Inherited rare variants in homologous recombination and neurodevelopmental genes are associated with increased risk of neuroblastoma

Abstract

Background: Neuroblastoma (NB) is the most common solid extracranial paediatric tumour. Genome-wide association studies have driven the discovery of common risk variants, but no large study has investigated the contribution of rare variants to NB susceptibility. Here, we conducted a whole-exome sequencing (WES) of 664 NB cases and 822 controls and used independent validation datasets to identify genes with rare risk variants and involved pathways.

Methods: WES was performed at 50× depth and variants were jointly called in cases and controls. We developed two models to identify mutations with high clinical impact (P/LP model) and to discover less penetrant risk mutations affecting non-canonical cancer pathways (RPV model). We performed a gene-level collapsing test using Firth's logistic regression in 242 selected cancer predisposition genes (CPGs) and a gene-sets burden analysis of biologically-informed pathways.

Findings: Twelve percent of patients carried P/LP variants in CPGs and showed a significant enrichment (P = 2.3 × 10^-4) compared to controls (6%). We identified P/LP variants in 45 CPGs enriched in homologous recombination (HR) pathway. The most P/LP enriched genes in NB were BRCA1, ALK and RAD51C. Additionally, we found higher RPV burden in gene-sets of neuron differentiation, neural tube development and synapse assembly, and in gene-sets associated with neurodevelopmental disorders (NDD).

Interpretation: The high fraction of NB patients with P/LP variants indicates the need of genetic counselling. Furthermore, inherited rare variants predispose to NB development by affecting mechanisms related to HR and neurodevelopmental processes, and demonstrate that NDD genes are altered in NB at the germline level.

Funding: Associazione Italiana per la Ricerca sul Cancro, Fondazione Italiana per la Lotta al Neuroblastoma, Associazione Oncologia Pediatrica e Neuroblastoma, Regione Campania, Associazione Giulio Adelfio onlus, and Italian Health Ministry.

Keywords: Genetic susceptibility; Neuroblastoma; Rare variants; Whole-exome sequencing.

Fig. 1

Workflow of WES and rare variant analysis. WES, whole genome sequencing; RPV, rare pathogenic variant; P/LP, pathogenic/likely pathogenic variant; CPG, cancer predisposition gene; NIG, Network of Italian Genomes.

Fig. 2

Proportion of NB patients with germline PLP variants detected in CPGs.(a) Proportions of NB patients and controls carrying P/LP variants involving all CPGs and CPGs with autosomal dominant (AD) or autosomal recessive (AR) mode of inheritance. ∗∗∗P = 2.3 × 10⁻⁴; ∗∗P = 2.2 × 10⁻³; ∗P = 0.02 (Fisher's exact test). (b) Percentage of P/LP variant carriers in NB cases and controls. (c) Distribution of P/LP carriers in the tested cohort (NB) and in the validation datasets (TARGET-NB and EGA-NB). Each cell shows the number of carriers for each gene with a P/LP variant in the tested cohort.

Fig. 3

Burden of RPV variants in selected gene-sets. The burden of RPV in the 56 gene-sets is shown on the x-axis (log-odds from logistic regression; error bars indicate the 95% confidence intervals); gene-sets are shown on the y-axis and annotated with a box indicating the respective gene-set category according to the legend. Gene-sets are ordered by increasing FDR with the dot colour proportional to the −log₁₀(FDR). Results with FDR above the significance threshold (logistic regression, FDR > 0.05) are shown in grey.