Abstract 405: Translocation detection in cancer using low-pass pore-c sequencing

Abstract

Abstract Complex chromosomal rearrangements, including translocations, play a critical role in oncogenesis and are often identified as recurrent genetic aberrations in hematologic malignancies and solid tumors[1]. Translocation detection by karyotyping of an individual’s metaphase chromosomes remains challenging for detection of balanced rearrangements, which have no gain or loss of genetic material. Rearrangement detection using whole-genome sequencing is a viable alternative, but it relies on breakpoint-spanning reads and requires high sequencing depth (30-60x) with long reads to achieve high sensitivity, especially in repetitive regions of the genome[2]. Here, we describe a workflow for translocation detection at low sequencing depth with Oxford Nanopore’s long read chromatin conformation capture technique, Pore-C[3]. Importantly, for translocation calling, Pore-C does not rely on breakpoint-spanning reads but rather the high intrachromosomal interaction frequency of genomic regions around the breakpoint, thus largely lowering sequencing depth requirements and reducing mapping issues in low complexity regions. We prepared, barcoded, and sequenced Pore-C libraries of 3 cancer cell lines including lung cancer (A549), Acute Monocytic Leukemia (THP-1), melanoma (COLO 829) and its matching normal (COLO 829 BL) on a single Q20+ MinION flow cell (FLO-MIN114). Genome-wide contact maps of low-pass data (<1.5 Gbps per sample) were compared against higher depth (>30 Gbps per sample) Hi-C maps [4], revealing that low-pass Pore-C successfully captured large-scale genomic rearrangement. For example, chromosomal pairs chr8-chr11 and chr15-chr19 in A549, chr9-chr11 and chr1-chr20 in THP1, and chr7-chr15 in Colo829 were detected at <0.5X depth of sequencing coverage. These translocation events were further validated by breakpoint analysis using adaptive sampling, where targeted regions were previously confirmed by independent studies[4],[5]. Low-pass Pore-C detects translocations in an unbiased manner and does not require prior knowledge of the translocation structure. Combined with its simple sample-preparation workflow and the capability to provide genome-wide copy-number information in a single experiment, it can serve as a cost-effective and comprehensive tool for cancer genomic studies. [1] Chromosomal translocations in human cancer, Nature, 372, 143 (1994) [2] Hi-C as a tool for precise detection and characterisation of chromosomal rearrangements and copy number variation in human tumors, Genome Biology, 18, 125 (2017) [3] Identifying synergistic high-order 3D chromatin conformations from genome-scale nanopore concatemer sequencing, Nature Biotechnology, 40, 1488(2022) [4] Chromosomal translocations detection in cancer cells using chromosomal conformation capture data, Genes (Basel), 13, 7 (2022) [5] A multi-platform reference for somatic structural variation detection, Cell Genomics, 2, 6 (2022) Citation Format: Scott Hickey, Xiaoguang Dai, Sergey Aganezov, John Beaulaurier, Eoghan Harrington, Sissel Juul. Translocation detection in cancer using low-pass pore-c sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 405.