Pathway-based analysis of genome-wide association study of circadian phenotypes

Abstract

Sleepiness affects normal social life, which attracts more and more attention. Circadian phenotypes contribute to obvious individual differences in susceptibility to sleepiness. We aimed to identify candidate single nucleotide polymorphisms (SNPs) which may cause circadian phenotypes, elucidate the potential mechanisms, and generate corresponding SNP-gene-pathways. A genome-wide association studies (GWAS) dataset of circadian phenotypes was utilized in the study. Then, the Identify Candidate Causal SNPs and Pathways analysis was employed to the GWAS dataset after quality control filters. Furthermore, genotype-phenotype association analysis was performed with HapMap database. Four SNPs in three different genes were determined to correlate with usual weekday bedtime, totally providing seven hypothetical mechanisms. Eleven SNPs in six genes were identified to correlate with usual weekday sleep duration, which provided six hypothetical pathways. Our results demonstrated that fifteen candidate SNPs in eight genes played vital roles in six hypothetical pathways implicated in usual weekday bedtime and six potential pathways involved in usual weekday sleep duration.

Keywords

circadian phenotypes / genome-wide association studies / pathway-based analysis

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Acknowledgments

This work was supported by the National Natural Science Foundation of China (No. 81470457 and No. 81700297). The authors acknowledge investigators gratefully for sharing the valuable GWAS data.

RIGHTS & PERMISSIONS

2018 2018 by the Journal of Biomedical Research.