Comparison of DNA methylation measured by Illumina 450K and EPIC BeadChips in blood of newborns and 14-year-old children
Autor: | Hong Quach, Gwen Tindula, J.L. MacIsaac, Michael J. Meaney, Lisa F. Barcellos, Brenda Eskenazi, Michael S. Kobor, Karen Huen, Olivia Solomon, Nina Holland |
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Rok vydání: | 2018 |
Předmět: |
Adult
Male 0301 basic medicine Cancer Research Adolescent Population Medical Biochemistry and Metabolomics Biology EPIC 850K California 450K Epigenesis Genetic 03 medical and health sciences Human health children Genetic Pregnancy Genetics 2.1 Biological and endogenous factors 2.2 Factors relating to the physical environment Humans Epigenetics Aetiology Pesticides education Molecular Biology Pediatric education.field_of_study DNA methylation Human Genome Infant Newborn Infant Methylation DNA Methylation Newborn 030104 developmental biology CpG site Maternal Exposure cord blood Female Biochemistry and Cell Biology Birth cohort Developmental Biology Epigenesis Demography |
Zdroj: | Epigenetics, vol 13, iss 6 |
ISSN: | 1559-2308 1559-2294 |
Popis: | 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. |
Databáze: | OpenAIRE |
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