Analyses of large population-based cohorts and clinical trials show that accounting for polygenic scores for PSA levels improves prostate cancer risk prediction, suggesting an approach for enhancing screening accuracy. Linda_Kachuri johnwitte
). Genetic data were imputed on the Michigan Imputation Server using 1000 Genomes phase 3 version 5 as the reference panel. For men with multiple PSA measurements, the median PSA was used.Data from multiple batches of genotyping of 4,069 MDCS participants using different Illumina Omni arrays were merged. For variants that appeared more than once under different names on the same Illumina array, those with the higher genotyping rate were retained.
To prepare genotype data for imputation with the TOPMed 5b reference panel, variants with MAF < 0.001, call rate < 98% or evidence of deviation from Hardy–Weinberg equilibrium were removed. After these QC steps, a total of 474,046 variants remained for PCPT, and 491,015 variants were retained for SELECT. Before submitting the data to the TOPMed Imputation Server, files were pre-processed using the check-bim.pl script .
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