The integration of transcriptome-wide association study and mRNA expression profiling data to identify candidate genes and gene sets associated with dental caries

Abstract

Objective: The aim of this study was to identify candidate genes and gene sets associated with dental caries by an integrative analysis of transcriptome-wide association study (TWAS) and messenger RNA (mRNA) expression profiling of dental caries.

Methods: A genome-wide association study (GWAS) dataset of dental caries was obtained from the UK Biobank. A TWAS of dental caries was conducted with the FUSION tool using the gene expression reference weights of musculoskeletal, whole blood, and peripheral blood genes. The dental caries-associated genes identified by the TWAS were further subjected to gene ontology (GO) and pathway enrichment analyses to explore dental caries-related gene sets. Finally, the TWAS results of dental caries were compared with genome-wide mRNA expression profiling of dental caries to detect common genes and gene sets.

Results: The TWAS identified 165 musculoskeletal genes, 110 whole blood genes, and 228 peripheral blood genes. GO analysis of the genes identified by the TWAS detected 57 GO terms. For pathway enrichment analysis, we detected 12 candidate pathways. After comparing the TWAS-identified genes with the mRNA expression profiling data, we detected 6 common genes. Further comparing the GO results of the TWAS and mRNA expression profiling identified 5 common GO terms.

Conclusion: We identified a group of dental caries-associated genes and GO terms, providing novel clues for understanding the genetic mechanisms of dental caries.

Keywords: Dental caries; Gene expression profiling; Genome-wide association study (GWAS); Transcriptome-wide association study (TWAS).