title: Automated design of paralogue ratio test assays for the accurate and rapid typing of copy number variation.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  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).
authors.affiliation: Department of Genetics, University of Leicester, Leicester, UK.
authors.forename: Colin D
authors.initials: CD
authors.lastname: Veal
authors.forename: Hang
authors.initials: H
authors.lastname: Xu
authors.forename: Katherine
authors.initials: K
authors.lastname: Reekie
authors.forename: Robert
authors.initials: R
authors.lastname: Free
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Hardwick
authors.forename: David
authors.initials: D
authors.lastname: McVey
authors.forename: Anthony J
authors.initials: AJ
authors.lastname: Brookes
authors.forename: Edward J
authors.initials: EJ
authors.lastname: Hollox
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Talbot
mesh_terms: D055028:Comparative Genomic Hybridization; D056915:DNA Copy Number Variations; D018628:Gene Dosage; D015894:Genome, Human; D023281:Genomics / Q000379:methods; D060005:Genotyping Techniques; D006801:Humans; D012984:Software