Initial studies to validate EHR-based phenotype approaches sought to replicate known associations between common single nucleotide polymorphisms (SNPs) and common diseases, established in multiple GWAS. An initial study in BioVU genotyped the first 9,483 samples accrued for common variants previously reported to be associated with rheumatoid arthritis, type II diabetes, multiple sclerosis, Crohn’s disease, and atrial fibrillation.13 Phenotyping algorithms identified 70-698 cases and 808-3,818 controls for the five phenotypes. A total of 21 tests of association were performed on SNPs with previously established odds ratios and each point estimate in BioVU was in the expected direction, and statistically significant associations were detected in all analyses that were adequately powered.
