population stratification by testing the correlation of CNV burden with ancestry of the samples, evaluated using PCA. The presence of large CNVs was not correlated with ancestry (p>0.05 for PCs 1 to 4). We also verified that OR estimates for large CNVs are consistent whether the CVCR cases are included (95% ci: 1.27–4.96) or not (95% ci: 1.08–5.95), but as expected from a reduction in sample size, when the burden analysis is restricted to Antioquia the significance decreases (one-sided Fisher’s exact test p = 0.16). Because cases and controls were genotyped in two batches (one batch of CVCR cases and one batch of Antioquia cases and controls), we also tested for correlation of genotyping batch with the presence of large CNVs, but found no significant effect.
