Expression profiling of primitive neuroectodermal tumours

Primitive neuro-ectodermal tumours (PNET) of the supratentorial region are rare, highly malignant embryonal brain tumours affecting young children. Although supratentorial PNET (sPNET) are histologically similar to infratentorial PNET/medulloblastoma, sPNET have more aggressive clinical phenotypes, which suggest sPNET represents distinct biological entities. In contrast to considerable progress in understanding the signalling pathways involved in medulloblastoma, little is known about sPNET pathogenesis. We utilized the Illumina Human-6 v2 Expression BeadChip platform to define pathways dysregulated in sPNET pathogenesis. Copy number analysis was also performed on an overlapping set of PNET tumours, also available on GEO with accession code GSE14087. Keywords: gene expression, pediatric brain tumour Raw BeadStudio output files (GSE14295_normalization-none*) linked below as Supplementary files. Supplementary File GSE14295_Array2SampleTitle_associations.txt maps Array IDs (e.g., 1814647101_B) to GEO Sample Titles (e.g., PNET2). A total of 56 primary sPNET samples were collected for this study from The Hospital for Sick Children, John Hopkins University, St. Jude Research Hospital, University of Cambridge, Children’s Hospital Boston, Virginia Commonwealth University, Instituto nazionale per lo studio e la cura dei tumori, and Texas Children’s Hospital, with local Institutional Research Ethics Board approval. Pineoblastoma and rhaboid tumours were specifically excluded, leaving 52 samples, 33 of which had good quality RNA available. These samples, in addition to normal fetal and adult brain reference samples (Clontech, Palo Alto, CA), were analyzed on Illumina Human-6 V2 Expression BeadChips.