Samples used in the analysis were predominantly of European single ancestry, and individuals with >15% minority ancestries were excluded (see Materials and Methods and summary data of imputation in Supplementary Material, Table S1).
After quality control (described in Supplementary Material, Table S1) and imputation, >2.3 million SNPs were examined.
To handle missing data, we tested five methods, including rolling back to a simpler model, excluding incomplete cases, EM algorithm, MI, and median imputation (see Materials and Methods).
Associations between biomarkers and 14-day mortality were estimated using Cox models with multiple imputation (see Supplementary Material).
The ORs for each of the five WQS indices were generally robust to the analyte imputation (see Supplemental Material, Figure S3).
For the majority of associations between self-harm and risk factors investigated the imputations made no material difference to our overall conclusions and so the estimates from simple logisitic regression models are presented within the paper.
In this study, the SNP genotype imputation is used as material preparation for the HLA allele prediction.
The Dutch samples thus far included in multi-center GWAS studies originate from several different places in the Netherlands and may thus optimally benefit from imputation when the reference material properly reflects this provenance.
All SNPs imputed well (all R for imputation quality > 0.72, mean = 0.978; Supplementary Material, Table S1), therefore, dosages from the imputed data were used in subsequent analyses (i.e. the estimated number of BMD-lowering alleles).
All 63 SNPs were common in this population (median BMD lowering allele frequency: 0.4, range: 0.07 0.72; Supplementary Material, Table S1) and they all imputed well (all R for imputation quality > 0.72).
