The difference between the heritability estimates calculated from imputed and directly genotyped data was not significant. However, the imputed heritability estimates were slightly but consistently lower compared to the estimates generated from the directly genotyped data. While we employed strict r2 thresholds, the dosage format of imputed data prevented it from being subjected to the same strict Hardy-Weinberg thresholds as the directly genotyped data. Therefore this small decrease in measured heritability may reflect additional noise in the imputed data contributed by lower quality SNPs. Alternatively, the decrease may reflect the possibility that even with very stringent QC some minor residual technical artifacts may have remained in the directly genotyped data. Perhaps most interesting though, is the observation that the imputed data did not show a significant increase in heritability, even with a substantial increase in the number of interrogated variants, suggesting that the directly genotyped data alone sufficiently captured the narrow-sense heritability present in SNP level data.
