Validating Infinium Methylation Array Data

We examined bisulfite-converted genomic DNA (EZ methylation kit by Zymo Research) by quantitative pyrosequencing analysis to confirm results from the Infinium Methylation arrays. Validation of methylation levels using pyrosequencing was performed on 20 cases and 15 controls. We performed pyrosequencing with appropriate oligos using the PyroMark Q24 System and advanced CpG Reagents (Qiagen^®) as per the manufacturer’s instructions. We confirmed methylation difference of top 25 CpG targets, concluding the chip-based cytosine methylations are true changes [57 (link),58 (link)]. A detailed methodology was published previously [57 (link)].

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Bahado-Singh R.O., Vishweswaraiah S., Aydas B., Mishra N.K., Guda C, & Radhakrishna U. (2019). Deep Learning/Artificial Intelligence and Blood-Based DNA Epigenomic Prediction of Cerebral Palsy. International Journal of Molecular Sciences, 20(9), 2075.

Publication 2019

EZ methylation kit PyroMark Q24 System advanced CpG Reagents

Bisulfite Chip Cytosine Genomic Methylations Oligos

Corresponding Organization : Oakland University

Other organizations : Albion College, University of Nebraska Medical Center

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Variable analysis

independent variables

Bisulfite conversion of genomic DNA

dependent variables

Methylation levels

control variables

Genomic DNA samples from 20 cases and 15 controls

controls

Positive control: Infinium Methylation arrays
Negative control: Not explicitly mentioned

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