Defining The Landscape Of Rare Inherited And De Novo Germline Structural Variation In Neuroblastoma
Date of Award
Doctor of Philosophy (PhD)
Cell & Molecular Biology
Sharon J. Diskin
John M. Maris
Neuroblastoma is a deadly cancer of the developing sympathetic nervous system with complex genetic influences. Linkage analysis, genome-wide association studies (GWAS), next-generation sequencing, and other approaches have demonstrated that both common and rare germline variants confer risk for neuroblastoma. Nevertheless, the role of rare germline structural variants (SVs), a broad class of variants that affect more than 50 base pairs, remained undefined. This dissertation addressed this knowledge gap through three studies. First, we conducted an unbiased GWAS of large (>500 kb), rare germline copy number variants (CNVs) in 5,585 neuroblastoma patients and 23,505 controls. We identified a 550-kb deletion on chromosome 16p11.2 that substantially increases risk for neuroblastoma (p=3.34x10-9, odds ratio=13.9, 95% confidence interval=5.8–33.4). Notably, 16p11.2 microdeletion has previously been associated with diverse phenotypes including autism spectrum disorder. Consistently decreased gene expression and absence of a clear second hit in matched tumors suggested multi-gene haploinsufficiency as a likely mechanism. Finally, 16p11.2 deletion arose de novo on the maternal haplotype in three patients for whom heritability could be ascertained. In a second study, we analyzed known neuroblastoma-associated genes in the same rare CNV cohort and identified three patients carrying ultra-rare germline deletions in BARD1, which were completely absent from control populations. Functional analysis of heterozygous BARD1 loss-of-function sequence variants in neuroblastoma cellular models revealed decreased BARD1 expression, widespread genomic instability, and DNA repair deficiency, suggesting that BARD1 mutations induce haploinsufficiency in neuroblastoma in the absence of a second hit. In a third study, we profiled germline SVs in whole-genome sequencing from 556 neuroblastoma patients and their parents. We identified 13 mostly-inherited candidate pathogenic SVs in known cancer predisposition genes, of which seven were highly likely to induce loss-of-function, such as a 700-kb deletion of the entire PHOX2B coding sequence, a 2-kb in-frame deletion abrogating the FHA domain of CHEK2, and a 5-kb frameshift-inducing duplication in FANCA. Altogether, this dissertation demonstrated that neuroblastoma patients harbor rare, pathogenic germline SVs that influence tumor phenotype. These findings advance biological understanding of neuroblastoma and inform genetic testing and treatment strategy.
Egolf, Laura E., "Defining The Landscape Of Rare Inherited And De Novo Germline Structural Variation In Neuroblastoma" (2022). Publicly Accessible Penn Dissertations. 5633.