Supplementary Material for: Population Stratification in a Case-Control Study of Brain Arteriovenous Malformation in Latinos

<i>Background:</i> Genetic association studies conducted in admixed populations may be confounded by population stratification resulting in spurious associations. The purpose of this pilot study was to determine the presence and effect of population stratification in a case-control study of brain arteriovenous malformation (BAVM). <i>Methods:</i> We tested 83 ancestry informative markers in BAVM cases and healthy controls of self-reported Latino race/ethnicity (n = 294). Individual ancestry estimates (IAE) were obtained using the Structure program, assuming 3 underlying subpopulations. Summary χ² tests comparing genotype frequency of ancestry informative markers were used to detect stratification and IAE were included as covariates in logistic regression analysis to account for differences in genetic background. <i>Results:</i> Admixture estimates for Latinos (overall 47% native American, 45% European and 8% African ancestry) revealed heterogeneity between individuals within ancestral groups. The summary χ² test was significant (p = 0.005), suggesting ancestral differences between cases and controls. Furthermore, genetic ancestry was associated with frequency differences in a promoter variant in the IL-6 gene (IL-6 –174G&gt;C). On average, subjects with the IL6 –174 GG genotype had 6% greater Native American ancestry (p = 0.023). Age- and sex-adjusted risk of BAVM associated with the IL-6 –174 GG genotype was 1.85 (95% CI 0.99–3.48, p = 0.055), and further adjustments for IAE yielded an OR of 1.96 (95% CI 1.03–3.72, p = 0.039). <i>Conclusion:</i> The IL-6 –174G&gt;C polymorphism was associated with increased risk of BAVM among Latinos after accounting for differences in ancestral background. These results suggest subtle, negative confounding and illustrate the importance of addressing population stratification in case-control studies conducted in admixed populations.

<i>背景：</i> 在混合人群中开展的遗传关联研究易受人群分层影响，进而产生虚假关联。本先导性研究旨在探讨脑动静脉畸形（brain arteriovenous malformation, BAVM）病例-对照研究中人群分层的存在情况及其效应。
<i>方法：</i> 我们对294名自我报告为拉丁裔种族/族裔的脑动静脉畸形病例及健康对照，共检测了83个祖先信息标记（ancestry informative markers）。基于3个潜在亚群的假设，采用Structure软件计算得到个体祖先估计值（individual ancestry estimates, IAE）。通过比较祖先信息标记基因型频率的汇总χ²检验识别人群分层，并将IAE作为协变量纳入logistic回归分析，以校正遗传背景差异。
<i>结果：</i> 拉丁裔人群的混合血统分析结果显示（总体血统构成：47%美洲原住民、45%欧洲血统及8%非洲血统），不同祖先类群内的个体间存在遗传异质性。汇总χ²检验结果具有统计学意义（p=0.005），提示病例组与对照组间存在祖先血统差异。此外，遗传血统与IL-6基因启动子区IL-6 –174G>C变异的频率差异显著相关。平均而言，携带IL6 –174 GG基因型的受试者的美洲原住民血统占比高出6%（p=0.023）。经年龄与性别校正后，携带IL-6 –174 GG基因型的受试者发生脑动静脉畸形的风险为1.85（95%置信区间：0.99–3.48，p=0.055）；进一步校正个体祖先估计值后，比值比（odds ratio, OR）升至1.96（95%置信区间：1.03–3.72，p=0.039）。
<i>结论：</i> 在校正祖先背景差异后，拉丁裔人群中IL-6 –174G>C多态性位点与脑动静脉畸形的发病风险升高相关。本研究结果提示存在轻微的负混杂偏倚，并阐明了在混合人群中开展病例-对照研究时校正人群分层的重要性。