title: Quantitative cross-validation and content analysis of the 450k DNA methylation array from Illumina, Inc.
abstract: BACKGROUND
  The newly released 450k DNA methylation array from Illumina, Inc. offers the possibility to analyze more than 480,000 individual CpG sites in a user friendly standardized format. In this study the relationship between the β-values provided by the Illumina, Inc. array for each individual CpG dinucleotide and the quantitative methylation levels obtained by pyrosequencing were analyzed. In addition, the representation of microRNA genes and imprinted loci on the Illumina, Inc. array was assessed in detail. Genomic DNA from 4 human breast cancer cell lines (IPH-926, HCC1937, MDA-MB-134, PMC42) and 18 human breast cancer specimens as well as 4 normal mammary epithelial fractions was analyzed on 450k DNA methylation arrays. The β-values for 692 individual CpG sites from 62 different genes were cross-validated using conventional quantitative pyrosequencing.
  
  
  RESULTS
  The newly released 450k methylation array from Illumina, Inc. shows a high concordance with quantitative pyrosequencing if identical CpG sites are analyzed in cell lines (Spearman r = 0.88, p ≪ 0.0001), which is somewhat reduced in primary tumor specimens (Spearman r = 0.86, p ≪ 0.0001). 80.7% of the CpG sites show an absolute difference in methylation level of less than 15 percentage points. If different CpG sites in the same CpG islands are targeted the concordance is lower (r = 0.83 in cell lines and r = 0.7 in primary tumors). The number of CpG sites representing microRNA genes and imprinted loci is very heterogeneous (range: 1 - 70 CpG sites for microRNAs and 1 - 288 for imprinted loci).
  
  
  CONCLUSIONS
  The newly released 450k methylation array from Illumina, Inc. provides a genome-wide quantitative representation of DNA methylation aberrations in a convenient format. Overall, the congruence with pyrosequencing data is very good. However, for individual loci one should be careful to translate the β-values directly into percent methylation levels.
authors.affiliation: Institute of Pathology, Medizinische Hochschule Hannover, Carl-Neuberg-Str, 1, D-30625, Hannover, Germany.
authors.forename: Jessica
authors.initials: J
authors.lastname: Roessler
authors.forename: Ole
authors.initials: O
authors.lastname: Ammerpohl
authors.forename: Jana
authors.initials: J
authors.lastname: Gutwein
authors.forename: Britta
authors.initials: B
authors.lastname: Hasemeier
authors.forename: Sumadi Lukman
authors.initials: SL
authors.lastname: Anwar
authors.forename: Hans
authors.initials: H
authors.lastname: Kreipe
authors.forename: Ulrich
authors.initials: U
authors.lastname: Lehmann
mesh_terms: D020029:Base Pairing / Q000235:genetics*; D001943:Breast Neoplasms / Q000235:genetics; D045744:Cell Line, Tumor; D019175:DNA Methylation / Q000235:genetics*; D005260:Female; D056426:Genetic Loci / Q000235:genetics; D018392:Genomic Imprinting / Q000235:genetics; D006801:Humans; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA / Q000295:instrumentation* / Q000379:methods* / Q000592:standards; D055517:snRNP Core Proteins / Q000235:genetics
chemical_list: C526417:SNRPN protein, human; D055517:snRNP Core Proteins