Long read sequencing reveals novel genomic and epigenomic alterations in repetitive regions of high grade serous ovarian cancer

Approximately half of high-grade serous ovarian carcinomas (HGSOCs) demonstrate homologous recombination deficiency (HRD) with characteristic genomic rearrangements. However, the impact of HRD on centromeres and transposable elements remains largely unexplored in HGSOC since conventional short-read sequencing is unable to interrogate these repetitive regions. We employed Oxford Nanopore long-read sequencing (LRS) to investigate genomic and epigenetic alterations in these regions. Pre-treatment archival cryopreserved tumor and matched blood samples were obtained for six patients with HGSOC. High-molecular-weight DNA was sequenced using Oxford Nanopore R10.4 flow cells and aligned to both the GRCh38 and the telomere-to-telomere T2T-CHM13 reference genome. Pathogenic gene mutations, allele-specific copy number variations, structural variants, and CpG methylation were analyzed. All six tumors had pathogenic TP53 mutations. Two carried germline BRCA1 mutations, while three showed CCNE1 amplifications. HRD scores and mutational signatures associated with HRD were elevated in the BRCA1-mutated tumors. Centromeric regions were significantly hypomethylated in tumors and their methylation profiles distinctly separated HRD tumors from non-HRD tumors. LINE1 and ERV transposable elements showed marked hypomethylation in tumors without germline BRCA1 mutations. Chromosome arm-specific telomere lengths were significantly shortened in tumors. Allele-specific hypermethylation in the TERT hypermethylated oncological region was detected in three tumors. LRS uncovered HRD-related genomic and epigenomic alterations in previously inaccessible repetitive regions of HGSOC, including centromeric and transposable element hypomethylation. These findings highlight the potential of such abnormalities as novel biomarkers for HGSOC and warrant further application of the methods to larger cohorts in future studies.