Germline 16p11.2 Microdeletion Predisposes to Neuroblastoma

Abstract

Neuroblastoma is a cancer of the developing sympathetic nervous system. It is diagnosed in 600-700 children per year in the United States and accounts for 12% of pediatric cancer deaths. Despite recent advances in our understanding of this malignancy's complex genetic architecture, the contribution of rare germline variants remains undefined. Here, we conducted a genome-wide analysis of large (>500 kb), rare (<1%) germline copy number variants (CNVs) in two independent, multi-ethnic cohorts totaling 5,585 children with neuroblastoma and 23,505 cancer-free control children. We identified a 550-kb deletion on chromosome 16p11.2 significantly enriched in neuroblastoma cases (0.39% of cases and 0.03% of controls; p = 3.34 × 10^-9). Notably, this CNV corresponds to a known microdeletion syndrome that affects approximately one in 3,000 children and confers risk for diverse developmental phenotypes including autism spectrum disorder and other neurodevelopmental disorders. The CNV had a substantial impact on neuroblastoma risk, with an odds ratio of 13.9 (95% confidence interval = 5.8-33.4). The association remained significant when we restricted our analysis to individuals of European ancestry in order to mitigate potential confounding by population stratification (0.42% of cases and 0.03% of controls; p = 4.10 × 10^-8). We used whole-genome sequencing (WGS) to validate the deletion in paired germline and tumor DNA from 12 cases. Finally, WGS of four parent-child trios revealed that the deletion primarily arose de novo without maternal or paternal bias. This finding expands the clinical phenotypes associated with 16p11.2 microdeletion syndrome to include cancer, and it suggests that disruption of the 16p11.2 region may dysregulate neurodevelopmental pathways that influence both neurological phenotypes and neuroblastoma.

Keywords: 16p11.2 microdeletion; chromosomal abnormalities; copy number variation; de novo; genetic predisposition; genome-wide association study; germline; neuroblastoma; pediatric cancer; rare variant.

Figure 1

Megabase-Scale Germline Chromosomal Abnormalities Including 2p Gain and 11q Loss Are Observed in 0.27% of Neuroblastoma Cases (A) Germline deletions and duplications larger than 5 Mb on autosomal chromosomes are plotted in a summary karyotype (karyoploteR⁷⁴) showing the entire cohort of 5,585 neuroblastoma cases. We observed 16 events affecting 15 individuals (the 1q44 terminal duplication and mosaic 17p13 terminal deletion were present in the same individual). (B) Log R ratio and B allele frequency plots for the 8.6-Mb germline duplication of 2p25.1-p24.2 (red shading) in a high-risk, MYCN-amplified case. The location of the MYCN oncogene is indicated by an arrow. (C) Log R ratio and B allele frequency plots for the 7.2-Mb 11q14 interstitial deletion (blue shading) in an intermediate-risk, MYCN-non-amplified case.

Figure 2

16p11.2 Microdeletion Associates with Neuroblastoma and Is Enriched in MYCN Non-Amplified, Low-Risk Cases (A) 16p11.2 microdeletions identified in neuroblastoma cases and cancer-free controls in each analysis cohort (discovery and replication) are plotted in UCSC Genome Browser. Minimum and maximum deletion coordinates approximated by SNP array are represented by the thick and thin blue bars, respectively. The red asterisk denotes one mosaic deletion identified in a control (the maximum end coordinate for this sample was extended to encompass a region of decreased probe intensity not called by the segmentation algorithm). The deletion coordinates reported by Kumar et al. are shown for reference (converted from hg18 to hg19 using UCSC liftOver⁷⁶). These coordinates match the 16p11.2 proximal CNV, a 550-kb critical region flanked by segmental duplications. This unique critical region (29.65–30.20 Mb) contains 25 annotated protein-coding genes. (B–C) 16p11.2 microdeletion was tested for association with clinical covariates in 21 cases with available annotation using Fisher’s exact test. The deletion associated significantly (p < 0.05) with MYCN amplification status (B) and Children’s Oncology Group risk classification (C).

Figure 3

16p11.2 Microdeletion Arises de novo in Neuroblastoma without Allelic Bias Coverage is plotted in 2-kb bins for four neuroblastoma cases with parental DNA available: two parent-child trios (A and B) and two mother-child duos (C and D). All parents show normal coverage within the 16p11.2 critical region (20.65–30.20 Mb, gray shading), whereas the children show a 50% decrease in coverage; this result confirms 16p11.2 microdeletion (blue shading). The number of low-frequency variants (<5% in 1000 Genomes) found within each child’s single remaining allele is displayed above the child’s coverage plot. The fraction of these variants the child shares with each parent is displayed above the parent’s plot.