Clinical targeted exome-based sequencing in combination with genome-wide copy number profiling: precision medicine analysis of 203 pediatric brain tumors

Abstract

Background: Clinical genomics platforms are needed to identify targetable alterations, but implementation of these technologies and best practices in routine clinical pediatric oncology practice are not yet well established.

Methods: Profile is an institution-wide prospective clinical research initiative that uses targeted sequencing to identify targetable alterations in tumors. OncoPanel, a multiplexed targeted exome-sequencing platform that includes 300 cancer-causing genes, was used to assess single nucleotide variants and rearrangements/indels. Alterations were annotated (Tiers 1-4) based on clinical significance, with Tier 1 alterations having well-established clinical utility. OncoCopy, a clinical genome-wide array comparative genomic hybridization (aCGH) assay, was also performed to evaluate copy number alterations and better define rearrangement breakpoints.

Results: Cancer genomes of 203 pediatric brain tumors were profiled across histological subtypes, including 117 samples analyzed by OncoPanel, 146 by OncoCopy, and 60 tumors subjected to both methodologies. OncoPanel revealed clinically relevant alterations in 56% of patients (44 cancer mutations and 20 rearrangements), including BRAF alterations that directed the use of targeted inhibitors. Rearrangements in MYB-QKI, MYBL1, BRAF, and FGFR1 were also detected. Furthermore, while copy number profiles differed across histologies, the combined use of OncoPanel and OncoCopy identified subgroup-specific alterations in 89% (17/19) of medulloblastomas.

Conclusion: The combination of OncoPanel and OncoCopy multiplex genomic assays can identify critical diagnostic, prognostic, and treatment-relevant alterations and represents an effective precision medicine approach for clinical evaluation of pediatric brain tumors.

Keywords: array CGH; brain tumor; clinical sequencing; pediatric neuro-oncology; precision medicine.

Fig. 1

Pediatric brain tumors can be distinguished by copy number profiles. (A) Unsupervised hierarchical clustering of 146 pediatric copy number profiles (arm-level events). (B) Percent of genome disruption in glial tumors (low-grade and high-grade) and embryonal tumors. Values represent mean level of disruption (± SEM). (C) Support vector machine classification of pediatric brain tumors.

Fig. 2

Targeted exome sequencing with OncoPanel detects clinically relevant genomic alterations in pediatric brain tumors. (A) Mutations and rearrangements identified in 117 tumors profiled by OncoPanel. Tier classification of mutations is shown. (B) Incidence of Tier 1, 2, 3, or 4 mutations in 117 tumors profiled by OncoPanel. (C) Clinically relevant rearrangements detected by OncoPanel. (D) Tiers 1 and 2 mutations detected by OncoPanel.

Fig. 3

Comprehensive genomic analysis with OncoPanel and aCGH aids genetic subgrouping of medulloblastoma. (A) Genomic landscape of 19 medulloblastomas profiled with combined OncoPanel and aCGH data. Focal copy number gains were reported to be likely subclonal amplifications based on patterns of occurrence in the literature and prior cases with fluorescence in situ hybridization validation. (B) Subgroup assignment with specific copy or mutation criteria used for individual tumor assignment. Single events and combined events were used to call genetic subgroup according to rules in Supplementary Table 4.

Fig. 4

OncoPanel guides the use of targeted inhibitors in PLGG. (A) Landscape of genomic alterations identified in 18 PLGGs profiled with both OncoPanel and aCGH. (B) Treatment of patients with BRAF-altered PLGG. (C) Hematoxylin and eosin BRAFV600E stains of ganglioglioma with BRAFV600E mutation. Scale bar represents 1.2 µm. (D) Axial postcontrast MRI of tumor at diagnosis, postsurgery, and following treatment with a BRAF inhibitor.

Fig. 5

Genomic alterations identified in 12 pediatric HGGs profiled with OncoPanel and aCGH. (A) Landscape of genomic alterations identified in 12 HGGs profiled with both OncoPanel and aCGH. (B) Genomic alterations for that for which either small molecule inhibitors exist or where they guide enrollment onto clinical trials.