{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,6]],"date-time":"2025-12-06T16:59:36Z","timestamp":1765040376872},"reference-count":18,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2010,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Multiplex Ligation-Dependent Probe Amplification (MLPA) is an application that can be used for the detection of multiple chromosomal aberrations in a single experiment. In one reaction, up to 50 different genomic sequences can be analysed. For a reliable work-flow, tools are needed for administrative support, data management, normalisation, visualisation, reporting and interpretation.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>Here, we developed a data management system, <jats:italic>MLPAInter<\/jats:italic> for MLPA interpretation, that is windows executable and has a stand-alone database for monitoring and interpreting the MLPA data stream that is generated from the experimental setup to analysis, quality control and visualisation. A statistical approach is applied for the normalisation and analysis of large series of MLPA traces, making use of multiple control samples and internal controls.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>\n              <jats:italic>MLPAinter<\/jats:italic> visualises MLPA data in plots with information about sample replicates, normalisation settings, and sample characteristics. This integrated approach helps in the automated handling of large series of MLPA data and guarantees a quick and streamlined dataflow from the beginning of an experiment to an authorised report.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-11-67","type":"journal-article","created":{"date-parts":[[2012,6,28]],"date-time":"2012-06-28T13:01:21Z","timestamp":1340888481000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["MLPAinter for MLPA interpretation: an integrated approach for the analysis, visualisation and data management of Multiplex Ligation-dependent Probe Amplification"],"prefix":"10.1186","volume":"11","author":[{"given":"Ronald","family":"van Eijk","sequence":"first","affiliation":[]},{"given":"Paul HC","family":"Eilers","sequence":"additional","affiliation":[]},{"given":"Remco","family":"Natt\u00e9","sequence":"additional","affiliation":[]},{"given":"Anne-Marie","family":"Cleton-Jansen","sequence":"additional","affiliation":[]},{"given":"Hans","family":"Morreau","sequence":"additional","affiliation":[]},{"given":"Tom","family":"van Wezel","sequence":"additional","affiliation":[]},{"given":"Jan","family":"Oosting","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2010,1,29]]},"reference":[{"key":"3524_CR1","doi-asserted-by":"publisher","first-page":"341","DOI":"10.1038\/ng1197-341","volume":"17","author":"A Petrij-Bosch","year":"1997","unstructured":"Petrij-Bosch A, Peelen T, van Vliet M, van Eijk R, Olmer R, Drusedau M, Hogervorst FB, Hageman S, Arts PJ, Ligtenberg MJ, et al.: BRCA1 genomic deletions are major founder mutations in Dutch breast cancer patients. Nat Genet 1997, 17: 341\u2013345. 10.1038\/ng1197-341","journal-title":"Nat Genet"},{"key":"3524_CR2","first-page":"55","volume":"51","author":"K Klinger","year":"1992","unstructured":"Klinger K, Landes G, Shook D, Harvey R, Lopez L, Locke P, Lerner T, Osathanondh R, Leverone B, Houseal T, et al.: Rapid detection of chromosome aneuploidies in uncultured amniocytes by using fluorescence in situ hybridization (FISH). Am J Hum Genet 1992, 51: 55\u201365.","journal-title":"Am J Hum Genet"},{"key":"3524_CR3","doi-asserted-by":"publisher","first-page":"569","DOI":"10.1016\/S0168-9525(01)02416-7","volume":"17","author":"P Devilee","year":"2001","unstructured":"Devilee P, Cleton-Jansen AM, Cornelisse CJ: Ever since Knudson. Trends Genet 2001, 17: 569\u2013573. 10.1016\/S0168-9525(01)02416-7","journal-title":"Trends Genet"},{"key":"3524_CR4","doi-asserted-by":"publisher","first-page":"1253","DOI":"10.1016\/S0002-9440(10)64076-X","volume":"158","author":"JM Nigro","year":"2001","unstructured":"Nigro JM, Takahashi MA, Ginzinger DG, Law M, Passe S, Jenkins RB, Aldape K: Detection of 1p and 19q loss in oligodendroglioma by quantitative microsatellite analysis a real-time quantitative polymerase chain reaction assay. Am J Pathol 2001, 158: 1253\u20131262.","journal-title":"Am J Pathol"},{"key":"3524_CR5","doi-asserted-by":"publisher","first-page":"4817","DOI":"10.1158\/0008-5472.CAN-04-0328","volume":"64","author":"EJ Douglas","year":"2004","unstructured":"Douglas EJ, Fiegler H, Rowan A, Halford S, Bicknell DC, Bodmer W, Tomlinson IP, Carter NP: Array comparative genomic hybridization analysis of colorectal cancer cell lines and primary carcinomas. Cancer Res 2004, 64: 4817\u20134825. 10.1158\/0008-5472.CAN-04-0328","journal-title":"Cancer Res"},{"key":"3524_CR6","doi-asserted-by":"publisher","first-page":"10188","DOI":"10.1158\/0008-5472.CAN-05-2486","volume":"65","author":"EH Lips","year":"2005","unstructured":"Lips EH, Dierssen JW, van Eijk R, Oosting J, Eilers PH, Tollenaar RA, de Graaf EJ, van't Slot R, Wijmenga C, Morreau H, et al.: Reliable high-throughput genotyping and loss-of-heterozygosity detection in formalin-fixed, paraffin-embedded tumors using single nucleotide polymorphism arrays. Cancer Res 2005, 65: 10188\u201310191. 10.1158\/0008-5472.CAN-05-2486","journal-title":"Cancer Res"},{"key":"3524_CR7","doi-asserted-by":"crossref","unstructured":"Schouten JP, McElgunn CJ, Waaijer R, Zwijnenburg D, Diepvens F, Pals G: Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification. Nucleic Acids Res 2002., 30(e57):","DOI":"10.1093\/nar\/gnf056"},{"key":"3524_CR8","doi-asserted-by":"publisher","first-page":"329","DOI":"10.1089\/109065703322783707","volume":"7","author":"A Erlandson","year":"2003","unstructured":"Erlandson A, Samuelsson L, Hagberg B, Kyllerman M, Vujic M, Wahlstrom J: Multiplex ligation-dependent probe amplification (MLPA) detects large deletions in the MECP2 gene of Swedish Rett syndrome patients. Genet Test 2003, 7: 329\u2013332. 10.1089\/109065703322783707","journal-title":"Genet Test"},{"key":"3524_CR9","doi-asserted-by":"publisher","first-page":"192","DOI":"10.1111\/j.1750-3639.2005.tb00520.x","volume":"15","author":"R Natte","year":"2005","unstructured":"Natte R, van Eijk R, Eilers P, Cleton-Jansen AM, Oosting J, Kouwenhove M, Kros JM, van Duinen S: Multiplex ligation-dependent probe amplification for the detection of 1p and 19q chromosomal loss in oligodendroglial tumors. Brain Pathol 2005, 15: 192\u2013197.","journal-title":"Brain Pathol"},{"key":"3524_CR10","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1097\/01.pas.0000146701.98954.47","volume":"14","author":"MC van Dijk","year":"2005","unstructured":"van Dijk MC, Rombout PD, Boots-Sprenger SH, Straatman H, Bernsen MR, Ruiter DJ, Jeuken JW: Multiplex ligation-dependent probe amplification for the detection of chromosomal gains and losses in formalin-fixed tissue. Diagn Mol Pathol 2005, 14: 9\u201316. 10.1097\/01.pas.0000146701.98954.47","journal-title":"Diagn Mol Pathol"},{"key":"3524_CR11","doi-asserted-by":"publisher","first-page":"396","DOI":"10.1093\/jnci\/djk067","volume":"99","author":"L Hameetman","year":"2007","unstructured":"Hameetman L, Szuhai K, Yavas A, Knijnenburg J, van Duin M, van Dekken H, Taminiau AH, Cleton-Jansen AM, Bovee JV, Hogendoorn PC: The role of EXT1 in nonhereditary osteochondroma: identification of homozygous deletions. J Natl Cancer Inst 2007, 99: 396\u2013406. 10.1093\/jnci\/djk067","journal-title":"J Natl Cancer Inst"},{"key":"3524_CR12","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1002\/ajmg.c.30132","volume":"145","author":"S Kantarci","year":"2007","unstructured":"Kantarci S, Donahoe PK: Congenital diaphragmatic hernia (CDH) etiology as revealed by pathway genetics. Am J Med Genet C Semin Med Genet 2007, 145: 217\u2013226.","journal-title":"Am J Med Genet C Semin Med Genet"},{"key":"3524_CR13","doi-asserted-by":"publisher","first-page":"4627","DOI":"10.1002\/elps.200800126","volume":"29","author":"P Kozlowski","year":"2008","unstructured":"Kozlowski P, Jasinska AJ, Kwiatkowski DJ: New applications and developments in the use of multiplex ligation-dependent probe amplification. Electrophoresis 2008, 29: 4627\u20134636. 10.1002\/elps.200800126","journal-title":"Electrophoresis"},{"key":"3524_CR14","doi-asserted-by":"publisher","first-page":"4327","DOI":"10.1002\/elps.200500390","volume":"26","author":"T Gerdes","year":"2005","unstructured":"Gerdes T, Kirchhoff M, Bryndorf T: Automatic analysis of multiplex ligation-dependent probe amplification products (exemplified by a commercial kit for prenatal aneuploidy detection). Electrophoresis 2005, 26: 4327\u20134332. 10.1002\/elps.200500390","journal-title":"Electrophoresis"},{"key":"3524_CR15","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1186\/1471-2350-8-9","volume":"8","author":"JW Ahn","year":"2007","unstructured":"Ahn JW, Ogilvie CM, Welch A, Thomas H, Madula R, Hills A, Donaghue C, Mann K: Detection of subtelomere imbalance using MLPA: validation, development of an analysis protocol and application in a diagnostic centre. BMC Med Genet 2007, 8: 9. 10.1186\/1471-2350-8-9","journal-title":"BMC Med Genet"},{"key":"3524_CR16","first-page":"323","volume":"30","author":"J Coffa","year":"2008","unstructured":"Coffa J, Wiel MA, Diosdado B, Carvalho B, Schouten J, Meijer GA: MLPAnalyzer: data analysis tool for reliable automated normalization of MLPA fragment data. Cell Oncol 2008, 30: 323\u2013335.","journal-title":"Cell Oncol"},{"key":"3524_CR17","doi-asserted-by":"publisher","first-page":"RESEARCH0034","DOI":"10.1186\/gb-2002-3-7-research0034","volume":"3","author":"J Vandesompele","year":"2002","unstructured":"Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F: Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 2002, 3: RESEARCH0034. 10.1186\/gb-2002-3-7-research0034","journal-title":"Genome Biol"},{"key":"3524_CR18","doi-asserted-by":"publisher","first-page":"10333","DOI":"10.1158\/0008-5472.CAN-08-2665","volume":"68","author":"WE Corver","year":"2008","unstructured":"Corver WE, Middeldorp A, ter Haar NT, Jordanova ES, van Puijenbroek M, van Eijk R, Cornelisse CJ, Fleuren GJ, Morreau H, Oosting J, van Wezel T: Genome-wide allelic state analysis on flow-sorted tumor fractions provides an accurate measure of chromosomal aberrations. Cancer Res 2008, 68: 10333\u201310340. 10.1158\/0008-5472.CAN-08-2665","journal-title":"Cancer Res"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-11-67.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T05:15:52Z","timestamp":1630473352000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-11-67"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,1,29]]},"references-count":18,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2010,12]]}},"alternative-id":["3524"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-11-67","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2010,1,29]]},"assertion":[{"value":"7 October 2009","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"29 January 2010","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"29 January 2010","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"67"}}