PhenoExplorer: An Interactive Web-based Platform for Exploring (Epi)Genome-Wide Associations Using a Swiss...

Area of Science:

• Genetics and Genomics
• Epigenetics
• Population Health

Background:

• High-throughput sequencing enables exploration of genetic and epigenetic contributions to complex traits.
• Population-based studies are crucial for understanding the genetic architecture of common diseases and phenotypes.

Purpose of the Study:

• To conduct large-scale Genome-Wide Association Studies (GWAS) and Epigenome-Wide Association Studies (EWAS) in a Swiss population.
• To investigate associations between Single Nucleotide Polymorphisms (SNPs) and Cytosine-Phospho-Guanine (CpG) markers with a wide range of phenotypes.
• To develop an accessible web-based platform (PhenoExplorer) for sharing study results.

Main Methods:

• Utilized data from the SKIPOGH cohort (N=1100) including 7.5 million SNPs, 420,000 CpGs, and 825 phenotypes.
• Performed GWAS for SNP-metabolite/metal associations and EWAS for CpG-phenotype associations.
• Adjusted for covariates including age, sex, recruitment center, familial structure, and seasonality for EWAS.

Main Results:

• Identified 2091 unique SNPs significantly associated with 103 phenotypes in GWAS.
• Discovered 2578 unique CpGs significantly associated with 109 phenotypes in EWAS.
• Developed and launched the PhenoExplorer web platform to provide open access to all GWAS and EWAS results.

Conclusions:

• This study provides a comprehensive overview of SNP and CpG associations with complex phenotypes in a Swiss population.
• The PhenoExplorer platform facilitates access to these findings, promoting further research into the role of molecular variants in human health.
• The results contribute to understanding the genetic and epigenomic underpinnings of diverse phenotypic traits.