Investigation of DNA damage response genes validates the role of DNA repair in pediatric cancer risk and identifies SMARCAL1 as novel osteosarcoma predisposition gene

Background Recent studies reveal that 5-18% of children with cancer harbor pathogenic variants in known cancer predisposing genes. However, DNA damage repair (DDR) genes, which are frequently somatically altered in pediatric tumors, have not been systematically examined as a source of novel cancer predisposing signals. Methods To address this gap, we interrogated 189 DDR genes for presence of germline predisposing variants (PV) among 5,993 childhood cancer cases and 14,477 adult non-cancer controls (discovery cohort). PV were determined using a tiered approach incorporating ClinVar annotations, InterVar classification, and in silico tools (REVEL, CADD, MetaSVM). Using logistic and firth regression, we identified genes with PV statistically enriched in tumors and replicated findings among 1,497additional childhood cancer cases across three independent cohorts. Findings Analysis across all cancers revealed enrichment of TP53 PV. Cancer-specific analyses confirmed known associations including germline TP53 PV in adrenocortical carcinoma, high-grade glioma (HGG), and medulloblastoma (MB), PMS2 in HGG and non-Hodgkin lymphoma (NHL), MLH1 in HGG, BRCA2 in NHL, and BARD1 in neuroblastoma. In addition, four novel associations were uncovered, including BRCA1 in ependymoma, SPIDR in HGG, SMC5 in MB, and SMARCAL1 in osteosarcoma (OS). Importantly, the SMARCAL1 :OS association was significant in the discovery (6/230, 2.6%, FDR logistic =0.0189) as well as all three replication cohorts (Childhood Cancer Survivor Study: 8/275, 2.9%; P Fisher <0.0001; German Childhood Cancer Registry: 4/135, 3%, P Fisher =0.002; INdividualized Therapy FOr Relapsed Malignancies in Childhood: 4/217, 1.8%, P Fisher =0.012). The remaining wildtype SMARCAL1 allele was deleted in three of four OS tumors with available data. Interpretation Our study confirms the relevance DDR genetic variation in pediatric cancer risk and establishes SMARCAL1 as a novel OS predisposing gene, providing insights into tumor biology and creating opportunities to optimize care for patients with this challenging tumor.