Open Access Highly Accessed Research article

DNA methylation in glioblastoma: impact on gene expression and clinical outcome

Amandine Etcheverry123, Marc Aubry3, Marie de Tayrac4, Elodie Vauleon15, Rachel Boniface1, Frederique Guenot23, Stephan Saikali6, Abderrahmane Hamlat7, Laurent Riffaud7, Philippe Menei8, Veronique Quillien15 and Jean Mosser123*

Author Affiliations

1 CNRS UMR6061 Institut de Génétique et Développement, Université de Rennes 1, UEB, IFR140, Rennes, France

2 Service de Génétique Moléculaire et Génomique, CHU Rennes, France

3 Plateforme Génomique Santé Biogenouest®, Rennes, France

4 INSERM U946, Fondation Jean Dausset, CEPH, Paris, France

5 Département de Biologie Médicale, Centre Eugène Marquis, Rennes, France

6 Service d'Anatomie et Cytologie Pathologique, CHU Rennes, France

7 Service de Neurochirurgie, CHU Rennes, France

8 Service de Neurochirurgie, CHU Angers, France

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BMC Genomics 2010, 11:701  doi:10.1186/1471-2164-11-701

Published: 14 December 2010

Additional files

Additional file 1:

Distribution of the β-values for GBM samples (n = 55) and control brain samples (n = 3).

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Additional file 2:

Genes differentially expressed between GBM and control brain.

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Additional file 3:

CpG sites differentially methylated between GBM and control brain.

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Additional file 4:

CpG sites displaying an inverse correlation between promoter methylation and expression levels.

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Additional file 5:

CpG sites significantly associated with overall survival - univariate Cox regression analysis.

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Additional file 6:

CpG sites significantly associated with overall survival - Log rank analysis.

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Additional file 7:

MGMT promoter sequence. Overlap between the sequence tested by the PyroMark Q96 CpG MGMT kit and the Illumina probe used to stratify patients (log rank test p-value = 9e-06). Numbers indicate positions on the reference genome.

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Additional file 8:

Kaplan-Meier estimation of overall survival in 50 GBMs treated in accordance with the STUPP protocol. Patients were assigned to groups according to the methylation status of (A) SOX10 site #1, (B) MGMT and FSD1, and (C) MGMT and DGKI. M: methylated; NM: non methylated. P-values for the difference in OS (log-rank test), size and median survival of each group are also reported. See Table 1 for β-values cut-offs.

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Additional file 9:

Contingency Table showing differentially expressed and differentially methylated enes.

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Additional file 10:

Kaplan Meier estimation of overall survival in 30 GBMs with methylated MGMT promoter. Patient were separated into two groups according to the methylation status of (A) FNDC3B, (B) TBX3, (C) DGKI, and (D) FSD1. See Table 1 for β-values cut-offs.

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