Department of Genetics, University of Leicester, Leicester, UK.
Bioinformatics. 2013 Aug 15;29(16):1997-2003. doi: 10.1093/bioinformatics/btt330. Epub 2013 Jun 6.
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.
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.
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).
基因组拷贝数变异（CNV）会影响常见疾病的易感性。高通量测量大量样本中的基因拷贝数是确认测序或阵列比较基因组杂交（CGH）观察结果的一个具有挑战性但至关重要的阶段。等位基因比率测试（PRT）是一种通过量化靶标和参考扩增子之间的扩增比率来准确确定拷贝数的简单、具有成本效益的方法。PRT 已成功应用于分析常见 CNV 的多项研究中。然而，由于检测设计的困难，其应用并不广泛。
我们提出了 PRTPrimer（www.prtprimer.org）软件，用于自动 PRT 检测设计。除了独立的软件外，该网站还包含一个人类基因组预设计检测的数据库，平均间隔为 6kb，以及一个用于定制检测设计的网络界面。其他参考基因组也可以通过软件的本地安装进行分析。PRTPrimer 的有用性在已知的 CNV 中进行了测试，结果显示可重复的定量。该软件和数据库提供了可以快速对大量样本进行 CNV 基因分型的检测，具有成本效益，并且将能够广泛采用 PRT。
PRTPrimer 有两种形式：一种是可以在 Linux 系统上从命令行运行的 Perl 脚本（版本 5.14 及更高版本），另一种是作为 PRTPrimer 网站（www.prtprimer.org）上的一项服务。
