Abstract 6288: Precise characterization of complex repeats in cancer genomes

The characterization of somatic variation, especially in complex genomic regions, is crucial for understanding the molecular drivers of cancer progression. Accurate PacBio long-read sequencing (HiFi) enables detection of all variant classes, from simple SNVs and INDELs up to complex structural variation, tandem repeats, and changes in epigenetic signatures. Complex and repetitive regions, while fully sequenced by HiFi reads, remain bioinformatically challenging, requiring tailored solutions. Here, we describe new tools to genotype understudied repetitive regions in cancer genomes, a task that has historically posed significant challenges to short-read sequencing.Our software tool, TRGT, resolves the sequence and methylation patterns of complex repetitive regions at a single-nucleotide resolution. A recent algorithmic improvement (vclust module) enables us to type expanded hyper-polymorphic regions, termed variation clusters. Variation clusters usually result in many incorrect variant calls in computational pipelines. By analyzing a variation cluster as a single region, rather than many small variants, we can accurately measure genetic variation. To demonstrate the importance of variation clusters in cancer, we comprehensively resolved repeat regions in five cell lines and 50 clinical tumor samples (with matched healthy tissue). We identified 5,500 new variation clusters across the tumors and an average of 46,220 (out of 4 million, 1%) loci that are contracted or expanded in a tumor compared to its matched normal tissue. We find 3% of these loci can be located within genes found in the Compendium of Cancer Genes, suggesting potentially oncogenic significance. In addition, using TRGT, we were able to detect microsatellite instability (MSI) in a tumor with a compound heterozygous coding mutation in MSH2. Lastly, we further analyzed haplotypes in selected variation clusters to detect and resolve sequences in somatic mosaicism. By incorporating this new class of variants—complex repeats—into our analysis, we significantly enhanced the capability of HiFi reads to detect a comprehensive spectrum of genomic variations. The inclusion of complex repeat genotyping with PacBio HiFi reads will enable a more detailed understanding of cancer genetics and open new avenues for research and clinical applications. Citation Format: Khi Pin Chua, Egor Dolzhenko, Zev N. Kronenberg, Seiya Imoto, Seiichi Mori, Michael A. Eberle. Precise characterization of complex repeats in cancer genomes [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 6288.