Tag Archives: dna data

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

How drug companies will mine your genes

Imagine a world where genetic sequencing is free, like Gmail. That’s where we’re headed. Genetic data is going the way the rest of our data has gone on the web. Companies will mine it, repackage it, and find a way to make money off it.

For eight years, personal genomics company 23andMe has been giving consumers access to their genes. It started off costing $999. Today it’s $99. In 2012, the company allowed consumers to share their data with third-party apps, the way you might link your Facebook profile to your Hulu account.

And this week, what could be seen as another step toward the full webification of our DNA went down, thanks to a new deal between 23andMe and Genentech, one of its early investors.

The Deal

To start, Genentech will pay to get access to the genetic and health information 23andMe has amassed from more than 10,000 of its customers with Parkinson’s disease, a disorder that affects movement. Genentech scientists will be able to see what medications they’re on, what other conditions they have, the symptoms they experience, along with whether they have tweaks in their DNA that put them at risk for developing the disease. (All these customers previously consented to be part of research by 23andMe and its partners.)

But the deal goes further. 23andMe will help Genentech identify approximately 3,000 customers who want to participate in more nuanced research.

23andMe only analyzes snippets of your DNA. Genentech needs the whole genome. So, it’s going to pay to sequence them, if they agree. Whether or not the patients will get that information back is still being worked out, 23andMe’s Emily Drabant Conley, who brokered the Genentech partnership, told me.

“We’re now starting to do [studies] at this really unprecedented scale,” she added. “Our database has hit a critical mass. These people can be recontacted. They’re engaged. The other thing that’s happening is pharma is seeing the value of bringing in genetics into the R&D pipeline earlier.”

You can see how this might evolve.

“With 23andMe,” wrote Lisa Miller in New York magazine last April. “[CEO Anne Wojcicki] wants to do with DNA what Google did for data—because, after all, DNA is data.” And what Google — and other web giants have done — is to create powerful platforms through which other companies can sell us stuff.

This vision of Googlized genetics thrives only in a world with minimal hurdles to getting data. It might take a decade or more, but eventually the cost will get low enough to allow companies to offer full genome sequencing for free, at massive scales.

“I would love that. It would be great…We want to have a product that’s accessible,” said 23andMe’s Drabant Conley. “I don’t foresee that happening in the near future. There are real costs involved.”

But when cost does hit that critical minimum, the true democratization of genetics will unfurl. It will just be something very different from what we were sold on.

The Promise

Eight years ago, when 23andMe first launched, it wooed technophiles with the idea that genetic information shouldn’t be locked away in a lab. It belonged to you. We had the right to spit in a tube and find out what diseases we might be at risk for, bureaucracy be damned.

Geneticist Misha Angrist, a senior fellow in Science & Policy at Duke University’s Social Science Research Institute, was one of the people who bought into that vision. He sent his DNA off to be analyzed by 23andMe and other companies that offered direct-to-consumer (DTC) genetic tests. This was the future.

Until it wasn’t.

Reports started coming out that genetic tests offered by different companies served up different interpretations of people’s genes. Sometimes, they were misleading. Genome wide association studies — the science upon which DTC genetics companies were built — started coming under fire. How much could you really tell from looking at individual mutations without analyzing the whole genome? Regulators started to notice. Then last year, the U.S. government slapped 23andMe with a cease-and-desist letter ordering it to stop marketing its spit-box genetic test as a health report. That reduced 23andMe, if only temporarily, to a glorified ancestry service since. The over-the-counter genetic testing industry, as we imagined it, seemed in jeopardy.

And then, this Genentech deal.

“I kind of think of this as a sad day. I think it’s sort of the final confirmation that direct-to-consumer genetics is not a viable business,” said Angrist. “I think this day was probably inevitable. It’s hard for me to feel betrayed. And you now if my genotype contributes to a blockbuster drug…and it improves people’s lives, I can’t be an asshole and say, ‘Boy that’s terrible!’, but given the rhetoric and the marketing of DTC genetics, which again, I admittedly bought into and wanted to buy into — I wanted it to be true — it’s hard for me to stand on the sidelines and say, ‘Yay! Rah-rah! Go Genentech.’”

That rhetoric harkened back a bit to the days of the early internet, when we learned to equate the sound of beeping modems to a superhighway of information that would empower us to be better. The information was seemingly accessible to all, for a fraction of the price it might have cost to access in the real world. That democratization morphed into something beyond our expectations, too.

“Just as it became clear that people didn’t want to pay money to AOL or Prodigy for email, Google found a way to give email away and derive ad revenue from somewhere else,” said Angrist. “It’s all the same business model,” a model in which you are the product. This internet-age adage is true, especially for DNA.

The new Genentech deal is only the beginning. Reset Therapeutics put out a press release saying it was going to use 23andMe’s massive database to study diseases related to circadian rhythms, the internal clocks that dictate when we sleep and eat. (Whether Reset will also be sponsoring its own genetic sequencing wasn’t clear.) And there are eight other deals coming, the details of which will trickle out in coming weeks. All the company would say for now is that they span a wide range of diseases and conditions.

As disappointing as the news may be to some, the strategy isn’t all bad. It could really open up new areas of research, in ways that current methods simply can’t.

“This is very exciting.  An integrated, enthusiastic cohort of 800,000 is far beyond academic capacity,” said George Church, one of the leaders of the Human Genome Project, in an email. (He’s also an advisor to 23andMe and was on the advisory board of a company recently acquired by Roche, Genentech’s parent company.) “I expect that the 23andMe cohort will continue to grow and be increasingly targeted to diseases of interest to pharma.”

Say Genentech wants to screen compounds for a new heart-disease drug they suspect might only work on a subset of patients with a certain genetic makeup. They can query 23andMe’s database, come up with potential candidates, and recontact them to sequence them. What’s more using new technologies like organoid chips, they can take skin cells from these patients, reprogram them, and build up tiny tissue-specific systems on which they can test their compounds. The results could give them a good indication of which ones might be toxic or work in individual patients. They could run multiple experiments at once, potentially speeding R&D up significantly.

For pharma companies, it’s a no brainer, especially with 23andMe customers at the ready, willing to supply more data in the hopes of finding a cure for the condition that ails them or their relatives.

As 23andMe co-founder Linda Avey put it on Twitter:

That economic value, though, will accrue to 23andMe.

The company’s terms of service clearly state that “by providing any sample…you acquire no rights in any research or commercial products that may be developed by 23and­Me or its collaborating partners.”

Daniella Hernandez, FUSION

23andMe turns spit into DNA data sales to Pfizer

23andMe Inc., the genetic-testing startup backed by Google, is sharing DNA data on about 650,000 individuals with Pfizer to help find new targets to treat disease and to design clinical trials.

The collaboration with Pfizer is the broadest announced so far in 23andMe’s ambitious plan to become a repository for humanity’s genetic makeup, and to turn data gathered from $99 saliva tests sold to consumers into multimillion-dollar deals with drugmakers.

The agreement unveiled Monday gives the U.S.’s largest drugmaker access to anonymous, aggregated information from consumers who bought 23andMe’s test over the past seven years to learn about their own genetic histories. It includes only people who agreed to let their data be used in research. Pfizer and 23andMe declined to give the deal’s value.

The Silicon Valley startup, named for the 23 pairs of chromosomes in human cells, is betting its growing troves of genetic data will prove essential to drug companies, medical researchers and even health and wellness companies.

Even as it seeks to expand its consumer tests around the world, the company is repairing relations with the Food and Drug Administration. An agency ruling in late 2013 left 23andMe unable to sell health analyses from the saliva tests.

While about two-thirds of 23andMe’s 800,000 customers agreed to let their test data be used in research, data-sharing agreements with drugmakers are likely to raise the hackles of privacy advocates who have questioned the wisdom of compiling highly personal information.

The deal gives Pfizer access to a broad cross-section of data, the first agreement in which a drugmaker has access 23andMe’s newly created research portal. 23andMe Chief Executive Officer Anne Wojcicki plans to pitch the service to other health companies this week at the JPMorgan Healthcare Conference in San Francisco. The company plans to announce a total of 10 similar deals with drugmakers and biotechnology companies this year.

23andMe, based in Mountain View, California, is near the Bay Area’s biggest technology companies, including Google, co- founded by Wojcicki’s husband Sergey Brin. The two are separated, though still legally married.

Google’s venture-capital arm and investors such as Russian billionaire Yuri Milner, Johnson & Johnson and venture-capital firm New Enterprise Associates have contributed $126 million in funding to date, according to 23andMe.

The company isn’t yet profitable, and it’s too early to consider an initial public offering, Wojcicki said.

While Pfizer has already worked with 23andMe to enroll 10,000 patients for irritable bowel disease research, the deal broadens their collaboration. Pfizer and 23andMe will also enroll 5,000 patients to conduct a study on the genetics of autoimmune disease lupus.

The company has also signed agreements on specific diseases, including one with Roche Holding’s Genentech unit announced last week, to study Parkinson’s disease patients.

Genentech will use the data to find the connection between patients’ symptoms and other personal traits, and their genetics,

said Alex Schuth, head of technology innovation and diagnostics in business development at Genentech, in a telephone interview.

Genentech is paying 23andMe $10 million upfront and as much as $50 million if the deal hits certain milestones.

The appeal to Pfizer and Genentech isn’t just the size of 23andMe’s data set – it’s the additional information that the company collects on users’ personal lives.

Every time consumers who bought the kit return to 23andMe’s website, they are prompted to answer more questions from an “infinite question box,” which quizzes them on everything from hair color to bra size, said Patrick Chung, a 23andMe board member and a partner in the Cambridge, Massachusetts-based venture capital firm Xfund. That additional information can help researchers make more connections about people’s characteristics and their health.

23andMe plans to debut in other countries this year, said President Andy Page in a telephone interview, though he declined to name the locations. The consumer spit kits, which

include reports on known risk factors for Alzheimer’s, Parkinson’s and cystic fibrosis, started sales in Canada and the U.K. last year.

The company has also given its kits away to get a more diverse set of genes for its database, including giving away 10,000 kits to black Americans one year, Wojcicki said. “You’ll see us in the future sponsoring those kinds of programs,” she said.

Caroline Chen Bloomberg News

Taking your Genome to the Bank

What’s more valuable than your money, equally vulnerable, and unique to you? Answer: Your genome. And just like your money, your genome should be stored securely as possible and those institutions that store your genome should be regulated on how they store it, use it, and potentially share it.

As medical science advances, it’s going to be increasingly important for people to be able to control and manage access to their personal genomes. To make this possible, we need to establish a formal, well-regulated system of genome banking. Just as the government regulates the banks that hold our money, we must also have it or an equivalent group/system to govern how institutions manage our genomic data. Because it is only by guaranteeing the security and use of that information that we will be able to exploit the full potential of the growing pool of genomic data for the betterment of the individual and for mankind.

Everyone’s genomic data, after all, is potentially life saving and life changing. We’ve long known that each of us has a unique string of three billion or so tiny molecules linked together in our own genetic code. That code governs much of our health and well being. It dictates the color of our eyes, how tall we can grow, our relative risk of developing cancer, and much more. Your genome also has big implications for your children and other members of your family. If a family member develops an inheritable disease such as breast cancer or Huntington’s, the information in your genome could be crucial to determine if other family members are also at risk. Think of this as the estate you pass on to your heirs.

Craig Venter was recently quoted in a Businessweek article saying ? “It’s going to be important to know what the variant is you got from your mother and from your father, and whether that correlates with 30 other variants across the genome that are associated with susceptibility for a certain type of cancer, for example.”

Genomic data is also becoming increasingly important in medical research. Studies of Alzheimer’s suggest that one reason so many clinical trials have failed so far is because the studies need to be done in people with earlier stage disease, which is currently very challenging to detect. In the future, it’s likely that people whose relatives have the disease will be able to get a simple blood test that will help estimate their own risk. Additional studies will then be used to select optimal candidates for early stages trial of new Alzheimer’s drugs.

But there’s also a dark side to genome sequencing. Hackers can sneak into databases and determine the owner of an “anonymous” genome using DNA identifiers. They can also uncover previously unrecognized sensitive information about someone’s genome, or unmask areas that researchers have attempted to keep from public view.

In probably the most famous example of this, James Watson (the co-discoverer of the DNA double helix) made almost his entire genome public in 2007. One gene—APOE, which helps predict risk of Alzheimer’s disease—had been masked before Watson’s genome was published. However, several geneticists said they could tell whether or not he carried the gene, based on other mutations that are commonly inherited with APOE. No one publicized his APOE status, but it became clear that publishing your genome could entail risk to your privacy.

Then in January 2013, a researcher at Massachusetts’ world-renowned Whitehead Institute tracked down five people who he selected at random from a DNA database. Using just their DNA, ages, and the states where they lived, in a matter of hours he identified the five as well as some of their relatives.

Such stories are unnerving to many, who worry that insurance companies or employers will use genetic information to discriminate against them. Even though it’s technically against the law, this is a widespread fear.

Some experts claim it’s time to simply accept that we are in a genomic era, and that will entail some risk to privacy. They are encouraging people to donate their DNA to large public databases so that we can more rapidly advance genomic testing and diagnosis. But for those who are not comfortable sharing their data (whether public or private unregulated entities) there should be an alternative that doesn’t involve simply trusting that our data will be safe. We should be able to have a guarantee that our genomes will be safe and managed according to standards. As we have done in the past—you can store you money in your mattress or you can choose to store it in a bank that is regulated and must abide by guidelines.

The system I am suggesting is one that would set up firm rules for how genomic data is stored, used, and transferred/loaned between institutions, just as we have rules for transferring money. Once those system and rules are in place and have been widely communicated, more people will trust the system. With greater confidence in the system, more people will start to participate and we can finally enter a truly genomic era that can profoundly affect the future of humanity. My challenge to lawmakers and policy makers is to not look at this area as something that is managed by researchers but something of significant value to society that affects every human being on earth. And if that is believed to be true—then this valuable asset should be rightfully standardized, regulated and managed to create a system that benefits all individuals both here and abroad.

Harry Glorikian , GEN

New Encryption Technique Promises to Keep Your Genetic Data Secure- For Now

Our genetic codes — the string of nucleotide “letters” that comprise our genomes — contain information about which diseases we may be susceptible to, or, what health conditions we have a predisposition for. However, this information is not absolute; having a gene or series of gene mutations that are biomarkers for a given disease, or spectrum of diseases, does not mean that our fate is sealed. Genetic information only provides an indication of probabilities — though what those probabilities are depends upon may other factors, many of which — like diet and exercise — are not in our genes at all.

And yet, medical research programs as well as medical insurance providers value this information and often use it to make treatment or research study participation decisions and insurance risk (and thus pricing) decisions, respectively. These are just two obvious uses of genetic data; there are other possible uses, no doubt, that we have yet to foresee. For these reason, issue of genetic privacy has emerged in recent years. This concern over protecting one’s genetic data will only increase as the cost of sequencing a genome drops more and more to the point where large numbers of people will have their genomes sequenced.

Further, recent reports of supposedly anonymous genetic data being correctly tied to its owner through more or less simple social media researching h as only intensified the concern. Yesterday at the annual Science/AAS meeting in Chicago, computational biologist Yaniv Erlich of the Whitehead Institution for Biomedical Research (Cambridge, Massachusetts) announced to those attending the symposium that he successfully matched anonymous genetic datato the exact person it came from in 12 percent of (anonymous) male genome donors.

So then, how does one protect one’s genomic data such that we control who sees it, and how much of it? This question has been asked fro several years now, but until recently, there were no promising answers.

But now there is a promising solution to this issue in the form of a fairly new encryption technique called homomorphic encryption.

The technique was presented at a symposium here at the annual Science meeting by cryptologist Kristin Lauter, research manager for the cryptography group at Microsoft Research in Redmond, Washington. The technique is a type of lattice-based cryptography scheme that allows users of the date to perform mathematical manipulations on it (like addition and multiplication) while still keep the data itself encrypted. This scheme was first developed by IBM in 2009.

During genome sequencing (the “DNA test”), genetic information is translated via a complex algorithm. This algorithm can be faithfully approximated using these mathematical operations. The lattice cryptology allowed homomorphic encryption which in turn allow computers to analyze the encrypted data (i.e., perform these mathematical operations) and produce encrypted results without ever actually decoding that genomic information. Thus the encryption technique allow researchers to analyze genetic data for genomic studies and research while simultaneously preserving patient privacy through protecting his/her genetic information.

Lauter compared the technique to “locking a gold brick in a safe with a pair of gloves attached to openings in the side. A jeweler could still use the gold to make jewelry without ever having full access to the gold brick.”

One drawback with this method is that more computational power and time is needed to encrypt the data compared to conventional encryption methods. but the research team is busy refining the technique to achieve “practical homomorphic encryption” which trades off computational flexibility for faster more efficient performance. The team was able to calculate a patient’s risk of a heart attack — based upon personal health data — in a fraction of a second.

The refinement is faster than “pure” homomorphic encryption, but according to the researchers, it’s still a billion times slower than it would be be due to the need to protect patient privacy (i.e., the patient’s identity and complete genomic sequence).

Wide-scale adoption of the technique with have to await standardization by the National Institute of Standards and Technology — a process that could take up to ten years.

While the technique will surely help keep a person’s genetic date more secure, genetic privacy critics point out that complete security is impossible. Combining the technique with other encryption and security methods could help improve DNA data security.

Regarding this, Lauter stated:

“Homomorphic encryption is a huge tool in our toolbox that we need to consider in policy discussions. We can’t solve all the problems using this method, but in combination with other, faster techniques it could provide a solution.”

But even this would not be full-proof, for long — especially as the cost of sequencing DNA continues to drop and consumer “bench top” gene sequencers become commonly available.  One could acquire a copy of someone’s genetic code simply by shaking hands with them and then swabbing his hands and sequencing the sample secretly and cheaply (in a form of genetic espionage).

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