Clinical and public health research using methylated DNA Immunoprecipitation (MeDIP): A comparison of commercially available kits to examine differential DNA methylation across the genome

Abstract

The methylated DNA immunoprecipitation method (MeDIP) is a genome-wide, high-resolution approach that detects DNA methylation with oligonucleotide tiling arrays or high throughput sequencing platforms. A simplified high-throughput MeDIP assay will enable translational research studies in clinics and populations, which will greatly enhance our understanding of the human methylome. We compared three commercial kits, MagMeDIP Kit TM (Diagenode), Methylated-DNA IP Kit (Zymo Research) and Methylamp™ Methylated DNA Capture Kit (Epigentek), in order to identify which one has better reliability and sensitivity for genomic DNA enrichment. Each kit was used to enrich two samples, one from fresh tissue and one from a cell line, with two different DNA amounts. The enrichment efficiency of each kit was evaluated by agarose gel band intensity after Nco I digestion and by reaction yield of methylated DNA. A successful enrichment is expected to have a 1:4 to 10:1 conversion ratio and a yield of 80% or higher. We also evaluated the hybridization efficiency to genome-wide methylation arrays in a separate cohort of tissue samples. We observed that the MagMeDIP kit had the highest yield for the two DNA amounts and for both the tissue and cell line samples, as well as for the positive control. In addition, the DNA was successfully enriched from a 1:4 to 10:1 ratio. Therefore, the MagMeDIP kit is a useful research tool that will enable clinical and public health genome-wide DNA methylation studies.

Keywords: :

• differential methylation
• Methylated DNA Immunoprecipitation (MeDIP)
• translational research genome-wide promoter methylation

Disclosure of Potential Conflicts of Interest

D. Sidransky owns Oncomethylome Sciences, SA stock, which is subject to certain restrictions under University policy. D. Sidransky is a paid consultant to Oncomethylome Sciences, SA, and is a paid member of the company's Scientific Advisory Board.

Financial support

This research was supported in part by the following grant awards: National Cancer Institute (NCI) 1K01CA164092–01; NCI Early Detection Research Network grant U01 CA84986; an NCI Supplement to Promote Diversity Award to U01 CA84986; a National Institute of Dental and Craniofacial Research (NIDCR) and NIH Specialized Program of Research Excellence grant (SPORE) P50DE019032; and NIDCR grant RC2 DE20957. The funding agencies had no role in the design of the study, data collection or analysis, the interpretation of the results, the preparation of the manuscript, or the decision to submit the manuscript for publication.

E. Soudry is recipient of a fellowship grant from the American Physicians Fellowship for Medicine in Israel.