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

By J. Sandoval, Holger Heyn, S. Moran, J. Serra-Musach, M. Pujana, M. Bibikova, Manel Esteller. Epigenetics, 2011

1,018 citations recorded by the source corpus.

DNA methylation is the most studied epigenetic mark and CpG methylation is central to many biological processes and human diseases. Since cancer has highlighted the contribution to disease of aberrant DNA methylation patterns, such as the presence of promoter CpG island hypermethylation-associated silencing of tumor suppressor genes and global DNA hypomethylation defects, their importance will surely become apparent in other pathologies. However, advances in obtaining comprehensive DNA methylomes are hampered by the high cost and time-consuming aspects of the single nucleotide methods currently available for whole genome DNA methylation analyses. Following the success of the standard CpG methylation microarrays for 1,505 CpG sites and 27,000 CpG sites, we have validated in vivo the newly developed 450,000 (450K) cytosine microarray (Illumina). The 450K microarray includes CpG and CNG sites, CpG islands/shores/shelves/open sea, non-coding RNA (microRNAs and long non-coding RNAs) and sites surrounding the transcription start sites (-200 bp to -1,500 bp, 5'-UTRs and exons 1) for coding genes, but also for the corresponding gene bodies and 3'-UTRs, in addition to intergenic regions derived from GWAS studies. Herein, we demonstrate that the 450K DNA methylation array can consistently and significantly detect CpG methylation changes in the HCT-116 colorectal cancer cell line in comparison with normal colon mucosa or HCT-116 cells with defective DNA methyltransferases (DKO). The provided validation highlights the potential use of the 450K DNA methylation microarray as a useful tool for ongoing and newly designed epigenome projects.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/a415b8c00b8c681707256e4fd0636bf0021e8657

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Citations in the corpus

Distinct DNA methylomes of newborns and centenarians (2012, methodology): “We used a newly developed DNA methylation microarray that assays the DNA methylation status of 450,000 CpG sites (28, 29).”
Differential DNA Methylation in Purified Human Blood Cells: Implications for Cell Lineage and Studies on Disease Susceptibility (2012, methodology): “Global DNA methylation was analyzed using the Illumina Infinium 450K microarray platform [29].”
Gene Body Methylation can alter Gene Expression and is a Therapeutic Target in Cancer (2014, background): “…for 482,421 CpG sites across the genome, covering 99% of RefSeq genes (more than 21,000 genes) with an average of 17 CpG sites per gene, and probes are distributed in promoters, gene bodies, Gene Body Methylation Alters Gene Expression enhancers, and intergenic regions (Sandoval et al., 2011).”
450K Epigenome-Wide Scan Identifies Differential DNA Methylation in Newborns Related to Maternal Smoking during Pregnancy (2012, methodology): “We measured methylation at 485,577 CpGs in cord blood using Illumina’s Infinium HumanMethylation450 BeadChip (Bibikova et al. 2011; Sandoval et al. 2011).”
A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data (2012, methodology): “A key statistical issue with the Illumina 450k beadchip is that probes come in two different designs, which causes the methylation values derived from these two designs to exhibit widely different distributions (Dedeurwaerder et al., 2011).”
A data-driven approach to preprocessing Illumina 450K methylation array data (2013, methodology): “The 450K BeadChip [2,3] achieves increased coverage by utilising two different probe types on each array: Infinium I (n=135,501) and Infinium II (n=350,076) probes.”
Integrative Analysis of Multi-omics Data for Discovery and Functional Studies of Complex Human Diseases (2016, methodology): “On the down side, it only represents ~2% of all DNAm sites of the human genome, and over-represents the genic regions (75% of sites) including promoter, gene body and 3’-UTR (Sandoval et al., 2011).”