6.0 genechip array

We estimate local ancestry on 313 Chilean admixed samples from two case–control studies, on Hantavirus infection (n=112) and 22q11 microdeletion syndrome (n=201), genotyped on an Affymetrix 6.0 GeneChip Array (Santa Clara, CA). Table 2 shows the distribution of the samples across the 15 political regions in Chile. Local Ethics Committees at each participating institution approved the study and informed consent was obtained from all participants, their parents or legal guardians. Local ancestry estimation requires reference panels from the ancestral populations, which for latinos correspond to Native-American, European and African populations. Our reference panels consist of 88 Native-Americans, 911 European and 229 Africans (Table 1 shows details on the populations). We filter SNPs for minor allele frequency (>0.01), Hardy–Weinberg Equilibrium (P value>10⁻⁵), call rates (>95%), missingness on SNPs and samples (10%) and discard A/T and C/G SNPs. We further filter out SNPs from the HLA region to avoid bias in the estimation of local ancestry58 (link). A total of 685,944 SNPs remain. Phase data are obtained using BEAGLE59 (link) on the CHL, NAT and SPN populations. To provide further demographic insights we grouped the Chilean sample into five zones from North to South (N,C1,C2,S1,S2) as shown in Fig. 4.

DNA was extracted from patient blood samples and genotyping was performed on the Affymetrix 6.0 GeneChip array using established protocols. We retained 838,221 SNPs after appropriate SNP quality control (QC) with PLINK [20 (link)]: SNP call rate ≥ 0.95, minor allele frequency (MAF) > 0.01, Hardy-Weinberg equilibrium (HWE) P-value > 1 x 10⁻⁵ and autosomal chromosome. Sample QC included sample call rate ≥ 0.95, removal of sex mismatch and related individuals. The EIGENSTRAT software [21 (link)] was used to assess the genetic ancestry of the samples (S1 Fig).