GE-25 * NEXT GENERATION COPY NUMBER ANALYSIS BY MOLECULAR INVERSION PROFILING - A HELPFUL TOOL IN DIAGNOSTICS AND PROGNOSTIFICATION OF TUMORS OF THE CNS

Abstract

Brain tumor entities are characterized by specific copy number alterations (CNA). Emerging technologies including SNP arrays, whole exome and whole genome sequencing are not suitable for degraded DNA derived from formalin-fixed, paraffin embedded (FFPE) samples. The aim of our study was to analyse the sensitivity and robustness of molecular inversion profiling (MIP) as a tool to identify CNA in brain tumor diagnostics and to compare this method to FISH and multiplex ligation probe analysis (MLPA). Genomic DNA was extracted from up to 20 years old FFPE materials and analyzed by MIP profiling (Oncoscan V2, Affymetrix) with more than 330,000 copy number probes. More than 1100 brain tumors covering most WHO entities were analysed. MIP revealed genome-wide copy number information from as little as 20 ng of degraded DNA; the drop-out rate was lower than 5%. In contrast to FISH and MLPA which enabled the analysis of only single or few genomic loci, MIP allowed a genome-wide analysis. It added significant information to the differential diagnosis as characteristic CNA were detected even with low input DNA, including BRAF duplications in pilocytic astrocytomas, chromosome 22 loss in ATRT, chromosome 10 loss and EGFR amplification in glioblastoma, 1p19q codeletion in oligodendroglial tumors, and chromosome 2 gain, C19MC amplification in ependymoblastoma. Prognostic markers including MYCC and MYCN copy number status in medulloblastomas and chromosome 1q gain in ependymomas were easily detected and validated by orthogonal methods. MIP also detected copy-neutral LOH and tumor-associated point mutations. Our data indicate that MIP is a sensitive and robust method to assess CNA in archival FFPE tumor material.