PheWAS - phenome-wide association studies

Current methods to identify gene-disease associations primarily rely on clinical trials or observational cohorts to identify patients.  At Vanderbilt, we have used an EMR-linked DNA biobank called BioVU to derive case and controls populations using data within the EMR to define clinical phenotypes.  Genetic data for these EMR-linked association studies are redeposited into BioVU for future EMR-linked studies.  This has opened the possibility of "reverse GWAS" or "Phenome-wide association studies" (PheWAS). 

PheWAS using ICD9 codes
Our initial studies in PheWAS have been performed using a custom-developed grouping of International Classification of Disease, 9th edition (ICD9) codes.  These grouping loosely follow the 3-digit (category) and section groupings defined with the ICD9 code system itself, but vary to include, for example, all hypertension codes (401-405) as one grouping.  Each custom PheWAS code group also has an associated control group that excludes other related conditions (e.g., a patient with psoriatic arthritis cannot be a control for rheumatoid arthritis).  Such grouping are based on other similar work.
 
The code included here performs genetic tests of association accross a single SNP or group of SNPs using ICD9 codes as its input.