A new method for exploring gene-gene and gene-environment interactions in GWAS with tree ensemble methods and SHAP values.

ABSTRACT:

Background

The identification of gene-gene and gene-environment interactions in genome-wide association studies is challenging due to the unknown nature of the interactions and the overwhelmingly large number of possible combinations. Parametric regression models are suitable to look for prespecified interactions. Nonparametric models such as tree ensemble models, with the ability to detect any unspecified interaction, have previously been difficult to interpret. However, with the development of methods for model explainability, it is now possible to interpret tree ensemble models efficiently and with a strong theoretical basis.

Results

We propose a tree ensemble- and SHAP-based method for identifying as well as interpreting potential gene-gene and gene-environment interacti

SUBMITTER: Johnsen PV 

PROVIDER: S-EPMC8097909 | biostudies-literature | 2021 May

REPOSITORIES: biostudies-literature