ArticleFrontiers in medicine2025
Accurate and rapid single nucleotide variation detection in
Article in Frontiers in medicine, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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Who cites it
2 citing papers in PubMed.
- From Phenotype to Genotype and Beyond: Insights into Familial Hypercholesterolemia and Familial Hypertriglyceridemia.Medicina (Kaunas, Lithuania) · 2026Review
- NanoSimFormer: an end-to-end transformer-based nanopore signal simulator with basecaller guidance.Bioinformatics (Oxford, England) · 2026Article
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Authors and funding
7 authors.
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Abstract
Background: Genetic testing is essential for disease screening, diagnosis, prognosis, and pharmacotherapy guidance. Oxford Nanopore Technologies (ONT) offers a cost-effective platform for long-read sequencing, yet its routine use in clinical diagnostics remains under evaluation. We tested different nanopore sequencing pipelines aimed at accurately detecting single-nucleotide variants (SNV) in a gene locus spanning ⁓25 kb. Methods: As a proof of concept, Results: The combination of super high accuracy (SUP) basecalling with Longshot variant calling demonstrated the highest performance across flow cells. MinION flow cell reached a perfect F1-score of 100%, while the more cost-effective Flongle flow cell remained a viable alternative (mean F1-score: 98.2% ± 4.2). Throughput analysis indicated that a single MinION flow cell could process up to 96 samples and ⁓40 long sequencing regions, whereas a Flongle flow cell could support sequencing of 96 samples and one long region. Conclusion: The proposed nanopore-based SNV identification workflows may support the development of long-read, targeted gene panels, offering a promising tool for both diagnostic and discovery applications, particularly in multi-gene settings such as oncology and cardiology.
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