{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,29]],"date-time":"2025-10-29T13:16:20Z","timestamp":1761743780193},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"16","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1214,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Genomic copy number variation (CNV) can influence susceptibility to common diseases. High-throughput measurement of gene copy number on large numbers of samples is a challenging, yet critical, stage in confirming observations from sequencing or array Comparative Genome Hybridization (CGH). The paralogue ratio test (PRT) is a simple, cost-effective method of accurately determining copy number by quantifying the amplification ratio between a target and reference amplicon. PRT has been successfully applied to several studies analyzing common CNV. However, its use has not been widespread because of difficulties in assay design.<\/jats:p>\n               <jats:p>Results: We present PRTPrimer (www.prtprimer.org) software for automated PRT assay design. In addition to stand-alone software, the web site includes a database of pre-designed assays for the human genome at an average spacing of 6 kb and a web interface for custom assay design. Other reference genomes can also be analyzed through local installation of the software. The usefulness of PRTPrimer was tested within known CNV, and showed reproducible quantification. This software and database provide assays that can rapidly genotype CNV, cost-effectively, on a large number of samples and will enable the widespread adoption of PRT.<\/jats:p>\n               <jats:p>Availability: PRTPrimer is available in two forms: a Perl script (version 5.14 and higher) that can be run from the command line on Linux systems and as a service on the PRTPrimer web site (www.prtprimer.org).<\/jats:p>\n               <jats:p>Contact: \u00a0cjt14@le.ac.uk<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt330","type":"journal-article","created":{"date-parts":[[2013,6,7]],"date-time":"2013-06-07T01:00:10Z","timestamp":1370566810000},"page":"1997-2003","source":"Crossref","is-referenced-by-count":9,"title":["Automated design of paralogue ratio test assays for the accurate and rapid typing of copy number variation"],"prefix":"10.1093","volume":"29","author":[{"given":"Colin D.","family":"Veal","sequence":"first","affiliation":[{"name":"1 Department of Genetics, University of Leicester, Leicester, LE1 7RH and 2Department of Cardiovascular Sciences, University of Leicester, LE3 9QP, UK"}]},{"given":"Hang","family":"Xu","sequence":"additional","affiliation":[{"name":"1 Department of Genetics, University of Leicester, Leicester, LE1 7RH and 2Department of Cardiovascular Sciences, University of Leicester, LE3 9QP, UK"}]},{"given":"Katherine","family":"Reekie","sequence":"additional","affiliation":[{"name":"1 Department of Genetics, University of Leicester, Leicester, LE1 7RH and 2Department of Cardiovascular Sciences, University of Leicester, LE3 9QP, UK"}]},{"given":"Robert","family":"Free","sequence":"additional","affiliation":[{"name":"1 Department of Genetics, University of Leicester, Leicester, LE1 7RH and 2Department of Cardiovascular Sciences, University of Leicester, LE3 9QP, UK"}]},{"given":"Robert J.","family":"Hardwick","sequence":"additional","affiliation":[{"name":"1 Department of Genetics, University of Leicester, Leicester, LE1 7RH and 2Department of Cardiovascular Sciences, University of Leicester, LE3 9QP, UK"}]},{"given":"David","family":"McVey","sequence":"additional","affiliation":[{"name":"1 Department of Genetics, University of Leicester, Leicester, LE1 7RH and 2Department of Cardiovascular Sciences, University of Leicester, LE3 9QP, UK"}]},{"given":"Anthony J.","family":"Brookes","sequence":"additional","affiliation":[{"name":"1 Department of Genetics, University of Leicester, Leicester, LE1 7RH and 2Department of Cardiovascular Sciences, University of Leicester, LE3 9QP, UK"}]},{"given":"Edward J.","family":"Hollox","sequence":"additional","affiliation":[{"name":"1 Department of Genetics, University of Leicester, Leicester, LE1 7RH and 2Department of Cardiovascular Sciences, University of Leicester, LE3 9QP, UK"}]},{"given":"Christopher J.","family":"Talbot","sequence":"additional","affiliation":[{"name":"1 Department of Genetics, University of Leicester, Leicester, LE1 7RH and 2Department of Cardiovascular Sciences, University of Leicester, LE3 9QP, UK"}]}],"member":"286","published-online":{"date-parts":[[2013,6,6]]},"reference":[{"key":"2023020305201443200_btt330-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":"2023020305201443200_btt330-B2","doi-asserted-by":"crossref","first-page":"4930","DOI":"10.1093\/hmg\/ddq411","article-title":"Measurement methods and accuracy in copy number variation: failure to replicate associations of beta-defensin copy number with Crohn\u2019s disease","volume":"19","author":"Aldhous","year":"2010","journal-title":"Hum. 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