Domains

biomedical, genomics, clinical, precision medicine

License

Warning: No license entered

Homepage

phewascat

Repository

GitHub

Infores ID

Unknown

FAIRsharing ID

Unknown

Product Summary

Contacts

Vanderbilt University Medical Center

Email: joshua.c.denny@vumc.org

URL: https://phewascatalog.org/phewas/#home

Publications

Systematic comparison of phenome-wide association study of electronic medical record data and genome-wide association study data Preferred

Products

From this Resource

ID	Name	URL	Category	Format	Description
phewascat.portal	PheWAS Catalog Portal	#home	GraphicalInterface	http	Web portal for browsing and accessing...
phewascat.associations	PheWAS Association Data	#home	Product	csv	PheWAS association results for SNPs f...
phewascat.phecodes	Phecode Maps	#home	Product	csv	Phecode mapping files for translating...
phewascat.rpackage	PheWAS R Package	phewas-r-package	ProgrammingInterface	http	R package for performing PheWAS analy...

From other Resources

ID	Name	URL	Category	Format	Description
disgenet.data	DisGeNET Data	www.disgenet.com	GraphProduct	❔	DisGeNET data, including gene to dise...

Relevant Taxa

Human (NCBITaxon:9606)

Details

PheWAS Catalog

The PheWAS Catalog is a comprehensive aggregator of phenome-wide association studies (PheWAS) that systematically analyzes associations between genetic variants and a wide range of phenotypes derived from electronic medical records (EMRs). This resource combines genetic data with clinical phenotypes to enable discovery of genetic associations across the phenome.

Key Features

Comprehensive Genetic-Phenotype Associations

Contains PheWAS results for over 3,144 single-nucleotide polymorphisms (SNPs) from the NHGRI GWAS Catalog
Analyzes 1,358 EMR-derived phenotypes for each genetic variant
Includes data from 13,835 European-ancestry individuals across five eMERGE network sites
Provides systematic comparison between PheWAS and traditional GWAS results

Phecode System

Uses standardized Phecode mapping system to translate ICD codes into phenotypes
Phecode Map 1.2 covers 1,866 phenotypes based on ICD-9 and ICD-10 codes
Extended Phecode Map X includes 3,612 phenotype groupings based on ICD-10
Enables consistent phenotype definitions across different healthcare systems

Validation and Replication

Successfully replicated 66% (51/77) of sufficiently powered prior GWAS associations
Identified 210/751 associations from all prior GWAS studies
Discovered 63 potentially pleiotropic associations with genome-wide significance
Provides independent validation cohort results for novel associations

Data Sources

Electronic Medical Records

eMERGE (Electronic Medical Records and Genomics) network data
Vanderbilt DNA biobank (BioVU) with linked EMR data
Multiple healthcare institutions contributing phenotype data
Standardized phenotype extraction and coding procedures

Genetic Data

NHGRI GWAS Catalog variants as of April 2012
High-quality genotyped and imputed SNPs
Population-stratified genetic association results
Quality control and validation of genetic variants

Clinical Phenotypes

ICD-9 and ICD-10 diagnostic codes from EMRs
Laboratory values and clinical measurements
Medication prescriptions and procedures
Longitudinal clinical data spanning multiple visits

Applications

Drug Discovery and Repurposing

Identification of pleiotropic genetic effects for drug target validation
Discovery of unexpected phenotype associations for drug repurposing
Safety signal detection through genetic association patterns
Biomarker identification for drug response prediction

Precision Medicine

Genetic risk prediction across multiple phenotypes
Personalized disease risk assessment using genetic profiles
Clinical decision support based on genetic associations
Population-specific genetic risk stratification

Genomic Medicine Research

Hypothesis generation for novel genetic associations
Validation platform for GWAS findings in clinical populations
Cross-phenotype genetic correlation analysis
Pleiotropy detection and characterization

Clinical Phenotyping

Standardization of EMR-derived phenotype definitions
Validation of electronic phenotype algorithms
Cross-institutional phenotype harmonization
Quality assessment of clinical data extraction

Technical Implementation

The PheWAS Catalog aggregates data through systematic analysis pipelines that process EMR data, apply Phecode mappings, perform genetic association testing, and provide statistical validation. The resource includes web-based tools for interactive exploration and programmatic access through R packages and APIs for computational workflows.