Identifying Therapeutically Actionable Events in Ameloblastomas Using Next Generation Sequencing

Objectives: There is an unmet need to study ameloblastoma, a rare odontogenic tumor, which has been limited by its rarity. Targeted DNA sequencing of these less well-studied tumor types could uncover the presence of actionable alterations, and also has the potential for discovery of novel driver mutations. The use of next generation sequencing (NGS) to identify these mutations in ameloblastoma could lead to the discovery of therapeutically actionable events. We aimed to identify genetic alterations in ameloblastoma tissue using IGNITE, which is a custom targeted DNA sequencing assay.
Methods: IGNITE targets 250 oncogenes and tumor suppressors to detect single-nucleotide variants (SNV) and copy-number variants (CNV). DNA was extracted from formalin fixed paraffin embedded (FFPE) tissue samples (12 samples for IGNITE), indexed libraries were constructed, hybridized and captured with custom oligonucleotide probes followed by sequencing on a MiSeq desktop sequencer. Data was processed and analyzed through in-house bioinformatics pipelines.
Results: The IGNITE assay identified the FGFR4 p.G388R mutation in 25%(3 of 12) of the samples sequenced with variant frequency ranging from 21.05 to 41.12% and BRAF p.V600E mutation in 41.7% (5 of 12)of the samples with variant frequency ranging from 25.89 to 37.08%. In addition, 8% (1 of 12) of the samples had an AKT1 p.E17K mutation with a variant frequency of 20.0%.
Conclusions: We identified recurrent FGFR4 mutations in cases of ameloblastoma, not previously described in literature for this tumor type. Results also confirm BRAF as a potential actionable target, as has been shown in other studies. Additionally, we identified a novel association of AKT1 p.E17K, an activating mutation, as a potential target for the AKT pathway in ameloblastoma. Investigation of these mutations in ameloblastoma as targets for novel therapies is warranted in these and other odontogenic tumors.