Adopting new technologies in scientific research can feel like a leap of faith. But imagine if that leap opens the door for your lab to help provide answers for patients with rare diseases. As labs around the globe continue to innovate, new approaches are redefining what’s possible for families who are searching for hope and solutions.
In this exclusive interview, we sat down with Professor Diana Baralle, President of the UK Clinical Genetics Society and leading researcher at the University of Southampton, about her team’s experience implementing PacBio RNA sequencing with Kinnex in their research. Dr. Baralle shares how this technology has enhanced her research in functional genomics, driving progress in the diagnosis of rare diseases. She also discusses the creation of an international working group to study the potential of RNA analysis in diagnostic settings to help accelerate the integration of full-length RNA sequencing into research protocols.
Q: Can you give us a brief overview of your research and your key focus areas?
Professor Baralle: I am a clinical researcher, which means I work for both the UK National Health Service as a consultant in clinical genetics seeing patients with rare disease, and as a Professor of Genomic Medicine undertaking research at the University of Southampton, Faculty of Medicine. I have a number of other roles including leading the genotype-phenotype research network at Genomics England and as President of the UK Clinical Genetics Society. My research group is an internationally renowned translational research group that drives forward functional genomics to improve clinical diagnosis and understand mechanisms of disease. We investigate novel causes for rare disorders and in particular the role of RNA, the transcriptome, and splicing in disease.
Q: What initially motivated you to explore RNA for rare disease research? What has been your experience with traditional RNA sequencing?
During my doctoral studies I investigated the NF1 gene and found that over half of the mutations causing disease affected RNA splicing. This led me to research more on the splicing process, which is a very complex but important mechanism in gene processing. During this time, sequencing technologies really took off and I looked to combine my work on this molecular mechanism with clinical utility. This meant researching all aspects of diagnostics, including what was being missed by DNA sequencing alone, the best ascertainment of patient cases, what sequencing technology to use, how to embed the testing and results into a health service, and very importantly, the best bioinformatic pipelines to use when interpreting the data.
It is important to make diagnoses for patients in order to make decisions for appropriate management and treatment, as well as ending what can be a grueling diagnostic odyssey.
Different RNA sequencing technologies have pros and cons for diagnostic application. Whilst short-read technology was well established and relatively easy to use, we found that some diagnoses were being missed when compared to long-read technology.
Q: How does isoform-level RNA sequencing with Kinnex kits contribute to better understanding of variants of uncertain significance and their potential role in pathogenicity?
We are still developing methods to identify new events in patient samples, but RNA sequencing with PacBio Kinnex kits certainly has been helpful in better understanding their significance. Full-length RNA sequencing with long-read technology can aid in the identification of alternative splicing events that can be difficult to detect using short-read technology, including intron retention events, genes with low mappability, and quantification of isoforms. It also allows for the detection of novel transcripts, which can be difficult to detect using short-read technology.
The Kinnex kit has a similar gene pick-up rate to short-read RNA-Seq so it’s a good alternative, especially with greater read depth. The final file size is compact, which is also a big advantage.
With short-read RNA sequencing in general, the disadvantage is that with a lot of data, discovering new events in patient samples with no candidate genes or variants becomes tricky. In contrast, long-read data excels at identifying a large number of transcripts that are unannotated and potentially unique to each patient, which is a significant step in determining the causal mechanisms of rare disease.
Q: What are some barriers to widespread adoption and potential clinical implementation of long-read RNA sequencing to help solve rare disease cases?
For a test to make it from development to an official test directory, we have to prove utility with large-scale testing. From my own research and collaborating with Genomics England looking at thousands of cases, we now have a good evidence base that new diagnoses can be made with RNA analysis. A barrier to widespread adoption has been the development of SOPs and reporting, but we have teamed up with a set of international researchers to work through some of these issues together. With this international working group, we plan to propose guidelines and potential plans for full clinical integration.
Q: How can RNA sequencing at full-length isoform resolution lead to potential treatments for rare disease cases?
Only once we can determine the mutation mechanism for a disease can we work on a potential therapeutic avenue. There has been significant success in gene replacement therapy recently by correcting genetic messages or abnormal splicing that occurs in some diseases. This method, called antisense oligonucleotide (ASO) therapy, can be customized to target the specific genetic defects in each patient, offering the potential of personalized treatment.
With the large number of samples we have analysed with RNA sequencing, we are now investigating how to efficiently correct abnormal splicing as a therapy, both for individual cases, and potentially across groups of patients who, for example, have the same type of mutation causing their disease. We are also collaborating with chemists who are working to optimize the chemistry for oligonucleotide treatment. The results of any successful mutation correction requires molecular validation, so we continue to use the knowledge we gain from RNA sequencing for therapy development. This being a rapidly accelerating field, I am most excited by the promise of this technology contributing more broadly to rare disease therapy.
Want to learn more about Professor Baralle’s work in rare disease research?
Interested in leveraging long-read RNA sequencing for your rare disease research? Learn more about full-length isoform sequencing with PacBio Kinnex kits at pacb.com/kinnex.