ArticleBioinformatics (Oxford, England)2024
mLiftOver: harmonizing data across Infinium DNA methylation platforms.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- DNA methylation profiling enables subclassification of mucinous ovarian carcinoma and distinguishes it from extraovarian mucinous metastases.Cell reports. Medicine · 2026Article
- Longitudinal Changes in Inflammation-Related Methylation Risk Score for C-Reactive Protein Among People with HIV.Epigenomes · 2026Article
- Spinal low-grade ependymal tumors harboring telomerase reverse transcriptase promoter mutation and chromosome 7 gain with methylation profile of spinal subependymoma.Acta neuropathologica communications · 2026Article
- DNA Methylation-Based Risk Stratification and Classification of Pediatric Thyroid Carcinoma.Clinical cancer research : an official journal of the American Association for Cancer Research · 2026Article
- Peripheral blood DNA methylation changes are predictive of incident radiographic osteoarthritis development: Data and biospecimens from the osteoarthritis initiative.Osteoarthritis and cartilage open · 2025Article
- CCNV: a user-friendly R package enabling large-scale cumulative copy number variation analyses of DNA methylation data.BMC bioinformatics · 2025Article
- Accounting for differences between Infinium MethylationEPIC v2 and v1 in DNA methylation-based tools.Life science alliance · 2025Article
- Accounting for differences between Infinium MethylationEPIC v2 and v1 in DNA methylation-based tools.bioRxiv : the preprint server for biology · 2025Article
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Authors and funding
2 authors.
Funding
Abstract
motivationInfinium 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 MethylationEPIC (EPIC) and the HumanMethylation450 (HM450) BeadChip.
resultsWe present mLiftOver, a user-friendly tool that harmonizes 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 IMPLEMENTATION: mLiftOver is implemented R and available in the Bioconductor package SeSAMe (version 1.21.13+): 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/raw/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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.