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Missing data imputation was performed by using the ImputeMissingValues.KNN module of GenePattern.
No missing data imputation was performed.
Missing data imputation was performed with the software Npute [ 65].
No data imputation was performed for several reasons.
Genotypic data imputation was performed after anchoring SNP tags to the POPSEQ assembly.
No data imputation was performed; therefore the sample size in the analyses may be lower than the number of respondents.
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In case of longitudinal missing data, imputation is performed with the last observation carried forward method.
Otherwise no missing data imputations were performed.
To address missing outcome data, multiple imputation was performed separately by treatment group using chained equations 13 to create 100 complete data sets, under the assumption that data were missing at random.
Because more than 97% of subjects had complete data, no imputation was performed for missing values.
The missing rate for our HLA data was very low (0.23%), therefore, no imputation was performed for the HLA genotype data.
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