A Do-It-Yourself Genomic Challenge to Myriad, the FDA and the Future of Genetic Tests
Over the weekend, Steven L. Salzberg and Mihaela Pertea published a short but significant article in the journal Genome Biology. In “Do-it-yourself genetic testing,” Salzberg and Pertea describe the creation of “a computational screen that tests an individual’s genome for mutations in the BRCA genes, despite the fact that both are currently protected by patents.”
The software-based test can be downloaded from the website of the University of Maryland’s Center for Bioinformatics & Computational Biology, where Salzberg is the director and Pertea is on the faculty. The test purports to test genomic sequence data against a set of known mutations in the BRCA genes. In addition to representing a conceptual alternative for those seeking to evaluate their risk of hereditary breast cancer, the so-called “Salzberg Screen” is also a direct challenge to Myriad Genetics, the FDA and the existing legal, regulatory and policy regimes that continue to struggle to keep pace with the science and technology of genomics and personalized medicine.
Below, we examine how the Salzberg Screen fits—or does not—within the current legal and regulatory landscape, as well as what it signals for the future of do-it-yourself genomics, whole-genome sequencing and the law.
The Past, Present and Future of DTC Genetic Testing Regulation
[Editor’s Note: Newsweek science editor Mary Carmichael has a DNA Dilemma. As Carmichael debates whether to take a direct-to-consumer (DTC) genetic test, she is soliciting feedback from the DTC community, from the public and from other commentators, including myself. At the end of the week, she will make her decision.
On Tuesday, Carmichael and five commentators examined what can be learned from a DTC genetic test. Yesterday, the topic was whether DTC genetic tests are trustworthy, and whether the results can be cause for concern. Today’s topic is the regulation of DTC genetic tests. In addition to several short commentaries, including a much shorter version of the piece below, Carmichael has also posted a lengthy interview with two top FDA officials on the subject of DTC genetic testing regulation.
The column below is an expanded version of what appears over at Newsweek. To see all of the commentaries in Carmichael’s series, click here.]
The recent media attention focused on direct-to-consumer (DTC) genetic tests has left companies, investors, consumers and even regulators scrambling to figure out what comes next.
As the situation stands today, companies and their investors live in a climate of unprecedented regulatory uncertainty, causing delays in the introduction of new products and rendering an already inhospitable economic climate – for both fundraising and sales – even more challenging. Commentators and regulators caution consumers that some DTC genetic tests may be unreliable or, worse, harmful, but have yet to provide clear tools and guidelines for evaluating competing tests. And regulators, including the FDA, must balance their mandate to protect the health and safety of the public with that same public’s desire for autonomy, while also recognizing that innovation is a prerequisite for a healthcare system that must continue to improve outcomes while reducing costs.
Clearly, something must change. But what will that change be? And how will the field of DTC genetic testing evolve? Will DTC be able to continue its current business while regulators and companies engage in protracted negotiations? Will oversight weed out the “snake oil salesmen” and permit legitimate companies to flourish? Will it drive all genetic testing (temporarily) out of the hands of consumers?
Or will the field change in a dramatic and completely unexpected way?
Personal Genomics Goes to Washington
Next week, the eyes of the personal genomics world will be focused on Washington, D.C., where the FDA and Congress will be meeting separately to consider the industry’s future. First, the FDA will convene a highly-anticipated public meeting (July 19th and 20th) to “discuss how the agency will oversee laboratory-developed tests (LDTs).” The FDA announced last month a proposal to develop a “risk-based” approach to oversight of all LDTs – a broad category that includes the vast majority of genetic tests, including high-complexity diagnostic tests (IVDMIAs) and direct-to-consumer (DTC) genetic tests. Hot on the heels of the FDA meeting, on July 22nd, the House of Representatives Committee on Energy and Commerce – which two months ago launched its own investigation into the personal genomics industry – will hold a subcommittee hearing on “Direct-to-Consumer Genetic Testing and the Consequences to the Public Health.”1
While the genomics and personalized medicine communities anxiously await the upcoming FDA and Congressional meetings, yesterday the future of personal genomics was being debated on the opposite coast, at a policy forum in San Francisco entitled “Genomics and the Consumer: The Present and Future of Personalized Medicine” (pdf). The forum, which was hosted by California State Senator Alex Padilla (sponsor of S.B. 482, the so-called “bioinformatics bill”) and personal genomics company 23andMe, was filled with speculation from personal genomics investors, providers, customers and commentators about what the FDA and Congress might have in store for the field.
Leveraging the Crowd to Understand Your Genome
Earlier this week Peter Aldhous of NewScientist magazine recounted an unusual experience with DTC genomics provider Decode Genetics. In reviewing his genetic data on the deCODEme website, Aldhous uncovered what appeared to be significant and bizarre errors in his mitochondrial DNA. Aldhous turned to Blaine Bettinger, The Genetic Genealogist, for help in diagnosing the problem with his mitochondrial DNA. Bettinger’s response: “This is a strange question, but are you sure this is Homo sapiens?”
Aldous, Bettinger and Decode investigated the problem and ultimately determined that the “errors” in the mitochondrial DNA were actually being introduced by a bug in the deCODEme software interface that allows users to browse their data. (Aldhous carefully points out that the software glitch was a rare one and that it did not seem to affect deCODEme’s disease-risk summaries or analysis.)
More than a simple software error, Aldhous’s experience highlights the complexity inherent in consumer genomes. Translating an individual’s saliva sample into a description of genetically influenced traits and risks is a multi-stage process with potential for error at every step in the chain. Or, as Daniel MacArthur of Genetic Future cleverly puts it, “There’s many a slip ‘twixt spit and SNP.”
Will Funding Break Through the Bioinformatics Bottleneck?
Earlier this month, the NIH announced the renewal of a grant program that awards up to $275,000 over two years to academic institutes, small businesses, non-profits and other groups, to support research aimed at developing new ways of managing, manipulating and interpreting genomic and other biological data. But the utility and necessity of such grants is not entirely clear.
To be sure, the biomedical community has recognized a potential for a “bioinformatics bottleneck” as the cost of genome sequencing plummets and the sheer quantity of raw data rises, potentially without a corresponding increase in the capacity to interpret that data. And the NIH’s focus on funding innovative, “high risk/high impact” research projects is certainly welcome. But it is far from clear that a handful of two-year, $275,000 grants will produce the right type of innovation, on the right time-scale, to put a dent in the problem. And perhaps more to the point, it is worth taking a closer look at whether any amount of public funding would address some of the other issues at the root of the impending shortfall in biomedical informatics and computational biology research and development.
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