Klin Padiatr 2011; 223 - A7
DOI: 10.1055/s-0031-1292588

First Results from the International Cancer Genome Consortium PedBrain Tumor Project on Whole-Genome Deep Sequencing in Medulloblastoma

DTW Jones 1, M Zapatka 1, N Jäger 2, Q Wang 2, A Stuetz 3, T Rausch 3, V Benes 4, J Blake 4, A Korshunov 5, 6, M Schmidt 7, C Bartholomae 7, O Witt 8, 9, MD Taylor 10, 11, C von Kalle 7, B Brors 2, R Eils 2, J Korbel 3, P Lichter 1 SM Pfister 1, 8 on behalf of the PedBrain Tumor Network
  • 1Division of Molecular Genetics, German Cancer Research Center, Heidelberg, Germany
  • 2Division of Bioinformatics, German Cancer Research Center, Heidelberg, Germany
  • 3Gene Expression Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
  • 4GeneCore Sequencing Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
  • 5Department of Neuropathology, University of Heidelberg, Heidelberg, Germany
  • 6Clinical Cooperation Unit Neuropathology, German Cancer Research Center, Heidelberg, Germany
  • 7Department of Translational Oncology, National Center for Tumor Diseases (NCT), Heidelberg, Germany
  • 8Department of Pediatric Oncology, Hematology and Immunology, University Hospital Heidelberg, Heidelberg, Germany
  • 9Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center, Heidelberg, Germany
  • 10Division of Neurosurgery
  • 11Neuro-oncology program, Division of Haematology/Oncology and The Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada

Introduction: The International Cancer Genome Consortium (ICGC) is a worldwide network of research groups aiming to provide comprehensive genomic, transcriptomic and epigenomic profiles of the 50 most clinically and societally relevant tumors. The PedBrain Tumor Project is one of three German contributions to this consortium, focusing on the integrated analysis of ˜300 of each of medulloblastoma (MB) and pilocytic astrocytoma (PA), the most common pediatric brain tumors. This will provide the clearest and most complete picture to date of the events underlying tumorigenesis in these entities, allowing the characterisation of novel diagnostic or prognostic markers, and therapeutic targets.

Methods: As a first phase, we have used Illumina HiSeq paired-end technology to produce whole-genome sequencing data at high coverage (˜30x) for 24 matched tumour-normal DNA pairs, representing a cross-section of MBs with different histology and expression subgroup (WNT, SHH, C & D). After optimisation of the bioinformatic pipeline and algorithms for the detection of single nucleotide variants and small insertion/deletion (InDel) events, verification rates were extremely high, with few false positives. In addition, the Agilent SureSelect 50Mb system was used to generate libraries for whole-exome sequencing in a further cohort of 24 cases to aid identification of recurrent mutation events.

Results: At the single nucleotide level, medulloblastomas seem to show a lower degree of aberration than previously studied adult tumors, with an average of ˜5 mutations per sample (compared with >30 in glioblastoma). Nearly all calls were successfully verified, as were a number of InDel events of between 1 and 26bp. Strikingly, very little overlap was seen in the specific genes altered in each sample, with relatively few mutations in genes with well-characterised cancer-associated functions. This highlights the importance for replication and validation in large sample cohorts to find commonly altered pathways.

Conclusion: This first phase of the project demonstrates the scale of the comprehensive data sets that will be obtained from sequencing-based analyses on additional tumors (MB & PA) in the future. Initial results show MB to be extremely heterogeneous, highlighting the importance of integrated systems approaches for better understanding the biological and clinical behavior of tumors and elucidating the role of mutational patterns in phenotype, prognosis, and response/resistance to therapy. Several partners in the network are integral parts of clinical studies in medulloblastoma and pilocytic astrocytoma, meaning validation cohorts for the translation of key findings into clinical settings are readily available.