title: Validation of a DNA methylation microarray for 850,000 CpG sites of the human genome enriched in enhancer sequences.
abstract: OBJECTIVE
  DNA methylation is the best known epigenetic mark. Cancer and other pathologies show an altered DNA methylome. However, delivering complete DNA methylation maps is compromised by the price and labor-intensive interpretation of single nucleotide methods.
  
  
  METHODS
  Following the success of the HumanMethylation450 BeadChip (Infinium) methylation microarray (450K), we report the technical and biological validation of the newly developed MethylationEPIC BeadChip (Infinium) microarray that covers over 850,000 CpG methylation sites (850K). The 850K microarray contains >90% of the 450K sites, but adds 333,265 CpGs located in enhancer regions identified by the ENCODE and FANTOM5 projects.
  
  
  CONCLUSIONS
  The 850K array demonstrates high reproducibility at the 450K CpG sites, is consistent among technical replicates, is reliable in the matched study of fresh frozen versus formalin-fixed paraffin-embeded samples and is also useful for 5-hydroxymethylcytosine. These results highlight the value of the MethylationEPIC BeadChip as a useful tool for the analysis of the DNA methylation profile of the human genome.
authors.affiliation: Cancer Epigenetics & Biology Program (PEBC), 08908 L'Hospitalet, Barcelona, Catalonia, Spain.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Moran
authors.affiliation: Cancer Epigenetics & Biology Program (PEBC), 08908 L'Hospitalet, Barcelona, Catalonia, Spain.
authors.forename: Carles
authors.initials: C
authors.lastname: Arribas
authors.affiliation: Cancer Epigenetics & Biology Program (PEBC), 08908 L'Hospitalet, Barcelona, Catalonia, Spain.|Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain.|Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.
authors.forename: Manel
authors.initials: M
authors.lastname: Esteller
mesh_terms: D018899:CpG Islands; D004742:Enhancer Elements, Genetic; D005557:Formaldehyde; D015894:Genome, Human; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D016612:Paraffin Embedding; D016707:Tissue Fixation / Q000379:methods
chemical_list: D005557:Formaldehyde
keywords: 5-hydroxymethylcytosine; CpG sites; DNA methylation; epigenetics; microarray; paraffin; validation