ALSPAC participants were genotyped from blood samples using the Illumina 550K custom chip (San Diego, CA, USA). Multi-dimensional scaling modeling seeded with HapMap Phase II release 22 reference populations was used to identify individuals of non-European descent. To reduce bias introduced by population stratification, individuals of non-European descent were removed from subsequent analyses. Those of European descent were imputed to HapMap Phase II (release 22, NCBI build 36, hg18) using the Markov Chain Haplotyping software (MACH v.1.0.16) [30]. SNPs that were in Hardy-Weinberg equilibrium (p > 5 × 10−7) with a final call rate of >95%, and minor allele frequency >1% were used in the imputation procedure. The 2,450,300 autosomal SNPs that exceeded an Rsq metric of 0.3 and had a minor allele frequency >1% following imputation were used in the GWAS. Additional, detailed GWAS data cleaning information for this sample are available in Fatemifar et al. [31].
