Collapsing SNP genotypes in case-control genome-wide association studies increases the type I error rate and power
Collapsing SNP genotypes in case-control genome-wide association studies increases the type I error rate and power
复制标题
病例对照全基因组关联研究中 SNP 基因型的崩溃增加了 I 型错误率和功效
DOI：
10.2202/1544-6115.1325
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发表时间：
2008-01-01
影响因子：
0.9
通讯作者：
Ott, Jurg
中科院分区：
文献类型：
--
作者：
Matthews, Abigail G.;Haynes, Chad;Ott, Jurg
全基因组关联研究现在是广泛使用的工具，用于确定可能有助于各种疾病发展的基因和/或区域。利用病例对照数据，可以为每个SNP构建2x3列联表，以进行基于基因的关联检验。为了提高检测关联的能力，一种越来越常见的技术是将每个2x3表折叠到一个表中，假定显性或隐性继承模式(2x2表)。我们考虑了三种不同的确定选择哪种遗传模型的方法，并表明这些折叠基因类型的方法中的每一种都会增加I型错误率(即假阳性率)。然而，与大多数遗传模型中通常的基于基因和等位基因的测试相比，这些方法中的一种确实导致了能力的增加。
Genome-wide association studies are now widely used tools to identify genes and/or regions which may contribute to the development of various diseases. With case-control data a 2x3 contingency table can be constructed for each SNP to perform genotype-based tests of association. An increasingly common technique to increase the power to detect an association is to collapse each 2x3 table into a table assuming either a dominant or recessive mode of inheritance (2x2 table). We consider three different methods of determining which genetic model to choose and show that each of these methods of collapsing genotypes increases the type I error rate (i.e., the rate of false positives). However, one of these methods does lead to an increase in power compared with the usual genotype- and allele-based tests for most genetic models.