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Torsten Pietsch, Marco Gessi, Anja zur Mühlen, Evelyn Dörner, Andy Last, Padma Sundar, OT-10
IMPLEMENTATION OF NEXT GENERATION COPY NUMBER AND MUTATIONAL ANALYSIS IN ROUTINE NEUROPATHOLOGY: MOLECULAR INVERSION PROFILING IS A HELPFUL TOOL IN DIFFERENTIAL DIAGNOSTICS AND PROGNOSTIFICATION OF PEDIATRIC BRAIN TUMORS, Neuro-Oncology, Volume 17, Issue suppl_3, June 2015, Pages iii30–iii31, https://doi.org/10.1093/neuonc/nov061.123Close - Share Icon Share
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Brain tumor entities are characterized by specific copy number alterations (CNA), allelic losses/disbalances and recurrend mutations. 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 these alterations in brain tumors and to compare this method to FISH and multiplex ligation probe analysis (MLPA). Genomic DNA extracted from up to 20 years old FFPE materials from more than 1300 brain tumors covering most WHO entities were analyzed by MIP profiling (Oncoscan V2/V3, Affymetrix). MIP revealed genome-wide copy number information from as little as 20 ng of degraded DNA; drop-out rate was <5%. In contrast to FISH and MLPA, MIP allowed a genome-wide analysis, adding significant information to the differential diagnosis. Characteristic CNA were detected, including BRAF duplications in pilocytic astrocytomas, chromosome 22 loss in ATRT, chromosome 10 loss, 7 gain and amplifications of PDGFR or EGFR in glioblastoma, 1p19q codeletion in oligodendroglial tumors, chromosome 2 gain and C19MC amplification in ependymoblastoma. Novel prognostic markers including MYCN amplification in CNS-PNET were identified. Established prognostic markers including MYC/MYCN amplifications in medulloblastomas and chromosome 1q gain in ependymomas were easily detected and validated by orthogonal methods. Extended chromosomal alterations including widespread hyperploidy in plexus papillomas or complex alterations such as chromosomal scattering of whole chromosomes (chromotripsis) in TP53 deficient medulloblastomas were easily uncovered. MIP also detected copy-neutral LOH and recurrent tumor-associated mutations (e.g BRAFV600E, IDH gene mutations). Our data indicate that MIP is a sensitive and robust method to assess CNA, allelic imbalances/losses and specific recurrent point mutations in FFPE tumor material, and therefore represents a novel tool for precise neuropathological tumor diagnostics and prognostic stratification.
