Abstract LB081: Concurrent characterization of somatic nucleotide mutations, 5mC, and 5hmC methylation in clinical research samples using a single nanopore sequencing assay

Abstract Genomic and epigenomic variants accumulate during cancer progression, resulting in a tumor consisting of heterogeneous collections of cells, or clones, with distinct profiles of genomic and/or epigenomic alterations. The ability to characterize a broad set of somatic (epi)genomic variations simultaneously, using a single sequencing assay, facilitates cancer research and can help inform treatment. Here we describe a comprehensive approach to analyze native tumor DNA with long nanopore reads. First, we demonstrate that shallow (<1x) whole genome nanopore sequencing provides sufficient information to observe large-scale copy number aberrations. This enables rapid and affordable screening of samples with an aim of selecting those that contain variation(s) of potential interest; such samples can then be sequenced to higher coverages for a higher resolution picture of specific structural variants. We further demonstrate an analysis workflow vimba for high coverage (>30x) nanopore sequencing of tumor/normal datasets that detects clone- and haplotype-resolved structural variations in patient-derived research samples. We provide an example of haplotype- and breakpoint-resolved compounded amplification and loss of heterozygosity (LOH) of a region containing the EGFR gene in an admixed kidney tumor sample. Finally, we describe the suitability of this assay to gather genome-wide (epi)genomic variations (e.g., SNPs, indels, SVs, microsatellite instability) across tumor samples of different cancer types. For the first time with native long nanopore reads we are able to capture 5mC and 5hmC methylation information and map it over some of the most challenging repetitive regions of the genome. This information can empower a better understanding of cancer-type-specific (epi)genomic alterations, which in turn can help map out the landscape for further research. Our approach demonstrates how nanopore sequencing can be used as a single comprehensive platform to better understand and resolve the complexity of (epi)genomic somatic alterations in tumor samples. Citation Format: Sergey Aganezov, Philipp Rescheneder, John Beaulaurier, Phillip James, Sissel Juul. Concurrent characterization of somatic nucleotide mutations, 5mC, and 5hmC methylation in clinical research samples using a single nanopore sequencing assay [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB081.