A rare disease can be an immense burden on patients and families, especially when it comes to childhood conditions. The path from symptoms to diagnosis to treatment is often long and challenging, making the journey even more difficult.
In honor of these challenges and Rare Disease Month, we are highlighting the latest advancements in research to shine a light on rare diseases and offer hope to affected families. For the second installment in our series, we spoke with Dr. Tomi Pastinen, director of the Genomic Medicine Center at Children’s Mercy, Kansas City. A leader in pediatric rare disease research and care, Dr. Pastinen shares how his team uses PacBio sequencing in their work with pediatric rare disease, and how the evolution of PacBio technology has transformed their research with the ultimate goal of shaping the future of clinical care.
Pioneering pediatric rare disease research
At the Genomic Medicine Center at Children’s Mercy, researchers are redefining how pediatric rare diseases are diagnosed and treated. A current focus of their research program is to use more comprehensive HiFi genome sequencing to help determine genetic causes of critical rare disease cases that often remain unresolved with traditional clinical testing. Many of these conditions, including movement and muscular disorders like infant hypotonia, ataxias, and dystonias, cannot be detected with standard short-read sequencing. By incorporating HiFi sequencing into their approach, Dr. Tomi Pastinen and his team aim to improve potential diagnostic findings and help provide life-changing answers for families navigating rare disease.
How commitment to advanced long-read sequencing technology leads to better insights
Children’s Mercy Genomic Medicine Center began their HiFi sequencing journey with a Sequel IIe system five years ago. As their research evolved, so did their technology. Today, the team operates five Revio systems, significantly expanding their capacity for high-resolution genomic analysis.
With HiFi sequencing’s growing capabilities, the team can now examine entire genomes at an unprecedented level of detail—offering far more comprehensive insights than short-read exome sequencing ever could.:
“We felt that the diagnostic rate for rare disease was low partially because we were not sequencing the whole genome and not all the types of variation that were in the genome. With PacBio we could initially resolve structural variants better, later on – methylation, and now even personal assemblies, allowing us to see the full genome of each child we sequence.”
Moving to multiomics
As PacBio technology has progressed, so has research at Children’s Mercy. HiFi sequencing has opened new doors beyond DNA, allowing researchers to explore epigenetics and transcriptomics for deeper insights into rare diseases. HiFi sequencing includes free, simultaneous methylation detection of 5mC with every sequencing run, without any additional library prep.
Methylation analysis has become an important tool for the Genomic Medicine Center. Recognizing its potential, Dr. Pastinen’s team expanded their focus on methylation in recent years, using it to analyze genomes where DNA sequencing alone couldn’t pinpoint potential causal variants.
“We tried to find methylation variation that was very unusual and could pinpoint towards a disease gene. And we actually did find a few cases through methylome variation that were unsolved before just by looking at nucleotide variation.
There are about 12 rare diseases that are caused by methylation defects. Those are detected concurrently with sequencing, but beyond that, we are using it as an R&D tool to find new types of variation and are developing pipelines to identify very rare methylation patterns in unsolved disease of children.”
The recent introduction of PacBio SPRQ chemistry on the Revio system only further enhances these capabilities by improving 5mC methylation detection accuracy and extending to 6mA calling, a marker of open chromatin in the Fiber-seq method.
Harnessing the power of RNA sequencing with Kinnex kits
The addition of HiFi RNA sequencing has also dramatically improved their rare disease research, especially for genetic variants that alter RNA structure and isoforms in ways that are difficult to predict.
Dr. Pastinen and his team began with PacBio Iso-Seq RNA sequencing, making significant progress in understanding these complex cases. But the introduction of Kinnex RNA sequencing—combined with the increased throughput of the Revio system—has expanded their research potential even further.
Dr. Pastinen is hopeful that the application of Kinnex and the throughput advancements on the Revio system have the potential to shed light on a significant number of unsolved cases, offering new hope for families searching for answers.
Changing the rare disease landscape with HiFi sequencing
HiFi sequencing is already reshaping the way pediatric rare diseases are studied and understood. As Dr. Pastinen explains:
“The potential diagnostic findings are just shy of 10 percentage points higher than it was with earlier genomic tests. The number of genomic tests is reduced because in the past, kids received multiple sequential tests, like sequencing, karyotyping, and microarray testing. It’s all now bundled into one HiFi genome sequencing test, so it is changing the standard of care for these critically ill newborns and children. At present, we are only sequencing critical cases, but hope to be able to offer it to outpatients in the future, which are a much larger pool of rare genetic disease.”
As discussed in last week’s Rare Disease Month blog, the “diagnostic odyssey” can drag over a span of several years. However, Dr. Pastinen’s research offers hope that this timeline could be significantly shortened for many families.
“The greatest insight we are experiencing from PacBio sequencing in the pediatric rare disease setting is that for the many cases with repeat expansion disorders, complex chromosomal aberrations, and complex structural variants that previously took years to solve, and now we can get the answer in two to three weeks from a single test.”
The future of rare disease diagnosis
Driven by increases in throughput and multiomic advances in HiFi sequencing, the landscape of rare disease research is rapidly evolving. As PacBio continues to innovate, we remain committed to supporting researchers in providing insight and hope to families affected by rare disease.
As Rare Disease Month continues, it is clear that institutions like Children’s Mercy are pioneering the future of rare disease research and care. We look forward to ongoing collaborations with this community and the hope it provides for the future of rare disease outcomes.
Learn more about how HiFi sequencing is playing a part at pacb.com/rare-disease.