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. 2014 Aug 15;30(16):2375-6.
doi: 10.1093/bioinformatics/btu197. Epub 2014 Apr 14.

R PheWAS: data analysis and plotting tools for phenome-wide association studies in the R environment

Robert J Carroll  1 , Lisa Bastarache  1 , Joshua C Denny  2
Affiliations

R PheWAS: data analysis and plotting tools for phenome-wide association studies in the R environment

Robert J Carroll et al. Bioinformatics. .

Abstract

Phenome-wide association studies (PheWAS) have been used to replicate known genetic associations and discover new phenotype associations for genetic variants. This PheWAS implementation allows users to translate ICD-9 codes to PheWAS case and control groups, perform analyses using these and/or other phenotypes with covariate adjustments and plot the results. We demonstrate the methods by replicating a PheWAS on rs3135388 (near HLA-DRB, associated with multiple sclerosis) and performing a novel PheWAS using an individual's maximum white blood cell count (WBC) as a continuous measure. Our results for rs3135388 replicate known associations with more significant results than the original study on the same dataset. Our PheWAS of WBC found expected results, including associations with infections, myeloproliferative diseases and associated conditions, such as anemia. These results demonstrate the performance of the improved classification scheme and the flexibility of PheWAS encapsulated in this package.

Availability and implementation: This R package is freely available under the Gnu Public License (GPL-3) from http://phewascatalog.org. It is implemented in native R and is platform independent.

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Figures

Fig. 1.
Fig. 1.
PheWAS Manhattan plot for rs3135388, with phenotypes ordered by PheWAS code
Fig. 2.
Fig. 2.
PheWAS Manhattan plot for maximum WBC, with phenotypes ordered within each phenotype category by P-value
See this image and copyright information in PMC

References

    1. De Jager PL, et al. Meta-analysis of genome scans and replication identify CD6, IRF8 and TNFRSF1A as new multiple sclerosis susceptibility loci. Nat. Genet. 2009;41:776–782. - PMC - PubMed
    1. Denny JC, et al. PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene–disease associations. Bioinformatics. 2010;26:1205–1210. - PMC - PubMed
    1. Denny JC, 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;89:529–542. - PMC - PubMed
    1. Denny JC, et al. Systematic comparison of phenome-wide association study of electronic medical record data and genome-wide association study data. Nat. Biotechnol. 2013;31:1102–1110. - PMC - PubMed
    1. Marchini J, et al. A new multipoint method for genome-wide association studies by imputation of genotypes. Nat. Genet. 2007;39:906–913. - PubMed

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