mLiftOver: Harmonizing Data Across Infinium DNA Methylation Platforms

Abstract

Infinium DNA methylation BeadChips are widely used for genome-wide DNA methylation profiling at the population scale. Recent updates to probe content and naming conventions in the EPIC version 2 (EPICv2) arrays have complicated integrating new data with previous Infinium array platforms, such as the EPIC and the HumanMethylation450 (HM450) BeadChip. We present mLiftOver, a user-friendly tool that transfers probe ID, methylation level, and signal intensity data across different Infinium platforms. It manages probe replicates, missing data imputation, and platform-specific bias for accurate data conversion. We validated the tool by applying HM450-based cancer classifiers to EPICv2 cancer data, achieving high accuracy. Additionally, we successfully integrated EPICv2 healthy tissue data with legacy HM450 data for tissue identity analysis and produced consistent copy number profiles in cancer cells. Availability and implementationmLiftOver is implemented R and available in the Bioconductor package SeSAMe (version 3.21.13+): https://bioconductor.org/packages/release/bioc/html/sesame.html Analysis of EPIC and EPICv2 platform-specific bias and high-confidence mapping is available at https://github.com/zhou-lab/InfiniumAnnotationV1/blob/main/Anno/EPICv2/EPICv2ToEPIC_conversion.tsv.gz The source code is available at https://github.com/zwdzwd/sesame/blob/devel/R/mLiftOver.R under the MIT license.