Response to “Different measures of ‘genome-wide’ DNA methylation exhibit unique properties in placental and somatic tissues”

Abstract

I found the research paper “Different measures of ‘genome-wide’ DNA methylation exhibit unique properties in placental and somatic tissues” by Price ME and colleagues in the June 2012 issue of Epigenetics to be an interesting read, but it contains errors in regards to the use of the MethylFlash Methylated DNA Quantification Kit. The text contained in the “Global DNA Methylation” paragraph under the “Methods” section of the paper claims that the kit was used by “following the manufacturer’s protocol.” I find that this is quite misleading to the reader as we have identified, based on the original electronic publication ahead of print, that the steps had not been correctly carried out.

The original text was the following: “DNA was hybridized to wells treated to have a high affinity for DNA. The wells were washed with a 5-mC-specific capture antibody followed by a detection antibody. The absorbance (or optical density) of each well was measured using a microplate spectrophotometer. Correlation of technical replicates was poor (r = 0.09, p = 0.72) using this kit.” However, the user guide of this kit clearly states that DNA is bound, not hybridized, to the strip wells and that the wells should be washed with the included Wash Buffer rather than a “5-mC-specific capture antibody.”

Therefore, it is not surprising that the result or correlation of replicates was poor and that the authors’ “results were variable” due to improper use of the kit. Based on our quality control tests and feedback from the vast amount of users of this popular kit, the variation between replicates should be less than 10% with R value > 0.9 (p < 0.01), assuming proper user performance according to the product manual.

I hope this helps to correct the misinformation presented in the paper as I feel that it is important to promote accuracy on behalf of the epigenetic research community. I also kindly encourage any users of an Epigentek product to work with our very knowledgeable technical support team should they have any difficulties.

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Different measures of “genome-wide” DNA methylation exhibit unique properties in placental and somatic tissues

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