Automated design of paralogue ratio test assays for the accurate and rapid typing of copy number variation..pdf (346.79 kB)
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Automated design of paralogue ratio test assays for the accurate and rapid typing of copy number variation

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posted on 21.01.2016, 12:54 by C. D. Veal, H. Xu, K. Reekie, R. Free, R. J. Hardwick, D. McVey, A. J. Brookes, Edward J. Hollox, C. J. Talbot
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).

History

Citation

Bioinformatics, 2013, 29 (16), pp. 1997-2003

Author affiliation

/Organisation/COLLEGE OF MEDICINE, BIOLOGICAL SCIENCES AND PSYCHOLOGY/MBSP Non-Medical Departments/Department of Genetics

Version

VoR (Version of Record)

Published in

Bioinformatics

Publisher

Oxford University Press (OUP)

issn

1367-4811

eissn

1460-2059

Acceptance date

02/06/2013

Copyright date

2013

Available date

21/01/2016

Publisher version

http://bioinformatics.oxfordjournals.org/content/29/16/1997

Language

en