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For each imputation method and for each imputed diagnostic test, we used complete data samples to train and validate the method.
For each imputation we generated 20 imputed datasets and combined coefficient estimates across these using Rubin's rules.
The success rates of imputation (defined as the percentage of correctly imputed genotypes) for each imputation method and each scenario, averaged across replicates, are presented in Table 2.
For each imputation model, the missing data were imputed 20 times and the regression analysis was performed on each completed dataset.
For each imputation model, separate KS tests were performed on each of the 20 imputed datasets, resulting in 20 p-values for each imputed variable.
Using the selected reference panels, we impute all the masked genotypes and compute the discordance rate for each imputation.
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For each imputed SNP, imputation accuracy was assessed using two measures: (i) the proportion of genotypes for the SNP that were correctly imputed among samples; and (ii) the correlation between the true and imputed genotypic allele counts across all samples (homozygote for allele 1, coded 0; heterozygous, coded 1; homozygous for allele 2, coded 2).
The inclusion of weights for each individual imputation makes it easier to ensure that the imputation model is appropriate (Rubin, 1996).
For each study, imputation was performed using the 1000 Genomes Project Phase 1 version 3 reference haplotypes, resulting in up to ∼10 million SNPs being available for the analysis for each cancer type.
For each individual, imputation accuracy was calculated using the same two measures: (i) the proportion of all of the horses' genotypes that were correctly imputed; and (ii) the correlation between the true and imputed genotypes across all the horses' SNPs when coded as above.
The impact of the number of nonmissing data points at a marker on the marker's imputation accuracy was assessed for each dataset-imputation method combination using data from all 10 replicates and versions NA20, NA50 and NA70 combined.
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