Abstract 3239: Single assay, tumor-only, somatic SNVs, SVs, and CNVs profiling using nanopore adaptive sampling

Abstract Background. Tumor-only (T-only) testing often trades high sensitivity at low allele fraction (AF) - when using amplicon or hybrid-capture based enrichment - against comprehensive structural and copy-number profiling and overall ease of use, when using whole genome sequencing. Nanopore adaptive sampling (AS) enriches targets by rejecting reads during sequencing if they don’t overlap with user-defined targets, yielding high-depth (100-200X) long read (8-15kb) data on target and shallow (5-15X and 500bp) sequencing off-target. As a result, AS simplifies experimental setup by not requiring PCR or pulldown-based enrichment, while at the same time enabling the detection of single nucleotide variants (SNVs), structural variants (SVs), and copy number variations (CNVs) in a single assay. Methods. Here, we evaluated variant calling accuracy for T-only AS on a highly aberrant genome (COLO829) and on a “synthetic,” less-aberrant genome constructed in silico from COLO829 and its matched normal, retaining only a small number of large-scale CNV events. Performance was assessed across coverage/purity ladders that emulate common conditions. Sequencing targeted a generic multi-region, 700+ cancer-gene-aware panel augmented to cover a range of SV types present in COLO829. SNVs and SVs were inferred with long-read tumor-only pipelines. SVs included translocations, deletions, duplications, and insertions. Genome-wide CNV profiles were derived from the same AS datasets by leveraging off-target reads. Results. SNVs. High (100-200X) on-target depth enabled confident recovery of somatic SNVs at relevant AFs, with high recall down to 0.05 AF and high precision down to 0.1-0.2 AF. These results were consistent across coverage/purity ladders. SVs. Long-read on-target data supported robust detection of inter- and intra-chromosomal rearrangements. Notably, events were recovered even when only partially overlapping with the target regions. CNVs. The high number of short off-target reads generated stable, genome-wide CNV segmentations from the same runs. Inferred CNV profiles demonstrated expected broad gains and losses on the highly aberrant genome as well as on the synthetic, less-aberrant construct across coverage/purity ladders. Conclusions. A single T-only nanopore AS run can (1) deliver sensitive SNV detection via high on-target coverage, (2) provide robust SV discovery, including one-breakend-on-target cases, and (3) yield genome-wide CNV profiles from off-target signal. By avoiding laborious panel-specific hybrid capture assays through simple software-defined targeting, AS offers a practical, streamlined, and highly flexible approach to single-assay tumor-only characterization that covers the full breadth of genomic variation found in cancer. Citation Format: Sergey Aganezov, Philipp Rescheneder, Rory Sinnott, Sissel Juul. Single assay, tumor-only, somatic SNVs, SVs, and CNVs profiling using nanopore adaptive sampling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 3239.