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Intra-Tumor DNA Methylation Heterogeneity in Glioblastoma; Implications for DNA Methylation-Based Classification.

Journal article
Authors Anna Wenger
Sandra Ferreyra Vega
Teresia Kling
Thomas Olsson
Asgeir Store Jakola
Helena Carén
Published in Neuro-oncology
Volume 21
Issue 5
Pages 616-27
ISSN 1523-5866
Publication year 2019
Published at Institute of Neuroscience and Physiology, Department of Physiology
Sahlgrenska Cancer Center
Department of Laboratory Medicine
Institute of Neuroscience and Physiology, Department of Clinical Neuroscience
Pages 616-27
Language en
Keywords DNA methylation; MGMT; classification; glioblastoma; heterogeneity
Subject categories Cell and Molecular Biology, Cancer and Oncology


A feature of glioblastoma (GBM) is cellular and molecular heterogeneity, both within and between tumors. This variability causes a risk for sampling bias and potential tumor escape from future targeted therapy. Heterogeneous intra-tumor gene expression in GBM is well documented, but little is known regarding the epigenetic heterogeneity. Variability in DNA methylation within tumors would have implications for diagnostics, as methylation can be used for tumor classification, subtyping and determination of the clinically used biomarker MGMT promoter methylation. We therefore aimed to profile the intra-tumor DNA methylation heterogeneity in GBM and its effect on diagnostic properties.Three to four spatially separated biopsies per tumor were collected from 12 GBM patients. We performed genome-wide DNA methylation analysis and investigated intra-tumor variation.All samples were classified as GBM IDH wild type (wt)/mutated by methylation profiling, but the subclass differed within five tumors. Some GBM samples exhibited higher DNA methylation differences within tumors than between, and many CpG sites (mean: 17,000) had different methylation levels within the tumors. MGMT methylation status differed in IDH mutated patients (1/1).We demonstrated that intra-tumor DNA methylation heterogeneity is a feature of GBM. Although all biopsies were classified as GBM IDH wt/mutated by methylation analysis, the assigned subclass differed in samples from the same patient. The observed heterogeneity within tumors is important to consider for methylation-based biomarkers and future improvements in stratification of GBM patients.

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