{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,16]],"date-time":"2026-01-16T13:07:18Z","timestamp":1768568838169,"version":"3.49.0"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"12","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: UPDtool is a computational tool for detection and classification of uniparental disomy (UPD) in trio SNP-microarray experiments. UPDs are rare events of chromosomal malsegregation and describe the condition of two homologous chromosomes or homologous chromosomal segments that were inherited from one parent. The occurrence of UPD can be of major clinical relevance. Though high-throughput molecular screening techniques are widely used, detection of UPDs and especially the subclassification remains complex. We developed UPDtool to detect and classify UPDs from SNP microarray data of parent\u2013child trios. The algorithm was tested using five positive controls including both iso- and heterodisomic segmental UPDs and 30 trios from the HapMap project as negative controls. With UPDtool, we were able to correctly identify all occurrences of non-mosaic UPD within our positive controls, whereas no occurrence of UPD was found within our negative controls. In addition, the chromosomal breakage points could be determined more precisely than by microsatellite analysis. Our results were compared with both the gold standard, microsatellite analysis and SNPtrio, another program available for UPD detection. UPDtool is platform independent, light weight and flexible. Because of its simple input format, UPDtool may also be used with other high-throughput technologies (e.g. next-generation sequencing).<\/jats:p>\n               <jats:p>Availability and implementation: UPDtool executables, documentation and examples can be downloaded from http:\/\/www.uni-tuebingen.de\/uni\/thk\/de\/f-genomik-software.html.<\/jats:p>\n               <jats:p>Contact: \u00a0christopher.schroeder@med.uni-tuebingen.de<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt174","type":"journal-article","created":{"date-parts":[[2013,4,16]],"date-time":"2013-04-16T00:15:15Z","timestamp":1366071315000},"page":"1562-1564","source":"Crossref","is-referenced-by-count":30,"title":["UPDtool: a tool for detection of iso- and heterodisomy in parent\u2013child trios using SNP microarrays"],"prefix":"10.1093","volume":"29","author":[{"given":"Christopher","family":"Schroeder","sequence":"first","affiliation":[{"name":"1 Department of Medical Genetics, University of T\u00fcbingen, Calwerstr. 7, 72076 T\u00fcbingen, Germany and 2Institute of Human Genetics, RWTH Aachen, Pauwelsstr. 30, 52074 Aachen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marc","family":"Sturm","sequence":"additional","affiliation":[{"name":"1 Department of Medical Genetics, University of T\u00fcbingen, Calwerstr. 7, 72076 T\u00fcbingen, Germany and 2Institute of Human Genetics, RWTH Aachen, Pauwelsstr. 30, 52074 Aachen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andreas","family":"Dufke","sequence":"additional","affiliation":[{"name":"1 Department of Medical Genetics, University of T\u00fcbingen, Calwerstr. 7, 72076 T\u00fcbingen, Germany and 2Institute of Human Genetics, RWTH Aachen, Pauwelsstr. 30, 52074 Aachen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ulrike","family":"Mau-Holzmann","sequence":"additional","affiliation":[{"name":"1 Department of Medical Genetics, University of T\u00fcbingen, Calwerstr. 7, 72076 T\u00fcbingen, Germany and 2Institute of Human Genetics, RWTH Aachen, Pauwelsstr. 30, 52074 Aachen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thomas","family":"Eggermann","sequence":"additional","affiliation":[{"name":"1 Department of Medical Genetics, University of T\u00fcbingen, Calwerstr. 7, 72076 T\u00fcbingen, Germany and 2Institute of Human Genetics, RWTH Aachen, Pauwelsstr. 30, 52074 Aachen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sven","family":"Poths","sequence":"additional","affiliation":[{"name":"1 Department of Medical Genetics, University of T\u00fcbingen, Calwerstr. 7, 72076 T\u00fcbingen, Germany and 2Institute of Human Genetics, RWTH Aachen, Pauwelsstr. 30, 52074 Aachen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Olaf","family":"Riess","sequence":"additional","affiliation":[{"name":"1 Department of Medical Genetics, University of T\u00fcbingen, Calwerstr. 7, 72076 T\u00fcbingen, Germany and 2Institute of Human Genetics, RWTH Aachen, Pauwelsstr. 30, 52074 Aachen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Bonin","sequence":"additional","affiliation":[{"name":"1 Department of Medical Genetics, University of T\u00fcbingen, Calwerstr. 7, 72076 T\u00fcbingen, Germany and 2Institute of Human Genetics, RWTH Aachen, Pauwelsstr. 30, 52074 Aachen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2013,4,14]]},"reference":[{"key":"2023012810440433900_btt174-B1","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1002\/humu.20198","article-title":"A rapid microarray based whole genome analysis for detection of uniparental disomy","volume":"26","author":"Altug-Teber","year":"2005","journal-title":"Hum. Mutat."},{"key":"2023012810440433900_btt174-B2","doi-asserted-by":"crossref","first-page":"847","DOI":"10.1136\/jmg.2005.032367","article-title":"Global analysis of uniparental disomy using high density genotyping arrays","volume":"42","author":"Bruce","year":"2005","journal-title":"J. Med. Genet."},{"key":"2023012810440433900_btt174-B3","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1111\/j.1399-0004.2008.01057.x","article-title":"Segmental maternal UPD(7q) in Silver-Russell syndrome","volume":"74","author":"Eggermann","year":"2008","journal-title":"Clin. Genet."},{"key":"2023012810440433900_btt174-B4","doi-asserted-by":"crossref","DOI":"10.1093\/med\/9780195375336.001.0001","volume-title":"Chromosome Abnormalities and Genetic Counseling","author":"Gardner","year":"2011"},{"key":"2023012810440433900_btt174-B5","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1016\/j.ygeno.2007.05.011","article-title":"Estimating genotyping error rates from Mendelian errors in SNP array genotypes and their impact on inference","volume":"90","author":"Saunders","year":"2007","journal-title":"Genomics"},{"key":"2023012810440433900_btt174-B6","doi-asserted-by":"crossref","first-page":"1225","DOI":"10.1002\/humu.20583","article-title":"Visualization of uniparental inheritance, Mendelian inconsistencies, deletions, and parent of origin effects in single nucleotide polymorphism trio data with SNPtrio","volume":"28","author":"Ting","year":"2007","journal-title":"Hum. Mutat."},{"key":"2023012810440433900_btt174-B7","first-page":"927","article-title":"Leigh syndrome transmitted by uniparental disomy of chromosome 9","volume":"36","author":"Tiranti","year":"1999","journal-title":"J. Med. Genet."},{"key":"2023012810440433900_btt174-B8","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1002\/ajmg.c.30270","article-title":"Uniparental disomy and human disease: an overview","volume":"154 C","author":"Yamazawa","year":"2010","journal-title":"Am. J. Med. Genet. C Semin. Med. Genet."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/12\/1562\/48886066\/bioinformatics_29_12_1562.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/12\/1562\/48886066\/bioinformatics_29_12_1562.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,28]],"date-time":"2023-01-28T12:26:22Z","timestamp":1674908782000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/29\/12\/1562\/291655"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,4,14]]},"references-count":8,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2013,6,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btt174","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2013,6,15]]},"published":{"date-parts":[[2013,4,14]]}}}