Thirty-seven SNPs in the dataset are ancestry informative markers that distinguished between non-Hispanic Caucasian and Hispanic ancestry in previous studies [51]. A principal components analysis using these SNPs indicated that the first component explained 18.99 % of the variance (eigenvalue = 7.03), the second explained 3.36 % (eigen-value = 1.24), and the third explained 3.11 % (eigen-value = 1.02). We used the 32 SNPs with loadings greater than 0.30 on the first principal component as indicators of a one-factor model using maximum likelihood estimation. The model fits the data well: χ2 (464) = 824.99, p < 0.001, RMSEA = 0.03, CFI = 0.94, SRMR = 0.03. Factor scores were saved and used as a covariate and were highly correlated with self-reported ethnicity (r = 0.86, p < 0.001), confirming that these markers differentiate between non-Hispanic Caucasian and Hispanic ancestry in our data. Higher factor scores indicate higher levels of Hispanic ancestry. See Table 1 for descriptive statistics.
