DeepPheWAS

DeepPheWAS implements generation and analysis of clinically curated composite phenotypes for phenome-wide association studies (PheWAS) in R, integrating quantitative primary-care measures, longitudinal trajectories, disease progression patterns, and drug response phenotypes.

Key Features:

• Clinically Curated Composite Phenotypes: Creates clinically curated composite phenotypes for use in PheWAS analyses.
• Integration of Quantitative Data: Integrates quantitative phenotypic data derived from primary care records.
• Longitudinal Trajectory Analysis: Supports analysis of longitudinal trajectories of quantitative measures within individuals.
• Disease Progression and Drug Response Phenotypes: Incorporates phenotypes describing disease progression patterns and drug response profiles.
• Flexible Genetic Analysis: Performs association analysis with any genetic input under multiple genetic models.
• Sex-Stratified Analysis Option: Enables sex-stratified analyses to identify sex-specific genetic associations.
• Novel Phenotype Development: Provides functionality to develop and characterize novel phenotypes.

Scientific Applications:

• Phenome-wide association studies: Enables PheWAS to discover genotype–phenotype associations across many clinical phenotypes.
• Genetics and genomics research: Supports investigation of genetic architecture of complex traits and diseases.
• Epidemiology and longitudinal studies: Facilitates epidemiological analyses using longitudinal measures and progression patterns.
• Pharmacogenomics and drug-response studies: Assesses genetic influences on drug response phenotypes.
• Personalized medicine: Links genetic variation to composite clinical phenotypes to inform personalized medicine approaches.

Methodology:

Integrates diverse phenotypic data types into a unified R-based framework and performs association analyses across different genetic models and stratifications.