Imputation was also conducted on an array-wise basis and has been described elsewhere.35 Following the pre-phase of the genotypes with Shape-IT v2.5,36 genetic markers were imputed from the cosmopolitan reference panel of the 1000 Genomes Project (phase I integrated release) using IMPUTE2 v2.3.1.37–39 As a QC metric, we used the info r2 from IMPUTE2, which estimates the correlation between the true and imputed genotype.40 Herein, we reported imputed markers with info-metric r2 ≥ 0.9 and MAF ≥ 1%; all reported genotyped markers exceeded a genotype call rate ≥ 98%, and a p-value ≥ 0.001 for Hardy-Weinberg equilibrium deviation.
