Work

P-Values for Two-Step Genome-Wide Gene–Environment Interaction Scans

Year: 2023

Type: preprint

Abstract: Two-step testing is the state-of-the art approach for performing genome-wide interaction scans (GWIS). It is computationally efficient and yields higher power than standard single-step-based GWIS for virtually all biologically plausible scenarios. However, while two-step tests control the genome-wide type I error rate at the desired level, the lack of associated valid p-values can make it difficult for users to compare with single step-results. We show how multiple-testing adjusted p-values can be defined for two-step test based on standard multiple-testing theory, and how they can be in turn scaled to make valid comparisons with single-step tests possible.

Source: medRxiv

DOI: 10.1101/2023.06.27.23291946

Authors: Juan Pablo Lewinger, Bo Yuan, Eric S. Kawaguchi, W. James Gauderman

Institution: University of Southern California

Language: English

Topic: Genetic Associations and Epidemiology

Subfield: Genetics

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

Funders: National Institutes of Health, National Cancer Institute, National Institute of Environmental Health Sciences

Awards: Environmental Genomics, Using functional genomics to inform gene environment interactions for colorectal cancer, Environmental Exposures, Host Factors and Human Disease, Statistical Methods for Integrative Genomics in Cancer