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Oxford Nanopore Technologies [ONT] Sequencing: Clinical Validation in Genetically Heterogeneous Disorders
Mario Urtis1, Chiara Paganini1, Viviana Vilardo1
1Centre for Inherited Diseases, Department of Research, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy.
Genes
|November 27, 2025
Summary
Long-read sequencing (LRS) using Oxford Nanopore Technologies (ONT) offers superior detection of complex genetic variants in inherited diseases compared to standard short-read sequencing (SRS). This validation confirms LRS
Area of Science:
- Genomics
- Molecular Diagnostics
- Bioinformatics
Background:
- Short-read sequencing (SRS) is the standard for genetic testing in inherited diseases but has limitations.
- SRS struggles with structural variants (SVs), copy number variations (CNVs), and deep intronic variants.
Purpose of the Study:
- Validate Oxford Nanopore Technologies (ONT) long-read sequencing (LRS) for clinical genetic testing.
- Assess LRS performance against established methods for inherited human diseases.
Main Methods:
- Analyzed 509 samples (393 with known pathogenic/likely pathogenic variants, 116 controls).
- Utilized ONT sequencing platforms (MinION, GridION, PromethION-2) with CE-IVD panels.
- Employed the 4eVAR pipeline for data analysis.
Main Results:
- Achieved 100% sensitivity in detecting known pathogenic/likely pathogenic variants.
- Identified a missed CNV in the *ENG* gene and precisely defined SV breakpoints.
- Improved detection in challenging genomic regions and deep intronic areas.
- Enabled rapid (<24h) testing for urgent clinical cases.
Conclusions:
- ONT LRS demonstrates diagnostic performance comparable to SRS for inherited diseases.
- LRS offers significant advantages in resolving complex and previously undetectable variants.
- Ongoing LRS advancements promise expanded clinical applications.
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