Abstract A044: The biology of childhood tumors with germline <i>CHEK2</i> loss of function variants

Abstract Germline CHEK2 pathogenic/likely pathogenic variants (GPV CHEK2 ) are associated with an increased risk of adult-onset malignancies such as breast cancer. However, their role in pediatric-onset cancer is unclear. Pediatric Precision Medicine Programs have reported GPV CHEK2 in some cases, suggesting a role in pediatric tumour development. Aims: To investigate the contribution of germline pathogenic CHEK2 variants (GPVCHEK2) to genetic cancer risk in children and explore their potential role in pediatric tumorigenesis. Methods: Patients under 21 years old with childhood cancer were enrolled in ZERO Childhood Cancer Program (2018-2025). We retrospectively analyzed clinical information, including demographics, diagnoses, treatment, and outcome data, obtained from medical records, and paired tumor-germline data from participants with GPV CHEK2 . Results: In total, 22 patients (0.94% of participants) harbored a GPV CHEK2 . Comparison of the rates of GPV CHEK2 between the ZERO cohort and gnomAD (Genome Aggregation Database) demonstrated a signal of statistical enrichment in the ZERO cohort. GPV CHEK2 were approximately 1.9 times more often in the ZERO cohort compared to gnomAD (q value (corrected p value) of 0.03; p value 0.003). Within the ZERO GPV CHEK2 cohort, there were 24 tumours and 26 episodes of paired tumor-germline profiling data (22 primary, 2 secondary and 2 relapsed cancers). The median age at diagnosis was 8 years old, 59% male, and a broad tumor spectrum including 6 hematological malignancies, and 18 non-hematological tumours (7 CNS tumours and 11 Solid tumours). We identified 10 distinct single nucleotide GPV CHEK2 ( no copy number changes were detected). Four patients had a second GPV in a cancer predisposition gene in addition to CHEK2. The CHEK2 c.1100del founder variant was seen in 64% of patients, with three patients harboring rare or novel variants. Half of them (55%) had high-risk tumors, 41% had non-high-risk tumors including 23% with rare tumors. Ploidy across the tumor samples ranged between 1.64 to 3.35 with a median of 2. Tumor Mutational Burden ranged between 0.08 to 48.46 mutation/Megabases (median 0.52mut/Mb). No homologous recombination deficiency (HRD) mutational signature was observed in the tumor samples. Genome Wide Loss of Heterozygosity across the samples ranged from 0% to 41.84%, with a median of 8.69%. Somatic second hits in CHEK2 were identified in two cases, both involving copy number variants. Additionally, each tumour also harbored an independent somatic driver in a different cancer gene deemed sufficient for tumorigenesis. Conclusions Germline pathogenic variants in CHEK2 are observed in children with diverse cancer types, without a clearly defined tumor spectrum. While no biomarkers of HRD were identified, some tumors exhibited biallelic inactivation of CHEK2 via a second somatic event on the wildtype allele. These findings suggest that GPV CHEK2 may contribute to genomic instability, enabling additional somatic alterations to occur and potentially cooperating with somatic drivers in tumorigenesis. Citation Format: Laura Raiti, Ann Altekoester, Sam El-Kamand, Gabi Ryan, Kathy Tucker, Meera Warby, Eliza Courtney, Paulette Barahona, Loretta Lau, Toby Trahair, Glenn Marshall, David Ziegler, Michelle Haber, Vanessa Tyrrell, Mark Cowley, Chelsea Mayoh, Mark Pinese, Dong-Anh Khuong-Quang, Noemi Fuentes-Bolanos. The biology of childhood tumors with germline CHEK2 loss of function variants [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Discovery and Innovation in Pediatric Cancer— From Biology to Breakthrough Therapies; 2025 Sep 25-28; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2025;85(18_Suppl_2):Abstract nr A044.