Please use this identifier to cite or link to this item: http://hdl.handle.net/2381/36348
Title: Automated design of paralogue ratio test assays for the accurate and rapid typing of copy number variation
Authors: Veal, C. D.
Xu, H.
Reekie, K.
Free, R.
Hardwick, R. J.
McVey, D.
Brookes, A. J.
Hollox, Edward J.
Talbot, C. J.
First Published: 15-Aug-2013
Publisher: Oxford University Press (OUP)
Citation: Bioinformatics, 2013, 29 (16), pp. 1997-2003
Abstract: 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. 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. 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).
DOI Link: 10.1093/bioinformatics/btt330
ISSN: 1367-4811
eISSN: 1460-2059
Links: http://bioinformatics.oxfordjournals.org/content/29/16/1997
http://hdl.handle.net/2381/36348
Version: Publisher Version
Status: Peer-reviewed
Type: Journal Article
Rights: Copyright © The Author(s) 2013. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Appears in Collections:Published Articles, Dept. of Genetics

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