Monthly Archives: May 2015

If Canada does not act to protect genetic data, we could see the rise of genetic discrimination

Earlier this month the Senate Human Rights Committee gutted a bill calling for a law against genetic discrimination in Canada. Instead of protecting Canadians from having their personal genetic information used against them, the bill now simply provides a definition of “disclose” and “genetic test,” and protects no one.

More than 26,000 genetic tests are now available to the public. Many do-it-yourself tests, like those offered by mail from the California-based company 23andMe, cost less than $200. As more Canadians elect to find out what their genetic blueprints say about them, Canada needs to protect their genetic information from being misused.

According to Senator James Cowan, who tabled the bill, most other Western democratic countries have laws like this already. In 2003, the United Nations’ scientific and cultural organization adopted the International Declaration on Human Genetic Data, which aims to prevent personal genetic information from being used against an individual or group.

Why isn’t Canada on board? The insurance industry opposed the original bill banning genetic discrimination, Senator Cowan said in the Senate.

Really? Should business interests be the reason this principle fails to become law?

Many Canadians who are sick and in need of treatment could be helped by genetic testing.

But with no law to protect them, they might decide not to get tested.

They might fear repercussions from their insurance company or employers down the road, if their tests indicate they carry genes that predispose them to a medical condition or disease.

Canadians may well decide not to get tested if there’s a risk their insurance premiums will go up, or that they will be denied insurance.

Ironically, when a patient is able to catch a genetic disease early through testing, they’re often able to take preventative measures that reduce the potential cost of their care for everyone involved ­— including themselves, the government and their insurers.

Genetic discrimination could come from anywhere, not just insurance companies. Should a hospital be allowed to deny a surgeon a job if he or she were found to be at risk for tremor-causing Parkinson’s disease? Would it be OK if a private school, whose reputation depends on its students’ test scores, rejected a student who carried a gene related to dyslexia?

We should not leave these decisions for Canadian organizations to make for themselves. As researchers discover more about the complicated human blueprint, Canadians will need increasing protection from discrimination that might arise from that information.

Stephanie Orford , Metro

Creepy Ads Use Litterbugs’ DNA to Shame Them Publicly

Next time you’re about to toss a cigarette butt on the ground, consider this freaky fact: It takes less than a nanogram (or less than one billionth of the mass of a penny) of your dried saliva for scientists to construct a digital portrait that bears an uncanny resemblance to your very own face. For proof look to Hong Kong, where a recent ad campaign takes advantage of phenotyping, the prediction of physical appearance based on bits of DNA, to publicly shame people who have littered.

If you walk around the city, you’ll notice portraits of people who look both scarily realistic and yet totally fake. These techno-futuristic most-wanted signs are the work of ad agency Ogilvy for nonprofit Hong Kong Cleanup, which is attempting to curb Hong Kong’s trash problem with the threat of high-tech scarlet lettering. It’s an awful lot like the Stranger Visions project from artist Heather Dewey-Hagborg, who used a similar technique a couple years back to construct sculptural faces as a way to provoke conversation around what we should be using these biological tools for.

In the case of Hong Kong’s Face Of Litter campaign, the creative team teamed up with Parabon Nanolabs, a company out of Virginia that has developed a method to construct digital portraits from small traces of DNA. Parabon began developing this technology more than five years ago in tandem with the Department of Defense, mostly to use as a tool in criminal investigations.

Parabon’s technique draws on the growing wealth of information we have about the human genome. By analyzing saliva or blood, the company is able to make an educated prediction of what you might look like. Most forensic work uses DNA to create a fingerprint, or a series of data points that will give a two-dimensional look at an individual that can be matched to pre-existing DNA samples. “We’re interested in using DNA as a blueprint,” explains Steven Armentrout, founder of Parabon. “We read the genetic code.”

The DNA found on the Hong Kong trash is taken to a genotyping lab, where a massive data set on the litterbug is produced. This data, when processed with Parabon’s machine-learning algorithms, begins to form a rough snapshot of certain phenotypes, or traits. Parabon focuses on what it describes as highly heritable traits—or traits that have the least amount of environmental variability involved. Things like eye color, hair color, skin color, freckling, and face shape are far easier to determine than height, age, and even hair morphology (straight, wavy, or curly).

The Ogilvy team says it accounted for age by studying market research on the types of litter it processed. For example, people ages 18-34 are more likely to chew gum, so any gum samples were automatically given an average age in that range. Whereas the portraits of cigarette litterers, more common among the 45-plus group, were depicted as slightly older.

It’s an imperfect science in some regards, and yet, the capabilities are astounding—and more than a little scary. Ogilvy says it received permission from every person whose trash they picked up, so in that way, it’s not a true case of unsolicited public shaming. And Parabon itself says its services are only available for criminal investigations (and, apparently, ad campaigns). But the message is still chilling. A project like The Face of Litter should serve as a provocation to talk critically about privacy, consent, and ethics surrounding the unsanctioned appropriation of someone’s DNA. So for now, the next time you drop that empty bag of Doritos onto the ground, you’re in the clear. But in the future? Just know it’s totally possible that you might be seeing your likeness plastered onto the subway walls.

Liz Stinson, Wired

Newborn screening collides with privacy fears

The wrinkled heel of nearly every baby in the United States is pricked at birth, and a few drops of blood are dabbed on filter paper and shipped off for analysis. Started in the 1960s, this newborn screening program tests for more than 30 rare and serious diseases that are treatable if caught early in life. Now, many public health experts who help run or advise the program are worried what the future holds. A new law shaped by a coalition of privacy advocates and conservative politicians requires consent for federally funded research on newborn blood spots, which include DNA but no names. Seeking consent sounds innocuous, even welcome. But experts are concerned that the law, which took effect in March, could hamstring not just fundamental research but also the kind of studies that routinely improve screening. Efforts to improve newborn testing often require studies on hundreds of thousands of stored blood samples; seeking consent for each one would be prohibitive and impractical. When California researchers sought informed consent to test a cuttingedge screening technology on blood spots from 400,000 newborns, for example, overworked hospital staff did not contact nearly half of eligible families, hampering the study. “Do you want genetic privacy at the expense of everything else?” asks David Orren, chief legal counsel of the Minnesota Department of Health in St. Paul.

When it began lumbering through Congress, the Newborn Screening Saves Lives Reauthorization Act of 2014 was unremarkable; it simply updated an expiring 2007 law that provided federal support for state-run newborn screening programs. In early 2014, the bill passed in the Senate—unanimously, and “in about 30 seconds,” says Cynthia Pellegrini of the March of Dimes in Washington, D.C., who advocated for the bill. The controversy began a few days before the House of Representatives voted on the bill last June, when a nurse named Twila Brase, who runs the Citizens’ Council for Health Freedom, a nonprofit in St. Paul that presses for medical privacy, reached out to the office of Michele Bachmann, a tea party icon whose district included the northern suburbs of Minneapolis-St. Paul until she retired from Congress earlier this year. Brase, who also opposes the federal mandate for electronic health records and the Affordable Care Act, had been fighting storage and research on newborn blood spots for years. Brase’s contact had its desired effect: When the bill reached the House floor, Bachmann delivered an emotional speech. “This legislation presumes that every parent of every newborn in the United States of America pre-agrees that the government can have their baby’s blood sample, which contains their DNA code,” she said. “Americans should not see the death of privacy, especially of the most sensitive private information that every American can have.”

Bachmann’s speech came too late to affect the House vote. The bill passed. But because legislators had added some minor tweaks to the language before voting, the bill had to return to the Senate, so that the two chambers were passing identical text. That gave time for Bachmann’s qualms to catch the attention of members of the conservative Senate Steering Committee, including Rand Paul (R–KY) and Patrick Toomey (R–PA). They sought input from her, as well as from officials from the March of Dimes, the National Institutes of Health (NIH), and other research and advocacy groups. After much discussion, the senators settled on the clause mandating informed consent when newborn blood spots were used in federally funded research. It passed both chambers and was signed into law by President Barack Obama a week before Christmas. At the crux of scientists’ and public health advocates’ concerns is what fits under the umbrella of “research,” which federal regulations define as investigations that “develop or contribute to generalizable knowledge.” Does testing a new screening technology qualify as research? What about studies of a test for a disease not currently on a screening panel, to determine whether it should be added? “There are public health functions that are mixed up with” what might be considered “pure” research, says Logan Spector, an epidemiologist at the University of Minnesota, Twin Cities. And some research that seems unrelated to newborn screening might not be: Probing leukemia’s origins, as researchers studying blood spots have done, could also represent nascent steps toward a test for leukemia risk.

Jeffrey Botkin, a pediatrician and bioethicist at the University of Utah in Salt Lake City, who is part of a federal advisory panel on newborn screening, worries about the impact of mandating informed consent. But he’s sympathetic to its appeal. “It’s good to be the subject of much more public dialogue and scrutiny,” Botkin says. Many acknowledge that screening programs could do a far better job of educating parents and doctors, ideally before a baby’s birth rather than in the distracted hours afterward. The Office for Human Research Protections is drafting guidelines on the law and plans to define what qualifies as research. In the meantime, scientists and state health departments are trying to anticipate the law’s effects. “We’ve essentially frozen” our repository, says Michael Watson, the executive director of the American College of Medical Genetics and Genomics in Bethesda, Maryland, which runs a virtual bank of dried blood spots. None of the four participating states plans to provide information from blood spots collected after March, when the law took effect. A pilot study to develop a test for detecting Duchenne muscular dystrophy “has been slowed down tremendously,” Watson says. There’s also a big question about whether the law is an early jolt of a larger seismic shift in how deidentified samples are handled. Until now, studying such samples, which carry no names or addresses and are not linked to an individual’s health records, hasn’t required informed consent. But in January, NIH began expecting grantees on genomic research to seek consent before using deidentified samples. The newborn screening law is turning that recommendation into a national requirement, at least for blood spots. (A handful of states already mandate consent.) Other samples, like tumor tissue or deidentified blood samples from adults, could be next. The Department of Health and Human Services is rewriting its “Common Rule” governing human subject research. An upcoming draft will reveal whether it wants consent for all deidentified samples. Once those regulations are finalized, perhaps within a couple of years, the newborn screening requirement for consent will be subsumed by the Common Rule. The Common Rule is Brase’s next frontier. She plans to comment on the proposed draft rules when they’re released, to urge that all deidentified samples be subject to informed consent before scientists can access them. “When researchers decide we’re theirs, that sets people up to oppose what’s happening in research,” she says.

Jennifer Couzin-Frankel, Science Magazine

Employer’s Use of DNA Test to Catch Employee Engaging in Inappropriate Workplace Behavior Violates Federal Law, Says U.S. District Judge

If someone continually, yet anonymously, defecated on the floor of your workplace, you’d probably want to use any and all legal means at your disposal to identify and discipline the perpetrator. Your methods might include surveillance or perhaps some form of forensic or other testing to link the offensive conduct to a specific individual. You would probably not be overly concerned that your efforts to rid the workplace of this malefactor might give rise to a discrimination claim, but is that really a safe assumption?

Background

In a case exemplifying the gentility of labor-management relations, a Georgia federal court grappled with how far an employer may go in this situation. In Lowe v. Atlas Logistics Group Retail Services, LLC, (N.D.Ga. May 5, 2015), the employer, Atlas Logistics Group Retail Services (Atlanta), LLC, which provides long-haul transportation and storage services for the grocery industry, discovered in 2012 that one or more employees had been using a common area in one of its warehouses as a lavatory. As part of its investigation into this matter, the company retained the services of a DNA testing lab and requested cheek swabs from two employees it considered suspects so that it could compare their DNA with that of the mystery defecator. After Atlas determined that neither employee was responsible for the unwelcome contributions to its workplace, the employees filed a lawsuit alleging that the company violated the Genetic Information Nondiscrimination Act (GINA) by requesting and requiring them to provide genetic information.

GINA prohibits discrimination on the basis of genetic characteristics and makes it unlawful for an employer to request, require or purchase genetic information with respect to an employee.

The Court Finds Atlas Violated GINA

The court held that Atlas’ argument that GINA only prohibited genetic testing that revealed an individual’s propensity for disease – which the test in this case did not do – was inconsistent with the statute’s text and legislative history as well as the applicable EEOC regulation. In the court’s view, this argument “render[ed] other language in GINA superfluous.” In particular, the court noted that the statute contained specific exceptions permitting certain testing that did not involve an individual’s propensity for disease, and if testing revealing a propensity for disease were the only prohibited testing, then those exceptions would not have been necessary. The court further rejected Atlas’ argument that GINA’s legislative history demonstrated an intent to limit violations to testing that revealed a propensity for disease, explaining that although a group of senators favored this interpretation during the legislative debate, all of the evidence indicated that Congress chose to reject this view in favor of a broad construction. Finally, the court held that an EEOC regulation listing eight examples of “genetic tests” did not support Atlas’ narrow definition of that term because the list included testing that also did not relate to one’s propensity for disease and, therefore, “would go beyond the scope of the statute” if the law were as narrow as Atlas claimed.

Conclusion

This case’s distasteful facts, which will undoubtedly remind many human resource specialists how coarse employee relations challenges often are in practice, should not distract employers that currently perform DNA tests from the fact that GINA may apply more broadly than some initially believed. Although the decision should not have a significant impact on the narrow range of situations where workplace DNA testing is a legitimate practice, such as those involving health and safety concerns, it should serve as notice to employers investigating misconduct that they should find methods other than DNA testing to identify culpable employees.

George Patterson, Employment Matters

Here’s how Apple, Google, and Microsoft are trying to get inside your genes-CRG in the News

Not satisfied by having our emails, chats, status updates, search histories, clicking behaviors, and shopping preferences, some of Silicon Valley’s most powerful tech titans are in an arms race to get access to your most personal information: your DNA.

Last week, for instance, the MIT Technology Review reported that Apple was looking to integrate genetic data into studies that run atop its new open-source research platform, ResearchKit. That should come as no surprise. There’s a national focus on personalized medicine, and since DNA information is becoming cheaper to get and store, the healthcare industry is hoping that personalized medicine will be part of the solution to rising costs.

Here’s a look at how three tech companies are preparing to dominate your DNA:

Apple

Apple’s ResearchKit platform may soon start integrating genetic information into its medical research efforts. The company has gone on the record saying that it’ll never see your health data. Instead, the data would most likely reside with the individual researchers whose studies were collecting DNA information. Alternately, it could be stored on servers maintained by the open-data nonprofit Sage Bionetworks, which worked with Apple to develop ResearchKit.

But the data that consumers willingly upload to HealthKit will be accessible to IBM’s Watson AI, according to InformationWeek:
As IBM receives Apple’s data, it will de-identify and store it in a secure and scalable cloud system. Researchers, doctors, and other health professionals will be able to view and share the data, as well as access data-mining and predictive analytics capabilities.

Applying artificial intelligence algorithms to health data, experts say, is where healthcare is heading. But because different types of data are often collected in disparate ways, drawing insights from it all is difficult. Apple, with the help of IBM, seems to be tackling that problem. And if they succeed, your iPhone and Apple Watch could become cutting-edge medical devices.

Google

Google has been investing in DNA-related companies, like 23andMe and DNAnexus, for years. More recently, the search giant offered cheap storage space to hospitals for their DNA data, through a new product called Google Genetics. For just $25 a year, a hospital could store a single copy of a person’s genome, according to the MIT Technology Review.

Doing analysis on that data will cost more, but that’s ultimately where the real value is — and where companies like Google could offer services that even some labs at at top-notch universities can’t afford. For years, the search giant has been recruiting experts in artificial intelligence to make sense of the world’s data. Deep learning is a subfield of artificial intelligence that’s especially good at pattern recognition, and it could help Google make inroads into serious life sciences research. In March, the company announced in a blog post that it would use its deep learning know-how for drug discovery. .

“Rather than just skimming the genome using superficial statistics,” Brendan Frey, an AI researcher at the University of Toronto who recently published a paper in the journal Science on using deep learning for genetic analysis, told me a few weeks ago, “the future lies in deep statistical analysis, also called deep learning, which will be used to find more profound patterns that relate elements in the genome to cellular activities and disease.”

Google’s medical efforts don’t end at DNA deep learning, though. The company has been on the hunt for synthetic chemists, and its research lab, Google X, is working on contact lenses that track glucose levels, in collaboration with pharmaceutical giant Novartis, and wristbands that can detect cancer cells.

Microsoft

Microsoft has been in the business of analyzing genetic information for some time, with products like HealthVault, an attempt at creating a health-data platform for consumers and doctors. The Cambridge branch of its research lab has an entire group dedicated to bioinformatics. Through collaborations with research organizations like MIT and the Wellcome Trust Sanger Institute, it’s developed several algorithms to try to tease out how environmental factors, like smoking or sunbathing, affect genetic predisposition to disease.

Microsoft is also leading the way on securing the DNA data it gathers. At the 2014 American Association for the Advancement of Science’s annual conference, Kristin Lauter, who heads up Microsoft’s cryptography research, discussed an encryption method she was developing, dubbed homomorphic encryption, that allows for scientists to encrypt genetic data, while letting researchers do experiments on it. She explained the technology to the Council for Responsible Genetics:
The primary new functionality enabled with homomorphic encryption is the ability to compute on encrypted data. This is very important for things like outsourcing storage and computation of data. The idea is that when using homomorphic encryption, the data owner – let’s say it’s a consumer or an enterprise – could encrypt the data locally and keep the key. Then they can upload that data to the cloud, and if they used homomorphic encryption, that data can still be operated on by the cloud and the encrypted results are available from the cloud to the data owner or anyone the data owner trusts to share the encryption key with. So it really allows a whole new functionality on encrypted data.

As she alludes to, this kind of technology could be useful for things like cloud-based medical records, another product Microsoft has worked on in the past.

Who will win?

None of this is purely charitable, of course. The tech company that wins the DNA research war will also make a fortune from selling its stores of data to pharmaceutical companies, research labs, and other buyers. The potential market for sequencing-driven treatments in oncology alone could be greater than $2 billion by 2018, according to a recent report by the consultancy McKinsey & Company. And the personalized-medicine market as a whole is estimated to be worth upwards of $230 billion, according to a report by PricewaterhouseCoopers.

So while you’re having your DNA sequenced and stored by a tech company, just remember: you may be getting some valuable insights about your health profile, but the company is making bank off your biology.

Daniela Hernandez , Fusion

Is DNA the next frontier in privacy?-CRG in the News

In late January, President Barack Obama announced what some have called a moonshot.

The $215 million Precision Medicine Initiative seeks to transform the health care system to target therapies to patients according to their unique genetics and environment.

The most ambitious part of the initiative is a proposal to enroll 1 million people in essentially a superstudy. Their genomes will be sequenced, their medical experiences will be chronicled through their electronic health records, and sensors worn by them will track their activities, behaviors and environmental exposures.

Participation in the program would be voluntary, but many are already concerned about the protection of the participants’ privacy. That includes the president.

“We’re going to make sure that protecting patient privacy is built into our efforts from Day One,” Obama said at the program’s announcement. “It’s not going to be an afterthought.”

Privacy is a reasonable concern for an undertaking that’s likely to generate exabytes of data (an exabyte is 1 quintillion bytes) on people’s bodies, behaviors and cellular makeup. And the issues range from protecting people’s identities and information to making sure participants have some level of control or knowledge of where the data generated is going and what it’s being used to study.

The effort complements other emerging for-profit ventures that are using large amounts of genetic data to try to help humans live healthier and likely longer lives.

Google, through its Google X life sciences division, intends to sequence thousands of people’s genomes and collect other physiological information to draw the clearest picture of human health yet and identify biological indicators of future disease. And Human Longevity, co-founded by maverick biologist Craig Venter, built the largest sequencing center in the world with the hope of processing 1 million genomes by 2020. It plans to combine those with data on people’s gut bacteria, health records and more to aid in the development of new therapies to prevent and treat disease.

“This is a bold, audacious kind of idea, but the time has come,” National Institutes of Health Director Francis Collins told “Fault Lines” in March about the government’s effort. “We have the chance to really find out what are the factors that keep people healthy or cause illness to happen and, when it happens, how to manage it.”

Target for cybercrime?

At a hearing about the Precision Medicine Initiative in front of the Senate Health, Education, Labor and Pensions Committee on May 5, Democratic Sen. Patty Murray of Washington state warned of the risks to privacy.

“In the last few months we’ve seen serious security breaches impacting families’ personal health information, and that’s unacceptable,” she said. “We need to be aware that data is being created that cybercriminals will want to exploit, and that means we will need to develop a strategy to protect privacy that meets today’s challenges.”

Collins responded that the White House, the NIH and the Office of the National Coordinator for Health Information Technology were all “deeply serious” about protecting the data of its volunteers.

He told “Fault Lines” that as a first step, he would de-identify the data, or remove any obvious identifiers — like names, addresses, Social Security numbers and dates of birth — from DNA samples and other health information.

But the lack of clear plan beyond that is troubling to some privacy advocates.

“I’ve heard almost nothing from any of the proponents of the Precision Medicine Initiative as to what structures they’re going to construct and put in place to protect this information,” said Jeremy Gruber, the president and executive director of the Council for Responsible Genetics. “I’m sure they’ll make all kinds of promises that they are appreciative of the issue and will address it.”

Details on security for the new effort may be scant, but medical centers all over the country are protecting sensitive information every day, largely successfully, noted Atul Butte. He heads the California Initiative to Advance Precision Medicine, which is starting two pilot research studies as a proof of principle for this approach to medicine.

“You could legitimately argue about how secure you can keep things on the Internet,” he said. “But would cybercriminals go after [genetic data] if there are banks with money storing their data online?”

Collins told “Fault Lines” that the Initiative aims to do the best it can to avoid obvious slip-ups that would leave volunteers’ data exposed.

“You can’t guarantee people that there’s no way that somebody — either accidentally or for nefarious purposes — might figure out who they are,” he said. “There’s no perfect way to deal with privacy in 2015.”

Concerns about data sharing

In the effort to build its cohort of 1 million, the Precision Medicine Initiative is likely to look for collaborators with information to marry into its database. Possible partners include the U.S. Department of Veterans Affairs, which is attempting to partially sequence 1 million veterans for its own research, and the extensive patient files at Kaiser Permanente of Northern California.

“We’re starting to see, very quickly in the last couple of years, particularly with these biobanks, an incredible effort to try to network now,” said Gruber. “So we’ve had the type of privacy protections that we’ve had not because any type of framework was in place to ensure them but simply because of the fact that these databases were separated.”

Sharing data is a key to the efficacy of precision medicine: the more data, the better when trying to find patterns and signals to develop possible treatments. But offering access to a data set can bring up issues of consent, with study participants not knowing what their information is being used for.

Take the case of 23andMe, a company in which Google is a major investor. Founded in 2006, 23andMe offered customers an analysis of their DNA that included assessments of their risk of developing various illnesses. In 2013 the U.S. Food and Drug Administration shut down that service.

In the past year, the company announced deals to share its database of 950,000 partial genome sequences with Pfizer and Genentech, among others, to study diseases. The moves prompted many critics, including Gruber, to accuse the company of misleading its customers by selling their data.

“More than 80 percent of 23andMe customers consent to research,” said a statement that the company provided to “Fault Lines.” “Ultimately, 23andMe customers own their data. Customers can decide to stop participating in research at any time and remove all of their information from our database.”

Hank Greely, a Stanford law professor who studies biomedical ethics, said that 23andMe customers might not have understood what they were agreeing to when they read the company’s consent form.

“It says, ‘I’m willing to let my data be shared for research into disease,’” he said. “It doesn’t say, ‘I’m willing to let you sell my data to Pfizer for $200 million.’”

When asked how he planned to avoid the sort of issues 23andMe had run into, Collins told “Fault Lines” that participants in the Precision Medicine Initiative would be treated as partners in the research and that they would have a say in deciding how much exposure they want their data to have.

He said it’s imperative that the program be flexible enough to accommodate people who will share anything if it will help others, as well as those who might later decide that they would like to limit the exposure their personal data gets.

“It’s going to be up to them to decide what’s an acceptable level of privacy and where are they willing to take risks,” said Collins. “And each individual, ideally, ought to be able to set that bar for themselves. Because we all differ.”

Nikhil Swaminathan, Al Jazeera

Apple Has Plans for Your DNA

Of all the rumors ever to swirl around the world’s most valuable company, this may be the first that could involve spitting in a plastic cup.

Apple is collaborating with U.S. researchers to launch apps that would offer some iPhone owners the chance to get their DNA tested, many of them for the first time, according to people familiar with the plans.

The apps are based on ResearchKit, a software platform Apple introduced in March that helps hospitals or scientists run medical studies on iPhones by collecting data from the devices’ sensors or through surveys.

The first five ResearchKit apps, including one called mPower that tracks symptoms of Parkinson’s disease, quickly recruited thousands of participants in a few days, demonstrating the reach of Apple’s platform.

“Apple launched ResearchKit and got a fantastic response. The obvious next thing is to collect DNA,” says Gholson Lyon, a geneticist at Cold Spring Harbor Laboratory, who isn’t involved with the studies.

Nudging iPhone owners to submit DNA samples to researchers would thrust Apple’s devices into the center of a widening battle for genetic information. Universities, large technology companies like Google (see “Google Wants to Store Your Genome”), direct-to-consumer labs, and even the U.S. government (see “U.S. to Develop DNA Study of One Million

People”) are all trying to amass mega-databases of gene information to uncover clues about the causes of disease (see “Internet of DNA”).

In two initial studies planned, Apple isn’t going to directly collect or test DNA itself. That will be done by academic partners. The data would be maintained by scientists in a computing cloud, but certain findings could appear directly on consumers’ iPhones as well. Eventually, it’s even possible consumers might swipe to share “my genes” as easily as they do their location.

An Apple spokeswoman declined to comment. But one person with knowledge of the plans said the company’s eventual aim is to “enable the individual to show and share” DNA information with different recipients, including organizers of scientific studies. This person, like others with knowledge of the research, spoke on condition of anonymity because of the company’s insistence on secrecy.

One of these people said the DNA-app studies could still be cancelled, but another said Apple wants the apps ready for the company’s worldwide developers’ conference, to be held in June in San Francisco.

Sophisticated data

Starting last year, Apple began taking steps to make its devices indispensable for “digital health.” Its latest version of the iOS operating system includes an app called Health, which has fields for more than 70 types of health data—everything from your weight to how many milligrams of manganese you eat (as yet, there’s no field for your genome). Apple also entered a partnership with IBM to develop health apps for nurses and hospitals, as well as to mine medical data.

Now Apple is closely involved in shaping initial studies that will collect DNA. One, planned by the University of California, San Francisco, would study causes of premature birth by combining gene tests with other data collected on the phones of expectant mothers. A different study would be led by Mount Sinai Hospital in New York.

Atul Butte, leader of the UCSF study and head of the Institute for Computational Health Sciences, said he could not comment on Apple’s involvement. “The first five [ResearchKit] studies have been great and are showing how fast Apple can recruit. I and many others are looking at types of trials that are more sophisticated,” Butte says. Noting that the genetic causes of premature birth aren’t well understood, he says, “I look forward to the day when we can get more sophisticated data than activity, like DNA or clinical data.”

To join one of the studies, a person would agree to have a gene test carried out—for instance, by returning a “spit kit” to a laboratory approved by Apple. The first such labs are said to be the advanced gene-sequencing centers operated by UCSF and Mount Sinai.

The planned DNA studies would look at 100 or fewer medically important disease genes (known as a “gene panel”), not a person’s entire genome.

These targeted tests, if done at large scale, would not cost more than a few hundred dollars each.

Like the ResearchKit apps released so far, the studies would be approved by Apple and by an institutional review board, a type of oversight body that advises researchers on studies involving volunteers.

The ResearchKit program has been spearheaded by Stephen Friend, a onetime pharmaceutical company executive and now the head of Sage Bionetworks, a nonprofit that advocates for open scientific research.

Friend’s vision for a data “commons” in which study subjects are active participants in scientific research was enthusiastically embraced by Apple starting in 2013. Friend, whom Apple describes as a medical technology advisor, declined an interview request through an assistant.

Silicon Valley companies are intent on using apps and mobile devices to overrun what Friend has called the “medical-industrial complex.” The problem is that hospitals and research groups are notorious for hoarding data, in many cases because they are legally bound to do so by state and federal privacy regulations. But no law stops individuals from sharing information about themselves. Thus one reason to “empower patients,” as rhetoric has it, is that if people collect their own data, or are given control of it, it could quickly find wide use in consumer apps and technologies, as well as in science.

One study that could get a boost from the iPhone is the Resilience Project, a joint undertaking by Sage and Mount Sinai to discover why some people are healthy even though their genes say they should have serious inherited diseases like cystic fibrosis. That project has already scoured DNA data previously collected from more than 500,000 people, and as of last year it had identified about 20 such unusual cases. But the Resilience Project was having difficulty contacting those people because their DNA had been collected anonymously. By contrast, recruiting people through iPhone apps could make ongoing contact easy.

Hard to handle

By playing this role in gene studies, Apple would join a short list of companies trying to excite people about what they might do with their own genetic information. Among them are the genealogy company Ancestry.com, the Open Humans Project, and 23andMe, a direct-to-consumer testing company that has collected DNA profiles of more than 900,000 people who bought its $99 spit kits.

That is one of the largest DNA data banks anywhere, but it took 23andMe nine years of constant media attention, such as appearance on Oprah, to reach those numbers. By comparison, Apple sold 60 million iPhones in just the first three months of this year, contributing to a total of about 750 million overall. That means DNA studies on the ResearchKit platform could, theoretically, have rapid and immense reach.

But DNA data remains tricky to handle, and in some cases what people can be told about it is regulated by the U.S. Food & Drug Administration.

One study launched this year by the University of Michigan, Genes for Good, uses a Facebook app to recruit subjects and carry out detailed surveys about their health and habits. In that study, participants will be sent a spit kit and will later gain access to DNA information via a file they can download to their desktops.

So far about 4,200 people have signed up, says Gonçalo Abecasis, the geneticist running the research. Abecasis says that the project will tell people something about their ancestry but won’t try to make health predictions. “There is tension in figuring out what is okay as part of our research study and what would be okay in terms of health care,” he says. “You can imagine that a lot of people have a good idea how to interpret the DNA … but what is appropriate to disclose isn’t clear.”

One issue facing Apple is whether consumers are even interested in their DNA. So far, most people still have no real use for genetic data, and common systems for interpreting it are lacking as well. “In 10 years it could be incredibly significant,” says Lyon, the Cold Spring Harbor geneticist. “But the question is, do they have a killer app to interact with their [DNA] quickly and easily.”

Some people have ideas. Imagine you could swipe your genes at a drugstore while filling a prescription, getting a warning if you’re predicted to have a reaction to the drug. Or perhaps an app could calculate exactly how closely related you are to anyone else. But Lyon believes that right now the story is mostly about helping researchers.

“They need people to donate their DNA,” he says. “One incentive is to have it on their phone where they can play with it.”

Antonio Regalado , MIT Technology Review

False positive highlights limitations of familial DNA searching

Michael Usry, a young New Orleans filmmaker, has a flair for the macabre. His award-winning output includes titles like “Murderabilia,” a dark production that spotlights the trade in collectibles related to real-life killings and other violent crimes.

Usry’s work can come off as gratuitously violent, as in a clip from the short film “Winding Down” in which his protagonist disembowels a corpse in a basement.

But for the Idaho Falls Police Department, his filmography seemed outright suspicious.

The authorities in that Idaho city targeted Usry last year as a suspect in the 1996 murder of Angie Dodge, a case that’s drawn national media attention amid claims that the wrong man was convicted.

The fatal stabbing remains steeped in mystery, as DNA from the crime scene failed to match any of the millions of genetic profiles on file in the national criminal database. Police still believe Dodge had multiple attackers, but traditional forensic testing has failed to identify the man whose semen was found on the 18-year-old’s body.

Investigators last year turned to a controversial technique known as familial searching, which seeks to identify the last name of potential suspects through a DNA analysis focusing on the Y chromosome. A promising “partial match” emerged between the semen sample and the genetic profile of Usry’s father, Michael Usry Sr. — a finding that excluded the father but strongly suggested one of his relatives had a hand in the young woman’s murder.

The results instantly breathed new life into a high-profile investigation in which Idaho Falls authorities have weathered intense criticism. But the story of how the police came to suspect the younger Usry and then eventually clear him of murder raises troubling questions about civil liberties amid the explosive — and increasingly commercial — growth of DNA testing.

The elder Usry, who lives outside Jackson, Mississippi, said his DNA entered the equation through a project, sponsored years ago by the Mormon church, in which members gave DNA samples to the Sorenson Molecular Genealogy Foundation, a nonprofit whose forensic assets have been acquired by Ancestry.com, the world’s largest for-profit genealogy company.

Ancestry.com received a court order last summer requiring it to reveal Usry’s name to the police, although it is listed as “protected” in the Sorenson Y-chromosome database, according to court records obtained by The New Orleans Advocate. Following this new lead, the police mapped out five generations of Usry’s family, narrowing their focus to three men.

Only one, the New Orleans filmmaker, fit the mold of a plausible suspect, according to an application for a search warrant. Usry, 36, had ties to Idaho, including two sisters who attended a private university about 25 miles from the crime scene.

In addition, some of Usry’s Facebook friends lived in the state. And in their search warrant application, police also mentioned Usry’s short films, which they said generally have “dealt with some sort of homicide or killings.”

“All of the circumstantial evidence was right,” said Sgt. James Hoffman, of the Idaho Falls Police Department. “He seemed like a really good candidate. But we’ve had that happen before.”

Days of suspense

Detectives traveled to New Orleans in December and persuaded a magistrate judge to sign a search warrant ordering Usry to provide his DNA for comparison. For about a month, Usry lived in a state of suspense, fearing he’d be taken into custody regardless of the test results.

“I had lots of days sitting at the house with the dog,” he recalled in an interview, “wondering if these guys were going to use a battering ram to bust open the door and shoot my dog after he started barking at them.”

On. Jan. 13, Usry received the email he’d been awaiting. His DNA, Hoffman wrote, did not match the semen from the scene of Dodge’s murder.

“It turned out to be nothing,” Hoffman said in a telephone interview. “I wish it wasn’t a dead end, but it was.”

Several experts agreed the Idaho Falls police had probable cause to take a swab from Usry. But his experience touches on the delicate balance between the right to privacy and public safety.

“It’s not very common to see this sort of thing, and I frankly hope it doesn’t become very common because an awful lot of people won’t bother testing” their DNA, said Judy G. Russell, a genealogist and attorney who writes The Legal Genealogist blog.

Ancestry.com did not respond to questions about how frequently it receives court orders in criminal investigations and whether it ever resists law enforcement requests to learn the identity of otherwise protected genetic information.

Erin Murphy, a professor at the New York University School of Law who has written about familial searching, said Usry’s case is the first she’s seen in which law enforcement used a publicly accessible database like Sorenson, as opposed to a private law enforcement database, to obtain an investigative lead.

“I think what we’re looking at is a series of totally reasonable steps by law enforcement,” Murphy said. “But it has this really Orwellian state feeling to it, and it is a huge indictment of private genetic testing companies and the degree to which people seamlessly share that information online.”

A controversial tool

Familial searching differs from traditional DNA testing, a mainstream tool used to identify criminals. In familial searching, the number of partial matches — in which genetic profiles share several common “alleles,” or variant forms of genes — can be overwhelming.

In Usry’s case, Hoffman’s search of the Sorenson database yielded 41 partial matches. Though the name was initially shielded, the strongest match was Usry’s father, with 34 of 35 alleles, which the Sorenson Forensics Lab in Utah deemed “exceptionally good” and indicative of a close family relation to the suspect.

Familial searching in law enforcement dates back over a decade to Great Britain, which employed the technique in the 2003 case of Craig Harman, who threw a brick through the windshield of a passing vehicle, causing the driver to suffer a fatal heart attack. British authorities could find no direct match between the DNA found on the brick — Harman’s blood — and a national database of criminal defendants.

But they found two dozen similar genetic profiles belonging to people from the surrounding region, including Harman’s brother, who represented the closest partial match to the blood sample. Further probing led investigators to Harman, who reportedly gave his DNA and confessed to the crime in the face of a match.

In the United States, the most notable use of familial searching was the case of the notorious Grim Sleeper. An alleged serial killer, Lonnie Franklin, was indicted in 2011 on 10 counts of murder in Los Angeles after authorities found similarities between crime scene evidence and the DNA of Franklin’s son, who recently had been jailed on a weapons charge.

The public debate largely has centered on the use of law enforcement databases like the FBI’s Combined DNA Index System.

Proponents argue familial searching is a harmless way for police to crack otherwise unsolvable cases. The closest partial matches can steer investigators toward a criminal’s family members, whose DNA profiles closely resemble those of a convicted or incarcerated relative.

Skeptics like Murphy, the NYU law professor, warn that the technique drastically expands DNA testing beyond the function envisioned by states that compel criminal defendants to submit DNA samples upon arrest. Many states lack formal legal rules governing the use of familial searching by law enforcement, while Maryland has explicitly outlawed the practice.

In Louisiana, familial searching by law enforcement appears to be exceedingly rare. The Louisiana State Police Crime Lab does not conduct that method of testing, said Capt. Doug Cain, a State Police spokesman.

“It’s not been a bone of contention here as it has in other states,” said Kevin Ardoin, director of the Acadiana Crime Lab. “I don’t believe we have any restrictions on it, though, probably because it’s not been pursued or challenged.”

Usry’s experience, Murphy noted, differs from a familial search involving a law enforcement database, in that Usry’s father voluntarily submitted his DNA as part of a genealogical project. But, she added, “that doesn’t mean that many people wouldn’t find it surprising — and troubling — to know that a DNA swab they sent in for recreational purposes” could years later land their child in an interrogation room.

“I think this case puts into stark relief some of the critical privacy concerns surrounding consumer genetic testing companies, public repositories of genetic information, DNA familial search practices and the general degree to which law enforcement should be able to access genetic information,” Murphy said.

A cloud of suspicion

The call came in early December, as Usry was visiting his parents in Mississippi. The caller identified himself as a law enforcement official in New Orleans and said he was investigating a hit-and-run in City Park.

“I didn’t take it as a big deal,” Usry said. “He said he wanted to get together, ask a couple of questions and take a couple pictures of my car.”

Knowing he had nothing to hide, Usry agreed to meet with the officer. After he returned to New Orleans, three lawmen arrived at his door, including two detectives from Idaho Falls. The other, Usry said, was a federal agent.

The officers led Usry to the 13th floor “of some building by the Superdome, an interrogation room with a one-way mirror.”

“They told me that it was not, in fact, about a hit-and-run,” Usry said. “They wanted to know about my travels to Idaho.”

Usry piqued the officers’ interest, he said, when he recounted a ski trip he’d taken when he was about 19 with three friends. While Usry couldn’t recall ever setting foot in Idaho Falls, his interrogators determined he must have passed through the city when driving to Rexburg, Idaho, to pick up a friend.

At the end of the interview, Usry said, the federal agent entered the small room with “gloves on, ready to go.” It finally occurred to him that he might want to consult a lawyer when the lawmen hovered over him and extended a long Q-tip into his mouth.

“It really took me until almost the end of the entire experience to realize that they were saying, ‘We think that you, Michael Usry, are a suspect in this murder,’ ” he said.

When the officers dropped Usry off at home, he said, “I just kind of stood on my sidewalk dazed for a few minutes.”

He called a friend, a co-producer of the short film “Murderabilia.”

“You’re not going to believe what just happened to me,” Usry told him.

It took his friend about 30 seconds to search “Idaho Falls cold case murder” online and determine the interrogation was related to the Dodge killing, he said.

Coming to terms

In the weeks since the questioning, Usry said, he’s wondered whether someone else in his family — perhaps a cousin or distant relative he hasn’t even met — had something to do with the killing.

Colleen M. Fitzpatrick, a well-known forensic genealogist, said a partial match of 34 of 35 alleles is “very close to a 100 percent” indication that the donor of the semen is an Usry. She suggested the authorities take a closer look at the family lineage.

“There’s still a small percent chance that it’s not an Usry due to an adoption or illegitimate” child in the family lineage, she noted.

Greg Hampikian, a professor at Boise State University who has worked on the Dodge case, also seemed impressed by the partial match. According to the search warrant application, he told police that Usry’s father “would probably be within three or four generations” of the unidentified suspect.

Asked whether police thought the semen donor might be someone else in Usry’s family, Hoffman, the Idaho Falls sergeant, said, “Not that I can see so far. We’re still investigating everything we can.”

Usry said he regarded his experience as an invasion of privacy, made even worse because his father’s DNA had been submitted during a church-sponsored event. But it also has emboldened Usry to try to find out the truth about the Dodge case — in the best way he knows how.

He is working on a documentary and researching the well-publicized case of Christopher Tapp, whose conviction in Dodge’s killing has drawn widespread criticism.

“I feel a connection to this case because I’ve been forced to be involved in it,” Usry said. “The guy that really killed Angie Dodge deserves to be put in jail.”

Jim Mustian, New Orleans Advocate