Post-imputation QC involved excluding any SNPs likely to be poorly imputed (specifically those with an 'info' score <0.5 or with minor allele frequency in controls <0.01).
Specifically, when genotypes were imputed in training and prediction animals with lower accuracy, the average r GEBV was larger than the accuracy of genomic evaluation, which we found was an artifact of lower estimates of the diagonal elements of the G matrix.
Using the imputation approach outlined in this paper, which was specifically designed to impute genotypes on sex chromosomes, did not always outperform the standard autosomal imputation procedure of AlphaImpute.
f90 was specifically designed to impute genotypes using large data sets and exploiting comprehensive pedigree information [ 6].
We also re-analysed both of our data sets using data generated in SNP2HLA because of the broad set of additional variations in the region it can impute: specifically, markers for the presence/absence of an amino acid residue, markers for the presence/absence of groups of amino acids residues given a multi-allelic amino acid position, HLA intragenic SNPs and insertion/deletions.
Specifically, the weight was first imputed using a formula based on the postpregnancy weight.
We did not find substantial differences in results, and we report multiple imputed data unless specifically indicated.
Specifically, SNPs for AA were imputed using both CEU (Utah residents with Northern and Western European ancestry from the CEPH collection) and YRI (Yoruba in Ibadan, Nigeria) data, SNPs for CA were imputed based on CEU data, and SNPs for HCA were imputed based on the CHB (Han Chinese in Beijing, China) and JPT (Japanese in Tokyo, Japan) data.
We did not observe a stronger association (P < 1 × 10−4) for either prostate cancer overall or specifically for nonaggressive prostate cancer using imputed genotype data (Supplemental Tables 7 and 8).
Imputation using chained equations does not require us to specifically order the variables that must be imputed because the software imputes, by default, the variables from the most observed to the least observed.
