Real-time genomic characterization of pediatric acute leukemia using adaptive sampling

Area of Science:

• Genomics
• Pediatric Oncology
• Molecular Diagnostics

Background:

• Accurate genomic classification is crucial for effective pediatric acute leukemia treatment.
• Current classification relies on multiple, time-consuming, and expensive techniques.

Purpose of the Study:

• To investigate the feasibility of a comprehensive single-assay classification using long-read sequencing.
• To assess the potential of real-time genome target enrichment for classifying acute leukemia.

Main Methods:

• Whole genome sequencing using long-read nanopore technology was performed on 57 pediatric acute leukemia samples.
• Real-time analysis with adaptive sampling was employed in 18 cases.
• Results were compared against standard-of-care clinical testing.

Main Results:

• The single-assay approach successfully characterized known karyotype abnormalities and structural variants.
• Subtype-defining genomic alterations were identified in all cases within 48 hours.
• Real-time analysis identified driving alterations in as little as 15 minutes for karyotype and 6 hours for complex variants.

Conclusions:

• Whole genome nanopore sequencing with adaptive sampling provides a comprehensive genomic classification of acute leukemia.
• This method has the potential to reduce cost and turnaround time compared to current standards.
• It offers a promising alternative for rapid and accurate diagnosis of pediatric acute leukemia.