The genetic landscape of high-risk neuroblastoma

Abstract

Neuroblastoma is a malignancy of the developing sympathetic nervous system that often presents with widespread metastatic disease, resulting in survival rates of less than 50%. To determine the spectrum of somatic mutation in high-risk neuroblastoma, we studied 240 affected individuals (cases) using a combination of whole-exome, genome and transcriptome sequencing as part of the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) initiative. Here we report a low median exonic mutation frequency of 0.60 per Mb (0.48 nonsilent) and notably few recurrently mutated genes in these tumors. Genes with significant somatic mutation frequencies included ALK (9.2% of cases), PTPN11 (2.9%), ATRX (2.5%, and an additional 7.1% had focal deletions), MYCN (1.7%, causing a recurrent p.Pro44Leu alteration) and NRAS (0.83%). Rare, potentially pathogenic germline variants were significantly enriched in ALK, CHEK2, PINK1 and BARD1. The relative paucity of recurrent somatic mutations in neuroblastoma challenges current therapeutic strategies that rely on frequently altered oncogenic drivers.

Figure 1. Landscape of genetic variation in neuroblastoma

Data tracks (rows) facilitate comparison of clinical and genomic data across neuroblastoma cases (columns). Data source: sequencing technology used, purple = WES from WGA (light) and native DNA (dark), green = Illumina WGS, yellow = Complete Genomics Inc. WGS. Striped blocks indicate cases analyzed using two approaches. Clinical variables: gender (male/female = blue/pink) and age (brown spectrum). Copy number alterations: ploidy measured by flow cytometry (hyperdiploid = DNA index > 1) and clinically relevant copy number alterations derived from sequence data. Significantly mutated: genes with statistically significant mutation counts given the background mutation rate, gene size, and expression in neuroblastoma. Germline: genes with significant numbers of germline ClinVar or loss-of-function cancer gene variants in our cohort. DNA repair: Genes that may be associated with increased mutation frequency in two apparently hyper-mutated tumors. Predicted effects of somatic mutations are color-coded by the provided legend.

Figure 2. Structural variation in neuroblastoma genomes

CIRCOS plots of cases with recurrent somatic alterations, labeled using TARGET identifiers. Chromosomes are arranged end-to-end in the outer-most ring. Mutations in significantly mutated genes are depicted in light blue outside of each diagram. The inside ring shows somatic copy number gains and losses (high-level gains are red, low-level gains are orange, losses are blue) detected by WGS. The innermost arcs depict genic structural aberrations (gene fusions are orange, all others are black) detected by RNA-seq and confirmed by local reassembly of WGS reads. Non-genic rearrangements are not shown. The top five cases have mutations in significantly mutated genes ALK, MYCN, and NRAS. The bottom three cases each have several rearrangements of NBAS, with expressed fusion transcripts as annotated.