Abstract 3525: Structural variation shapes clonal evolution in pediatric cancer

Abstract Tumor clonal evolution is driven by the selection or acquisition of mutations that confer an advantage under the pressures of therapeutic intervention. Much of the knowledge of clonal evolutionary trajectories is based upon single nucleotide variants (SNVs), a mutation type well-suited for detecting subclones and estimating their cancer cell fraction by deep sequencing. To explore the role of structural variants (SVs) in the evolutionary process, we analyzed 13 pediatric cancer patients with multiple spatiotemporally distinct tumor samples and patient-derived xenografts (PDXs) profiled by whole-genome sequencing (WGS). In addition to de novo SV calling, the SV presence across all tumor samples from the same patient was analyzed by Fuzzion2, which uses pattern matching to find SVs at a sensitivity as low as a single read pair. We found that clonal architectures defined by SVs largely mirrored those of SNVs, although the branch lengths could differ if SV formation was not affected by therapy-related mutagenesis (e.g. cisplatin). SV-based mutational processes, such as RAG-mediated recombination in leukemia, can be active from diagnosis to relapse, and complex SVs caused by chromothripsis may not be selected for despite their predominant presence at diagnosis. A trio of diagnosis-relapsed rhabdomyosarcoma samples exhibited an intriguing pattern of sharing an ancestral extrachromosomal amplicon of MDM2, which co-existed with a second amplicon distinct at diagnosis and relapse. RNA sequencing confirmed each amplicon led to overexpression of different subsets of genes, and SVs derived from WGS indicated that the amplicon private to relapse may have merged with the ancestral MDM2 amplicon. Validation of this finding is currently underway, leveraging long-read sequencing and cells derived from PDX models of these tumors. Our study emphasizes the importance of examining SVs to gain perspective on the dynamic changes that impact driver genes and amplicon architecture during therapy and may offer new insights on strategies to overcome therapeutic resistance. Citation Format: Robert Greenhalgh, Bensheng Ju, Samuel W. Brady, John Easton, Sivaraman Natarajan, Jinghui Zhang, . Structural variation shapes clonal evolution in pediatric cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 3525.