Abstract LB347: Telomere-to-telomere long read whole genome sequencing provides novel insights into ovarian cancer genomics

Abstract Background: High-grade serous ovarian carcinoma (HGSOC) is driven by chromosomal instability and patterns of genomic rearrangement have predictive and prognostic value in this disease. Nearly all next generation sequencing performed to date rely on short read sequencing, which is unable to resolve complex rearrangements or analyze repetitive centromeric or telomeric regions. Here we combine long-read sequencing (LRS) platform with the recently completed telomere-to-telomere (T2T-CHM13) reference genome to report the first comparison of whole genome variation in BRCA1-mutated and CCNE1-amplified HGSOC. Methods: High-molecular-weight DNA was extracted from cryopreserved, pre-treatment tumor and matched blood samples from six HGSOC patients and sequenced using Oxford Nanopore PromethION platform. Base-called reads were aligned to both the GRCh38 and T2T-CHM13 reference genomes for the analysis of SNVs, indels, allele-specific CNVs, complexed structural variants, transposable element insertions, and CpG methylation patterns. Results: Somatic pathogenic TP53 mutations were identified in all tumors (P1-P6). Germline pathogenic BRCA1 mutations were present in two cases (P1, P2), while CCNE1 amplification was observed in the remaining four cases (P3-P6). Homologous recombination deficiency (HRD) scores were elevated in BRCA1-mutated tumors (73 and 84) compared to CCNE1-amplified tumors (71, 43, 53, and 29, respectively). Complete loss of heterozygosity in chromosome 17 was observed in all tumors. Chromoplexy was detected in five tumors (P1, P2, P4-P6). Focal amplifications associated with extrachromosomal DNA and breakage-fusion-bridge cycles were observed in P2 and P6. Telomere length was significantly shortened in all tumors compared to matched normal samples. Additionally, CpG methylation levels were significantly reduced in centromeric satellite repeats and inserted transposable elements in all tumors than in normal samples. Conclusion: This study establishes the first LRS-based analysis workflow for comprehensive genomic characterization of HGSOC, uncovering novel alterations in previously inaccessible genomic regions. These findings highlight the potential of LRS as a new gold standard for whole genome analysis in HGSOC, warranting further investigation for its clinical and research applications. Citation Format: Shiro Takamatsu, Jian Li, Thomas Welte, Eleonora Khlebus, Veena Vuttaradhi, Allison Brodsky, Barrett Lawson, Robert T. Hillman. Telomere-to-telomere long read whole genome sequencing provides novel insights into ovarian cancer genomics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_2):Abstract nr LB347.