Molecular inversion probes (MIPs) identify novel copy number changes in pediatric gliomas

Abstract

13006 Background: Childhood brain tumors (CBT) are the most common solid pediatric cancer and the leading cause of pediatric cancer mortality. More than half of all CBTs are gliomas. Despite their high prevalence, little is known about the genetic events that contribute to the development and progression of pediatric gliomas (PGs). In this study, we used Molecular Inversion Probes (MIPs) to identify recurrently amplified or deleted genomic loci in advancing stages of pediatric astrocytomas (PAs). Our results help define the molecular characteristics of PAs, which may lead to the development of novel biomarkers and therapeutic agents. Methods: DNA was extracted from 14 flash- frozen PA biopsies (WHO grade II [n=3, mean age 7 yr]; grade III [n=2, mean age 6 yr]; grade IV [n=9, mean age 12 yr]). DNA was also extracted from 5 adult-gliosis biopsies to use as non-neoplastic controls. The MIP assay was run using 37 ng genomic DNA/sample on a customized Affymetrix 24K Cancer Panel representing oncogenes, tumor suppressor, DNA repair, cell growth, and metabolism genes. Copy number (CN) changes were identified by comparing probe signal intensity between brain tumor and controls. Results: We observed the full spectrum of genomic CN aberrations including regions of single copy gain and loss, homozygous deletions, and high-level focal amplifications. Grade-III and -IV tumors showed more CN alterations relative to grade II tumors. CN changes ranged from < 1000 basepairs to entire chromosome arms. Deleted genes included: DRD3 (3q13), GAP43 (3q13), DHFR (5q14), SOX8 (16p13.3), ADAMTS18 (16q23.1), WWOX (16q23.1). Amplified genes included: PTPN7 (1q32), GPR160 (3q26), PGDFRA (4q12), KIT (4q12), TBXAS1 (7q34), PLAG1 (8q12.1), CHCHD7 (8q12.1), MYC (8q24.1), FOXM1 (12p13), CCND2 (12p13), ERC1 (12p13), WNT5B (12p13), MEGF8 (19q13.2), TUBGCP6 (22q13.33). Several amplifications ranged as high as CN of 80. Conclusions: MIPs can identify both known and novel areas of CN events in PGs using minimal DNA. PGs display increasing molecular CN changes with advancing clinical stages. Areas of amplifications and deletions range from microscopic to macroscopic. Further exploration with larger sample sets (including paraffin-embedded specimens) may increase our understanding of the biology and behavior of PGs. No significant financial relationships to disclose.