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

Priscilla Brebi-Mieville, Carmen Ili-Gangas, Pamela Leal-Rojas, Maartje G. Noordhuis, Ethan Soudry, Jimena Perez, Carlos Juan Roa, David Sidransky, Rafael Guerrero-Preston

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish (US)
Pages (from-to)106-112
Number of pages7
JournalEpigenetics
Volume7
Issue number1
DOIs
StatePublished - Jan 2012

Keywords

  • Differential methylationsolexa
  • Methylated DNA immunoprecipitation (MeDIP)
  • Translational research genome-wide promoter methylation

ASJC Scopus subject areas

  • Molecular Biology
  • Cancer Research

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