Abstract 710: Germline whole genome sequencing and nanopore long-read sequencing reveal high incidence of pathogenic variants in childhood cancer survivors with subsequent malignant neoplasms

Abstract Background: Childhood cancer survivors with cancer-predisposing variants are at increased risk of developing subsequent malignant neoplasms (SMNs). Although panel sequencing is commonly used for diagnostics, its overall yield has been lower than expected. Methods: From 1, 435 pediatric solid tumor patients diagnosed or treated between 1994 and 2014, we previously identified 72 individuals who developed SMNs; germline DNA samples were available for 40 of them. Whole genome sequencing (WGS) was performed on these 40 survivors using Illumina sequencing to investigate deleterious germline variants in 205 known cancer predisposition genes (CPGs). We further assessed candidate structural variants with Oxford Nanopore long-read sequencing in 10 patients who showed no pathogenic variants but were highly suspicious for genetic predisposition. Results: Pathogenic or likely pathogenic (P/LP) variants were identified in 18 patients (45%), with 11 patients (27%) carrying P/LP variants in known autosomal dominant CPGs. Excluding RB1, the incidence remained high at 32% (10 out of 31 patients). Patients with P/LP variants in known CPGs developed a second tumor at a significantly younger age (P = 0.031), more pronounced in autosomal dominant CPGs (P = 0.008). Excluding RB1 cases, patients with any P/LP variants were more likely to have a family history of cancer among second-degree relatives (P = 0.034). Nanopore long-read sequencing revealed pathogenic structural variants in two highly suspicious cases not identified by Illumina sequencing. Specifically, a structural variant in the MLH1 gene was discovered in a patient with colorectal cancer and microsatellite instability, leading to a Lynch syndrome diagnosis. Additionally, a structural variant was found in the RB1 gene of a patient with a family history of retinoblastoma. Conclusions: Our study demonstrates a high incidence of pathogenic germline variants in childhood cancer survivors who develop SMNs. Integrating long-read sequencing technologies, such as Oxford Nanopore sequencing, enhances the detection of structural variants missed by traditional short-read WGS. These findings underscore the importance of comprehensive genomic profiling—including both short-read and long-read sequencing—in accurately identifying genetic predispositions in high-risk populations. Early identification of these variants can inform surveillance strategies and guide clinical management to improve patient outcomes. Citation Format: Eun Seop Seo, Ji Hwan Moon, Woong-Yang Park, Ji Won Lee. Germline whole genome sequencing and nanopore long-read sequencing reveal high incidence of pathogenic variants in childhood cancer survivors with subsequent malignant neoplasms [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 710.