19.06.2023 – 09:12
Oxford Nanopore Technologies
Oxford, England (ots)
As part of a pilot project, four German competence centers are provided with sequencing reagents from Oxford Nanopore Technologies. Long-read sequencing technology is intended to enable higher diagnosis rates for patients.
Oxford Nanopore Technologies plc. (Oxford Nanopore) announced a research collaboration agreement with the Clinical Long-Read Genome Initiative (lonGER). This is an initiative to evaluate clinical and scientific applications of nanopore sequencing with the aim of gaining a better understanding of rare diseases.
The scientists from four German universities – Uniklinik RWTH Aachen (Ingo Kurth, Florian Kraft); Institute for Medical Genetics and Human Genetics, Charité – Universitätsmedizin Berlin and Berlin Institute of Health in the Charité (BIH) (Nadja Ehmke, Janine Altmüller, Manuel Holtgrewe); Hannover Medical School (Bernd Auber, Gunnar Schmidt) and the University of Tübingen (Tobias Haack, Stephan Ossowski) – will test Oxford Nanopore’s technology to characterize genetic diseases. The technology allows DNA fragments of any length (from short to extremely long) to be sequenced. The universities will examine a multi-centre patient cohort with rare diseases that have not yet been deciphered, including neurological diseases, neurodevelopmental disorders and imprinting diseases.
In the two-year pilot study, the advantages and possible use of Nanopore genome sequencing in clinical practice in Germany are to be tested, with the long-term goal of using the results of the pilot study as a blueprint for implementation at other sequencing centers.
Sequencing is performed at the various sites using PromethION P2 and P24 sequencers. The P24 can analyze up to 24 human genomes simultaneously, enabling high sample throughput and fast data analysis. In this way, researchers can simultaneously identify different classes of disease-causing variants in the genome, including single nucleotide variants (SNV), structural variants (SV) and methylation alterations, using a single method.
The study builds on structured diagnostic processes that were established and evaluated in the previous TRANSLATE-NAMSE study. More than 200 physicians and scientists were involved in this three-year prospective study in Germany. The study aimed to assess the clinical value of exome sequencing using short-read sequencing methods for people living with extremely rare diseases.
More comprehensive data on rare diseases
Oxford Nanopore’s technology is ideally suited to lonGER’s goal of improving the analysis of the causes of rare diseases by now also being able to sequence very long DNA fragments – in contrast to the “short-read” sequencing used up to now.
This has been shown to offer specific advantages over short reads when researching genetic diseases. The generation of extremely long reads allows genetic variants to be assigned to their haplotype, which is important for clinical interpretation of the genome in relation to the identification of compound heterozygous variants and their parental origin.
Nanopore sequencing can also resolve so-called “dark” regions of the genome that were previously inaccessible with short-read sequencing, but which account for up to 8% of the genome and may contain clinically relevant variants.
Oxford Nanopore’s scalability with plug-and-play sequencing equipment and ready-to-use workflows makes it easy to scale to other sites. In addition, the research consortium benefits from additional flexibility through the possibility of sequencing the samples in the order in which they arrive without having to create batches.
Gordon Sanghera, CEO, Oxford Nanopore Technologies:
“We look forward to working with this diverse, dedicated team dedicated to translational research into rare diseases.
Oxford Nanopore’s read-any-length sequencing technology shows that comprehensive insights across the entire genome can be gained from previously unanalyzed regions.
Together with the lonGER consortium, we can realize the potential of nanopore sequencing, advance breakthrough discoveries and transform the lives of those affected by these rare diseases.”
Bernd Auber, Team Leader Hereditary Risk, Institute for Human Genetics, Hannover Medical School:
“Long-read sequencing technology is overcoming the limitations of short-read sequencing. Scalable sequencing technology with long-read capability can potentially improve the accuracy and completeness of genomic analysis, thereby revealing new disease mechanisms of rare diseases.
For example, in critically ill children, comparing genetic variants using rapid sequencing of long reads could be very helpful in both diagnosis and the choice of individualized therapy for pediatric ICU patients.”
Nadja Ehmke, Head of the Department of Clinical Genomics, Institute for Medical Genetics and Human Genetics, Charité – Universitätsmedizin Berlin:
“We are convinced that the integration of genome sequencing with long reads into everyday clinical practice will help us to further close the diagnostic gap in patients with monogenic diseases.
For the first time it is possible to sequence complex regions, determine structural variants and carry out haplotype analyses. In addition, we can detect methylation patterns. This enables us to better understand disease mechanisms and develop therapies.”
Tobias Haack, Deputy Institute Director, Institute for Medical Genetics and Applied Genomics, University of Tübingen:
“In addition to improved accuracy in detecting genomic changes, the organizational structure of our consortium and unified processes will create the data background for the clinical classification of etiologically unclear variants and gene-disease associations.
The translation of this multicentric concept into reliable diagnoses is supported by established networks and the combined expertise of multidisciplinary teams of clinicians, geneticists and translational researchers.”
Florian Kraft, Head of the Long-Read Sequencing Group, Institute for Human Genetics and Genome Medicine, University Hospital RWTH Aachen:
“We are excited about the genomic analysis of rare disease patients using Nanopore sequencing and believe it can shape the future of research and diagnostics in this area.
The new V14 chemistry in combination with the PromethION P24 is a real game changer in the application of long-read sequencing in everyday clinical practice.
We see a huge improvement in fidelity and a dramatic drop in DNA input along with approximately 50x genomic coverage from a single PromethION flow cell.
The improved data quality will make it easier to identify the pathomechanisms of rare genetic disorders.”
About Oxford Nanopore Technologies
Oxford Nanopore Technologies believes in serving society as a whole and aims to create analytical capabilities that are accessible to everyone, anytime, anywhere. The company has created a new generation of Nanopore sensor technology that makes high-quality, real-time DNA and RNA analysis scalable and accessible to all. The technology is used in more than 120 countries to understand the biology of people and diseases such as cancer, plants, animals, bacteria, viruses and entire environments. Oxford Nanopore Technologies products are intended for molecular biology applications and not for diagnostic purposes. www.nanoporetech.com
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