Detection of Pleiotropy through a Phenome-Wide Association Study (PheWAS) of Epidemiologic Data as Part of the Environmental Architecture for Genes Linked to Environment (EAGLE) Study

Abstract

We performed a Phenome-wide association study (PheWAS) utilizing diverse genotypic and phenotypic data existing across multiple populations in the National Health and Nutrition Examination Surveys (NHANES), conducted by the Centers for Disease Control and Prevention (CDC), and accessed by the Epidemiological Architecture for Genes Linked to Environment (EAGLE) study. We calculated comprehensive tests of association in Genetic NHANES using 80 SNPs and 1,008 phenotypes (grouped into 184 phenotype classes), stratified by race-ethnicity. Genetic NHANES includes three surveys (NHANES III, 1999–2000, and 2001–2002) and three race-ethnicities: non-Hispanic whites (n = 6,634), non-Hispanic blacks (n = 3,458), and Mexican Americans (n = 3,950). We identified 69 PheWAS associations replicating across surveys for the same SNP, phenotype-class, direction of effect, and race-ethnicity at p<0.01, allele frequency >0.01, and sample size >200. Of these 69 PheWAS associations, 39 replicated previously reported SNP-phenotype associations, 9 were related to previously reported associations, and 21 were novel associations. Fourteen results had the same direction of effect across more than one race-ethnicity: one result was novel, 11 replicated previously reported associations, and two were related to previously reported results. Thirteen SNPs showed evidence of pleiotropy. We further explored results with gene-based biological networks, contrasting the direction of effect for pleiotropic associations across phenotypes. One PheWAS result was ABCG2 missense SNP rs2231142, associated with uric acid levels in both non-Hispanic whites and Mexican Americans, protoporphyrin levels in non-Hispanic whites and Mexican Americans, and blood pressure levels in Mexican Americans. Another example was SNP rs1800588 near LIPC, significantly associated with the novel phenotypes of folate levels (Mexican Americans), vitamin E levels (non-Hispanic whites) and triglyceride levels (non-Hispanic whites), and replication for cholesterol levels. The results of this PheWAS show the utility of this approach for exposing more of the complex genetic architecture underlying multiple traits, through generating novel hypotheses for future research.

Phenome-Wide Association Studies: Embracing Complexity for Discovery

“…This is important, as much of GWAS has been pursued in individuals of European ancestry, and PheWAS provides a high-throughput way to contrast association results across populations in addition to identifying novel associations in understudied populations such as African-Americans. Pleiotropy has been highlighted in some of the studies in which SNPs were associated with multiple phenotypes [106,107,114] and replicated in independent datasets [106,107,112,113] . The PheWAS approach continues to develop, in part because the number of datasets that can be used for a PheWAS continues to grow as the amount of highthroughput genotypic and phenotypic data increases.…”

“…PheWAS began with exploring the association between SNPs and up to thousands of phenotypes, using high-throughput linear or logistic regression depending on the phenotypes [104,105] . These studies using SNPs for PheWAS have been pursued with 116 a range of data sets, such as data from a series of epidemiological studies across genetic ancestry from the Population Architecture Using Genomics and Epidemiology (PAGE) I Study [106] as well as with data from the NHANES conducted by the CDC accessed by the Epidemiologic Architecture for Genes Linked to Environment (EAGLE) [107] . These PheWAS analyses included survey, laboratory, and medical data coupled with genetic data for exploring associations.…”

“…In addition, these studies have also identified hypothesisgenerating novel associations. Several of these studies have investigated associations across diverse genetic ancestries [106,107,114] . This is important, as much of GWAS has been pursued in individuals of European ancestry, and PheWAS provides a high-throughput way to contrast association results across populations in addition to identifying novel associations in understudied populations such as African-Americans.…”

Large-Scale Simultaneous Testing of Cross-Covariance Matrices with Applications to PheWAS

“…PheWAS enables the discovery of genetic markers with pleiotropic effects, and thus may provide a broader view of the relationship between genetic variation and networks of phenotypes (Pendergrass et al, 2013;Hall et al, 2014). This is highly desirable since recent genetic studies have suggested that many genetic loci appear to harbor variants associated with multiple traits (Solovieff et al, 2013).…”

Functional Analysis of Genomic Variation and Impact on Molecular and Higher Order Phenotypes

“…For example, a SNP (rs3135388) that was previously associated with multiple sclerosis was also found to be associated with erythematous conditions. Several recent studies have successfully exploited PheWAS to identify novel SNP-disease associations [54,57,59,64,66,67]. Whereas GWAS focuses on only one disease at a time, PheWAS has the ability to measure genetic associations with potentially thousands of traits and diseases simultaneously, enabling systematic detection of genetic variants with pleiotropic effects [56,58,67].…”