The effect of genotyping errors on the robustness of composite linkage disequilibrium measures

Abstract

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 $\Delta^{\prime}_{AB}$ and r _AB , and compared the robustness of $\Delta^{\prime}_{AB}$ and r _AB in the presence of genotyping errors. The results showed that $\Delta^{\prime}_{AB}$ and r _AB 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, r _AB is more robust than $\Delta^{\prime}_{AB}$ except some special cases and the difference of robustness between $\Delta^{\prime}_{AB}$ and r _AB becomes less severe as the difference between the frequencies of two SNP alleles A and B becomes smaller.