Abstract B07: Prospective germline next-generation sequencing in pediatric patients with neuroblastoma identifies frequent alterations in genes involved in DNA damage repair
Authors: Sarah Cohen-Gogo, Karin Langenberg-Ververgaert, Anita Villani, Winnie Lo, Ted Young, Nisha Kanwar, Scott Davidson, Nathaniel Anderson, Bailey Gallinger, Mehdi Layeghifard, Larissa Waldman, Daniel Morgenstern, Ledia Brunga, Stephen Meyn, David Malkin, Adam Shlien, Meredith Irwin
Journal: Cancer Research (2020)

Abstract Background: The role of germline ALK and PHOX2B variants in genetic predisposition to neuroblastoma (NB) is well established; however, alterations in genes associated with other syndromes, including RASopathies, Fanconi anemia, and Li-Fraumeni, have also been detected. Emerging data suggest potential roles for DNA damage repair (DDR) pathway genes in NB predisposition. The use of next-generation sequencing (NGS) technologies facilitates the unbiased detection of both known and novel germline variants. Methods: Patients (pts) with newly diagnosed and relapsed malignancies, including 43 NB pts, were referred to our institutional pediatric oncology NGS study to sequence germline DNA, tumor DNA, and RNA. Germline DNA was sequenced using a custom pediatric cancer panel (Agilent Sure Select capture technology) targeting 15,000 exons across 864 genes (1000x coverage). Variant pathogenicity was classified according to ACMG (American College of Medical Genetics and Genomics) criteria and evaluated at multidisciplinary molecular tumor boards. Rare variants of uncertain significance (VUS) with supportive corresponding somatic data, patient phenotypes, literature, and/or in-silico functional analyses were termed “Variants of uncertain significance with limited evidence for pathogenicity” (VUS-LEP). Results: Analyses have been completed for 41/43 enrolled NB pts. Patient history was retrospectively categorized as “high genetic predisposition risk” (HGPR) in 14/41 pts based on ≥1 of the following criteria: (1) family history of NB and/or significant family history of other cancer(s); (2) patient with NB and another metachronous or synchronous malignancy; (3) NB with congenital abnormalities; (4) multifocal NB. Germline pathogenic (P), likely pathogenic (LP) variants, or VUS-LEP in a known cancer predisposition gene were identified in 6/14 HGPR pts (43%), predominantly in DDR-related genes (PALB2, BRCA1/CHEK2, CHEK2/PALB2, NF1, DICER1, MITF). Of note, no ALK or PHOX2B germline variants were identified for the five pts with NB family history. For the 27 non-HGPR pts, germline P, LP variants or VUS-LEP in DDR genes were most prevalent and detected in 8/27 pts (30%), in genes such as BAP1, BARD1 (n=2), BLM, BRCA2, CHEK2, RAD51, RAD51D/NBN. In this non-HGPR population, we also identified a germline P TP53 variant (n=1), a LP FH variant (n=1) as well as additional germline VUS-LEPs in EZH2 (n=1) and ERCC2 (n=1). Conclusion: Prospective sequencing identified frequent germline variants in NB pts, predominantly in genes involved in DDR and homologous recombination, regardless of classification as HGPR. We intend to complete and report somatic characterization of the tumors, with a focus on mutational signatures and 11q loss encompassing ATM. Our findings may have implications for future targeted treatment recommendations (e.g., PARP inhibitors) as well as for appropriate genetic counseling for pts and families. Citation Format: Sarah Cohen-Gogo, Karin Langenberg-Ververgaert, Anita Villani, Winnie Lo, Ted Young, Nisha Kanwar, Scott Davidson, Nathaniel Anderson, Bailey Gallinger, Mehdi Layeghifard, Larissa Waldman, Daniel Morgenstern, Ledia Brunga, Stephen Meyn, David Malkin, Adam Shlien, Meredith Irwin. Prospective germline next-generation sequencing in pediatric patients with neuroblastoma identifies frequent alterations in genes involved in DNA damage repair [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr B07.