The individuals were genotyped using the Illumina OmniExpress 700K chip, imputed to the 1000 genome imputation panel. After imputation we selected SNPs from the HapMap3 panel since this SNP set was optimized to capture common genetic variation,21 (link) which is required for the GREML analysis. For quality control, SNPs with a minor allele frequency less than 1%, a higher missing rate than 0.03 and that failed the Hardy-Weinberg equilibrium for a threshold of 10-6 were removed. The first 20 principal components are included as covariates to adjust for population stratification.22 (link)
Protocol detail
Genotyping and QC for GREML analysis
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Corresponding Organization :
Other organizations : University of Groningen, University of Oxford, Karolinska Institutet, University Medical Center Groningen
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Variable analysis
independent variables
- Genotyping using the Illumina OmniExpress 700K chip
- Imputation to the 1000 genome imputation panel
- Selection of SNPs from the HapMap3 panel
- Not explicitly mentioned
- Removal of SNPs with minor allele frequency less than 1%
- Removal of SNPs with a higher missing rate than 0.03
- Removal of SNPs that failed the Hardy-Weinberg equilibrium for a threshold of 10^-6
- Inclusion of the first 20 principal components as covariates to adjust for population stratification
- Not specified
- Not specified
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