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首页> 美国卫生研究院文献>American Journal of Human Genetics >Exact Tests of Hardy-Weinberg Equilibrium and Homogeneity of Disequilibrium across Strata
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Exact Tests of Hardy-Weinberg Equilibrium and Homogeneity of Disequilibrium across Strata

机译：跨地层的Hardy-Weinberg平衡和不平衡同质性的精确测试

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摘要

Detecting departures from Hardy-Weinberg equilibrium (HWE) of marker-genotype frequencies is a crucial first step in almost all human genetic analyses. When a sample is stratified by multiple ethnic groups, it is important to allow the marker-allele frequencies to differ over the strata. In this situation, it is common to test for HWE by using an exact test within each stratum and then using the minimum P value as a global test. This approach does not account for multiple testing, and, because it does not combine information over strata, it does not have optimal power. Several approximate methods to combine information over strata have been proposed, but most of them sum over strata a measure of departure from HWE; if the departures are in different directions, then summing can diminish the overall evidence of departure from HWE. An exact stratified test is more appealing because it uses the probability of genotype configurations across the strata as evidence for global departures from HWE. We developed an exact stratified test for HWE for diallelic markers, such as single-nucleotide polymorphisms (SNPs), and an exact test for homogeneity of Hardy-Weinberg disequilibrium. By applying our methods to data from Perlegen and HapMap—a combined total of more than five million SNP genotypes, with three to four strata and strata sizes ranging from 23 to 60 subjects—we illustrate that the exact stratified test provides more-robust and more-powerful results than those obtained by either the minimum of exact test P values over strata or approximate stratified tests that sum measures of departure from HWE. Hence, our new methods should be useful for samples composed of multiple ethnic groups.
机译：在几乎所有人类遗传分析中，检测标记基因型频率与哈迪-温伯格平衡（HWE）的偏离都是至关重要的第一步。当样本由多个种族分层时，重要的是允许标记等位基因频率在各个层次上不同。在这种情况下，通常通过在每个层中使用精确测试然后将最小P值用作全局测试来测试HWE。这种方法不能解决多重测试问题，并且由于它没有组合分层信息，因此没有最佳性能。已经提出了几种在层上组合信息的近似方法，但是大多数方法在层上求和是偏离HWE的一种方法。如果偏离方向不同，则求和可以减少偏离HWE的总体证据。精确的分层测试更具吸引力，因为它使用整个分层中基因型构型的概率作为全球偏离HWE的证据。我们为HWE开发了一种精确的分层测试，以评估诸如单核苷酸多态性（SNP）的拨号标记，以及Hardy-Weinberg不平衡性的均一性。通过将我们的方法应用于来自Perlegen和HapMap的数据（总共超过五百万个SNP基因型，三到四个阶层，层大小从23到60个对象不等），我们说明了准确的分层测试可提供更强大的功能-强大的结果，而不是通过层上确切的测试P值的最小值或相加HWE偏离度量的近似分层测试获得的结果。因此，我们的新方法应适用于由多个种族组成的样本。

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