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Rare Pathogenic Germline Variants Were Observed in Sporadic Pediatric Neuroblastoma Cases and Were Inherited

PHILADELPHIA – Pediatric patients with sporadic neuroblastoma harbored rare pathogenic variants in cancer predisposition genes that were inherited and associated with worse disease outcomes, according to data presented during Week 1 of the virtual AACR Annual Meeting 2021, held April 10-15.

Neuroblastoma is a pediatric cancer arising from the sympathetic nervous system. Approximately 1-2 percent of all cases have a positive family history of disease, and are classified as familial neuroblastoma, explained presenting author Emily Blauel, MD, an attending physician at the Children’s Hospital of Philadelphia. In these cases, patients are likely to have an underlying pathogenic germline mutation in the ALK or PHOX2B gene.

The remaining cases, which represent the vast majority, are thought to arise sporadically, Blauel added. While recent studies have estimated that 8-10 percent of pediatric patients spanning all cancer types harbor a rare pathogenic or likely pathogenic germline variant in a cancer predisposition gene, the heritability of such germline variants remains largely unknown due to limited parental data.

“Despite the richness of prior studies, they were unable to definitively determine if the germline variants were inherited due to scarcity of parental germline data,” Blauel explained.

With support from the Gabriella Miller Kids First Program (led by John Maris, MD, and Sharon Diskin, PhD), and in collaboration with bioinformatics scientist Zalman Vaksman, PhD, Blauel and colleagues performed whole-genome sequencing of germline DNA from 556 patients with neuroblastoma and one or both of their biological parents. The study included whole genome sequencing (WGS) from 457 patients with both of their biological parents and 99 patients with one of their biological parents. Sequencing of matched tumor DNA and RNA was also performed, including WGS on 336 tumor DNA samples, whole exome sequencing on 326 tumor DNA samples, and RNA sequencing on 207 tumor RNA samples.

The analysis identified 93 pathogenic or likely pathogenic germline variants in known cancer predisposition genes across 90 patients, representing 16 percent of the cohort. Sequencing data from biological parents were available for 85 of these patients, which revealed that 94 percent of the identified germline variants were inherited, with an equal distribution between maternally and paternally inherited patterns. One canonical ALK mutation was identified, but no PHOX2B mutations were identified.

“This large-scale study allowed us to identify rare pathogenic germline variants and—for the first time—assess whether these variants are inherited or acquired de novo,” said Blauel. “The results from this study have large implications for patients and their families, and they may aid genetic counseling.”

Enrichment of pathogenic or likely pathogenic variants was observed in several known cancer predisposition genes, including CHEK2, BARD1, and NSD1, suggesting that these variants may increase the risk of developing neuroblastoma, Blauel explained. All pathogenic and likely pathogenic germline variants were also observed in the tumor DNA of patients whose tumor sequences were available.

Furthermore, the presence of a pathogenic or likely pathogenic germline variant in a cancer predisposition gene was associated with worse outcomes, including lower odds of 10-year event-free survival (66.9 percent vs. 79.7 percent) and 10-year overall survival (76.5 percent vs. 89.4 percent), compared with those without such variants.

“The observed associations of pathogenic and likely pathogenic germline variants with worse outcomes suggest that we need a more thorough genetic evaluation of patients with neuroblastoma than is currently performed as standard of care,” Blauel noted.

Blauel, Vaksman, and colleagues are currently exploring why parents with pathogenic or likely pathogenic germline variants did not develop neuroblastoma. As this study focused on variants in known cancer predisposition genes, it did not evaluate if pathogenic variants in other genes or in non-coding regions of the genome are associated with neuroblastoma incidence and outcomes. Future plans include extending their analyses genome-wide.

A limitation of the study is that the functional relevance to neuroblastoma is not yet known for many of the pathogenic or likely pathogenic variants identified in this study. The study was supported by the National Institutes of Health. Blauel declares no conflicts of interest.