UCSF

Abstract

BACKGROUND

Analysis of tumors via next-generation sequencing is now routinely used in clinical practice. The UCSF500 NGS panel became available starting in June 2015. In Dec 2017, a glioblastoma precision medicine initiative started at our institution to sequence all newly-diagnosed WHO grade IV diffuse gliomas. We review our experience over a 3-year period.

METHODS

The UCSF500 Cancer Panel assesses approximately 500 cancer-associated genes for mutations, copy number alterations, and structural rearrangements, including fusions. The test can be run on tumor DNA alone or compared with normal DNA, allowing for discrimination of germline variants. Sequencing results are analyzed by a neuropathologist with genomics expertise (D.A.S.). Results from the 165 adult WHO grade IV diffuse glioma cases sequenced to date were analyzed, including 136 glioblastomas, IDH-wildtype; 19 glioblastomas, IDH-mutant; and 10 diffuse midline gliomas, H3 K27M-mutant.

RESULTS

Among the 136 IDH-wildtype glioblastomas, the most common alterations were in TERT, EGFR, CDKN2A, PTEN, NF1, TP53, PIK3R1, PDGFRA, CDK4, MDM2, LZTR1, and STAG2. Among the 19 IDH-mutant glioblastomas, the most common additional alterations were in TP53, ATRX, CDKN2A, and PDGFRA. Paired germline sequencing was performed on 71 patients, ten of which were found to harbor a germline mutation associated with increased cancer risk, including the CHEK2, MSH2, and NF1 genes. Somatic hypermutation was present in nine cases, four at initial resection and five at recurrence with a temozolomide-associated mutational signature. Among the four treatment-naïve glioblastomas with hypermutation, two were Lynch syndrome-associated in patients with damaging germline mutations in MSH2, and two were sporadic tumors that harbored somatic mutations in mismatch repair genes. CONCLUSIONS: Genomic profiling in adult glioblastoma patients results in identification of potentially actionable genetic alterations and also previously unknown germline mutations associated with increased cancer risk. A subset of glioblastomas (approximately 5%) harbor somatic hypermutation, indicating potential utility of immune checkpoint inhibition.