Investigation of DNA Damage Response Genes Validates the Role of DNA Repair in Pediatric Cancer Risk and Identifies <i>SMARCAL1</i> as a Novel Osteosarcoma Predisposition Gene.

Abstract

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. 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 noncancer controls (discovery cohort). PV were determined using a tiered approach incorporating ClinVar annotations, InterVar classification, and <i>in</i> <i>silico</i> tools (REVEL, CADD, and MetaSVM). Using logistic and firth regression, we identified genes with PV statistically enriched in the germline of children with tumors and replicated findings among 1,497 additional childhood cancer cases across three independent cohorts. Analysis across all cases with cancer revealed enrichment of <i>TP53</i> PV. Cancer-specific analyses confirmed known associations including germline <i>TP53</i> PV in adrenocortical carcinoma, high-grade glioma (HGG), and medulloblastoma (MB), <i>PMS2</i> in HGG and non-Hodgkin lymphoma (NHL), <i>MLH1</i> in HGG, <i>BRCA2</i> in NHL, and <i>BARD1</i> in neuroblastoma. In addition, four novel associations were uncovered, including <i>BRCA1</i> in ependymoma, <i>SPIDR</i> in HGG, <i>SMC5</i> in MB, and <i>SMARCAL1</i> in osteosarcoma (OS). Importantly, the <i>SMARCAL1</i>:OS association was significant in the discovery (6/230, 2.6%, false discovery rate [FDR]_logistic = 0.0189) as well as all three replication cohorts (Childhood Cancer Survivor Study: 8/275, 2.9%; <i>P</i>_Fisher < .0001; Cancer Predisposition Syndrome-German Childhood Cancer Registry: 4/135, 3%, <i>P</i>_Fisher = .002; Individualized Therapy for Relapsed Malignancies in Childhood: 4/217, 1.8%, <i>P</i>_Fisher = .012). The remaining wild-type <i>SMARCAL1</i> allele was deleted in three of four OS tumors with available data. Our study confirms the relevance DDR genetic variation in pediatric cancer risk and establishes <i>SMARCAL1</i> as a novel OS predisposing gene, providing insights into tumor biology and creating opportunities to optimize care for patients with this challenging tumor.