Use of targeted next generation sequencing (NGS) to assess mutational load in glioblastoma (GBM).

Abstract

2027 Background: Trials of immune checkpoint inhibitors in GBM are ongoing. Evidence from other tumors suggests that high mutational load predicts response to these agents. We estimated mutational load in adults with newly diagnosed GBM using targeted NGS and assessed its association with other clinicopathologic parameters. Methods: NGS was performed for all patients diagnosed with isocitrate dehydrogenase wild-type (IDH-WT) GBM at our institution since September 1, 2016. Our panel performs targeted exome sequencing of 153 cancer-related genes (+/- 10 bp at intron/exon boundaries) and detects insertions, deletions, and single nucleotide variants at an allele frequency of 2%. Polymorphisms present in > 0.1% of the population according to the ExAC database and 1000 Genomes Project were filtered to reduce germline variants in the absence of matched normals. To avoid upward skewing of mutational load due to the panel’s preferential detection of genes recurrently mutated in cancer, alterations with known or likely functional disruption per the COSMIC database and/or our internal variant knowledge base were also not counted. The number of mutations counted was divided by the coding region target territory of the NGS panel (~0.5 Mb) to extrapolate mutational load to the whole exome. The Mann-Whitney U test was used to compare mutational load according to sex, age (≥65 vs. < 65), and MGMT methylation status (positive vs. negative). Results: Of 28 patients, median age was 65, 75% were male, and 37% were MGMT-methylated. Mean mutational load was 3.6 mutations/Mb (range 0-8, standard deviation 2.3) and was higher in males (4.3, 95% CI 3.3-5.3) compared to females (1.4, 95% CI 0.03-2.8) (p = 0.004). Mutational load did not differ according to age or MGMT methylation. Conclusions: In newly diagnosed IDH-WT GBM, targeted NGS revealed an estimated mutation rate similar to that reported in whole exome sequencing studies. In addition, we detected a higher mutational load in males compared to females. The latter finding adds to recent evidence suggesting sex-specific differences in the biology of GBM, and implies that future studies should account for sex when assessing mutational load as a predictive marker of immune checkpoint inhibition.