PheWAS analysis on large-scale biobank data with PheTK.

ABSTRACT:

Summary

With the rapid growth of genetic data linked to electronic health record (EHR) data in huge cohorts, large-scale phenome-wide association study (PheWAS) have become powerful discovery tools in biomedical research. PheWAS is an analysis method to study phenotype associations utilizing longitudinal EHR data. Previous PheWAS packages were developed mostly with smaller datasets and with earlier PheWAS approaches. PheTK was designed to simplify analysis and efficiently handle biobank-scale data. PheTK uses multithreading and supports a full PheWAS workflow including extraction of data from OMOP databases and Hail matrix tables as well as PheWAS analysis for both phecode version 1.2 and phecodeX. Benchmarking results showed PheTK took 64% less time than the R PheWAS package to co

SUBMITTER: Tran TC 

PROVIDER: S-EPMC11709244 | biostudies-literature | 2024 Dec

REPOSITORIES: biostudies-literature