In February we are observing Rare Disease Month, a time to shine a light on the experiences of rare disease patients and their families. At PacBio, we are committed to advancing technology that can help alleviate the diagnostic challenges associated with rare disease.
This year, we kick off Rare Disease Month by showcasing the incredible work of Radboudumc, which is leveraging HiFi sequencing to provide insights for patients and help transform rare disease diagnostics.
The diagnostic odyssey of rare disease
For families affected by rare disease, the journey to a genetically confirmed diagnosis — often called the “diagnostic odyssey” — can take years. Many patients undergo a complex and costly series of traditional testing, which may include karyotyping, fluorescence in situ hybridization (FISH), genomic microarrays, Southern blotting, multiplex ligation-dependent probe amplification (MLPA), and short-read whole exome or whole genome sequencing. With such sequential testing, each negative result increases the cost and time spent on this diagnostic odyssey. The long wait for answers can be frustrating and, in many cases, delays access to appropriate medical interventions.
A turning tide for rare disease diagnostics
Increasingly, researchers and clinicians are turning to long-read genome sequencing as a comprehensive solution to streamline the diagnostic process by potentially consolidating these legacy assays onto a single test. Because its highly accurate long reads grant access to certain regions of the genome and types of variants that may not be reached by other technologies, PacBio HiFi sequencing is progressively being considered as a single genomic alternative to this battery of testing. Radboud University Medical Center (Radboudumc) is at the forefront of this shift, actively initiating the potential implementation of HiFi sequencing into their clinical pathway.
HiFi sequencing identifies 93% of pathogenic variants
As an initial step of potentially bringing HiFi sequencing to the clinic, Radboudumc researchers assessed its readiness in a study published last month in the American Journal of Human Genetics. This study, led by Professors Alexander Hoischen, Christian Gilissen, and Lisenka Vissers, examined 100 rare disease patient samples with 145 clinically-relevant germline variants that are difficult to detect using short-read sequencing and conventional testing methods.
The results were outstanding: At 30x coverage, HiFi sequencing successfully identified 93% of pathogenic variants, including complex structural variants, single nucleotide variants (SNVs) or indels in homologous/paralogous sequences, and expansions of short tandem repeats, that were missed by other methods. Even more remarkable, the researchers show that 90% of all automatically called variants could still be detected at 15x HiFi coverage.
These findings underscore the promise of HiFi sequencing for clinical adoption, reducing the need for sequential testing and helping to enable potentially faster, more accurate diagnoses.
Radboudumc’s commitment to transforming clinical diagnostics
Building on the success of this study, Radboudumc is scaling up its efforts to integrate HiFi sequencing into their routine clinical workflow. They have committed to sequencing 5,000 genomes using their Revio fleet with SPRQ chemistry, with formal workflow implementation expected this summer. The new SPRQ chemistry enables two 20x human genomes per SMRT Cell, which allows for increased throughput and scale. As evidence of their momentum, nearly 1,000 genomes have already been sequenced from the project’s initiation in August 2024.
To further support this effort, Radboudumc has streamlined its automated library prep workflows on the PacBio Revio system. By leveraging automated library preparation and expanding sequencing throughput capabilities, their workflow will significantly increase the potential diagnostic findings efficiently and with more accessibility for rare disease patients.
What HiFi sequencing can do for the clinic
The possible clinical adoption of HiFi sequencing has profound implications for rare disease diagnostics. A single, comprehensive assay could eliminate the need for multiple, sequential diagnostic tests, reducing both the cost and time required to reach a diagnosis in the long run. More importantly, an accurate and timely genetic diagnosis can open the door to targeted treatments, better patient management, and improved outcomes.
Dr. Alexander Hoischen, Professor of Genomic Technologies at Radboudumc, emphasizes the impact a comprehensive genomic test could have on rare disease patients:
“A lot of our rare disease patients remain undiagnosed, despite quite extensive testing. While exome sequencing and other legacy tests are the standard of care, they don’t provide answers for more than half of patients. However, from technical studies that we and others have performed, we now know that HiFi genomes find many more variants, in particular structural variants and repeat expansions, where other technologies fail to give us the full set.”
Dr. Hoischen’s team has a particular focus on rare immune diseases, where genetic insights can be especially impactful:
“The beauty to finding a genetic answer to a rare immune disease is that a lot of these diseases are actionable, so our colleagues in immunology at Radboudumc and other experts can begin their work on the case straight away.”
The power of HiFi sequencing
The power of the technology driving the potential adoption of HiFi sequencing into clinical practice is clear: its comprehensive variant detection, scalability, and operational efficiency instill unwavering confidence in its transformative clinical capabilities. Its highly accurate comprehensive coverage of the genome allows for the capture of large and challenging genomic regions and resolve complex structural variants, repetitive sequences, and segmental duplications linked to rare disease, as well as provide phasing information that traditional technologies often miss.
Additionally, simultaneous methylation detection of 5mC is included for free with every sequencing run, providing a layer of epigenetic information without any additional library prep. This enhanced resolution into the genome is critical for identifying rare or novel pathogenic variants in rare disease, where small changes can have significant impact on disease etiology or progression.
This exceptional performance is equipped for the scalability needed for clinical implementation, with SPRQ chemistry enabling a 33% increase in data output per SMRT Cell, from ~90 Gb to 120 Gb of HiFi reads. This advance powers each Revio system to generate up to 2,500 human whole genomes per year at a cost of ~$500 per genome at 20x coverage. This throughput coupled with streamlined protocols and automation, enables the possible adoption of HiFi sequencing into existing clinical workflows as a first-tier assay with the potential to replace multiple traditional diagnostic methods.
A pivotal moment in clinical genomics
As Radboudumc continues its mission to sequence 5,000 genomes and make transformative progress on diagnostic workflows, the widespread adoption of HiFi sequencing for rare disease clinicians is on the horizon. This is now made even more accessible with the launch of the Vega benchtop system, further broadening the reach of high-quality clinical genomics into individual labs.
Dr. Hoischen sees this as a pivotal moment in clinical genomics:
“There’s great promise in this type of genomics-informed clinical practice that can be thought of as a prototype to personalized medicine. From seeing the completeness of HiFi genomes, I have great hope that there are many discoveries to come for rare diseases.”
The future of rare disease genomics
This demonstrated ability to detect previously inaccessible clinically-relevant genomic variants and deliver insights on rare disease cases showcases the revolutionary power of HiFi technology and its potential pathway into clinical practice. As Radboudumc leads the charge in bringing this technology to rare disease patients, the future of rare disease diagnostics looks brighter than ever.
This Rare Disease Month, PacBio stands with the rare disease community and is proud to support and highlight the pioneering efforts of Radboudumc. Stay tuned for more stories throughout the month that showcase how HiFi sequencing is transforming rare disease research.
Learn more about how HiFi sequencing is powering rare disease research at pacb.com/rare-disease.