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

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.