An effective processing pipeline for harmonizing DNA methylation data from Illumina's 450K and EPIC platforms for epidemiological studies.

Lauren A VanderlindenRandi K JohnsonPatrick M CarryFran DongDawn L DeMeoIvana V YangJill M NorrisKaterina Kechris

Published in: BMC research notes (2021)

We found normalization and probe filtering had the biggest effect on data harmonization. Employing a meta-analysis was an effective and easily executable method for accounting for platform variability. Correcting for genomic inflation also helped with harmonization. We present guidelines for studies seeking to harmonize data from the 450K and EPIC platforms, which includes the use of technical replicates for evaluating numerous pre-processing steps, and employing a meta-analysis.

Keyphrases

dna methylation
electronic health record
big data
gene expression
mental health
genome wide
high throughput
copy number
machine learning
clinical practice