Frequency and Clinical Significance of Clonal and Subclonal Driver Mutations in High-Risk Neuroblastoma at Diagnosis: A Children's Oncology Group Study.

Purpose: Relapsed high-risk neuroblastomas (NBLs) are enriched for targetable mutations in ALK and RAS-MAPK pathways, yet the prognostic effect of these aberrations and relevance of subclonal mutations at diagnosis remain undefined. We describe the spectrum and clinical significance of clonal and subclonal pathogenic alterations in high-risk NBL.

Methods: We developed a focused high-risk NBL sequencing panel including ALK, NRAS, KRAS, HRAS, BRAF, PTPN11, TP53, and ATRX genes for ultra-deep sequencing and applied this assay to 242 pretherapy tumors from patients enrolled on the phase III trial Children's Oncology Group ANBL0532. We assessed the effect of clonal and subclonal mutations on event-free survival (EFS) and overall survival (OS).

Results: ALK-activating mutations occurred in 21.5% of tumors (n = 52, 30 clonal, 22 subclonal), and 3.3% (n = 8) showed ALK amplification. EFS and OS for patients with any ALK-aberrant tumor were inferior to patients with wild-type (WT) ALK tumors (5-year OS 37.7% v 66.3%; hazard ratio [HR], 1.992; P = .0007). EFS and OS for patients with tumors harboring activating ALK mutations ≥5% variant allele frequency (VAF) were inferior to ALK WT (5-year OS 37.7% v 66.3%; HR, 1.966; P = .0041). The 5-year EFS and OS for patients with ALK-amplified tumors were 25.0%. RAS pathway mutations occurred in 7.9% of tumors (n = 19; four clonal, 15 subclonal), with EFS and OS for those with VAF ≥5% inferior to RAS-WT patients (5-year OS 19.1% v 60.0%; HR, 3.021; P = .0168).

Conclusion: Ultra-deep sequencing of high-risk NBLs demonstrates that oncogenic aberrations are more prevalent at diagnosis than previously recognized. ALK and RAS pathway aberrations confer inferior outcomes in patients treated with contemporary therapy, emphasizing the need for novel therapeutic approaches.