Infinitum 660 w quad

The discovery GWAS included genotyped as well as imputed SNPs for better coverage. Sample genotypes were phased and missing markers were imputed using the software IMPUTE2 (ref. 54 (link)). Phased data of 1,094 samples from the 1000 Genomes Project (www.1000genomes.org) were used as the reference data set. These samples are from African, African American, Asian, Caucasian and Native American populations. We excluded SNPs with an information coefficient value <0.5 and minor allele frequency <1%. For markers in the MEC data, we conducted additional stringent quality-control analyses to exclude SNPs with different minor allele frequencies in controls typed on or imputed from different genotyping platforms. SNPs that exhibited differences in minor allele frequencies between the controls genotyped with the Illumina Infinitum 660 W-Quad or Omni 2.5 M platforms at P<0.01, and/or had ORs >10 or <0.1 were excluded. The final GWAS analysis included 7,229,558 SNPs.

The SFBCS, NC-BCFR and GALA1 samples were genotyped with the Affymetrix 6.0 array according to the manufacturer’s instructions in the Laboratory of Esteban Gonzalez Burchard at UCSF. The MEC samples were genotyped with the Illumina Infinitum 660 W-Quad or the Omni 2.5 array in the Genomics Center at USC and at the Broad Institute (Cambridge, MA, USA).
Before imputation, we excluded 15 cases and 30 controls from the SFBCS/NC-BCFR/GALA1 set that had a genotyping call rate <95% or showed either known or cryptic relatedness. We excluded 26 cases and 8 controls from the MEC because of unexpected relatedness. The final analysis included 1,497 cases and 3,213 controls (1,699 individuals from the SFBCS/NC-BCFR/GALA1 set (977 cases and 722 controls) and 3,011 from the MEC (520 cases and 2,491 controls)).
A scatter plot of the first and second principal components estimated for the US Latina samples included in the discovery phase of the study showed the expected distribution for this population, with most samples spreading between the European and Asian axes (and beyond the Asian cluster towards what would be the Indigenous American cluster) and a smaller proportion of samples deviating towards the African cluster (Supplementary Fig. 5).