Targeted Adaptive Sampling Long-Read Sequencing for Pediatric Leukemia Genome Profiling
Overview
Targeted adaptive sampling long-read sequencing (TAS-LRS) was successfully applied to genome profiling in 28 pediatric leukemia patients, enabling rapid and comprehensive detection of structural variations (SVs), copy number variations (CNVs), and single-nucleotide variants (SNVs). TAS-LRS identified genomic subtypes in 85.7% of patients, including variants missed by conventional clinical tests, demonstrating its utility for precise diagnosis and risk stratification.
Background
Genome profiling is critical in leukemia treatment for diagnosis, risk stratification, and therapeutic targeting. Conventional next-generation sequencing (NGS) methods have limitations in detecting structural and copy number variations and require lengthy processing times. Nanopore sequencing with adaptive sampling offers long-read sequencing advantages, including improved SV detection and faster turnaround. Pediatric leukemia, characterized by frequent SVs and CNVs, benefits from rapid and comprehensive genome analysis, motivating evaluation of TAS-LRS in this context.
Data Highlights
Metric
Median (Range)
Mean Depth (Tumor samples)
21.3× (16.1×–31.1×)
N50 Read Length
11,089 bp (8,423–12,654 bp)
Mean Base Quality
15.8 (14.3–19.1)
Variants Identified
498 SNVs, 35 small indels, 632 SVs
Driver Alterations
22 SNVs (4.4%), 15 small indels (42.9%), 71 SVs (11.2%)
Genomic Subtypes Determined
24/28 patients (85.7%)
Turnaround Time
~72 hours from library preparation to results
Key Findings
TAS-LRS successfully profiled tumor/normal paired samples in all 28 pediatric leukemia patients with a rapid ~72-hour turnaround.
Genomic subtypes were identified in 85.7% of patients, including 12 cases where TAS-LRS detected subtypes missed by clinical testing.
Long-read sequencing enabled precise breakpoint mapping of SVs, including cryptic fusions and large deletions overlooked by conventional methods.
Chromosome-level and focal CNVs were sensitively detected, complementing G-banding results and revealing additional alterations.
Tumor-only analysis detected more variants but included many germline or sequencing errors; tumor/normal-paired analysis improved specificity but missed some driver variants.
Comparison with short-read whole genome sequencing showed high precision for SNVs (100%) and SVs (73.7%) but moderate recall, indicating TAS-LRS’s strong specificity and reasonable sensitivity.
Clinical Implications
TAS-LRS offers a rapid, comprehensive genome profiling tool for pediatric leukemia, improving detection of clinically relevant structural and copy number variants that impact diagnosis and classification. Its ability to identify cryptic rearrangements and provide haplotype-aware variant calls supports more precise risk stratification and therapeutic decision-making. Integration of TAS-LRS into clinical workflows could enhance genetic testing efficiency and accuracy in pediatric hematologic malignancies.
Conclusion
Targeted adaptive sampling long-read sequencing is a feasible and effective method for comprehensive genome profiling in childhood leukemia, enabling rapid detection of diverse genomic alterations critical for diagnosis and treatment. This approach holds promise to complement or enhance current clinical genetic testing paradigms.
References
University of Tokyo Hospital Study 2024 -- Targeted Adaptive Sampling Long-Read Sequencing for Genome Profiling in Childhood Leukemia
