Genomic Profiling of Childhood Tumor Patient-Derived Xenograft Models to Enable Rational Clinical Trial Design.

Accelerating cures for children with cancer remains an immediate challenge as a result of extensive oncogenic heterogeneity between and within histologies, distinct molecular mechanisms evolving between diagnosis and relapsed disease, and limited therapeutic options. To systematically prioritize and rationally test novel agents in preclinical murine models, researchers within the Pediatric Preclinical Testing Consortium are continuously developing patient-derived xenografts (PDXs)-many of which are refractory to current standard-of-care treatments-from high-risk childhood cancers. Here, we genomically characterize 261 PDX models from 37 unique pediatric cancers; demonstrate faithful recapitulation of histologies and subtypes; and refine our understanding of relapsed disease. In addition, we use expression signatures to classify tumors for TP53 and NF1 pathway inactivation. We anticipate that these data will serve as a resource for pediatric oncology drug development and will guide rational clinical trial design for children with cancer

Defining The Landscape Of Rare Inherited And De Novo Germline Structural Variation In Neuroblastoma

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 (\u3e500 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

OpenPBTA: The Open Pediatric Brain Tumor Atlas

Pediatric brain and spinal cancers are collectively the leading disease-related cause of death in children; thus, we urgently need curative therapeutic strategies for these tumors. To accelerate such discoveries, the Children\u27s Brain Tumor Network (CBTN) and Pacific Pediatric Neuro-Oncology Consortium (PNOC) created a systematic process for tumor biobanking, model generation, and sequencing with immediate access to harmonized data. We leverage these data to establish OpenPBTA, an open collaborative project with over 40 scalable analysis modules that genomically characterize 1,074 pediatric brain tumors. Transcriptomic classification reveals universal dysregulation in mismatch repair-deficient hypermutant high-grade gliomas and loss as a significant marker for poor overall survival in ependymomas and H3 K28-mutant diffuse midline gliomas. Already being actively applied to other pediatric cancers and PNOC molecular tumor board decision-making, OpenPBTA is an invaluable resource to the pediatric oncology community