phewascat

is an Aggregator.

The PheWAS Catalog is an aggregator of phenome-wide association studies that systematically analyzes many phenotypes compared to single genetic variants. It aggregates results from electronic medical record (EMR) data analysis, combining genetic association data from multiple biobanks and clinical databases to enable comprehensive phenotype-genotype association discovery.

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Domains

biomedical, genomics, clinical, precision medicine

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Homepage

phewascat

Repository

GitHub

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Unknown

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Product Summary

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 phewas-catalog.csv.zip (7.8 MB) Product csv PheWAS association results for SNPs f...
phewascat.phecodes Phecode 1.2 Maps Phecode_map_v1_2_icd9_icd10cm.csv.zip (1.1 MB) Product csv Phecode 1.2 definitions and ICD-9/ICD...
phewascat.phecodex PhecodeX Maps phecodeX_info.csv.zip (54.8 KB) Product csv PhecodeX version 1.0 extended phenoty...
phewascat.rpackage PheWAS R Package phewas-r-package ProgrammingInterface http R package for performing PheWAS analy...
phewascat.phetk PheTK PheTK ProcessProduct http PheTK Python library for PheWAS analy...
From other Resources
ID Name URL Category Format Relation Description
disgenet.data DisGeNET Data www.disgenet.com GraphProduct ❔ had primary source DisGeNET data, including gene to dise...

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.

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Created: September 24, 2025 | Last modified: June 12, 2026