Genome-wide Methylation Analysis

Epigenetics describes the study of heritable changes in gene function that occur without a change in the nuclear DNA sequence. A major epigenetic mechanism in higher eukaryotes is DNA methylation. It involves the covalent addition of a methyl group to the 5'-carbon of cytosine usually in a CpG dinucleotide.

Many, if not all, human tumors exhibit an altered methylation signature. This aberrant methylation pattern is often characterized by global hypomethylation and locus specific hypermethylation, which often occurs in promoter regions of tumorsuppressor genes such as p16 or RASSF1 (Esteller, 2007).

Methylation patterns are maintained during replication (semi-conservative duplication of DNA) by DNA Methyltransferase 1 (DNMT1). De novo methylation of CpG sites is carried out by DNMT3A and DNMT3B. The methylation patterns allow distinctions according to cell types, age, or cancer (vs. normal).

At Microarray Core Facility, we provide full service for the analysis of DNA methylation on a genome-wide level in human and in mouse samples (genomic DNA) making use of the well established Infinium technology of Illumina.

Infinium MethylationEPIC BeadChip

The HumanMethylationEPIC is the next generation of Infinium Methylation and builds upon the HumanMethylation450k with 93.3% of the original CpGs plus roughly additional 350.000 CpGs in enhancer regions.

The interrogated sites have been selected to represent the following content:

• coverage of all designable RefSeq genes (also with lacking CpG islands), including promoter, 5'- and 3'-regions
• CpG islands and shores
• CpG sites outside of CpG islands
• Non-CpG methylated sites identified in human stem cells
• Differentially methylated sites identified in tumor versus normal CpG islands outside of coding regions
• FANTOM5 enhancers
• ENCODE open chromatin and enhancers
• DNase hypersensitive sites
• miRNA promoter regions
• Disease-associated regions identified through GWAS

The MethylationEPIC array provides an unprecedented view of 864.928 CpGs in an 8 sample per chip format. This allows a genome-wide and cost effective insight into the human methylome at single-nucleotide resolution. Sample requirements can be found in the table below.

Infinium Mouse Methylation BeadChip

Finally, there is the possibility to study epigenetic changes cost-effectively and at a higher throughput, even in modified mouse strains, many of which were created to model human disease.

The Infinium Mouse Methylation BeadChip interrogates > 285k methylation sites per sample at single-nucleotide resolution and is designed for 18 common laboratory mouse strains. It provides balanced coverage of CpG islands, translation start sites, enhancers, imprinted loci, hypermethylated regions in cancer and other regions for a comprehensive view of the methylation landscape in the murine genome.

The BeadChip enables a broad range of applications e.g. epigenome-wide association studies, studies in Developmental Biology and Epigenetic Aging and can also be used in Preclinical Research, and for Patient-derived xenograft models e.g. of cancer.

Sample requirements can be found in the table below. Please provide sample sets of 12 samples each.

Methylation studies on human FFPE samples are enabled with a modified version of the Infinium Methylation protocol. The quality of such material strongly varies depending on applied FFPE protocol and storage period. Therefore, we perform an initial quality control with all incoming samples using fluorescence based quantification followed by quantitative Real-Time PCR. Only samples passing this additional QC will be bisulfite converted and processed in a special restore step followed by the standard hybridisation workflow. Due to this additional effort an extra FFPE fee per sample will be charged.

YOU supply

• Completion of sample sheet
• DNA Sample Concentration and Volume Requirements:
   

 For lower DNA amounts please inquire.
 

WE perform

• QC of DNA sample (applied methods depend on the DNA's origin)
• Bisulfite treatment (incl. QC)
• Restore procedure (only for human FFPE samples)
• Infinium assay (technical reproducibility >0,98, PCR free assay)
• Basic data analysis

WE provide (see example expression data)

• Raw data
• Methylation information on all CpG sites tested (in MS Excel compatible format)
• Medium term storage of all data for at least 12 months
• Discussion on the results
   

Pricing per DNA sample is provided on our pricelist. For further details concerning methylation analysis, please feel free to contact Dr. Melanie Bewerunge-Hudler.

Citing our service

Please cite our service in the acknowledgements part of your paper in case we've just performed the standard service. The following statement has been used in the past.:

"We thank the Microarray Core Facility of the DKFZ for providing the Illumina methylation arrays and related services."

Selected Publications

Find below a selection of publications making use of data generated at the Microarray Core Facility using HumanMethylationEPIC.

Koelsche C, Schrimpf D, Stichel D, Sill M, et al.
Sarcoma classification by DNA methylation profiling.
Nat Commun. 2021 Jan 21;12(1):498. 
PMID: 33479225 

Zhang Y, et al.
Blood-derived DNA methylation predictors of mortality discriminate tumor and healthy tissue in multiple organs.
Mol Oncol. 2020 Sep;14(9):2111-2123. 
PMID: 32506842

Capper D,  et al.
Nature. 2018;555(7697):469-74.
DNA methylation-based classification of central nervous system tumours.
PMID: 29539639