Real-time genomic characterization of pediatric acute leukemia using adaptive sampling.
Julie Geyer1, Kofi B Opoku2,3, John Lin2
1Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Leukemia
|March 25, 2025
Summary
Long-read sequencing offers a faster, more cost-effective method for classifying pediatric acute leukemia. This single assay identifies key genomic alterations, improving diagnostic speed and efficiency for better treatment outcomes.
Area of Science:
- Genomics
- Molecular Diagnostics
- Pediatric Oncology
Background:
- Accurate genomic classification is crucial for effective pediatric acute leukemia treatment.
- Current classification methods (flow cytometry, FISH, karyotyping, PCR, microarrays) are time-consuming and expensive.
Purpose of the Study:
- To assess the feasibility of a comprehensive single-assay classification using long-read sequencing.
- To rapidly identify chromosomal abnormalities and structural variants in pediatric acute leukemia.
Main Methods:
- Whole genome sequencing using long-read nanopore technology with real-time adaptive sampling.
- Analysis of DNA from 57 pediatric acute leukemia cases.
- Comparison of results with standard-of-care clinical testing.
Main Results:
- Identified known, clinically relevant karyotype abnormalities and structural variants concordant with standard methods.
- Subtype-defining genomic alterations detected in all cases within 48 hours.
- Real-time analysis identified driving alterations in as little as 15 minutes for karyotype and up to 6 hours for complex variants.
Conclusions:
- Whole genome nanopore sequencing with adaptive sampling can accurately classify pediatric acute leukemia.
- This approach has the potential to significantly reduce diagnostic cost and turnaround time compared to current standards.
