler H, Carr P, Douglas EJ, Burford DC, Hunt S, Scott CE, Smith J, Vetrie D, Gorman P, Tomlinson IP, Carter NP: DNA microarrays for comparative genomic hybridization based on DOP-PCR amplification of BAC and PAC clones. Genes Chromosomes Cancer 2003, 36: 361\u2013374. 10.1002\/gcc.10155","journal-title":"Genes Chromosomes Cancer"},{"key":"410_CR13","doi-asserted-by":"publisher","first-page":"483","DOI":"10.1101\/gr.169601","volume":"11","author":"K Osoegawa","year":"2001","unstructured":"Osoegawa K, Mammoser AG, Wu C, Frengen E, Zeng C, Catanese JJ, de Jong PJ: A bacterial artificial chromosome library for sequencing the complete human genome. Genome Res 2001, 11: 483\u2013496. 10.1101\/gr.169601","journal-title":"Genome Res"},{"key":"410_CR14","doi-asserted-by":"publisher","first-page":"3651","DOI":"10.1093\/nar\/gkh700","volume":"32","author":"M Krzywinski","year":"2004","unstructured":"Krzywinski M, Bosdet I, Smailus D, Chiu R, Mathewson C, Wye N, Barber S, Brown-John M, Chan S, Chand S, Cloutier A, Girn N, Lee D, Masson A, Mayo M, Olson T, Pandoh P, Prabhu AL, Schoenmakers E, Tsai M, Albertson D, Lam W, Choy CO, Osoegawa K, Zhao S, de Jong PJ, Schein J, Jones S, Marra MA: A set of BAC clones spanning the human genome. Nucleic Acids Res 2004, 32: 3651\u20133660. 10.1093\/nar\/gkh700","journal-title":"Nucleic Acids Res"},{"key":"410_CR15","unstructured":"MPI array CGH protocols[http:\/\/www.molgen.mpg.de\/~abt_rop\/molecular_cytogenetics\/ProtocolsEntry.html]"},{"key":"410_CR16","unstructured":"arrayCGHbase- Matrix CGH Reloaded[http:\/\/medgen.ugent.be\/arrayCGHbase\/]"},{"key":"410_CR17","unstructured":"L'Institut Curie: Bioinformatics[http:\/\/www.curie.fr\/recherche\/themes\/detail_equipecfm\/lang\/_gb\/id_equipe\/303htm]"},{"key":"410_CR18","doi-asserted-by":"publisher","first-page":"e15","DOI":"10.1093\/nar\/30.4.e15","volume":"30","author":"YH Yang","year":"2002","unstructured":"Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP: Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 2002, 30: e15. 10.1093\/nar\/30.4.e15","journal-title":"Nucleic Acids Res"},{"key":"410_CR19","doi-asserted-by":"publisher","first-page":"829","DOI":"10.1080\/01621459.1979.10481038","volume":"74","author":"WS Cleveland","year":"1979","unstructured":"Cleveland WS: Robust Locally Weighted Regression and Smoothing Scatterplots. Journal of the American Statistical Association 1979, 74: 829\u2013836.","journal-title":"Journal of the American Statistical Association"},{"key":"410_CR20","doi-asserted-by":"publisher","first-page":"1003","DOI":"10.1126\/science.1072047","volume":"297","author":"JA Bailey","year":"2002","unstructured":"Bailey JA, Gu Z, Clark RA, Reinert K, Samonte RV, Schwartz S, Adams MD, Myers EW, Li PW, Eichler EE: Recent segmental duplications in the human genome. Science 2002, 297: 1003\u20131007. 10.1126\/science.1072047","journal-title":"Science"},{"key":"410_CR21","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1136\/jmg.2003.013813","volume":"41","author":"DP Locke","year":"2004","unstructured":"Locke DP, Segraves R, Nicholls RD, Schwartz S, Pinkel D, Albertson DG, Eichler EE: BAC microarray analysis of 15q11\u2013q13 rearrangements and the impact of segmental duplications. J Med Genet 2004, 41: 175\u2013182. 10.1136\/jmg.2003.013813","journal-title":"J Med Genet"},{"key":"410_CR22","doi-asserted-by":"publisher","first-page":"74","DOI":"10.1016\/S0168-9525(02)02592-1","volume":"18","author":"P Stankiewicz","year":"2002","unstructured":"Stankiewicz P, Lupski JR: Genome architecture, rearrangements and genomic disorders. Trends Genet 2002, 18: 74\u201382. 10.1016\/S0168-9525(02)02592-1","journal-title":"Trends Genet"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-6-85.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/1471-2105-6-85\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-6-85.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,10,7]],"date-time":"2024-10-07T12:10:09Z","timestamp":1728303009000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-6-85"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2005,4,5]]},"references-count":22,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2005,12]]}},"alternative-id":["410"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-6-85","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2005,4,5]]},"assertion":[{"value":"18 November 2004","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"5 April 2005","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"5 April 2005","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"85"}}