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This article is from the In-Depth Report Personalized Medicine in the Genomic Era

Genome Sequencing for the Rest of Us

Even as scans get faster and cheaper, many diseases still have unknown or sketchy genetic correlates. How much stock should consumers put in personal genome sequencing?
individual gets swab dna test, which the fda is considering regulating



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We all carry our DNA around with us—in every cell of our bodies—but some biotech trailblazers are toting their genomes with them, too. In a recent talk Jay Flatley, president and CEO of sequencing giant Illumina, recalled being asked by his doctor to get a certain genetic test. But Flatley was able to pull up his full genome on his iPad then and there instead of sending a spit sample off to the lab.

Although most people are not yet able—or willing—to obtain or share their own personal genome sequence, many already see a genome-empowered future dawning. In the quest to better know one's self, however, more and more people are turning to genome sequencing to uncover information about their ancestral histories, impending health risks, and disorders of potential progeny. After the U.S. Food and Drug Administration (FDA) prevented Pathway Genomics' direct-to-consumer DNA kits from reaching drugstore shelves in May, however, the technology—and companies who offer it—have come under finer scrutiny from the public as well as the government.

Despite the completion of the generalized human genome draft a decade ago, connections between diseases and genetic variations have proved to be evermore complex and elusive.

"We naively thought that there would be a few genes involved in risks for a variety of common disorders," says Barbara Bernhardt, an associate professor of medicine and genetic counselor at the Hospital of the University of Pennsylvania (Penn).

Some conditions, such as cystic fibrosis (pinpointed even before the completion of the human genome), are caused by single gene mutations, and clinical genetic tests for these types of diseases have been useful diagnostic tools. But other diseases, such as Alzheimer's, have no uniform genetic signature—or clear way of avoiding them—leaving many to wonder about the science and utility behind the results many genome scans offer casual consumers. Other information gleaned from sequences—for example, the drug metabolic-rate estimates for medications such as the blood-thinner Warfarin—could be used directly for medical treatment decisions.

"They certainly do provide medical information to people," Bernhardt says of the direct-to-consumer genomic tests. "From that perspective, they do need to be regulated as medical devices."

The FDA, which had provided relatively loose rules for consumer genetic testing, is now revaluating the industry's methods and will begin asking companies to provide data about how they interpret the scans for customers.

In a 2006 Scientific American article, Harvard Medical School geneticist George Church called for genome sequencing for all. But four years later, is the technology ready for the mass market?

Testing the market
The first complete individual human genome was finished less than three years ago and cost hundreds of millions of dollars. Now many companies offer a similar service, which promises a personalized laundry list of disease risks assessed from a simple cheek swipe or spit test, available online for thousands—and in some cases, for less complete scans, hundreds—of dollars.

Despite the drastic decline in price and increase in availability, direct-to-consumer genome sequencing has been relatively slow to catch on. The Google-backed sequencing company 23andMe has gone through two rounds of staff cuts in the past several months, and the Iceland-based deCODE genetics was delisted from public trading on Nasdaq earlier this year after its market value dropped.

Additionally, a mishap earlier this month at a lab under contract with 23andMe resulted in as many as 96 customers receiving the wrong genetic reports.

"The consumer market for whole genome sequencing and interpretation has yet to evolve," says Nathan Pearson, director of research at Knome, a company that offers full genome sequencing. Recent studies have also found other applications for genetic tests, such as ancestry profiles, to be rather unreliable. And many consumers are reluctant to submit their DNA for private sequencing—let alone inclusion in genetic studies—fearing privacy issues.

Even so, research shows that genetic insight into health risks is in high demand in some consumer groups. In an ongoing study of attitudes toward genetic testing at Penn's School of Medicine, Bernhardt and her colleagues have found that their subjects generally embraced and understood their genetic test results and risk levels. Their volunteers were primarily people who took an active interest in their health, she notes, and results were presented only for a single condition for which preventive actions could be taken (such as risk for heart disease), rather than a fuller scan of multiple risks that many of the direct-to-consumer tests offer.

But for conditions in which there is currently no cure or effective prevention there is concern that just downloading a personal genetic risk profile at home might cause undue stress or even depression. Bernhardt and others recommend that consumers meet with a genetic counselor before tests to prepare for what information might come back—and for how it should be used.

The family doctor, however, might not be ready to help in interpreting genetic test results. Bernhardt notes that a lot of general practitioners often do not know what to do with this genetic information.

Recoding the code
Even for genetic tests that offer just a snapshot of relatively common disease-linked variations, the amount of data such a scan generates is immense and requires distillation before relevant information can be presented to consumers. This process of interpretation, however, is one place where the science can get murky.

Most companies offer genetic data in terms of relative risk for particular conditions. Some, including Knome, provide links to scientific studies about genetic variants that appear in your genome, allowing a customer to judge what a particular difference might mean for them. Their personal scans, however, have primarily been limited to a few dozen "healthy and wealthy" customers who are motivated to dive into the literature and explore health implications for themselves.

"Dealing with the huge haystack of data that you get is a really difficult task," Pearson says. And that service is not likely to disappear, even as sequencing prices drop. "When sequencing is free or nearly free, there will always be room for expert interpretation," he says. "That's our stock and trade," he says of his work with Knome.

That approach could have limitations for much of the public who might not be interested in sifting through a decade of scientific literature about a particular mutation they carry. "They're going to get overwhelmed," Pearson notes about consumers who get inundated with mountains of data about their 3.3-billion base-pair genome. Finding ways to convey results "judiciously, securely and wisely" will be a long-term challenge for the industry, Pearson says.

No magic markers
Another challenge to consumer genetic testing has been consistency. Although most sequencing processes are similar, and the DNA itself is a unique code, reports from various groups for a single person can have striking differences. "People interpret the information that comes out of the sequence differently," notes John Boyce, co-founder of Delphi Bio, a biotech consulting firm, who also founded the annual Consumer Genetics Conference.

The main problem, as explained by Boyce and others, is that solid, predictive biomarkers have not been agreed on for most conditions. And because one company might select a different set of biomarkers for a disease than another, "the estimates of odds conferred may vary widely," Pearson says.

Genome-wide association studies, in which genetic variants are matched with different health outcomes across a study population, promised to give researchers a tidy map of diseases and related genetic variations. But, particularly in studies that use short-cut sequencing methods in which common variants are sampled rather than full genomes, the results so far have been disappointing to many population geneticists. As Pearson points out, "a spelling variant does not get to be common in the population if it's really harmful," which means that most harmful variants are rare—and confidently predicting risk for an individual based on a relatively small sample population can be problematic.

"The sample populations are not large enough to truly find the predictive biomarkers," Boyce says. These relatively small sample sizes could hamper companies' ability to make exacting correlations between genetic variations and health or disease risk.

Another company Boyce is involved with, GnuBio, aims to drop the cost of sequencing to $30 per genome in the next two years. With fast and cheap sequencing, he expects the number of logged genomes will skyrocket. "Once the numbers [of genomes] are high enough," Boyce says, "we should have the power to see deeper into the genome and find the predictive biomarkers."

Showing the science
Most of the companies offering personal genome scans use their own algorithms for calculating a person's disease risk or other health information, and the validity of the results has remained relatively unexamined.

Since the Pathway Genomics consumer test controversy this spring the FDA has sent public letters to five companies requesting meetings to discuss the regulatory future of the latter's genetic products. Four of the firms—23andME, deCODE, Knome and Navigenics—offer direct-to-consumer genome scans (Personal Genome Service; Complete Scan; KnomeCOMPETE; and Health Compass, respectively), which the FDA has labeled as medical devices and, as such, they would be subject to closer inspection and possibly premarket approval.

"It is important that [the scans] be analytically and clinically accurate so that individuals are not misled by incorrect test results or unsupported clinical interpretations," Alberto Gutierrez, head of the Office of In Vitro Diagnostics at the FDA, wrote in letters to the companies.

Rather than pulling all of the tests off the market immediately, however, the FDA plans to evaluate the claims each company is making and the data they have to back them up.

"By law, they're medical devices," Gutierrez explains of the tests. Depending on how vital or potentially risky the information the tests claim to provide is, services might be evaluated differently. If one test is "going to give people a risk assessment that a kid is going to be bald when they grow up, I think that's a very low risk," he says. However, if a test is offering to predict how a person's body is going to metabolize a drug, "the risk of that information being misused is something that we would be concerned with."

Some working in the industry have voiced support for more government guidance. "We welcome the interest," Pearson says of the FDA's inquiries. He adds that his group shares the agency's concern that, "that new technologies are used reliably and accurately."

But the FDA—already spread thin as it deals with other regulatory challenges, including food safety and drug approval—might need to rally additional resources to provide premarket approval if the consumer genetic testing market expands as rapidly as many are predicting. "It would be impossible for them to sustain the burden of all the new tests," says Paul Kim, a partner at the law firm Foley Hoag, who has studied the regulation of the industry.

Boyce agrees, noting that if interest in personal genome sequencing is "going to become such a tidal wave at some point, it's going to be hard to regulate." He also worries that premarket approval could stifle innovation and new company start-ups.

Until the FDA meets with companies to assess the data backing up their claims and conclusions, the fate of these tests remains unknown. Gutierrez notes that the agency might simply seek to verify that product labeling is truthful and complete enough for consumers to know what kind of answers and information they might—or might not—get from a genetic test as well as whether they will be able to act on that information. The agency might also take a broader approach to ensure support for consumers who choose to dive into their genome. "It wouldn't be out of the question for us to require [that there be] genetic counseling on hand," Gutierrez says.

Back in the lab
Most commercial tests are not entire genome scans, but rather analyses of common genetic alterations that have been linked to disease risk and other health issues. This shorthand version, although more economical and efficient, can leave much of the genome unexamined. Such details might not concern someone specifically looking for their family's risk of age-related macular degeneration, whereas for purposes of future discovery leaving out so much of the genome can be problematic, much as a partial population census would likely fail to bring back crucial details about a community.

With individual customers currently few and far between, some companies have fashioned themselves into research-ready firms, able to help scientists sequence and interpret genetic information for their studies.

Many clinical tests for single mutations, however, have already been having a meaningful impact for years. Testing for certain known genetic mutations that cause different kinds of breast cancer, for example, can help tell oncologists what kinds of treatment will be most effective—and least harmful—to the patient. But with all of the head-scratching over full-genome scan fallibilities, these single-gene mutation tests are "the kind of things people are losing sight of," Bernhardt says.

Despite a bumpy start and uncertain regulatory future, many who follow the consumer genomic testing industry are optimistic: Boyce projects that when electronic medical records become more prevalent, people will be able to add their genomic scans, which could help them and their doctors manage personal health; but it could also be a boon to researchers if individuals make them available for study. With millions of health records and related genomes available researchers might eventually have access to study populations of unprecedented size, breadth and depth, in turn making individual genomic-based predictions more accurate, reliable and perhaps more appealing.

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