By Matt Luchette
July 24, 2013 | The Supreme Court’s 9-0 decision last month in favor of the Association for Molecular Pathology in its case against Myriad Genetics marked a tide change in the genetic testing industry and the Open Science movement.
Open science is not a new goal; scientific progress has always predicated on the free and open exchange of ideas. As Isaac Newton famously expressed in a letter to his rival, the scientist Robert Hooke, in 1676, “If I have seen further, it is by standing on the shoulders of giants.”
But since Newton’s day the challenges to Open Science have grown. In a 2003 correspondence to Nature, John P. Walsh, then a professor of Sociology at the University of Illinois, and Wei Hong, a research assistant at the school, argued that secrecy in science “is increasing in step with competition.” It’s a fear every professor knows all too well: when the significance of her research findings is closely linked to the funding she’s awarded, a professor’s fear that her research will be scooped prevents open dialogue and collaboration with outside labs.
Competition, however, should not be confused with commercialization. Walsh and Hong argued, “Although commercial activity may reduce formal activities such as publication or sharing of materials, it may have fewer negative effects on informal communication among researchers” than funding concerns and other competitive factors inherent in academia.
Supporters of Open Science argue that for-profit research, and the proprietary restrictions, copyright walls, and patent protections they create, encourages the same culture of secrecy that Walsh and Hong describe. But while the authors agree that secrecy is toxic to inspiring scientific insight, they say industry restraints and economic incentives are not primarily to blame, suggesting instead that “increases in US government funding for science, if they are sustained, may help to lower the intensity of competition.” (Needless to say, a decade later, they were not sustained.)
The Walsh-Hong letter is particularly relevant in the wake of last month’s Supreme Court decision, which ruled that Myriad could not hold patents on the naturally-occurring genes BRCA1 and BRCA2. Mutants of the two genes are associated with a higher risk of breast cancer, with as many as 60% of women who inherit a harmful BRCA1 or BRCA2 mutation developing the disease. Patenting the genes would grant Myriad exclusivity in developing genetic tests for BRCA1 and BRCA2, and restrict other labs from researching them further.
Yet because the genes are products of nature, the court determined that they could not be patented. “Myriad found the location of the BRCA1 and BRCA2 genes, but that discovery, by itself, does not render the BRCA genes ‘new [...] composition[s] of matter,’ [...] that are patent eligible,” wrote Justice Thomas in the court’s majority opinion.
The decision is a win for both Open Science and scientific commercialization. Biotech companies and academic labs alike are now free to perform their own experiments on BRCA1 and BRCA2 and develop cheaper tests for the genes. Yet even without the patents, Myriad still has control of a valuable piece of information: their stockpile of patient data that they have kept private since 2006. Multiple BRCA1 and BRCA2 variants exist, and without details on the severity of those variants, doctors have no way of differentiating a benign mutation from a more serious one.
The Free the Data effort, a collaboration between a number of non-profit and for-profit organizations, hopes to make that data freely available by going directly to the source. Each Myriad client received a report with their genetic results that detailed the severity of their specific BRCA1 or BRCA2 variant; Free the Data hopes to compile the information contained in those reports from thousands of Myriad clients and make it freely available online for doctors, patients, and genetic researchers.
The potential benefits of this open data initiative stretch throughout academic research and the biotech industry. One of the group’s founding partners, InVitae, a genetic diagnostics company based in San Francisco, hopes to leverage the valuable patient variant data that Free the Data is collecting to create an all-in-one genetic test. The company’s goal, according to CEO Randy Scott, is to bring “comprehensive genetic testing to a billion people on the planet.”
“Everyone is carrying 50-100 genetic mutations,” said Scott. “We just don’t know, at this stage, what they are.” And for the mutations that have already been discovered, such as BRCA1 and BRCA2, most have their own unique test, making broad-spectrum genetic testing cumbersome and costly.
To help make genetic testing more feasible for a billion patients, InVitae plans to, “aggregate all the world’s known genetic tests into a single test for less than $1000,” according to Scott. The company has currently cataloged over 32,000 genetic variants pertaining to over 500 genetic conditions in a database that is curated and updated regularly from scientific journals by staff scientists. But through Free the Data, the company hopes to tap into the most important data points: the actual patients with those variants.
“We’re still discovering new genetic variations all the time,” said Scott. But when these variants are seen in the clinic, typically the most useful technology geneticists have to determine the severity of a variant has been around since before genes were even discovered: the telephone.
“Lab directors will call each other to see if they’ve seen certain variants before” and whether or not they’re severe, Scott explained, adding, “We need a better way to share genetic variation data.” Users of InVitae’s genetic tests can access detailed clinical reports on their results from the company’s curated database of variants. And with their clients’ permission, InVitae plans to make clinically-observed variant data publicly available to physicians and patients on open, searchable genetic databases, like ClinVar.
But despite InVitae’s contributions to the Open Science community, Scott defends the company’s for-profit model. Open Science has innumerable benefits for researchers, Scott explained, but “there’s a role for proprietary programs as well, and at times it’s good for those systems to compete,” adding that the biotech industry’s economic incentives encourage scientists to “move as quickly as possible.”
“Broad access to information will have a great benefit to healthcare,” said Scott. But as Big Data experts like Atul Butte have stated, the most challenging part of open access to information is not collecting the information, but deriving meaning from the data. Scott believes for-profit ventures, like InVitae are best fit for the task. “We need to think like Google, eBay, or Yahoo!,” said Scott. “How [will] we organize the information and create value?”
This insistence on optimizing value to the consumer may be just the sort of motivation companies like InVitae will need to bring clinically-actionable genetic testing to patients.
“This is a very exciting future,” said Scott, “The dawn of a new age in genetic medicine.”