SAN FRANCISCO (GenomeWeb) – Under funding from Genome Canada, researchers from the Hospital for Sick Children in Toronto are developing an RNA sequencing test to help diagnose rare genetic diseases and profile cancer patients' tumors.
Last week, Genome Canada partnered with the Canadian federal government as well as with provincial governments, businesses, and research groups to provide C$56 million ($42.2 million) in funding for 37 winners of three of Genome Canada's funding competitions. A team composed of two SickKids research groups focused on rare genetic disease and cancer won C$3 million ($2.3 million) from the Disruptive Innovations in Genomics competition to develop transcriptome-based diagnostics.
The group is being co-led by Adam Shlien, associate director of translation genetics; James Dowling, a clinician-scientist in neurology; Michael Wilson, a senior scientist; and Michael Brudno, director of the Center for Computational Medicine.
The goal is to launch a clinical test within one year out of the SickKids clinical genomics laboratory, Shlien said.
The collaboration came about because both Shlien and Dowling had been studying the genomics of cancer and rare genetic disorders, independently, and saw the value that RNA sequencing added to DNA sequencing.
"There are some things we see in cancer, like structural variants that are really complicated, that RNA sequencing helps work out," he said.
"Similarly, there have been some patients with a pretty convincing clinical phenotype for Duchenne muscular dystrophy, but genome sequencing alone wasn't revealing," Dowling said. That's because the causative gene also has a pseudogene that can make interpretation of DNA sequencing difficult. But, because RNA-seq only sequences transcribed genes, it does not sequence the pseudogene, so can often clarify the diagnosis, Dowling added.
The grant from Genome Canada will support the second phase of the development project. In the first phase, the researchers demonstrated the feasibility of using RNA-seq to identify relevant gene fusions and rearrangements in both cancer and rare disease. In that phase, Shlien's and Dowling's research teams each demonstrated separately that RNA-seq was useful for both cancer and genetic disease.
The second phase involves bringing the two research teams together and also developing a commercially viable test that can be run in a clinical hospital lab. That will involve a significant amount of automation, Shlien said, including the library prep and the variant calling and bioinformatics.
"The most important thing is figuring out how this can be worked into the normal processes of a clinical lab," Shlien said.
Shlien said that on the cancer side, researchers from SickKids and elsewhere published a study in Science last year using genome and RNA sequencing in a cohort of patients with Ewings sarcoma, showing how RNA sequencing could help untangle complex rearrangements. In unpublished work, he said that the team has analyzed a few hundred patients with hard to treat pediatric cancers and found that RNA-seq had "massive utility." He said that for about 50 percent of cases, RNA-seq would have clinical utility, including both for identifying treatment-relevant gene fusions and also for subtyping tumors by doing pathway and expression analysis.
The team has not yet published a technical or clinical validation of its assay, but plans to in the future.
For rare diseases, Dowling said that current clinical utility estimates are based on research of neuromuscular disorders. For those cases, about half are negative from an exome or genome sequencing test, and of those, transcriptome sequencing can solve between 30 percent and 40 percent. He anticipated that similar to diagnostic exome sequencing, the yield would increase over time.
"With more samples, we'll be able to classify more of what are now variants of unknown significance," he said. "Thinking about the trajectory of exome sequencing, initially, the ability to interpret was limited," Dowling added. "But now, our ability to interpret is so much more robust" due to the sheer number of exomes that have now been sequenced. Similarly, with transcriptome sequencing, while there are currently a limited set of known alterations, over time, the clinical utility will increase.
The researchers anticipated that the test would be used in slightly different ways depending on whether it was being ordered for a cancer patient or rare disease patient. For cancer, Shlien anticipated that both DNA and RNA would be analyzed together. He said most likely, the RNA portion would employ bioinformatics to focus on certain fusions known to be drivers of pediatric cancers.
For rare genetic disease testing, RNA sequencing would likely be used slightly differently, Dowling said. In that case, a gene panel, exome, or whole-genome test would likely be used as a first-line test, with RNA-seq added as a reflex test in non-informative cases.
Another goal, Dowling noted, would be to build evidence to convince the provincial healthcare system to cover the test. In Canada, reimbursement is determined at the province level by the local ministry of health. The Ontario Ministry of Health has generally been supportive of NGS-based clinical tests, Dowling said, supporting exome sequencing for rare disease, including sending tests out of province and out of country for testing. But, that's not the case everywhere. In Alberta, for instance, exome sequencing is not approved, he said. And currently, there is not a clinical transcriptome sequencing test being offered in Canada, Dowling said, so, "we think we'll have a unique position in the diagnostic market."