European Consortium Will Advance Long-Read Sequencing in Clinics
A new consortium aims to make long-read sequencing routine in clinical diagnostics across Europe.
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A pan-European consortium will redefine how genetic diseases are diagnosed.
The recently launched European Long Read Innovation Network (ELRIN) consortium, led by the University of Tübingen, features 21 labs across 11 countries that will work together to set new standards for clinical genetic testing in Europe.
The UK-based company Oxford Nanopore Technologies announced that it has partnered with ELRIN to help bring nanopore whole-genome sequencing (WGS) – a third-generation sequencing platform – into wider clinical practice for the diagnosis of rare disease, familiar cancers and other areas of unmet need in healthcare. By integrating long-read sequencing into routine diagnostics, ELRIN promises more precise, timely and comprehensive genomic insights, helping to improve patient care.
Technology Networks recently interviewed Cerissa French, sales director, clinical sales specialists, EMEAI at Oxford Nanopore Technologies, to discuss the limitations of legacy sequencing technologies, how next-generation sequencing (NGS) is being used in clinical practice and the need for ELRIN.
French highlighted how ELRIN leverages long-read sequencing to capture complex structural variations and epigenomic modifications, improving diagnostic rates for rare diseases and advancing oncology applications.
What are some of the limitations of legacy sequencing technologies in clinical practice?
Cerissa French (CF):
When using legacy sequencing technologies, it can be difficult to get the complete picture. There are parts of the genome that short reads simply can’t map – for example, long repeat regions that are critical for diagnosing certain rare diseases. These technologies are also very one-dimensional in terms of the data they produce. Native base modifications can’t be interrogated in the same test, meaning an additional assay is required to generate methylation data, which adds both time and cost.
Another key limitation is the need to batch samples to make the economics work. This means samples are sitting and waiting to be analyzed, delaying results that could be used to guide patient care.
MC:
Can you discuss the use of NGS in clinical practice at this stage? Why is it challenging to achieve wider incorporation?
CF:
NGS is already quite widely adopted in many clinical labs, although this varies by country. Today there are many targeted NGS panels deployed routinely in the clinic, for example, in comprehensive genomic profiling of tumors, HLA region testing and for some single gene testing. The adoption of WGS is not as widely adopted but is increasing. The full benefits of whole-genome analysis, particularly in oncology diagnostics, are still being evaluated.
The biggest challenge to wider adoption, in my opinion, is the lack of understanding by clinicians as to the benefits of NGS – such as enabling more comprehensive insights in a single assay – and the fact that many clinicians aren’t being trained sufficiently to incorporate genomic medicine into their practice.
However, this is changing and I’m hearing more and more that it’s the clinicians pushing the laboratories for NGS analysis, including long-read read sequencing, once they know the benefits it can bring.
MC:
Can you explain why there is a need for ELRIN and what it aims to achieve?
CF:
The rare and inherited disease community is becoming increasingly aware of the need for sequencing technologies that can capture any read length to improve diagnostic rates. Currently, around half of patients with a rare and inherited disease are still without a diagnosis. Since the application of long read sequencing in WGS for rare disease testing is still in its early days, there are some gaps in enabling a seamless adoption.
The ELRIN consortium is committed to setting new standards for clinical genetic testing, leveraging any-read length sequencing and ensuring that the tools needed for adoption are accessible and practical for clinical use. This involves creating a robust infrastructure for access to and sharing reference data, procedures and analyses. It is also dedicated to building a sustainable, future-proof framework that incorporates any-read length sequencing into routine clinical practice, ensuring long-term benefits for healthcare systems across European member states.
MC:
What will the day-to-day operations of the consortium look like, and which countries will be involved?
CF:
Currently there are 21 countries participating in ELRIN with more looking to join.
Ideally, we would have representatives from every country in Europe. The consortium, of over 75 individual members, currently meets online monthly to discuss specific topics around the handling of samples with respect to the benchwork and bioinformatics analysis, plus other relevant topics of the field.
New applications using long-read data, such as
leveraging methylation and interesting cases, are presented and discussed. The
first in-person kick-off meeting will take place this April (2025) and will
catalyze the collaboration required for a successful initiative.
MC:
What are your hopes for the future of NGS in clinical diagnostics?
CF:
I hope that technologies enabling a more comprehensive view of the genome will close the diagnostic gap for people living with rare diseases and that a better understanding of genomics and epigenomics might lead to new therapies for many diseases that are still without treatment.
We have already come a long way, but there is still a way to go before we realize the full potential of third-generation sequencing technologies.
In the longer term, I hope that we can leverage genomics for preventative health, stopping people from getting sick in the first place or catching things early enough that their chances of survival are massively increased.
