Capturing clinically actionable copy number alterations in Wilms tumor using nanopore sequencing.

Area of Science:

• Genomics
• Molecular Diagnostics
• Pediatric Oncology

Background:

• Copy number alterations (CNVs) on chromosomes 1p, 1q, 16q, and 11p15 are critical for Wilms tumor (WT) risk stratification.
• Current detection methods for CNVs and 11p15 loss of imprinting (LOI) in WT are time-consuming and costly.
• 11p15 LOI is a key adverse predictor in WT, necessitating accurate detection.

Purpose of the Study:

• To evaluate the feasibility of nanopore sequencing for detecting CNVs and 11p15 LOI in Wilms tumor (WT).
• To assess the turnaround time and cost-effectiveness of nanopore sequencing compared to existing methods for WT genomic analysis.

Main Methods:

• Whole-genome sequencing (WGS) using the MinION nanopore platform was performed on 15 patient-derived WT xenografts.
• Adaptive sampling was applied to enrich for clinically relevant genomic regions.
• Sequencing data were analyzed for CNVs and compared with existing characterization data (WES, MLPA).

Main Results:

• Nanopore WGS successfully detected 94% of clinically relevant CNVs in WT with high accuracy (no false positives).
• Adaptive sampling demonstrated concordance with WGS for CNV detection and enabled sample multiplexing.
• Current nanopore sequencing depth was insufficient for reliable assessment of 11p15 methylation status (LOI).

Conclusions:

• Nanopore sequencing is a feasible approach for rapid and cost-effective CNV assessment in Wilms tumor.
• The technology holds potential for integrated genomic analysis, including CNVs and 11p15 LOI, pending improvements in sequencing depth.
• Higher throughput nanopore platforms are needed for successful clinical integration of this diagnostic approach for WT.