2025 Volume 62 Issue 5 Pages 294-305
Background: The real-time nature of nanopore sequencing allows for targeted adaptive sampling long-read sequencing (TAS-LRS), an in silico targeted sequencing method. However, their use for cancer genome profiling remains unclear.
Methods: TAS-LRS was performed in 28 children with acute leukemia (10 with acute myeloid leukemia, 13 with B-cell acute lymphoblastic leukemia [ALL], and five with T-ALL). After three-day sequencing, single-nucleotide variants (SNVs), structural variations (SVs), and copy number variations were determined. The results from 21 samples were compared with those obtained using short-read whole-genome sequencing (WGS).
Results: The median coverage was 21.0×, and the N50 was 11,191 bps in the on-target regions. Subtype-defining genomic abnormalities were detected in 24 patients. Among the variants identified by WGS, TAS-LRS detected 60.9%, 17.6%, and 89.2% of SNVs, small indels, and SVs, respectively. TAS-LRS had poor efficiency for variants with low variant allele frequencies; however, it uniquely detected some rearrangements of immunoglobulin/T-cell receptor genes that WGS overlooked because of low mapping quality. Potential clinical applications of this method were demonstrated, including NUDT15 diplotyping, which leverages long-read sequencing, and a fusion-based minimal residual disease assay using fusion breakpoint coordinates.
Conclusions: TAS-LRS enables rapid and precise genomic profiling of pediatric leukemia, which is particularly advantageous for identifying SVs. This may enhance the clinical practice of leukemia treatment.
