Data from: "Comparison of enzymatic- and bisulfite conversion of circulating cell-free tumor DNA for DNA methylation analyses"

Abstract Detection of DNA methylation biomarkers in circulating cell-free DNA (cfDNA) has great clinical potential for cancer management, but method optimization and standardization is needed. Bisulfite conversion is the gold-standard pre-treatment method for methylation analyses, but causes DNA fragmentation and loss. Enzymatic conversion of DNA represents a promising alternative due to the more gentle treatment. The aim of this study was to evaluate and compare enzymatic- and bisulfite conversion to identify the best pre-treatment method for detecting DNA methylation biomarkers in cfDNA from plasma using droplet digital PCR (ddPCR). The performance of the NEBNext Enzymatic Methyl-seq Kit and the EpiTect Plus DNA Bisulfite Kit was evaluated and compared using normal cfDNA and tumor cfDNA samples from colorectal cancer patients. Enzymatic conversion resulted in longer DNA fragments with higher peak fragment sizes compared to bisulfite conversion, but the DNA recovery was considerably lower after enzymatic conversion compared to bisulfite conversion. DNA methylation of the biomarker BCAT1 was detected at similar rates in parallel tumor cfDNA samples pre-treated with either enzymatic- or bisulfite conversion. However, enzymatic conversion resulted in lower number of positive droplets for both target and control ddPCR assays, in line with the lower DNA recovery after conversion. Altogether, bisulfite conversion emerges as the best pre-treatment method due to higher DNA recovery after conversion and higher number of positive droplets in the ddPCR reactions.