Abstract 2853: Comparison of methods for detection of hemispheric gliomas of infancy and their characteristic oncogenic tyrosine kinase gene fusions
Authors: Pietsch Torsten , Gielen Gerrit , Waha Andreas , Dörner Evelyn , Dreschmann Verena , Kramm Christof , Vokuhl Christian 
Published: March 2024

Abstract
Introduction High grade hemispheric gliomas in infancy (IHG) are characterized by a more favorable outcome compared to high grade gliomas in older children. We have shown in previous studies that these tumors are characterized by a stable genome. The occurrence of tyrosine kinase gene fusions in high-grade hemispheric gliomas of infancy may represent therapeutic targets.
Methods: 33 high-grade hemispheric gliomas occurring in children younger than three years were retrieved from the archives of the Brain Tumor Reference Center, Institute of Neuropathology, University of Bonn. DNA and RNA were extracted from FFPE tumor samples. Methylation-based classification was done by hybridization to Illumina methylation arrays and subsequent use of the Heidelberg brain tumor classifier versions v11b4, v12.5 and v12.8. In addition UMAP plots were used to visualize similarities of methylation profiles. Gene fusions were identified on the DNA level by FISH using break-apart probes for ALK, NTRK1, -2, -3, ROS1 and MET and Molecular Inversion Probe (MIP) methodology. On the RNA level, fusion transcripts were detected by targeted RNA sequencing as well as Nanostring assay with fusion-specific probes.
Results: 32 IHG occurred in the first year of life, one at the age of two years. 23/33 IHG were classified as such by methylation arrays; 6 further cases could be annotated to the IHG group by UMAP plots. 18/33 cases (54.5 %) showed fusions of ALK to different partners; all occurred in the first year of life. Fusions of ROS1 were found in 4, MET in 2, NTRK1 and -3 in 7 cases. 2 cases showed no fusions. The different methods for fusion detection led to comparable results. Only recurrent fusions with known fusion partners were detectable with Nanostring probes designed for the fusion sequence, and library construction for targeted RNA sequencing was not successful in a fraction of cases. Break-apart FISH led to reliable results on the next day, and MIP technology represented the most sensitive method for analysis of FFPE samples.
Conclusions: Gene fusions involving the tyrosine kinase genes ALK, MET, ROS1 and NTRK1 and -3 occurred in 93 % of high grade hemispheric gliomas of infancy; the most frequent were ALK fusions occurring in children younger than 1 year. DNA-based MIP technology represented the most robust and sensitive assay. A combination of RNA- and DNA-based methods to detect these fusions with high reliability is recommended.
Citation Format: Torsten Pietsch, Gerrit Gielen, Andreas Waha, Evelyn Dörner, Verena Dreschmann, Christof Kramm, Christian Vokuhl. Comparison of methods for detection of hemispheric gliomas of infancy and their characteristic oncogenic tyrosine kinase gene fusions [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2853.