Infinium omni2.5m 8 array

Automated DNA extraction from buffy coat samples was performed using the QiaSymphony DNA mini kit (Qiagen, Toronto, Canada). Genotypes were determined with the Illumina Infinium Omni2.5M-8 array (Illumina, San Diege, CA, USA). PLINK tool set [37 (link)] (http://pngu.mgh.harvard.edu/purcell/plink/) was used to: 1) filter gender mismatches, 2) filter missingness at both the sample-level (< 5%) and SNP-level (< 5%), 3) assess sample heterozygosity and 4) filter SNPs in Hardy-Weinberg disequilibrium (p>0.001). Reference alleles on GRCh37 coordinates were set according to the forward strand and the final .vcf file was send to Sanger Imputation Service [38 (link)] (https://imputation.sanger.ac.uk). Pre-phasing was performed with SHAPEIT2 [39 (link)] and PBWT [40 (link)] was used for imputation with the 1000 Genomes (phase 3) selected as reference panel. Only post-imputed SNPs with an info score > 0.7 were kept. For PCSK9 locus, a total of 168 SNPs spanning the genomic region 55 496 039–55 530 526 on GRCh37 coordinates were computed for the expression quantitative trait loci (eQTL) analysis.