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Open Access Highly Accessed Technical Note

Quantitative cross-validation and content analysis of the 450k DNA methylation array from Illumina, Inc.

Jessica Roessler1, Ole Ammerpohl2, Jana Gutwein2, Britta Hasemeier1, Sumadi Lukman Anwar1, Hans Kreipe1 and Ulrich Lehmann1*

Author Affiliations

1 Institute of Pathology, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, D-30625, Hannover, Germany

2 Institute of Human Genetics, University Hospital Schleswig Holstein, Kiel, Germany

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BMC Research Notes 2012, 5:210  doi:10.1186/1756-0500-5-210

Published: 30 April 2012

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.

Findings

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.