NEW YORK (GenomeWeb News) – Next-generation sequencing may not yet have a solid footing in the clinical environment, but Ottawa Hospital in Ontario has plans to use the technology as part of a new personalized medicine initiative that it hopes to embark on in the next year.
The initiative is still in the planning stage, details of the hospital's strategy are blurry, and no funding has yet been secured, but David Stewart, head of medical oncology at the hospital, told GenomeWeb Daily News recently that he anticipates that in a year he and his colleagues will be able to use the next-generation sequencing-based multiplex tests developed in house to better match patients with the most effective therapies.
Like other clinical settings, Ottawa Hospital has been using personalized approaches such as HER2/neu testing for years, but the advent of new molecular diagnostic technologies offer the potential to improve patient care dramatically by providing detailed genetic information about patients. In his own specialty area, oncology, "'what we know is that it's likely to be molecular characteristics of tumors that will predict the probability of a person benefitting from therapy," Stewart said.
Though the health benefits and the cost-effectiveness of genomics-based technologies in clinical settings are still unclear, and some say that it could be several years before the technologies have meaningful clinical use, the impetus to use technologies such as next-gen sequencing and other 'omics-based methods in clinical practice is growing.
As such, it behooves institutions such as Ottawa Hospital to adopt such technologies, Stewart said.
"Having seen the rate at which things have changed over the past few years and trying to extrapolate how it's going to go over the next few years, that's what makes me think that" investments into such technologies need to be made, he said.
Although Ottawa Hospital is "actively involved in many clinical trials," a new genomics-based initiative would open up a new research area, pharmacogenetics, to the hospital, he added.
Another benefit of creating multiplex tests in house is that the hospital would no longer have to send tests elsewhere, lengthening the time needed to get test results. Less patient sample could also be used in order to get test results.
For example, in the case of lung cancer, there have been instances when the hospital has had an EGFR test return negative. A KRAS test then needs to be done, and "eventually, "we run out of sample because of the sequential way that it's currently done," Stewart said.
The plans are for Ottawa Hospital to initially develop multiplex tests using technologies such as RT-PCR. Stewart said, though, that it also hopes to bring next-gen sequencing to the fold, and specifically it is developing plans to incorporate exome sequencing, which is steadily gaining footing as a clinical diagnostics tool.
As GenomeWeb Daily News sister publication Clinical Sequencing News reported recently, Duke University researchers plan to expand their exome sequencing program after a pilot project suggested the method may help discover causal mutations in a significant proportion of difficult-to-diagnose cases. A number of commercial and academic centers have also recently launched clinical exome sequencing tests and services or plan to do so.
Stewart has filed a pre-application with Genome Canada for funding in support of a study using RNA sequencing on formalin-fixed, paraffin-embedded samples to identify biomarkers that may predict resistance to certain treatments for non-small cell lung cancer, or that may predict which patients are best responders to other therapies. He said he expects to hear next month whether his proposal has been chosen for the next phase, in which a full application will need to be submitted.
The funding request was made in response to a new grants program from the Canadian government for projects that use genomics-based research to advance personalized healthcare.
The focus of the hospital's new initiative would be on oncology first because that's the application area in which personalized therapies are furthest along, Stewart said. Plans also exist "to look at whole genome SNPs to see how they impact outcome and how they're influenced [by] and interact with the presence of mutations in the tumor," he said.
No decision has been made yet on whether Ottawa Hospital would buy its own sequencer or collaborate with another facility that already has an instrument. Its sister hospital down the road, the Children's Hospital of Eastern Ontario — a walkway joins the two facilities — has an Illumina MiSeq instrument and initially, at least, next-gen sequencing-based assays could be developed on CHEO's instrument, Stewart said.
No formal agreement has yet been established for such an arrangement, a CHEO spokesperson said, adding that the hospital has not yet used the platform for clinical applications.
Ottawa Hospital has not committed financially to a genomics personalized medicine initiative, but Stewart said, it has signaled its support for such a plan.
"They've said, 'This is important, let's see what we can do to make it happen,'" he said.
Organizers have also had discussions with unnamed pharmaceutical firms to fund the initial start-up costs, he added.