Blog Post April 02, 2013

The U.K.'s audacious clinical genomics project

Oxford University announced the launch of a gene-sequencing test for cancer patients in the U.K.’s National Health Service (NHS). The test will assess 46 genes in which mutations can drive the growth of solid tumors, hopefully allowing for better therapy selection up front. It costs £300 but offers the potential for better patient care and economic benefits.

The initial press release provides few technical details, but the test looks very similar to one offered by the Baylor College of Medicine. Its use will begin within the Oxford University Hospital system, but scientists intend to scale it up quickly for use throughout the NHS within a year.  

Normally this would be big news on its own. As interesting as the large-scale tumor genotyping effort may be, however, it’s mostly a stepping-stone within a much more ambitious—some would say audacious—program. In late 2012 Prime Minister David Cameron announced plans for the NHS to sequence the genomes of 100,000 patients, focusing mostly on those with cancer and rare diseases. The government is earmarking a whopping £100M for the project. There are, as they say, many details to work out before the sequencing can begin on such a large scale, however, so implementation is expected to take three to five years.

This isn’t the first plan to perform genome sequencing on a large scale within a population. The Faroe Islands program, FarGen, which looks to sequence all 50,000 residents, and the U.S. Veteran’s Administration’s plans to sequence 1 million genomes among its members spring to mind. But the NHS effort may represent the most promising opportunity yet to implement clinical genomics within mainstream healthcare.

If anything has become clearer in the early days of whole-genome sequencing and analysis, it’s that small sample size provides small amounts of insight. The NHS project allows for the collection, storage and use of a huge amount of data in a highly coordinated manner within a national healthcare system. The 1,000-genome project seemed massive a very short time ago. It’s exciting to think of how much we’ll learn as the data grows to include 100,000 and even 1 million genome sequences within a single resource.

Details, details

So what details need to be worked out? A couple are included right in the “Notes to Editors” at the bottom of the government announcement. Note #2 says “Whole genome sequence data will be completely anonymised apart from when it is used for an individual’s own care.” While that’s a noble goal, many theorize that it may be impossible to achieve, and recent research has reinforced that concern. The NHS and U.K. government overall will need to look very carefully at their informed-consent process. It would be a shame to see the project impeded because of an inability to follow through on assurances made.

Note #3 is “A number of ways to store this data will be investigated. The privacy and confidentiality of NHS patients will be paramount in this decision.” These two short sentences foreshadow massive amounts of work. Not just storage but data formatting and handling demands will create headaches for computer experts and bioinformaticians alike. The competing goals of making the data useful in both research and clinical settings while keeping it as secure as possible are not new in the field, but the scale of the data may be.

Finally, there are many skeptics who point out discrepancies between the project’s assumptions about progress versus what actually exists today. On the personal genomics blog Genomes Unzipped, Caroline Wright posted “£100M for whole patient genomes—revolutionising genetic diagnostics or squandering NHS cash?” Wright’s answer is clear, formatted as it is in bold type: “It would be a mistake to implement whole genome sequencing in the NHS now.” In addition to pointing out the plan’s dependence on rapid decreases in genome sequence pricing, she raises valid questions regarding the wisdom of using whole-genome sequencing for every patient if clinical outcomes are the focus. More focused genetic tests and panels, such as the one for cancer just announced, may be far more cost-effective and sufficiently effective for many patients. Also, issues with genome sequencing accuracy and analysis bottlenecks have hampered the use of clinical genomics on any scale to this point, and they will need to be solved for benefits to be realized by NHS patients.

Bold moves

Clinical genomics is facing a paradox at this time. Although there are many examples of success, the cost-to-benefit ratio is still daunting. And we still don’t understand the vast majority of what our genomes can tell us. But to achieve better understanding, benefits and pricing, we need to sequence hundreds of thousands if not millions more people, both healthy and those with disease. We also need to share the data among researchers and clinicians while safeguarding, as much as possible, subject privacy and security.

Therefore significant progress in the field depends a certain amount on some entity with substantial resources—a government, an industry (pharma?), a consortium—to take a risk. It’s a process that comes with a lot of uncertainties, including exactly how individual patients will benefit. But the returns to this point are so promising, so exciting, that it seems like a good risk to take.

So it’s great news that the U.K. is willing to step forward with an ambitious plan. And before anyone accuses me of applauding the effort from afar (and with no skin in the game, literally or figuratively), I hope the VA effort in the United States goes forward as well. If either project can leverage their data to solve some of clinical genomics’ thorniest issues, one can only hope that they reap significant benefits—in patient care, in financial return, and in receiving the credit they will be due for such a bold move.