Li Yu Mei, Xiang Yang
Department of Mathematics, Huaihua University, Huaihua, Hunan 418008, People's Republic of China.
J Genet. 2011 Dec;90(3):453-7. doi: 10.1007/s12041-011-0110-x.
We conclude that composite linkage disequilibrium (LD) measures be adopted in population-based LD mapping or association mapping studies since it is unaffected by Hardy-Weinberg disequilibrium. Although some properties of composite LD measures have been recently studied, the effects of genotyping errors on composite LD measures have not been examined. In this report, we derived deterministic formulas to evaluate the impact of genotyping errors on the composite LD measures Δ'AB and rAB, and compared the robustness of Δ'AB and rAB in the presence of genotyping errors. The results showed that Δ'AB and rAB depend on the allele frequencies and the assumed error model, and show varying degrees of robustness in the presence of errors. In general, whether there is HWD or not, rAB is more robust than Δ'AB except some special cases and the difference of robustness between Δ'AB and rAB becomes less severe as the difference between the frequencies of two SNP alleles A and B becomes smaller.
我们得出结论，在基于人群的连锁不平衡（LD）定位或关联定位研究中应采用复合连锁不平衡（LD）测量方法，因为它不受哈迪-温伯格不平衡的影响。尽管最近已经研究了复合LD测量方法的一些特性，但尚未研究基因分型错误对复合LD测量方法的影响。在本报告中，我们推导了确定性公式，以评估基因分型错误对复合LD测量方法Δ'AB和rAB的影响，并比较了在存在基因分型错误的情况下Δ'AB和rAB的稳健性。结果表明，Δ'AB和rAB取决于等位基因频率和假定的错误模型，并且在存在错误的情况下表现出不同程度的稳健性。一般来说，无论是否存在哈迪-温伯格不平衡，除了一些特殊情况外，rAB比Δ'AB更稳健，并且随着两个单核苷酸多态性（SNP）等位基因A和B频率之间的差异变小，Δ'AB和rAB之间稳健性的差异变得不那么明显。
