Droplet digital PCR is a powerful technique to demonstrate frequent FGFR1 duplication in dysembryoplastic neuroepithelial tumors

// Frédéric Fina 1 , Doriane Barets 2 , Carole Colin 3 , Corinne Bouvier 2, 3 , Laëtitia Padovani 4 , Isabelle Nanni-Metellus 1 , L’Houcine Ouafik 1 , Didier Scavarda 5 , Andrey Korshunov 6 , David T.W. Jones 6 , Dominique Figarella-Branger 2, 3 1 Assistance Publique Hôpitaux de Marseille (AP-HM), Hôpital Nord, Service de Transfert d'Oncologie Biologique, Laboratoire de Biologie Médicale Marseille, France 2 APHM, Hôpital de la Timone, Service d’Anatomie Pathologique et de Neuropathologie, Marseille, France 3 Aix-Marseille Université, Inserm, CRO2 UMR_S 911, Marseille, France 4 APHM, Hôpital de la Timone, Service de Radiothérapie, Marseille, France 5 APHM, Hôpital de la Timone, Service de Neurochirurgie Pédiatrique, Marseille, France 6 Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany Correspondence to: Dominique Figarella-Branger, email: dominique.figarella-branger@univ-amu.fr Keywords: dysembryoplastic neuroepithelial tumor (DNT), low grade neuroepithelial tumor (LGNT), FGFR1, droplet digital PCR (DDPCR™), MAP kinase pathway Received: June 15, 2016 Accepted: October 13, 2016 Published: October 25, 2016 ABSTRACT Dysembryoplastic neuroepithelial tumors (DNT) share V600E mutation in the BRAF gene with other low grade neuroepithelial tumors (LGNTs). FGFR1 internal tandem duplication of the tyrosine-kinase domain ( FGFR1 -ITD), another genetic alteration that also leads to MAP kinase pathway alteration, has been previously reported in LGNTs by whole-genome sequencing. In the present study we searched for FGFR1 -ITD by droplet digital PCR (DDPCR™) and for FGFR1 point mutations by HRM-sequencing in a series of formalin-fixed paraffin-embedded (FFPE) LGNTs including 12 DNT, 2 oligodendrogliomas lacking IDH mutation and 1p/19q co- deletion (pediatric-type oligodendrogliomas; PTOs), 3 pediatric diffuse astrocytomas (PDAs), 14 gangliogliomas (GGs) and 5 pilocytic astrocytomas (PAs). We showed by DDPCR™ that 5/12 DNT, but none of the other LGNTs, demonstrated FGFR1 -ITD. In addition, these cases also accumulated phosphorylated-FGFR1 protein as shown by immunohistochemistry. FGFR1 G539R point mutation was only recorded in one DNT that also showed FGFR1 -ITD. Interestingly, these FGFR1 alterations were mutually exclusive from BRAF V600E mutation that was recorded in 13 LGNTs (3 DNTs, 1 PTO, 2 PDAs, 5 GGs and 2 PAs). Therefore, FGFR1 alteration mainly represented by FGFR1 -ITD is a frequent event in DNT. DDPCR™ is an easy and alternative method than whole-genome sequencing to detect FGFR1 -ITD in FFPE brain tumors, in routine practice.