biostudies-literaturePeters TJNational Health and Medical Research CouncilNational Breast Cancer Foundation251https://www.ebi.ac.uk/biostudies/studies/S-EPMC10916044biostudies-literatureUnknown25(1)<h4>Background</h4>The Illumina family of Infinium Methylation BeadChip microarrays has been widely used over the last 15 years for genome-wide DNA methylation profiling, including large-scale and population-based studies, due to their ease of use and cost effectiveness. Succeeding the popular HumanMethylationEPIC BeadChip (EPICv1), the recently released Infinium MethylationEPIC v2.0 BeadChip (EPICv2) claims to extend genomic coverage to more than 935,000 CpG sites. Here, we comprehensively characterise the reproducibility, reliability and annotation of the EPICv2 array, based on bioinformatic analysis of both manifest data and new EPICv2 data from diverse biological samples.<h4>Results</h4>We find a high degree of reproducibility with EPICv1, evidenced by comparable sensitivity and precisBMC genomicsCharacterisation and reproducibility of the HumanMethylationEPIC v2.0 BeadChip for DNA methylation profiling.PMC1091604417-02IIRS-21-0471156408IIRS-22-0602010156Meyer BAchinger-Kawecka JRyan LLoi-Luu PPidsley RClark SJNair SSong JPeters TJCampbell EMStricker PLim EStirzaker CQu WfalseCharacterisation and reproducibility of the HumanMethylationEPIC v2.0 BeadChip for DNA methylation profiling.<h4>Background</h4>The Illumina family of Infinium Methylation BeadChip microarrays has been widely used over the last 15 years for genome-wide DNA methylation profiling, including large-scale and population-based studies, due to their ease of use and cost effectiveness. Succeeding the popular HumanMethylationEPIC BeadChip (EPICv1), the recently released Infinium MethylationEPIC v2.0 BeadChip (EPICv2) claims to extend genomic coverage to more than 935,000 CpG sites. Here, we comprehensively characterise the reproducibility, reliability and annotation of the EPICv2 array, based on bioinformatic analysis of both manifest data and new EPICv2 data from diverse biological samples.<h4>Results</h4>We find a high degree of reproducibility with EPICv1, evidenced by comparable sensitivity and precis2024-01-01T00:00:00Z2024 Mar2026-07-15T16:03:25.179Z2026-07-07T03:08:19.3ZS-EPMC109160443844882010.1186/s12864-024-10027-5