Title: Pathway-based analysis of genome-wide association study of circadian phenotypes
Authors: Didi Zhu1, Jiamin Yuan2, Rui Zhu1, Yao Wang1, Zhiyong Qian1, Jiangang Zou1
Institutions: 1Department of Cardiology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China; 2Department of Cardiology, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, China.
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
Full Text: JBR-2017-0102.pdf
J Biomed Res published on Epub 19 February 2018, https://doi.org/10.7555/JBR.32.20170102