{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Solomon O"],"funding":["National Institute of Environmental Health Sciences","NIDA NIH HHS","NIEHS NIH HHS","California Environmental Protection Agency","National Institutes of Health","NIH HHS"],"pagination":["655-664"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC6140901"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["13(6)"],"pubmed_abstract":["Analysis of DNA methylation helps to understand the effects of environmental exposures as well as the role of epigenetics in human health. Illumina, Inc. recently replaced the HumanMethylation450 BeadChip (450K) with the EPIC BeadChip, which nearly doubles the measured CpG sites to >850,000. Although the new chip uses the same underlying technology, it is important to establish if data between the two platforms are comparable within cohorts and for meta-analyses. DNA methylation was assessed by 450K and EPIC using whole blood from newborn (n = 109) and 14-year-old (n = 86) participants of the Center for the Health Assessment of Mothers and Children of Salinas. The overall per-sample correlations were very high (r >0.99), although many individual CpG sites, especially those with low variance of methylation, had lower correlations (median r = 0.24). There was also a small subset of CpGs with large mean methylation β-value differences between platforms, in both the newborn and 14-year datasets. However, estimates of cell type proportion prediction by 450K and EPIC were highly correlated at both ages. Finally, differentially methylated positions between boys and girls replicated very well by both platforms in newborns and older children. These findings are encouraging for application of combined data from EPIC and 450K platforms for birth cohorts and other population studies. These data in children corroborate recent comparisons of the two BeadChips in adults and in cancer cell lines. However, researchers should be cautious when characterizing individual CpG sites and consider independent methods for validation of significant hits."],"journal":["Epigenetics"],"pubmed_title":["Comparison of DNA methylation measured by Illumina 450K and EPIC BeadChips in blood of newborns and 14-year-old children."],"pmcid":["PMC6140901"],"funding_grant_id":["R01ES012503","P01 ES009605","R24 ES028529","R01 ES023067","UG3 OD023356","UG3OD023356","R01 ES012503","F31 ES027751","RD83273401","R01 DA035300","R24ES028529","P01ES009605","R01 ES021369","RD83171001","R01ES021369"],"pubmed_authors":["Meaney MJ","Kobor MS","Barcellos LF","Tindula G","MacIsaac J","Holland N","Huen K","Solomon O","Eskenazi B","Quach H"],"additional_accession":[]},"is_claimable":false,"name":"Comparison of DNA methylation measured by Illumina 450K and EPIC BeadChips in blood of newborns and 14-year-old children.","description":"Analysis of DNA methylation helps to understand the effects of environmental exposures as well as the role of epigenetics in human health. Illumina, Inc. recently replaced the HumanMethylation450 BeadChip (450K) with the EPIC BeadChip, which nearly doubles the measured CpG sites to >850,000. Although the new chip uses the same underlying technology, it is important to establish if data between the two platforms are comparable within cohorts and for meta-analyses. DNA methylation was assessed by 450K and EPIC using whole blood from newborn (n = 109) and 14-year-old (n = 86) participants of the Center for the Health Assessment of Mothers and Children of Salinas. The overall per-sample correlations were very high (r >0.99), although many individual CpG sites, especially those with low variance of methylation, had lower correlations (median r = 0.24). There was also a small subset of CpGs with large mean methylation β-value differences between platforms, in both the newborn and 14-year datasets. However, estimates of cell type proportion prediction by 450K and EPIC were highly correlated at both ages. Finally, differentially methylated positions between boys and girls replicated very well by both platforms in newborns and older children. These findings are encouraging for application of combined data from EPIC and 450K platforms for birth cohorts and other population studies. These data in children corroborate recent comparisons of the two BeadChips in adults and in cancer cell lines. However, researchers should be cautious when characterizing individual CpG sites and consider independent methods for validation of significant hits.","dates":{"release":"2018-01-01T00:00:00Z","publication":"2018","modification":"2026-06-08T03:24:20.068Z","creation":"2019-03-26T23:56:25Z"},"accession":"S-EPMC6140901","cross_references":{"pubmed":["30044683"],"doi":["10.1080/15592294.2018.1497386"]}}