Reshaping rare disease diagnosis — an end to the diagnostic odyssey?

Considering the 300 to 400 million individuals around the world living with a rare disease^1,2, the term ‘rare’ feels cruelly ironic. Nearly 70% of rare diseases strike in childhood¹, replacing the exciting and joyful experiences of growing up with multiple clinic visits, appointments with various specialists, and countless tests — the so-called ‘diagnostic odyssey’. And, despite around 80% of rare diseases having a genetic cause¹, the reality is that, after all these tests, less than 50%^3-5 of individuals with rare conditions receive a genetic diagnosis. Devastatingly, 30% of children with a rare disorder die before their fifth birthday¹.

For the individuals with rare diseases, and their families, there is a pressing need to provide a genetic resolution to end their diagnostic odyssey. In this blog, discover how hope may lie in the form of Oxford Nanopore sequencing^*.

Longer reads, higher hopes

Over the last decade, short-read sequencing, be it targeted, exome, or, increasingly, whole-genome analyses, has been introduced into the clinic to tackle rare disease diagnosis. This has increased the diagnostic yield for a range of disorders. Yet, due to inherent limitations of the technology, such as its read length restrictions, many disease-causing variants have remained hidden.

An increasing number of studies (several referenced in this 2025 review) have demonstrated that Oxford Nanopore technology holds the potential to address the diagnostic odyssey head-on, partly because it can produce reads of any length, including ultra-long (megabases). This provides a significantly greater capacity to identify clinically relevant structural variants⁶. The ability to detect methylation information, and the speed at which you can obtain results with Oxford Nanopore sequencing, also combine with the power of long reads to provide a platform capable of producing a more holistic picture of the genome.

It is for these reasons that clinician researcher Danny Miller boldly claims ‘long-read sequencing will fundamentally change clinical genetic testing within 5 years’, ‘even if the cost of generating other types of data falls to $0’⁷.

Unleashing the technology’s potential

With that in mind, let’s explore the latest in that growing body of published research showing how Oxford Nanopore sequencing holds the potential to increase diagnostic yield for rare diseases in the future. This short list only reflects what has been published over the past few months, and demonstrates the variety of variants, disorders, and ultimately questions, that the technology could resolve.

1. Negi et al. Advancing long-read nanopore genome assembly and accurate variant calling for rare disease detection. AJHG (2025).

Researchers at the University of California, Santa Cruz, explored how nanopore reads could resolve disease-associated variants inaccessible to short-read sequencing, to bridge the diagnostic gap. They sequenced each sample on a single PromethION Flow Cell (~36x depth). With 26% (11/42) of cases genetically resolved with nanopore sequencing, versus 19% (8/42) with short-read sequencing, the team emphasised the ‘potential to enhance diagnostic yield for rare monogenic diseases, implying utility in future clinical genomics workflows’.
Take-home: accessing previously inaccessible areas of the human genome using Oxford Nanopore technology represents a potential breakthrough for advancing rare disease diagnosis.

2. Kamolvisit et al. Singleton rapid long-read genome sequencing as first tier genetic test for critically ill children with suspected genetic diseases. EJHG (2025).

This proof-of-concept study in a real-world clinical setting explored the potential use of Oxford Nanopore sequencing as a first-tier genetic test for critically ill children in intensive care. Having unsuccessfully provided a molecular diagnosis for two individuals in their cohort through exome sequencing, they applied nanopore technology to all 18 children. The team identified causative pathogenic variants in 11/18 individuals. Nanopore sequencing also revealed greater genomic information, leading to the reclassification of single nucleotide variants (SNVs) in three instances.
Take-home: with further development, whole-genome nanopore sequencing has potential utility as a first-tier diagnostic approach.

3. de Boer et al. Nanopore long-read sequencing as a first-tier diagnostic test to detect repeat expansions in neurological disorders. Int. J. Mol. Sci. (2025).

Looking to establish a workflow for analysing short tandem repeats (STRs) in neurological disorders, the researchers created a custom panel sequencing nine genes associated with spinocerebellar ataxia and fragile X syndrome. Applying their ‘raw data to report’ nanopore workflow to samples from 12 affected individuals, they achieved concordance with results from current diagnostic tests for 22/23 STRs. Notably, the ability to concurrently detect SNVs, indels, and methylation offers the potential for a ‘one-test-fits-all' solution.
Take-home: nanopore technology shows similar performance to current testing methods in detecting causal STR expansions, with additional variant and methylation information that offers the future potential to improve prognosis and diagnosis.

Figure: Variant interpretation report (VIP) which could be used in a clinical setting. The report shows results for targeted STRs (a), including the interpretation (far right column) and detailed results for a specific variant (b) — here being the ATXN3 repeat. Figure taken from de Boer et al. 2025 and made available under Creative Commons License (creativecommons.org/licenses/by/4.0). The pre-print on MOLGENIS VIP provides further details on the pipeline.

4. Sinha et al. Long-read sequencing enhances pathogenic and novel variation discovery in patients with rare diseases. Nat. Comm. (2025).

Ahmad Abou Tayoun and colleagues applied a whole-genome nanopore sequencing workflow to a research cohort of undiagnosed patients. For 51 individuals with negative testing using short-read sequencing, additional potential diagnoses were uncovered in nearly 10% of cases (5/51). They also uncovered a novel methylation signature that could be incorporated into routine genetic testing for spinal muscular atrophy (SMA).
Take-home: in future, nanopore data could increase diagnostic yield in individuals with prior negative short-read testing.
Read Dr. Tayoun’s story on developing a ‘unified platform for clinical genetic testing’.

5. Rudaks et al. Targeted long-read sequencing as a single assay improves the diagnosis of spastic-ataxia disorders. Ann. Clin. Transl. Neurol. (2025).

Researchers applied targeted Oxford Nanopore sequencing to investigate genetically unresolved cases of spastic-ataxia. Causative variants were identified in 14/34 (41%) samples, including 9/23 (39%) samples that were undiagnosed after prior short-read sequencing.
Take-home: one targeted nanopore sequencing assay could potentially ‘streamline the testing pathway [for spastic-ataxia] by capturing all known genetic causes in a single assay’.

Figure: Overview of genetic findings for the research cohort of 34 individuals with spastic-ataxia spectrum disorders, including those with prior negative-genetic testing, and those who were testing naive. Figure taken from Rudaks et al. 2025 and made available under Creative Commons License (creativecommons.org/licenses/by/4.0).

6. Lam et al. The implementation of genome sequencing in rare genetic diseases diagnosis: a pilot study from the Hong Kong Genome Project The Lancet: Regional Health (2025).

In this prospective pilot study undertaken by the Hong Kong Genome Project, the potential diagnostic yield of short-read genome sequencing, complemented by Oxford Nanopore sequencing, was assessed for rare genetic disease samples. With short-read sequencing, the researchers successfully identified causative variation in 24% (125/520) samples. The subsequent application of nanopore sequencing to 21 samples with unresolved genetic findings identified the causative variation in all cases.
Take-homes: at population level, nanopore data shows potential for broader clinical application in rare diseases.

Transforming human health

Let’s finish by looking at the preliminary results from the first study using Oxford Nanopore sequencing in a large, independent, investigator-led clinical research initiative in rare diseases.

In the BEACON project, the team are exploring how Oxford Nanopore sequencing could potentially improve the diagnostic accuracy of rare, undiagnosed genetic disorders. They are sequencing research samples from a total of 1,000 individuals from a range of high-level rare disease categories. All the samples come from individuals who have remained unresolved after short-read sequencing. Results from 141 cases revealed 34 (24%) instances where the underlying genetic basis was resolved.

Looking back at their short-read data, ‘there's no way in the world I would have picked this up from what we did before’ said Wendy Chung, clinical and molecular geneticist at Boston Children’s Hospital, presenting the data at the Annual Clinical Genetics Meeting (ACMG) 2025.

The growing body of evidence sends a clear message — the potential future of rare disease diagnosis is rapidly unfolding, are you ready to be a part of it?

Watch Wendy Chung's ACMG talk

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*Oxford Nanopore Technologies products are not intended for use for health assessment or to diagnose, treat, mitigate, cure, or prevent any disease or condition.