Long-read sequencing improves clinical diagnostics
In response to the growing demand for more comprehensive, sensitive, and rapid diagnostic methods, long-read sequencing is emerging as a revolutionary technology. This advanced sequencing technique offers unparalleled detection of genetic variants and holds significant promise for improving clinical diagnostics, patient care and clinical outcomes.
Long-read sequencing can detect all types of genetic variants, including complex structural variants often missed by traditional methods. It has great potential to improve diagnostics of a range of diseases (see text box at the bottom). The expectation is that within the next few years, several clinical tests based on other methods will be replaced by long-read sequencing. Additionally, long-read sequencing holds promise for the development of new clinical tests for genetic variants that cannot be analyzed today.
“There is a continuous demand from healthcare for more comprehensive, sensitive, rapid, yet cost-effective, diagnostic methods. Within hematology, targeted long-read sequencing and transcriptome sequencing can offer streamlined detection of rare fusion genes and other genetic variants”, says Panagiotis Baliakas, senior consultant in hematology and clinical genetics and Director of Clinical Genomics Uppsala.
Applications within rare diseases and infectious diseases
Beyond hematology, there are many applications of long-read sequencing for rare diseases, other types of cancer, and infectious diseases.
“The Clinical Genomics platform was recently involved in a study highlighting the power of long-read sequencing to detect complex genomic rearrangements, such as repeat expansions, that cannot be resolved with short-read sequencing. Such rearrangements often play a role in rare inherited diseases. The introduction of long-read sequencing-based tests is expected to increase the diagnostic yield for this patient group”, says Marie-Louise Bondeson, clinical laboratory geneticist and leader of the work focusing on inherited diseases at Clinical Genomics Uppsala.
Long-read sequencing was also used for lineage determination during the SARS-CoV-2 pandemic, and offers rapid testing for other clinical microbiology applications. Clinical Genomics Uppsala is also involved in a collaborative project investigating the role of viruses in cancer etiology with an in-house developed long-read sequencing-based method. This method enables identification of virus type, lineage and specific genomic features that may influence cancer development.
Clinical Genomics Uppsala and NGI are pioneers in long-read sequencing-based clinical diagnostics
Clinical Genomics Uppsala coordinates the work on long-read sequencing at the national Clinical Genomics platform. This work is a collaboration with the other nodes at the platform, the National Genomics Infrastructure (NGI) and Genomic Medicine Sweden (GMS). Clinical Genomics Uppsala has a long-standing collaboration with long-read sequencing specialists at the Uppsala Genome Center (part of NGI). This collaboration comprises joint development work, shared staff, equipment, and organization of a bi-annual international conference on long-read sequencing.
“Ten years ago, we jointly implemented one of the first long-read sequencing-based clinical tests globally. This test analyzed mutations conferring therapy resistance in a fusion transcript in chronic myeloid leukemia. To select the most appropriate treatment”, says Adam Ameur, associate professor and bioinformatician at Uppsala Genome Center.
NGI is also constructing a long-read whole-genome dataset for Sweden’s population, as part of the Genome of Europe project. It will consist of data from at least 1,000 individuals and will be an important reference dataset for future clinical diagnostics.
Different long-read sequencing platforms offer distinct advantages for clinical use
Long-read sequencing technologies have undergone rapid development in recent years, being selected as the method of the year by Nature Methods in 2022. The clinical potential is highlighted by investments in both Oxford Nanopore Technologies (ONT) and PacBio instruments by several university hospitals and Clinical Genomics platform nodes.
“Various long-read sequencing technologies have unique features, making them suitable for specific clinical applications. For example, the PacBio Revio is a high-throughput instrument that generates high-quality sequence data. This is important for the accurate detection of SNPs and indels, and essential for the replacement of short-read technologies. ONT offers real-time analysis and can generate rapid results in applications where time is critical, explains Ida Höijer, senior research engineer at Clinical Genomics Uppsala and Uppsala Genome Center.
Uppsala University Hospital and Clinical Genomics Uppsala have recently acquired a new PacBio Revio instrument. A launch event for the new instrument will be arranged at the Rudbeck Laboratory on May 20. Read more and register here
Read more
- Detection of complex structural variants in rare disease (Eisfeldt et al, Genome Res. 2024)
- Method of the year 2022: long-read sequencing (Marx, Nature Methods 2022)
- Early long-read sequencing-based detection of fusion gene resistance mutations (Cavelier et al, BMC Cancer, 2015)
Examples of long-read sequencing tests expected to be introduced in the clinic within the next few years
- Whole-genome long-read sequencing is a comprehensive test to detect all types of genetic variation, including complex structural rearrangements and variants in homologous regions, and is expected to replace short-read sequencing in some rare disease diagnostics.
- Analysis of repeat expansions that are important to assess disease severity and progression in, for example, Huntington’s disease and Fragile X Syndrome. Targeted long-read sequencing is expected to provide more accurate measurements than traditional methods, such as PCR or fragment analysis.
- Targeted and transcriptome long-read sequencing in leukemia is expected to replace current methods, such as short-read sequencing, chromosome analysis and Fluorescence In Situ Hybridization (FISH), and result in more comprehensive variant detection and faster clinical workflows.
- Whole-genome and targeted sequencing of microbes for outbreak surveillance, species determination or resistance typing.
These projects are carried out with support from MedTech4Health, the Regional Cancer Centrum, Genomic Medicine Sweden, and the Ministry of Social Affairs. In addition to core facility funding for the Clinical Genomics platform.
Photo: Mikael Wallerstedt
