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Related Experiment Video

Updated: Feb 7, 2026

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
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Capturing clinically actionable copy number alterations in Wilms tumor using nanopore sequencing.

Larissa V Furtado1, Carolyn Jablonowski2, Pandurang Kolekar3

  • 1Department of Pathology, St. Jude Children's Research Hospital.

Research Square
|February 6, 2026
PubMed
Summary

Nanopore sequencing shows promise for detecting copy number alterations (CNVs) in Wilms tumor (WT) rapidly and affordably. While effective for CNVs, current methods need improvement for 11p15 loss of imprinting (LOI) analysis in WT.

Keywords:
ONTWilms tumorcopy number alterationsmethylationnanoporesequencing

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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.