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首页> 外文期刊>Heredity: An International Journal of Genetics >Testing for Hardy-Weinberg equilibrium at biallelic genetic markers on the X chromosome
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Testing for Hardy-Weinberg equilibrium at biallelic genetic markers on the X chromosome

机译：在X染色体上的双等位基因遗传标记处测试Hardy-Weinberg平衡

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摘要

Testing genetic markers for Hardy-Weinberg equilibrium (HWE) is an important tool for detecting genotyping errors in large-scale genotyping studies. For markers at the X chromosome, typically the chi(2) or exact test is applied to the females only, and the hemizygous males are considered to be uninformative. In this paper we show that the males are relevant, because a difference in allele frequency between males and females may indicate HWE not to hold. The testing of markers on the X chromosome has received little attention, and in this paper we lay down the foundation for testing biallelic X-chromosomal markers for HWE. We develop four frequentist statistical test procedures for X-linked markers that take both males and females into account: the chi(2) test, likelihood ratio test, exact test and permutation test. Exact tests that include males are shown to have a better Type I error rate. Empirical data from the GENEVA project on venous thromboembolism is used to illustrate the proposed tests. Results obtained with the new tests differ substantially from tests that are based on female genotype counts only. The new tests detect differences in allele frequencies and seem able to uncover additional genotyping error that would have gone unnoticed in HWE tests based on females only.
机译：测试Hardy-Weinberg平衡（HWE）的遗传标记是检测大规模基因型研究中基因型错误的重要工具。对于X染色体上的标记，通常仅对雌性进行chi（2）或精确测试，而半合子雄性被认为是没有信息的。在本文中，我们证明了男性是相关的，因为男性和女性之间等位基因频率的差异可能表明HWE不成立。 X染色体上的标记测试很少受到关注，在本文中，我们为测试HWE的双等位X染色体标记奠定了基础。我们针对X链接标记开发了四个频繁的统计测试程序，将男性和女性都考虑在内：chi（2）测试，似然比测试，精确测试和置换测试。包括男性在内的精确测试显示出更好的I型错误率。 GENEVA项目关于静脉血栓栓塞的经验数据用于说明拟议的测试。新测试获得的结果与仅基于女性基因型计数的测试有很大不同。新的检测方法可以检测等位基因频率的差异，并且似乎能够发现其他仅基于女性的HWE检测中未注意到的基因分型错误。

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