Dr. Andrew Stergachis: ‘We were able to precisely resolve the genetic and molecular basis of (the individual patient’s) condition, thereby providing both her family and care team with answers to help support her moving forward.’
[Editor’s Note: Recently, Nature Genetics published, “Synchronized long-read genome, methylome, epigenome and transcriptome profiling resolve a Mendelian condition.” The corresponding author is BBI’s Andrew Stergachis, M.D., Ph.D. The paper represents a groundbreaking demonstration of using long-read multi-omic sequencing to resolve the genetic and molecular basis of a Mendelian condition.]
How are findings in this paper moving researchers toward a greater understanding of genetic variants?
One of the biggest challenges in clinical genomics is that we have a very limited understanding of which genetic variants actually contribute to human disease. Emerging genomic sequencing technologies are well-equipped to accurately identify genetic variants. But the challenge is that each individual has over 4 million genetic variants, with the far majority of these being in genomic regions that we do not understand well. So genomic sequencing alone will result in the identification of 4 million potential variants in each individual that could be contributing to their health.
The premise of the paper is that rather than just measuring whether a genetic variant is present or not, “Can we, at the exact same time, measure whether or not that variant is impacting how a cell is actually functioning?” However, the challenge comes down to: How do we measure all the different diverse functions of the cell in a streamlined manner that gives us an accurate reflection of what’s going on?
There have been approaches before where people have thrown the proverbial kitchen sink at the problem – but those methods have not been robust, and are unable to resolve the function of many genetic variants, due to technical limitations. Resolving this challenge required us to build a new toolkit for mapping the sequence and function of the human genome.
What is the key question this paper answers?
The key question is “Can we devise an experimental paradigm that would synchronously co-measure both the sequence and function of an individual’s genome?” We demonstrated in the paper that yes, we can do this.
Specifically, our approach utilizes the Fiber-seq method that our lab invented, in combination with long-read transcript sequencing. This provides an accurate map of an individual’s genome, how that genome is methylated, how that genome is structured in terms of chromatin, and how that genome is transcribed into RNA. This approach demonstrates both the power and potential of long-read sequencing for resolving the function of the human genome. In addition to simply showing that we can synchronously co-measure both the sequence and function of an individual’s genome, we also wanted to see whether this was clinically useful. Consequently, we applied our approach to an individual enrolled in the Pacific Northwest Undiagnosed Diseases Network who had a previously unsolved condition. By applying this approach to cells from her, we were able to precisely resolve the genetic and molecular basis of her condition, thereby providing both her family and care team with answers to help support her care moving forward.
How does this study achieve a greater understanding of genetic variants?
Traditionally, when a genetic variant of interest was identified in an individual, researchers have to do a host of different time-consuming experiments to determine the function of that variant. As you can imagine, because each individual has about million genetic variants, this is often not a practical approach. Importantly, our methods enable us to quickly filter the 4 million genetic variants in an individual to only the handful that appear to be functionally significant.
What’s next in your endeavors to translate this research for clinicians?
We’re now applying this to samples from individuals we are seeing as part of the Undiagnosed Disease Network at the UW, with the hope is that this will enable us to make precise molecular diagnoses for these individuals. We have already made an additional diagnosis in the pilot study, and have been able to return this to the family and his care team.
We also are exploring ways to get this method and the data we are generating from this method out to other researchers and clinicians. Specifically, we have been working with ClinVar, which is a major repository of clinical genetic information, to enable them to encode functional data directly in ClinVar in a manner that can be disseminated to clinicians. Moreover, we are working with Drs. Lea Starita and Doug Fowler to offer this approach across different rare disease patient groups. The goal is to leverage this approach to better understand not only why individuals have these rare diseases, but also, potentially, to identify therapeutic options.
