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Stanford Clinical Genomics Pilot Offering Illumina Whole-Genome Sequencing to Select Patient Groups


Stanford Hospital and Clinics and the Lucile Packard Children's Hospital Stanford have begun offering clinical whole-genome sequencing using Illumina's Rapid Track sequencing service, beginning with a pilot phase limited to select disease areas.

The new Clinical Genomics Service is currently officially available only to patients with “mystery” diseases with a likely genetic origin, unexplained hereditary cancer risk, patients with inherited cardiovascular or neurological disease, and those with severe, unexplained drug reactions. But the new service's co-director Euan Ashley told Clinical Sequencing News that the group would potentially accept other referred patients on a case-by-case basis.

"We picked a couple of areas that are [main areas] for Stanford clinically and hopefully high yield for the technology to work with first … But though we've identified these groups as an initial focus, we are open to referrals from any physician … really to any patient that could potentially benefit," he said.

According to Ashley, while several Stanford physicians have been taking advantage of clinical whole-genome sequencing services offered by other groups like Baylor College of Medicine for some time, the hospital had held off on launching its own service.

"We wanted to take a very close look at what we could say about the data: things like what the coverage of key genes was, whether we could make a call at every position, how good we are with new technology at indel calling," he said.

About a year of lead-up time allowed the group to explore these questions, which Ashley said are discussed in an upcoming paper recently accepted for publication.

"Overall, the sense we got was that we are very good at SNVs, and we still have a ways to go on other types [of alterations], but we felt we have gotten to the point where a [Stanford] genome sequencing service was reasonable to pilot," he said. "We thought there was something we could add in having our own service."

The initial pilot phase of the new service, which is co-led by Ashley and his colleague Jason Merker, is intended to last 18 months. At least in its current iteration, the group is utilizing Illumina's rapid turnaround whole-genome sequencing service, which Ashley said has already returned results for several patients within five days, allowing the group to then return a clinical report to ordering physicians within about 10 days.

Moving forward, Ashley said the group is not wedded to the Illumina Rapid Track, and could potentially adopt other commercial clinical sequencing offerings or switch to sequencing patient genomes in house at Stanford, although he did not detail any distinct plans to make changes to the service in the near-term.

As Stanford has developed the strategy for the new service, Ashley said it has been working with the university’s ethics department to develop a plan for consenting subjects for whole-genome sequencing.

According to Ashley, when a physician seeks out the service and their patient is deemed eligible, the patient goes through a process of genetic counseling that includes a category-based choice of what types of findings they would like to receive.

"The approach is that we ask every patient — we give them categories [of clinical genomic findings] and ask whether they want to hear about those categories," Ashley said.

"So if they have a specific disease and only want to know about that, that's all we will return. And if they want to hear more broadly, they have the option. If they want to hear incidental findings in the 56 genes ACMG came up with, we'll do that, but we won't share anything unless they want it," he explained.

According to Ashley, after a patient is accepted for the service, a blood sample is taken and processed initially at Stanford's pathology lab before being sent to Illumina for rapid whole-genome sequencing.

Ashley said that though the group has already processed several patients, the reimbursement landscape for the service is still mostly an unknown.

However, he said, in talking to colleagues at Baylor and other centers like the Medical College of Wisconsin, which have adopted clinical sequencing services, it seems that the field is "beginning to get a sense of where payors fall."

"In many cases, the patients for whom we are doing whole-genome sequencing are patients for whom a panel approach has failed and who are now looking at potentially going on to a number of other panels," he said. "Each payor is coming up with their own recommendations for this, but they do appreciate that this technology can actually save money. So given that WGS might now [be at a cost of] maybe two-panels worth of reimbursement, we expect to get at least some reimbursement."

While Stanford's current clinical genomics service is focused on whole-genome sequencing only, Ashley said that the center's experience in the field may lead it to integrate other approaches into its clinical efforts in the future.

"Especially when we start to think about tumor-normal sequencing, which is one of the next things on our horizon, we are going to be very interested in transcriptome [sequencing]," he said. "And epigenome is just a step from that."

"We are very interested, in general, in what happens post-genome, including modeling systems and other approaches that can help us determine causality," Ashley added. "That is something that is beginning to be explored, and no one is clear yet how that should interact with a clinical service, but we are very much engaged in what that looks like and it’s something we would look to add on in the next year or two."