Phenome-wide association studies (PheWAS) analyze many phenotypes compared to a single genetic variant (or other attribute). This method was originally described using electronic medical record (EMR) data from EMR-linked in the Vanderbilt DNA biobank, BioVU, but can also be applied to other richly phenotyped sets.

PheWAS Catalog

The PheWAS catalog contains the PheWAS results for 3,144 single-nucleotide polymorphisms (SNPs) present in the NHGRI GWAS Catalog as of 4/17/2012 in 13,835 European-ancestry individuals from five sites of the Electronic Medical Records and Genomics (eMERGE) network. A total of 1,358 EMR-derived phenotypes were analyzed for each SNP. This PheWAS replicated 66% (51/77) of sufficiently powered prior GWAS associations, and 210/751 of all prior GWAS associations. We also identified 63 potentially pleiotropic associations with p < 4.6x10-6 (false discovery rate < 0.1); the strongest of these novel associations replicated in an independent cohort (n=7,406). The catalog contains all associations with p < 0.05 (uncorrected).

EMR-based PheWAS using ICD9 codes

These current studies using PheWAS have been performed using a custom, hierarchical grouping of International Classification of Disease, 9th edition (ICD9) codes applied to EMR data from. There are a total of 1645 PheWAS case groups (typically diseases), each with a corresponding control group. These groupings loosely follow the 3-digit (category) and section groupings defined with the ICD9 code system itself, and have been revised based on statistical co-occurrence, code frequency, and human review. For more information, see the references below.

How to Cite the PheWAS catalog

Denny JC, Bastarache L, Ritchie MD et al. Systematic comparison of phenome-wide association study of electronic medical record data and genome-wide association study data. Nat Biotechnol. 2013 Dec;31(12):1102-10.[Article]

PheWAS References

  1. Denny JC, Bastarache L, Ritchie MD et al. Systematic comparison of phenome-wide association study of electronic medical record data and genome-wide association study data. Nat Biotechnol. 2013 Dec;31(12):1102-10.[Article] [Pubmed]
  2. Denny JC, Ritchie MD, Basford M, et al. PheWAS: Demonstrating the feasibility of a phenome-wide scan to discover gene-disease associations. Bioinformatics. 2010 May 1;26(9):1205-10.[Article] [PubMed]
  3. Denny JC, Crawford DC, Ritchie MD, et al. Variants near FOXE1 are associated with hypothyroidism and other thyroid conditions: using electronic medical records for genome- and phenome-wide studies. Am J Hum Genet. 2011 Oct 7;89(4):529-42. [Article] [PubMed]
  4. Ritchie MD, Denny JC, Zuvich RL, et al. Genome- and phenome-wide analyses of cardiac conduction identifies markers of arrhythmia risk. Circulation. 2013 Apr 2;127(13):1377-85. [Article] [PubMed]