A practical case-control association test for detecting a susceptibility allele at a copy number variation locus
A practical case-control association test for detecting a susceptibility allele at a copy number variation locus
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DOI：
10.1038/jhg.2009.8
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发表时间：
2009-03-01
影响因子：
3.5
通讯作者：
Ohashi, Jun
中科院分区：
文献类型：
--
作者：
Ohashi, Jun
拷贝数变异（CNV）与疾病易感性之间的关系已引起广泛关注。在这项研究中，一个病例对照关联检验的CNV基因座与多个等位基因的建议，检测一个单一的CNV等位基因与疾病。在关联检验中，使用期望最大化（EM）算法分别估计病例和对照组的CNV等位基因频率，并计算每个CNV等位基因的卡方（2）值，以比较它们之间的估计频率。置换过程用于获得每个CNV等位基因的经验P值，并用于控制全局I型错误率。通过具有多个参数设置的计算机模拟分析来评估本关联测试的统计功效。结果表明，不同拷贝数的CNV等位基因的统计功效存在显著差异，拷贝数最低或最高的易感等位基因的统计功效高于拷贝数居中的易感等位基因。Journal of Human Genetics（2009）54，169-173; doi：10.1038/jhg.2009.8; 2009年2月6日在线发表
The association between a copy number variant (CNV) and susceptibility to disease has drawn much attention. In this study, a case-control association test for a CNV locus with multiple alleles is proposed for detecting a single CNV allele associated with a disease. In the association test, CNV allele frequencies are estimated for cases and controls separately using an expectation-maximization (EM) algorithm, and the chi(2) values are calculated for each CNV allele to compare the estimated frequency between them. A permutation procedure is used to obtain an empirical P-value for each CNV allele and for controlling a global type I error rate. The statistical power of the present association test was evaluated by a computer simulation analysis with several parameter settings. The results revealed that the statistical power was markedly different among CNV alleles with different copy numbers, and a higher power could be achieved for a susceptible allele with the lowest or highest copy number in comparison with those with intermediate copy numbers. Journal of Human Genetics (2009) 54, 169-173; doi: 10.1038/jhg.2009.8; published online 6 February 2009