Human omniexpress 12v1 h

Genomic DNA from participants was extracted from peripheral whole blood, and genotyped at deCODE Genetics (Reykjavik, Iceland) on either the Human OmniExpress-12v-1-1_B (Illumina, San Diego, CA, USA) or Human OmniExpress-12v1_H (Illumina, San Diego, CA, USA) platforms in accordance with the manufacturer’s standard protocol. Genotypes were assigned in concordance with the standard Illumina protocol in GenomeStudio software V2011.1 version 1.9.4. We performed a standard pre-imputation quality control, where markers exhibiting high rates of genotyping missingness (>95%), minor allele frequency (MAF) <1% or showing departure from the Hardy Weinberg equilibrium (p<1.00E-05) were excluded from the analyses. Also, individuals exhibiting high rates of genotyping missingness (>5%), cryptic relatedness (PI_HAT>15%) or genome-wide heterozygosity (outside mean ± 4SD of the sample) were removed from the analyses, as well as individuals with incoherent sex assessment based on the homozygosity estimate of X chromosome markers implemented in PLINK [39 (link)]. Finally, we restricted our data by excluding individuals with non-European ancestry (outside 3SD range of either one of the first two genetic principal components).MACH (http://www.sph.umich.edu/csg/abecasis/MACH) was used to impute the genotypes onto the reference haplotypes from the 1000 Genomes Project (build 37, assembly Hg19).

Participants were genotyped on either Human OmniExpress-12v1-1_B (Illumina, San Diego, CA, USA) or Human OmniExpress-12v1_H (Illumina, San Diego, CA, USA) platforms. Genotyping was performed according to the standard Illumina protocol at Decode facility (Reykjavik, Iceland). Genotypes were assigned according to the standard Illumina protocol in GenomeStudio software, version V2011.1.
Individuals exhibiting high rates of genotype missingness (above 98%) or genome-wide heterozygosity (outside mean±3SD of the sample); cryptic relatedness (PI_HAT above 15%) or non-European ancestry were excluded from the analyses. Sex check was performed based on the homozygocity estimate of X chromosome markers implemented in PLINK. Given high concordance between the reported and estimated sex (>98% in our dataset), this method was also used to impute the missing sex information.
SNPs exhibiting high rates of missingness (above 95%), minor allele frequency (MAF) below 1% or failing Hardy-Weinberg equilibrium test (p<1.00E-05) were excluded from the analyses.