OTHR-26. MINIMALLY-INVASIVE MOLECULAR DIAGNOSIS OF DIFFUSE LEPTOMENINGEAL GLIONEURONAL TUMOR (DLGNT) USING CEREBROSPINAL FLUID CELL-FREE DNA SEQUENCING IN PEDIATRIC AND YOUNG ADULT PATIENTS

Abstract

Abstract BACKGROUND Diffuse leptomeningeal glioneuronal tumor (DLGNT) presents with nodular leptomeningeal disease throughout the neuroaxis and is characterized by the presence of KIAA1549::BRAF fusion and chromosome arm 1p deletion. Concomitant gain of chromosome arm 1q is associated with poor prognosis. Diagnosis by meningeal biopsy is often non-diagnostic due to sampling error or yields insufficient material for molecular testing. We hypothesized that analysis of cell free DNA (cfDNA) from cerebrospinal fluid (CSF) could represent a superior diagnostic modality. METHODS We analyzed CSF samples from 9 suspected DLGNT patients, median age of 19.5 years with a 5:4 male:female ratio using MSK-IMPACT, a hybridization capture-based next-generation DNA sequencing panel, including matched germline. RESULTS Prior tissue biopsy was done in 7 patients; 6 were negative for the KIAA1549:BRAF fusion and 1 was positive. Of the 6 biopsies negative for the fusion, analysis of CSF cfDNA detected KIAA1549::BRAF fusion in 3/6 (50%) of patients, who were all subsequently started on MEK inhibitor therapy. The other 3 patients were negative for KIAA1549:BRAF fusion on both biopsy and CSF cfDNA. One patient received biopsy confirmation of KIAA1549::BRAF fusion after CSF cfDNA analysis detected the mutation. In addition, in one patient with prior tissue-confirmed KIAA1549::BRAF fusion, the fusion was not detected in CSF cfDNA during/after treatment with a MEK inhibitor, but additional somatic alterations and DNA copy number profiles were similar to those found in prior biopsies. Additional somatic alterations were identified in ATRX, BCOR, RARA, STAT5A, SPOP, PPM1D, MED12, KMT2C, RECQL andSETD2, including likely oncogenic secondary driver alterations that have not been previously reported in DLGNT. CONCLUSIONS Given the high molecular diagnostic yield and concordance with open biopsy, cfDNA CSF sequencing should be considered as a first line diagnostic maneuver for patients with suspected DLGNT, followed by surgical biopsy only if CSF testing is non-diagnostic.