Research article
Array-based DNA methylation profiling of primary lymphomas of the central nervous system
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* Corresponding author: Reiner Siebert rsiebert@medgen.uni-kiel.de
- † Equal contributors
1 Institute of Human Genetics, University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel, Germany
2 Department of Neuropathology, University of Cologne, Cologne, Germany
3 Illumina Inc., San Diego, CA, USA
4 Molecular Neuro-Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
BMC Cancer 2009, 9:455 doi:10.1186/1471-2407-9-455
Published: 21 December 2009Additional files
Additional file 1:
Table of DNA-methylation data (beta-values) obtained from the microarray analysis (0: unmethylated; 1: fully methylated). Additionally, this table contains information about the sequence analyzed, the promoter class and whether the gene is a putative PcG target gene.
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Additional file 2:
DNA samples used as controls in the present study (according to Hummel et al., 2006).
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Additional file 3:
List of genes differentially methylated between controls, PCNSL and DLBCL
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Additional file 4:
GeneVenn Diagramm http://www.bioinformatics.org/gvenn/ webcite of genes differentially methylated between 5 samples of PCNSL and 10 hematopoietic controls (control-PCNSL, red circle), between 49 cases of systemic DLBCL and 10 haematopoietic controls (control-DLBCL, yellow circle) or between 5 cases of PCNSL and 49 cases of systemic DLBCL (PCNSL-DLBCL, green circle), respectively. There is a significant overlap of genes differentially methylated in both malignancies compared to controls. A detailed list of genes is presented in Additional file 3.
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Additional file 5:
Hierarchical cluster analysis of DNA methylation data obtained from 4 differentially methylated CpG loci in 5 cases of PCNSL (orange boxes in the bar blot below the dendrogramm) and 49 cases of systemic DLBCL (yellow boxes). PCNSL and systemic DLBCL samples were not delineated according to their DNA methylation pattern.
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Additional file 6:
List of genes unmethylated in normal controls and methylated in PCNSL (meP/umC), unmethylated in normal controls and unmethylated in PCNSL (umP/umC) or methylated in normal controls and methylated in PCNSL (meP/meC).
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Additional file 7:
GeneOntology terms of genes differentially methylated in PCNSL (vs. controls) and DLBCL (vs. controls). RR, OR and p-value are shown.
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Additional file 8:
Comparision of the methylation frequency [%] of genes previously determined by other authors (Chu et al., 2006; Gonzalez-Gomez et al., 2003) using MSP and this study. To calculate frequency based on the date obtained from the GoldenGate array, AVG-beta values above 0.3 where considered as methylated.
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