Assessing the Readiness of Oxford Nanopore Sequencing for Clinical Genomics Applications

Authors

• Judith Arres
• Santosh Elavalli
• Shalini Behl
• Daniel Matias Sanchez
• Ayesha Al Ali
• Abdelrahman Ahmed Yehia Abdelaziz Saad
• Azza Attia
• Cyla Minas
• Sharika Pariyachery
• Shariq Ahmed
• Fatmah Aldhuhoori
• Nitu Thulasidharan
• Gurunath Katagi
• Omar Soliman
• Shilp Purohit
• Vinay Kusuma
• Raony Cardenas
• Thyago Cardoso
• Luis F Paulin
• Philippe Sanio
• Joseph Mafofo
• Haiguo Wu
• Val Zvereff
• Albarah El-Khani
• Fahed Al Marzooqi
• Tiago R Magalhães
• Fritz J Sedlazeck
• Javier Quilez

Language

English

Publication Date

3-2-2026

Journal

Genome Research

DOI

10.1101/gr.280134.124

PMID

41672886

PMCID

PMC12951962

PubMedCentral® Posted Date

3-1-2026

PubMedCentral® Full Text Version

Post-print

Abstract

Long-read sequencing (LRS) technologies, namely, Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio), have emerged as promising solutions to overcome the limitations of short-read sequencing (SRS). Nevertheless, the still higher sequencing error rates compared with SRS, need for customized pipelines, rapidly updating software, and incipient scalability continue to present challenges for adopting ONT in standard clinical practice. Here we assess the performance of ONT (R9 and R10 chemistries) in comparison to Illumina and MGI across 17 well-characterized reference samples with 11 clinical variants representing nine different genetic diseases. To enable this, we have implemented a production-ready pipeline including SNV, indel, STR, SV, and CNV detection, alongside reporting key summary metrics to ensure high-quality data at the production sequencing level. Our results show high accuracy of ONT across SNVs (F-score 0.978–0.983) and SVs (F-score = 0.75) but still weaknesses across indels (F-score 0.659–0.758). However, we highlight that ONT accurately detected all four pathogenic indels as well as the performance improvement in exons and with the newer R10 chemistry. We further demonstrated the importance of long reads to detect clinically impactful variants such as a FMR1 pathogenic expansion, often misclassified by SRS as being in the premutation range. Our multiplatform analysis and Sanger validation uncovered a 1 bp error in the Coriell annotation for a cystic fibrosis–causing indel in GM07829. This work underscores the growing readiness of ONT for clinical applications, highlighting both its advancements and its potential for broader adoption in clinical genomics and large-scale operations.

Keywords

Humans, Nanopore Sequencing, Genomics, High-Throughput Nucleotide Sequencing, INDEL Mutation, Sequence Analysis, DNA, Polymorphism, Single Nucleotide, DNA Copy Number Variations, Genome, Human

Published Open-Access

yes

Recommended Citation

Arres, Judith; Elavalli, Santosh; Behl, Shalini; et al., "Assessing the Readiness of Oxford Nanopore Sequencing for Clinical Genomics Applications" (2026). Faculty, Staff and Students Publications. 8660.
https://digitalcommons.library.tmc.edu/baylor_docs/8660