A validation of Illumina EPIC array system with bisulfite-based amplicon sequencing.

Area of Science:

• Epigenetics
• Genomics
• Molecular Biology

Background:

• The Illumina Infinium MethylationEPIC BeadChip (EPIC array) is the gold standard for genome-wide DNA methylation analysis.
• Targeted validation of EPIC array findings in larger cohorts is essential for hypothesis generation and pilot studies.
• A need exists for accurate, smaller-scale targeted techniques that generate CpG-level data comparable to the EPIC array.

Purpose of the Study:

• To evaluate bisulfite-based amplicon sequencing (BSAS) as a method for validating DNA methylation sites identified by the EPIC array.
• To assess the correlation between BSAS and EPIC array data at individual CpG sites.
• To determine the suitability of BSAS for targeted validation and discovery in epigenomic research.

Main Methods:

• Bisulfite-based amplicon sequencing (BSAS) was employed to analyze DNA methylation.
• BSAS data was compared with data generated from the Illumina Infinium MethylationEPIC BeadChip array.
• Correlation analysis was performed on CpG site methylation levels between the two techniques.

Main Results:

• BSAS demonstrated high correlation with EPIC array data for differential DNA methylation at some CpG loci.
• Correlation between BSAS and EPIC array data was lower in instances where the magnitude of change detected by the EPIC array exceeded 5%.
• BSAS allows for the analysis of CpGs not present on the EPIC array, facilitating the discovery of novel sites and differentially methylated regions.

Conclusions:

• BSAS serves as a valid tool for validating specific DNA methylation sites identified by the EPIC array.
• Individual locus-by-locus comparison is recommended when using BSAS for validation, particularly for loci with substantial methylation changes.
• BSAS offers advantages over probe-based arrays by enabling analysis of broader genomic regions and discovery of novel epigenetic marks.