The linkage disequilibrium (LD) score regression method tests whether there is an association between the LD score and allele frequency differences between cases and controls. It makes the assumption that there is no association between LD score and allele frequency differences among populations and hence that any observed association is the result of a polygenic effect rather than population stratification. This assumption was previously tested only using European cohorts. In comparisons among more diverse HapMap populations, we observe that there is indeed an association between the LD score and allele frequency differences. However, this effect is small and when we carry out simulations of large case-control samples, the effect becomes negligible. We conclude that if the intercept is small then any increase in mean chi-squared does indeed reflect a polygenic effect rather than population stratification.

中文翻译：

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LD 分数与种群之间等位基因频率的差异有关，但 LD 分数回归仍然可以区分混杂和多基因性

连锁不平衡 (LD) 评分回归方法测试 LD 评分与病例和对照之间的等位基因频率差异之间是否存在关联。它假设 LD 分数与种群之间的等位基因频率差异之间没有关联，因此任何观察到的关联都是多基因效应的结果，而不是种群分层的结果。这一假设以前仅使用欧洲队列进行过测试。在更多样化的 HapMap 群体之间进行比较时，我们观察到 LD 分数和等位基因频率差异之间确实存在关联。然而，这种影响很小，当我们对大型病例对照样本进行模拟时，这种影响变得可以忽略不计。