EPCO-22. IDENTIFYING NEOANTIGENS FOR A PERSONALIZED MUTATION-DERIVED GENOMIC VACCINE IN PATIENTS WITH NEWLY DIAGNOSED GLIOBLASTOMA

Abstract

Abstract BACKGROUND Glioblastomas (GBM) are known for having a lower mutational burden than many other tumor types. Nevertheless, somatic variants that occur in GBM mutational processes may give rise to neoantigens, which can be targeted in a personalized genomic vaccine to elicit a patient-specific anti-tumor response. METHODS Normal and tumor DNA and tumor RNA are extracted from tumor specimens and PBMCs. Exome and RNA sequencing and HLA typing is performed for each patient. Neoantigens are identified using the OpenVax computational pipeline, which calls somatic variants in the DNA and prioritizes corresponding candidate neoantigens for vaccination based on tumor RNA expression and predicted MHC class I binding affinity for each of the patient’s HLA alleles. This work is the base for a phase I trial of personalized neoantigen vaccines in combination with Tumor Treating Fields for GBM (NCT03223103). RESULTS For each of the 9 patients enrolled in the trial, an average of 1005 somatic mutations were identified (range 299–2441), of which 118 were coding variants (range 52–198), 20 were coding and expressed in the tumor RNA (range 9–45), and 16 were coding, expressed and resulted in predicted MHC class I ligands (range 7–33). An average of 2.3% of all somatic variants identified in each tumor gave rise to predicted neoantigens. Sufficient numbers of neoantigens were identified in all tumor samples of the patients enrolled in the study. The overall somatic mutation landscape for the tumors revealed 4/9 PIK3R1 deletions, 2/9 IDH1 substitutions, as well as disruptions in PTEN, TP53, and ATRX, among others. CONCLUSIONS Identifying sufficient neoantigens for inclusion in the personalized genomic vaccine is computationally feasible despite a typically low GBM mutational burden. Driver and passenger mutations can be identified through the same computational pipeline utilized for other tumor types.