Abstract 3030: Heritability of cancer predisposition gene mutations in 556 neuroblastoma patients with paired parental DNA whole genome sequences
Authors: Blauel Emily , Vaksman Zalman , Lee Alex , Kaufman Rebecca , Egolf Laura , Olshan Andrew , Maris John , Sharon Diskin 
Published: July 2021

Background: Neuroblastoma is a childhood cancer that arises from the sympathetic nervous system. Approximately 1% of patients have a family history of disease with causal germline mutations in neuroblastoma predisposition genes, ALK or PHOX2B. Recent genome-wide association studies (GWAS) of sporadic cases have identified over two dozen susceptibility loci, and next-generation sequencing studies estimate that 8-10% of children with cancer harbor a rare pathogenic (P) or likely pathogenic (LP) germline variant in a cancer predisposition gene (CPG). To date, the heritability and clinical significance of germline P/LP variants remains unknown due to a lack of parental germline DNA.

Methods: Through the Gabriella Miller Kids First program, we performed whole genome sequencing (WGS) at 30x depth on patient-parent triads (n=457) and dyads (n=99), along with WGS and exome sequencing on matched tumor DNA (n=336) and RNA-sequencing on matched tumor RNA (n=207). Rare variants (allele frequency &lt;0.1% in ExAC, 1000 Genomes, and gnomAD) in a predefined set of CPGs (n=197) were annotated, and pathogenicity was assessed using ClinVar, InterVar, and manual review. Gene-based enrichment was performed by comparison to gnomAD WGS data (n=143,068), excluding TCGA samples. Heritability was evaluated using family-based variant calling. Tumor DNA sequencing was analyzed for second hits or somatic enrichment of the germline P/LP variant. Tumor RNA sequencing was interrogated to identify expressed P/LP variants and preferential allelic expression. Ongoing analyses are utilizing polygenic risk scores from our GWAS study to inform tumor penetrance.

Results: We observed 78 P/LP germline variants in CPGs in 75 probands (13.5%). Of the 72 probands with trio data, 95% of the P/LP variants were inherited (54% maternal, 46% paternal). Several CPGs showed enrichment of P/LP variants, including BARD1 (p=0.001; OR 16.16; 95% CI 3.21-50.45). We observed one canonical ALK mutation (R1275Q), but no PHOX2B mutations. For patients with corresponding tumor samples, all germline P/LP variants were observed in the tumor DNA. Germline P/LP variants were associated with high-risk disease as defined by risk group (high vs. low/intermediate, p=0.005), INRG stage (stage M vs stage L1/L2/MS, p=0.024), and MYCN amplification status (amplified vs not amplified, p=0.016).

Conclusions: Here we show that approximately 13.5% of patients with neuroblastoma harbor a rare P/LP germline variant in a CPG, and the vast majority of these are inherited. Neuroblastoma patients with P/LP germline variants are more likely to have high-risk disease and several variants suggest potential therapeutic opportunities. Work is ongoing to understand the genetic factors that explain why parents harboring the same P/LP variant did not develop neuroblastoma, and to determine the genetic counseling implications of these data.

Citation Format: Emily Blauel, Zalman Vaksman, Alex Lee, Rebecca Kaufman, Laura Egolf, Andrew Olshan, John Maris, Diskin Sharon. Heritability of cancer predisposition gene mutations in 556 neuroblastoma patients with paired parental DNA whole genome sequences [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 3030.