一个用于识别和基因分型与疾病相关的常见 CNVs 的外显子组测序管道，应用于银屑病。
An exome sequencing pipeline for identifying and genotyping common CNVs associated with disease with application to psoriasis.
机构信息
BGI-Shenzhen, Shenzhen, 518083, China.
出版信息
Bioinformatics. 2012 Sep 15;28(18):i370-i374. doi: 10.1093/bioinformatics/bts379.
MOTIVATION
Despite the prevalence of copy number variation (CNV) in the human genome, only a handful of confirmed associations have been reported between common CNVs and complex disease. This may be partially attributed to the difficulty in accurately genotyping CNVs in large cohorts using array-based technologies. Exome sequencing is now widely being applied to case-control cohorts and presents an exciting opportunity to look for common CNVs associated with disease.
RESULTS
We developed ExoCNVTest: an exome sequencing analysis pipeline to identify disease-associated CNVs and to generate absolute copy number genotypes at putatively associated loci. Our method re-discovered the LCE3B_LCE3C CNV association with psoriasis (P-value = 5 × 10e-6) while controlling inflation of test statistics (λ < 1). ExoCNVTest-derived absolute CNV genotypes were 97.4% concordant with PCR-derived genotypes at this locus.
AVAILABILITY AND IMPLEMENTATION
ExoCNVTest has been implemented in Java and R and is freely available from www1.imperial.ac.uk/medicine/people/l.coin/.
CONTACT
动机
尽管人类基因组中存在大量的拷贝数变异（CNV），但仅报道了少数常见 CNV 与复杂疾病之间的明确关联。这可能部分归因于使用基于阵列的技术在大型队列中准确基因分型 CNV 的困难。外显子组测序现在已广泛应用于病例对照队列，并为寻找与疾病相关的常见 CNV 提供了令人兴奋的机会。
结果
我们开发了 ExoCNVTest：一种外显子组测序分析管道，用于识别与疾病相关的 CNV 并生成假定相关基因座的绝对拷贝数基因型。我们的方法重新发现了 LCE3B_LCE3C CNV 与银屑病的关联（P 值= 5×10e-6），同时控制了测试统计数据的膨胀（λ < 1）。在该基因座处，ExoCNVTest 衍生的绝对 CNV 基因型与 PCR 衍生的基因型的一致性为 97.4%。
可用性和实现
ExoCNVTest 已用 Java 和 R 实现，并可从 www1.imperial.ac.uk/medicine/people/l.coin/ 免费获得。
联系方式
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