Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome

Sandoval, Juan; Heyn, Holger; Morán, Sebastian; Serra-Musach, Jordi; Pujana, Miguel Ángel; Bibikova, Marina; Esteller, Manel

doi:10.4161/epi.6.6.16196

Cited by 900 publications

(828 citation statements)

References 45 publications

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“…We also used minfi to analyze methylation patterns at the level of epigenomic substructures, such as CpG islands, shores, shelves, and open sea regions (Irizarry et al ., 2009; Sandoval et al ., 2011). The results again indicated only minor differences between the young and old samples for most substructures, but revealed a robust and highly significant ( P = 2.0e‐171) hypermethylation of CpG islands in the old samples (Fig.…”

Section: Resultsmentioning

confidence: 99%

Reduced DNA methylation patterning and transcriptional connectivity define human skin aging

et al. 2016

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SummaryEpigenetic changes represent an attractive mechanism for understanding the phenotypic changes associated with human aging. Age‐related changes in DNA methylation at the genome scale have been termed ‘epigenetic drift’, but the defining features of this phenomenon remain to be established. Human epidermis represents an excellent model for understanding age‐related epigenetic changes because of its substantial cell‐type homogeneity and its well‐known age‐related phenotype. We have now generated and analyzed the currently largest set of human epidermis methylomes (N = 108) using array‐based profiling of 450 000 methylation marks in various age groups. Data analysis confirmed that age‐related methylation differences are locally restricted and characterized by relatively small effect sizes. Nevertheless, methylation data could be used to predict the chronological age of sample donors with high accuracy. We also identified discontinuous methylation changes as a novel feature of the aging methylome. Finally, our analysis uncovered an age‐related erosion of DNA methylation patterns that is characterized by a reduced dynamic range and increased heterogeneity of global methylation patterns. These changes in methylation variability were accompanied by a reduced connectivity of transcriptional networks. Our findings thus define the loss of epigenetic regulatory fidelity as a key feature of the aging epigenome.

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Section: Resultsmentioning

confidence: 99%

Reduced DNA methylation patterning and transcriptional connectivity define human skin aging

et al. 2016

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“…DNA was whole-genome amplified, enzymatically fragmented, purified, and applied to the Illumina Infinium HumanMethylation450 BeadChips (Illumina, San Diego, CA) according to the Illumina methylation protocol [11,12]. Both EPIC and 450K chips were analyzed using the Illumina Hi-Scan system.…”

Section: Methodsmentioning

confidence: 99%

Comparison of DNA methylation measured by Illumina 450K and EPIC BeadChips in blood of newborns and 14-year-old children

et al. 2018

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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.

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“…Transcription start sites (TSS) were used to set Bpromoter regionsâ t 4000 bp upstream plus 1000 bp downstream of each TSS. CG islands (Gardiner-Garden and Frommer 1987) not present in repeat regions (18,411), i.e., masked CG islands, were downloaded from UCSC (Rosenbloom et al 2015), and CG island shores and shelves (Irizarry et al 2009;Sandoval et al 2011) were defined as 4000 bp up and downstream of the masked CG islands (Fig. 1a).…”

Section: Probe Designmentioning

confidence: 99%

“…Thus, while RRBS is a powerful discovery tool, comprehensive coverage of regions of interest and consistent methylation quantitation across multiple samples and multiple experimental groups can be difficult to achieve. Microarrays which combine bisulfite conversion with an existing SNP platform technology (Illumina 450K Array (Sandoval et al 2011)) have also been widely used but cover relatively few CG and non-CG sites of the genome and are currently only available for human studies. Thus, while these existing techniques are useful, they do not combine genome-wide scope with sufficient sample throughput for genome-wide discovery and hypothesis-generating studies.…”

Section: Introductionmentioning

confidence: 99%

Bisulfite oligonucleotide-capture sequencing for targeted base- and strand-specific absolute 5-methylcytosine quantitation

Masser

Stanford

Hadad

et al. 2016

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Epigenetic regulation through DNA methylation (5mC) plays an important role in development, aging, and a variety of diseases. Genome-wide studies of base-and strand-specific 5mC are limited by the extensive sequencing required. Targeting bisulfite sequencing to specific genomic regions through sequence AGE (2016) capture with complimentary oligonucleotide probes retains the advantages of bisulfite sequencing while focusing sequencing reads on regions of interest, enables analysis of more samples by decreasing the amount of sequence required per sample, and provides base-and strand-specific absolute quantitation of CG and non-CG methylation levels. As an example, an oligonucleotide capture set to interrogate 5mC levels in all rat RefSeq gene promoter regions (18,814) and CG islands, shores, and shelves (18,411) was generated. Validation using whole-genome methylation standards and biological samples demonstrates enrichment of the targeted regions and accurate base-specific quantitation of CG and non-CG methylation for both forward and reverse genomic strands. A total of 170 Mb of the rat genome is covered including 6.6 million CGs and over 67 million non-CG sites, while reducing the amount of sequencing required by~85 % as compared to existing wholegenome sequencing methods. This oligonucleotide capture targeting approach and quantitative validation workflow can also be applied to any genome of interest.

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Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome

Cited by 900 publications

References 45 publications

Reduced DNA methylation patterning and transcriptional connectivity define human skin aging

Reduced DNA methylation patterning and transcriptional connectivity define human skin aging

Comparison of DNA methylation measured by Illumina 450K and EPIC BeadChips in blood of newborns and 14-year-old children

Bisulfite oligonucleotide-capture sequencing for targeted base- and strand-specific absolute 5-methylcytosine quantitation

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