This article is part of a special issue on epigenomics.

Open Access Research

Genome-wide promoter methylation analysis in neuroblastoma identifies prognostic methylation biomarkers

Anneleen Decock1, Maté Ongenaert1, Jasmien Hoebeeck12, Katleen De Preter1, Gert Van Peer1, Wim Van Criekinge345, Ruth Ladenstein6, Johannes H Schulte7, Rosa Noguera8, Raymond L Stallings109, An Van Damme11, Geneviève Laureys12, Joëlle Vermeulen13, Tom Van Maerken114, Frank Speleman1 and Jo Vandesompele1*

Author Affiliations

1 Center for Medical Genetics, Department of Pediatrics and Genetics, Ghent University, De Pintelaan 185, 9000 Ghent, Belgium

2 Faculty of Education, Health and Social Work, University College Ghent, 9000 Ghent, Belgium

3 Department of Mathematical Modelling, Statistics and Bio-informatics, Ghent University, Coupure Links 653, 9000 Ghent, Belgium

4 MDxHealth, Tour 5 GIGA, Avenue de l'Hôpital 11, 4000 Liège, Belgium

5 NXTGNT, Ghent University, De Pintelaan 185, 9000 Ghent, Belgium

6 Children's Cancer Research Institute, St Anna Kinderkrebsforschug, Zimmermannplatz 10, A-1090 Vienna, Austria

7 University Children's Hospital Essen, Hufelandstraße 55, 45122 Essen, Germany

8 Department of Pathology, Medical School, University of Valencia, Blasco Ibañez 17, 46010 Valencia, Spain

9 National Children's Research Centre, Our Lady's Children's Hospital, Crumlin, Dublin 12, Ireland

10 Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, York House, York Street, Dublin 2, Ireland

11 Department of Pediatrics, Brussels University Hospital, Laarbeeklaan 101, 1090 Brussels, Belgium

12 Department of Pediatric Hematology and Oncology, Ghent University Hospital, De Pintelaan 185, 9000 Ghent, Belgium

13 Pédiatrie, Hôpital de Jolimont, Rue Ferrer 159, 7100 La Louvière (Haine-Saint-Paul), Belgium

14 Department of Clinical Chemistry, Microbiology and Immunology, Ghent University Hospital, De Pintelaan 185, 9000 Ghent, Belgium

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Genome Biology 2012, 13:R95  doi:10.1186/gb-2012-13-10-r95

Published: 3 October 2012

Additional files

Additional file 1:

Clinical patient annotation, MSP assays and results on the BioTrove discovery platform.

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Open Data

Additional file 2:

Visualization of the protocadherin beta gene cluster and the HIST1H3C promoter region in the Integrative Genomic Viewer. Eight neuroblastoma cell lines (SK-N-AS, CLB-GA, SH-SY5Y, SJNB-1, CHP-902R, IMR-32, LAN-2 and N206) and the MBD-seq results are displayed.

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Additional file 3:

Clinical patient annotation, summary of clinical characteristics, MSP assays, results and summarized results (per clinical parameter) on the LC480 platform for 89 NB patient samples. Assays differentially methylated between prognostic groups and between neuroblastoma risk factors are discussed in detail, as well as extended analyses on the MSP data (hierarchical clustering (heatmap) and survival analysis according to the number of methylation events (Kaplan-Meier plot)).

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Additional file 4:

Quantitative PCR and MSP assays for HIST1H3C and ACSS3 and matched results (expression levels - methylation call) for a panel of 31 NB cell lines.

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Additional file 5:

Clinical annotation, summary of clinical characteristics, qPCR assays and results of qPCR experiments on 366 NB patient samples (SIOPEN/GPOH cDNA library). Boxplots of the expression levels for CNR1, GRB10, KRT19, PRPH and QPCT in each of the five different NB stages (stages 1, 2, 3, 4 and 4S). A Kaplan-Meier plot shows overall survival according to the relative mRNA expression levels of CNR1, GRB10, KRT19, PRPH and QPCT.

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