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MIT TECH REVIEW PART THREE: 10 Breakthrough Technologies 2015(PART 3 OF 3)

8.  BRAIN ORGANOIDS
[A new method for growing human brain cells could unlock the mysteries of dementia, mental illness, and other neurological disorders.]


Clumps of Living Human Brain Tissue Could Reshape Medical Research | MIT Technology Review Availability: now Breakthrough: Three-dimensional clusters of living neurons that can be grown in a lab from human stem cells. Why It Matters: Researchers need new ways of understanding brain disorders and testing possible treatments. Key Players: Madeline Lancaster and Jürgen Knoblich, Institute of Molecular Biotechnology Rudolph Tanzi and Doo Yeon Kim, Massachusetts General Hospital As Madeline Lancaster lifts a clear plastic dish into the light, roughly a dozen clumps of tissue the size of small baroque pearls bob in a peach-­colored liquid. These are cerebral organoids, which possess certain features of a human brain in the first trimester of development—including lobes of cortex. The bundles of human tissue are not exactly “brains growing in a dish,” as they’re sometimes called. But they do open a new window into how neurons grow and function, and they could change our understanding of everything from basic brain activities to the causes of schizophrenia and autism. Top Photo: Madeline Lancaster figured out a way to keep neurons growing in a dish until they develop characteristics of living human brains. Middle: Magdalena Renner, a graduate student in the lab, examines organoids under a microscope. Bottom: A variety of organoids are kept alive on a shaker plate in an incubator. Before it grows in one of Lancaster’s dishes, a brain organoid begins as a single skin cell taken from an adult. With the right biochemical prodding, that cell can be turned into an induced pluripotent stem cell (the kind that can mature into one of several types of cells) and then into a neuron. This makes it possible to do things that were impossible before. Now scientists can directly see how networks of living human brain cells develop and function, and how they’re affected by various drug compounds or genetic modifications. And because these mini-brains can be grown from a specific person’s cells, organoids could serve as unprecedentedly accurate models for a wide range of diseases. What goes wrong, for example, in neurons derived directly from someone with Alzheimer’s disease? The prospect of finding answers to such questions is leading pharmaceutical companies and academic researchers to seek collaborations with Lancaster and Jürgen Knoblich, whose lab at the Institute of Molecular Biotechnology (IMBA) in Vienna, Austria, is where Lancaster developed the organoids as a postdoc. READ MORE...

ALSO: 9. Supercharged Photosynthesis
[Advanced genetic tools could help boost crop yields and feed billions more people.]


The supercharged process, called C4 photosynthesis, boosts plants’ growth by capturing carbon dioxide and concentrating it in specialized cells in the leaves. That allows the photosynthetic process to operate much more efficiently. It’s the reason corn and sugarcane grow so productively; if C4 rice ever comes about, it will tower over conventional rice within a few weeks of planting. Availability: 10-15 years Breakthrough: Engineering rice plants to extract energy from sunlight far more efficiently than they do now. Why It Matters: Crop yields aren’t increasing fast enough to keep up with demand from a growing population.
Key Players: Paul Quick, International Rice Research Institute Daniel Voytas, University of Minnesota Julian Hibberd, University of Cambridge Susanne von Caemmerer, Australian National University In December, geneticists announced that they’d made a major advance in engineering rice plants to carry out photosynthesis in a more efficient way—much as corn and many fast-growing weeds do. The advance, by a consortium of 12 laboratories in eight countries, removes a big obstacle from scientists’ efforts to dramatically increase the production of rice and, potentially, wheat. It comes at a time when yields of those two crops, which together feed nearly 40 percent of the world, are dangerously leveling off, making it increasingly difficult to meet rapidly growing food demand. The supercharged process, called C4 photosynthesis, boosts plants’ growth by capturing carbon dioxide and concentrating it in specialized cells in the leaves. That allows the photosynthetic process to operate much more efficiently. It’s the reason corn and sugarcane grow so productively; if C4 rice ever comes about, it will tower over conventional rice within a few weeks of planting. Researchers calculate that engineering C4 photosynthesis into rice and wheat could increase yields per hectare by roughly 50 percent; alternatively, it would be possible to use far less water and fertilizer to produce the same amount of food. The December results, achieved by the C4 consortium and led by Paul Quick at the International Rice Research Institute (IRRl) in the Philippines, introduced key C4 photosynthesis genes into a rice plant and showed that it carried out a rudimentary version of the supercharged photosynthesis process. “It’s the first time we’ve seen evidence of the C4 cycle in rice, so it’s very exciting,” says Thomas Brutnell, a researcher at the Danforth Plant Science Center in St. Louis. Brutnell is part of the C4 Rice Consortium headed by IRRI, which has funding from the Bill & Melinda Gates Foundation, but was not directly involved in the most recent breakthrough. READ MORE...

ALSO: 10. Internet of DNA
[A global network of millions of genomes could be medicine’s next great advance.]


Networks of Genome Data Will Transform Medicine | MIT Technology Review Availability: 1-2 years Breakthrough: Technical standards that let DNA databases communicate. Why It Matters: Your medical treatment could benefit from the experiences of millions of others. Key Players: Global Alliance for Genomics and Health Google Personal Genome Project
Noah is a six-year-old suffering from a disorder without a name. This year, his physicians will begin sending his genetic information across the Internet to see if there’s anyone, anywhere, in the world like him. A match could make a difference. Noah is developmentally delayed, uses a walker, speaks only a few words. And he’s getting sicker. MRIs show that his cerebellum is shrinking. His DNA was analyzed by medical geneticists at the Children’s Hospital of Eastern Ontario. Somewhere in the millions of As, Gs, Cs, and Ts is a misspelling, and maybe the clue to a treatment. But unless they find a second child with the same symptoms, and a similar DNA error, his doctors can’t zero in on which mistake in Noah’s genes is the crucial one. In January, programmers in Toronto began testing a system for trading genetic information with other hospitals. These facilities, in locations including Miami, Baltimore, and Cambridge, U.K., also treat children with so-called ­Mendelian disorders, which are caused by a rare mutation in a single gene. The system, called MatchMaker Exchange, represents something new: a way to automate the comparison of DNA from sick people around the world. One of the people behind this project is David Haussler, a bioinformatics expert based at the University of California, Santa Cruz. The problem Haussler is grappling with now is that genome sequencing is largely detached from our greatest tool for sharing information: the Internet. That’s unfortunate because more than 200,000 people have already had their genomes sequenced, a number certain to rise into the millions in years ahead. The next era of medicine depends on large-scale comparisons of these genomes, a task for which he thinks scientists are poorly prepared. “I can use my credit card anywhere in the world, but biomedical data just isn’t on the Internet,” he says. “It’s all incomplete and locked down.” Genomes often get moved around in hard drives and delivered by FedEx trucks. Haussler is a founder and one of the technical leaders of the Global Alliance for Genomics and Health, a nonprofit organization formed in 2013 that compares itself to the W3C, the standards organization devoted to making sure the Web functions correctly. Also known by its unwieldy acronym, GA4GH, it’s gained a large membership, including major technology companies like Google. Its products so far include protocols, application programming interfaces (APIs), and improved file formats for moving DNA around the Web. But the real problems it is solving are mostly not technical. Instead, they are sociological: scientists are reluctant to share genetic data, and because of privacy rules, it’s considered legally risky to put people’s genomes on the Internet. The unfolding calamity in genomics is that a great deal of life-saving information, though already collected, is inaccessible. READ MORE...

ALSO: Here’s why the Internet of DNA is going to be the Next Big Thing in Fighting Disease Written by Stefan Wolf 11 months ago Posted: February 19, 2015 at 12:19 pm


SUPERHUMANS-SECRET WORLD OF HUMAN DNA; #WAVEGENETICS OF BIOLOGICAL INTERNET #TRANSMIGRATION #DNA #OM | Yogini TrueKrishnaPriya | LinkedIn We have the Internet of Things, why not DNA, right? Let’s ponder over a scenario: Adam is a seven-year-old suffering from a disorder without a name. This very year, his physicians will begin sending his genetic information across the Internet to see if there’s anyone, anywhere, in the world who is like unto him. If by some force majeure there is a match, it could make all the difference. Adam is developmentally delayed, uses a walker, quips only a few words. Trouble is, he’s getting sicker. MRIs indicate that his cerebellum is diminishing. Thing is, his DNA goes through analysis by medical geneticists at a Children’s Hospital. Somewhere in the millions of As, Gs, Cs, and Ts is a mis-arrangement (these are the building blocks of DNA and RNA, you have heard of them in your biological studies-Adenine, Guanine, Cytosine, and Thymine), and maybe the clue to a treatment. But unless they find a second child with the same symptoms, and DNA error akin to Adam’s, then there isn’t much his doctors can do to zero in on which mistake in Adam’s genetic code is the crucial one. The above scenario is based on a true story that I read in an article, but I shall not go into the details. At the beginning of the year, programmers in Toronto began testing a system for trading genetic information with other hospitals. These facilities, in locations including Miami, Baltimore, and Cambridge, U.K., also treat children with so-described ¬Mendelian disorders (you do remember who Mendel was, the so-dubbed father if modern Genetics) , which are caused by an obscure mutation in a single gene. The system, called MatchMaker Exchange, represents something new: a way to automate the comparison of DNA from sick people around the world. I like the sound of that, but weary at the same time-I just hope the scientific value will not go ahead of itself to sacrifice even the slightest sense of decency or morality. So who is This Guy Haussler? One of the people behind this project is David Haussler, a bioinformatics expert based at the University of California, Santa Cruz. Haussler has to contend with the fact that genome sequencing is largely detached from our greatest tool for sharing information: the Internet. That’s unfortunate because more than 200,000 people have already had their genomes sequenced (I want my genome sequenced then I can pay Google $25 to store my DNA, right? Wrong, no company is storing my DNA, what if they make a replica of me or sells my DNA for Research, or whatever, those are valid concerns, yeah?), a number certain to rise into the millions in years ahead. The next era of medicine is predicated on large-scale comparisons of these genomes, a task for which our good fellow Monsieur Haussler thinks scientists are poorly prepared, and the business opportunities are enormous according to me. “I can use my credit card anywhere in the world, but biomedical data just isn’t on the Internet,” he says. “It’s all incomplete and locked down.” Genomes often get moved around in hard drives and delivered under strict supervision. READ MORE...


READ FULL MEDIA REPORTS:

PART 3 OF 3: 10 Breakthrough Technologies 2015

8.
Brain Organoids:
[A new method for growing human brain cells could unlock the mysteries of dementia, mental illness, and other neurological disorders.]


Clumps of Living Human Brain Tissue Could Reshape Medical Research | MIT Technology Review

CYBERSPACE, JANUARY 18, 2016 (MIT TECHNOLOGY REVIEW) Availability: now Breakthrough: Three-dimensional clusters of living neurons that can be grown in a lab from human stem cells. Why It Matters: Researchers need new ways of understanding brain disorders and testing possible treatments. Key Players: Madeline Lancaster and Jürgen Knoblich, Institute of Molecular Biotechnology Rudolph Tanzi and Doo Yeon Kim, Massachusetts General Hospital

As Madeline Lancaster lifts a clear plastic dish into the light, roughly a dozen clumps of tissue the size of small baroque pearls bob in a peach-­colored liquid. These are cerebral organoids, which possess certain features of a human brain in the first trimester of development—including lobes of cortex. The bundles of human tissue are not exactly “brains growing in a dish,” as they’re sometimes called.

But they do open a new window into how neurons grow and function, and they could change our understanding of everything from basic brain activities to the causes of schizophrenia and autism.

Top Photo: Madeline Lancaster figured out a way to keep neurons growing in a dish until they develop characteristics of living human brains.

Middle: Magdalena Renner, a graduate student in the lab, examines organoids under a microscope.

Bottom: A variety of organoids are kept alive on a shaker plate in an incubator.

Before it grows in one of Lancaster’s dishes, a brain organoid begins as a single skin cell taken from an adult. With the right biochemical prodding, that cell can be turned into an induced pluripotent stem cell (the kind that can mature into one of several types of cells) and then into a neuron. This makes it possible to do things that were impossible before.

Now scientists can directly see how networks of living human brain cells develop and function, and how they’re affected by various drug compounds or genetic modifications. And because these mini-brains can be grown from a specific person’s cells, organoids could serve as unprecedentedly accurate models for a wide range of diseases. What goes wrong, for example, in neurons derived directly from someone with Alzheimer’s disease?

The prospect of finding answers to such questions is leading pharmaceutical companies and academic researchers to seek collaborations with Lancaster and Jürgen Knoblich, whose lab at the Institute of Molecular Biotechnology (IMBA) in Vienna, Austria, is where Lancaster developed the organoids as a postdoc.

READ MORE...

The first of these collaborations was an investigation of microcephaly, a disorder characterized by small brain size, with Andrew Jackson of the University of Edinburgh. Using cells derived from a patient with microcephaly, the team cultured organoids that shared characteristics with the patient’s brain. Then the researchers replaced a defective protein associated with the disorder and were able to culture organoids that appeared partially cured.

This is just the beginning, says Lancaster. Researchers such as Rudolph Jaenisch at MIT and Guo-li Ming at Johns Hopkins are beginning to use brain organoids to investigate autism, schizophrenia, and epilepsy.

What makes cerebral organoids particularly useful is that their growth mirrors aspects of human brain development. The cells divide, take on the characteristics of, say, the cerebellum, cluster together in layers, and start to look like the discrete three-dimensional structures of a brain. If something goes wrong along the way—which is observable as the organoids grow—scientists can look for potential causes, mechanisms, and even drug treatments.

The breakthrough in creating these organoids happened as part of a side project. Other researchers had grown neurons in a dish before, and like them, Lancaster started by using a flat plate to “play” with neural stem cells—the kind that form into neurons and other cells in the nervous system.

Sometimes, she says, “I’d get neural stem cells that wouldn’t really stay in 2-D, and they would kind of fall off the plate and they’d make 3-D clumps—and rather than ignoring them or throwing them away, I thought, ‘Those are cool—let’s see what happens if I let them keep growing.’” But there was a major challenge: how to keep the tissue at the center of the organoids fed without the benefit of veins. ­Lancaster’s solution was to encapsulate each organoid in a matrix known to nurture cells, put a dozen of these blobs in a nutritious bath, and shake or spin it all to keep the organoids awash in cellular food.


A stained section of an organoid is seen in close-up.

Since publishing her method, Lancaster has pushed the brain tissue to further levels of complexity with neurons at later stages of development. The number of possible applications grows with each advance. Most tantalizing to Lancaster herself is the prospect that cerebral organoids might solve the deepest of mysteries: what happens in our brains to set us apart from other animals? “I’m mainly interested,” she says, “in figuring out what it is that makes us human.”


—Russ Juskalian
is a freelance writer & photographer who covers science, culture, and adventure. His work has appeared in: Discover, Smithsonian, Wired (UK), The New York Times, Newsweek, The Boston Globe, Orion Magazine, Popular Science, Columbia Journalism Review, Technology Review, and other newspapers and magazines. His reporting has brought him from the Meth Lab at the New York State Psychiatric Institute, to a semi-abandoned railroad in the Cambodian countryside, to the halls of Congress. Russ teaches Journalism to undergraduates at UMass, Amherst. His passion is storytelling...

Credit: Photos by Regina Huegli Tagged: Biomedicine, brain, EmTechMIT2015, neuroscience, autism, schizophrenia, Alzheimer’s Disease, Massachusetts General Hospital


9. Supercharged Photosynthesis:
[Advanced genetic tools could help boost crop yields and feed billions more people.]


The supercharged process, called C4 photosynthesis, boosts plants’ growth by capturing carbon dioxide and concentrating it in specialized cells in the leaves. That allows the photosynthetic process to operate much more efficiently. It’s the reason corn and sugarcane grow so productively; if C4 rice ever comes about, it will tower over conventional rice within a few weeks of planting.

Availability: 10-15 years

Breakthrough: Engineering rice plants to extract energy from sunlight far more efficiently than they do now.

Why It Matters: Crop yields aren’t increasing fast enough to keep up with demand from a growing population.

Key Players: Paul Quick, International Rice Research Institute Daniel Voytas, University of Minnesota Julian Hibberd, University of Cambridge Susanne von Caemmerer, Australian National University

In December, geneticists announced that they’d made a major advance in engineering rice plants to carry out photosynthesis in a more efficient way—much as corn and many fast-growing weeds do.

The advance, by a consortium of 12 laboratories in eight countries, removes a big obstacle from scientists’ efforts to dramatically increase the production of rice and, potentially, wheat. It comes at a time when yields of those two crops, which together feed nearly 40 percent of the world, are dangerously leveling off, making it increasingly difficult to meet rapidly growing food demand.

The supercharged process, called C4 photosynthesis, boosts plants’ growth by capturing carbon dioxide and concentrating it in specialized cells in the leaves. That allows the photosynthetic process to operate much more efficiently. It’s the reason corn and sugarcane grow so productively; if C4 rice ever comes about, it will tower over conventional rice within a few weeks of planting.

Researchers calculate that engineering C4 photosynthesis into rice and wheat could increase yields per hectare by roughly 50 percent; alternatively, it would be possible to use far less water and fertilizer to produce the same amount of food.

The December results, achieved by the C4 consortium and led by Paul Quick at the International Rice Research Institute (IRRl) in the Philippines, introduced key C4 photosynthesis genes into a rice plant and showed that it carried out a rudimentary version of the supercharged photosynthesis process.

“It’s the first time we’ve seen evidence of the C4 cycle in rice, so it’s very exciting,” says Thomas Brutnell, a researcher at the Danforth Plant Science Center in St. Louis. Brutnell is part of the C4 Rice Consortium headed by IRRI, which has funding from the Bill & Melinda Gates Foundation, but was not directly involved in the most recent breakthrough.

READ MORE...

Despite the genetic changes, the altered rice plants still rely primarily on their usual form of photosynthesis. To get them to switch over completely, researchers need to engineer the plants to produce specialized cells in a precise arrangement: one set of cells to capture the carbon dioxide, surrounding another set of cells that concentrate it. That’s the distinctive wreath anatomy found in the leaves of C4 plants.

However, scientists still don’t know all the genes involved in producing these cells and suspect that they could number in the dozens.

New genome editing methods that allow scientists to precisely modify parts of plant genomes could help solve the problem. Using conventional breeding to manipulate more than one or two genes is a “nightmare,” Brutnell says, let alone trying to engineer a plant with dozens of gene changes. Genome editing could make it possible to change a large number of genes easily. Says Brutnell: “Now we have the toolbox to go after this.”

It can be a decade or more before even simple crop modifications reach farmers, let alone changes as complex as reëngineering how plants carry out photosynthesis. But once scientists solve the C4 puzzle in a plant such as rice, they hope, the method can be extended to dramatically increase production of many other crops, including wheat, potatoes, tomatoes, apples, and soybeans.


—Kevin Bullis
is Senior Editor, My reporting as MIT Technology Review’s senior editor for materials has taken me, among other places, to the oil-rich deserts of the Middle East and to China, where mountains are being carved away to build the looming cities.
Growing up, I lived for a time in the Philippines, where I knew people who lit their tiny homes with single lantern batteries or struggled to breathe through the dense diesel fumes of Manila, so I have a feel for the pressing need around the world for both cheap energy and clean energy.

Credit: Illustration by Luke Shuman; Data sources: Food and Agriculture Organization of the United Nations; Cornell University; International Rice Research Institute; Patricio Grassini, et al., Nature Communications; Deepak Ray et al., PLOSone Tagged: Materials, EmTechMIT2015, crops


10.

Internet of DNA A global network of millions of genomes could be medicine’s next great advance.


Networks of Genome Data Will Transform Medicine | MIT Technology Review

Availability: 1-2 years

Breakthrough: Technical standards that let DNA databases communicate.

Why It Matters: Your medical treatment could benefit from the experiences of millions of others.

Key Players: Global Alliance for Genomics and Health Google Personal Genome Project

Noah is a six-year-old suffering from a disorder without a name. This year, his physicians will begin sending his genetic information across the Internet to see if there’s anyone, anywhere, in the world like him.

A match could make a difference.

Noah is developmentally delayed, uses a walker, speaks only a few words. And he’s getting sicker. MRIs show that his cerebellum is shrinking. His DNA was analyzed by medical geneticists at the Children’s Hospital of Eastern Ontario. Somewhere in the millions of As, Gs, Cs, and Ts is a misspelling, and maybe the clue to a treatment.

But unless they find a second child with the same symptoms, and a similar DNA error, his doctors can’t zero in on which mistake in Noah’s genes is the crucial one.

In January, programmers in Toronto began testing a system for trading genetic information with other hospitals.

These facilities, in locations including Miami, Baltimore, and Cambridge, U.K., also treat children with so-called ­Mendelian disorders, which are caused by a rare mutation in a single gene.

The system, called MatchMaker Exchange, represents something new: a way to automate the comparison of DNA from sick people around the world.


Bioinformatics expert David Haussler awarded Oxford's Weldon Memorial Prize

One of the people behind this project is David Haussler, a bioinformatics expert based at the University of California, Santa Cruz.

The problem Haussler is grappling with now is that genome sequencing is largely detached from our greatest tool for sharing information: the Internet. That’s unfortunate because more than 200,000 people have already had their genomes sequenced, a number certain to rise into the millions in years ahead.

The next era of medicine depends on large-scale comparisons of these genomes, a task for which he thinks scientists are poorly prepared.

“I can use my credit card anywhere in the world, but biomedical data just isn’t on the Internet,” he says. “It’s all incomplete and locked down.” Genomes often get moved around in hard drives and delivered by FedEx trucks.

Haussler is a founder and one of the technical leaders of the Global Alliance for Genomics and Health, a nonprofit organization formed in 2013 that compares itself to the W3C, the standards organization devoted to making sure the Web functions correctly. Also known by its unwieldy acronym, GA4GH, it’s gained a large membership, including major technology companies like Google.

Its products so far include protocols, application programming interfaces (APIs), and improved file formats for moving DNA around the Web. But the real problems it is solving are mostly not technical. Instead, they are sociological: scientists are reluctant to share genetic data, and because of privacy rules, it’s considered legally risky to put people’s genomes on the Internet.

The unfolding calamity in genomics is that a great deal of life-saving information, though already collected, is inaccessible.

READ MORE...

But pressure is building to use technology to study many, many genomes at once and begin to compare that genetic information with medical records. That is because scientists think they’ll need to sort through a million genomes or more to solve cases—like Noah’s—that could involve a single rogue DNA letter, or to make discoveries about the genetics of common diseases that involve a complex combination of genes.

No single academic center currently has access to information that extensive, or the financial means to assemble it.

Haussler and others at the alliance are betting that part of the solution is a peer-to-peer computer network that can unite widely dispersed data. Their standards, for instance, would permit a researcher to send queries to other hospitals, which could choose what level of information they were willing to share and with whom. This control could ease privacy concerns. Adding a new level of complexity, the APIs could also call on databases to perform calculations—say, to reanalyze the genomes they store—and return answers.

The day I met Haussler, he was wearing a faded ­Hawaiian shirt and taking meetings on a plastic lawn chair by a hotel pool in San Diego. Both of us were there to attend one of the world’s largest annual gatherings of geneticists. He told me he was worried that genomics was drifting away from the open approach that had made the genome project so powerful.

If people’s DNA data is made more widely accessible, Haussler hopes, medicine may benefit from the same kind of “network effect” that’s propelled so many commercial aspects of the Web.

The alternative is that this vital information will end up marooned in something like the disastrous hodgepodge of hospital record systems in the United States, few of which can share information.

One argument for quick action is that the amount of genome data is exploding. The largest labs can now sequence human genomes to a high polish at the pace of two per hour. (The first genome took about 13 years.) Back-of-the-envelope calculations suggest that fast machines for DNA sequencing will be capable of producing 85 petabytes of data this year worldwide, twice that much in 2019, and so on. For comparison, all the master copies of movies held by Netflix take up 2.6 petabytes of storage.

“This is a technical question,” says Adam Berrey, CEO of Curoverse, a Boston startup that is using the alliance’s standards in developing open-source software for hospitals. “You have what will be exabytes of data around the world that nobody wants to move. So how do you query it all together, at once? The answer is instead of moving the data around, you move the questions around. No industry does that. It’s an insanely hard problem, but it has the potential to be transformative to human life.”

Today scientists are broadly engaged in what is, in effect, a project to document every variation in every human gene and determine what the consequences of those differences are. Individual human beings differ at about three million DNA positions, or one in every 1,000 genetic letters.

Most of these differences don’t matter, but the rest explain many things that do: heartbreaking disorders like Noah’s, for example, or a higher than average chance of developing glaucoma.

RUNNING DNA's ON TUMORS

So imagine that in the near future, you had the bad luck to develop cancer. A doctor might order DNA tests on your tumor, knowing that every cancer is propelled by specific mutations. If it were feasible to look up the experience of everyone else who shared your tumor’s particular mutations, as well as what drugs those people took and how long they lived, that doctor might have a good idea of how to treat you.

 The unfolding calamity in genomics is that a great deal of this life-saving information, though already collected, is inaccessible. “The limiting factor is not the technology,” says David Shaywitz, chief medical officer of DNAnexus, a bioinformatics company that hosts several large collections of gene data. “It’s whether people are willing.”

Last summer Haussler’s alliance launched a basic search engine for DNA, which it calls Beacon. Currently, Beacon searches through about 20 databases of human genomes that were previously made public and have implemented the alliance’s protocols. Beacon offers only yes-or-no answers to a single type of question.

You can ask, for instance, “Do any of your genomes have a T at position 1,520,301 on chromosome 1?” “It’s really just the most basic question there is: have you ever seen this variant?” says Haussler. “Because if you did see something new, you might want to know, is this the first patient in the world that has this?” Beacon is already able to access the DNA of thousands of people, including hundreds of genomes put online by Google.


David Altshuler

One of the cofounders of the Global Alliance is David ­Altshuler, who is now head of science at Vertex Pharmaceuticals but until recently was deputy chief of the MIT-Harvard Broad Institute, one of the largest academic DNA-sequencing centers in the United States.

The day I visited Altshuler in his Broad office, his whiteboard was covered with diagrams showing genetic inheritance in families, as well the word “Napster” written in large blue letters—a reference to the famously disruptive music-sharing service of the 1990s.

Altshuler has his own reasons for wanting to connect massive amounts of genetic data. As an academic researcher, he hunted for the genetic causes of common diseases like diabetes. That work was carried out by comparing the DNA of afflicted and unafflicted people, trying to spot the differences that come up most often. After burning through countless research grants this way, geneticists realized there would be no easy answers, no common “diabetes genes” or “depression genes.”

It turns out that common diseases aren’t caused by single, smoking-gun defects. Instead, a person’s risk, scientists have learned, is determined by a combination of hundreds, if not tens of thousands, of rare variations in the DNA code.

That’s created a huge statistical headache. Last July, in a report listing 300 authors, Broad looked at the genes of 36,989 people with schizophrenia. Even though schizophrenia is highly heritable, the 108 gene regions identified by the scientists explained only a small percentage of a person’s risk for the disease. Altshuler believes that big gene studies are still a good way to “crack” these illnesses, but he thinks it will probably take millions of genomes to do it.

The way the math works out, sharing data no longer looks optional, whether researchers are trying to unravel the causes of common diseases or ultra-rare ones. “There’s going to be an enormous change in how science is done, and it’s only because the signal-to-noise ratio necessitates it,” says Arthur Toga, a researcher who leads a consortium studying the science of Alzheimer’s at the University of Southern California. “You can’t get your result with just 10,000 patients—you are going to need more. Scientists will share now because they have to.”

Privacy, of course, is an obstacle to sharing.

People’s DNA data is protected because it can identify them, like a fingerprint—and their medical records are private too. Some countries don’t permit personal information to be exported for research. But Haussler thinks a peer-to-peer network can sidestep some of these worries, since the data won’t move and access to it can be gated.

More than half of Europeans and Americans say they’re comfortable with the idea of sharing their genomes, and some researchers believe patient consent forms should be dynamic, a bit like Facebook’s privacy controls, letting individuals decide what they’ll share and with whom—and then change their minds. “Our members want to be the ones to decide, but they aren’t that worried about privacy. They’re sick,” says Sharon Terry, head of the Genetic Alliance, a large patient advocacy organization.

The risk of not getting data sharing right is that the genome revolution could sputter. Some researchers say they are seeing signs that it’s happening already. Kym Boycott, head of the research team that sequenced Noah’s genome, says that when the group adopted sequencing as a research tool in 2010, it met with immediate success. Over two years, between 2011 and 2013, a network of Canadian geneticists uncovered the precise molecular causes of 146 conditions, solving 55 percent of their undiagnosed cases.

But the success rate appears to be tailing off, says ­Boycott. Now it’s the tougher cases like Noah’s that are left, and they are getting solved only half as often as the others. “We don’t have two patients with the same thing anymore. That’s why we need the exchange,” she says. “We need more patients and systematic sharing to get the [success rate] back up.” In late January, when I asked if MatchMaker Exchange had yielded any matches yet, she demurred, saying that it could be a matter of weeks before the software was fully operational. As for Noah, she said, “We are still waiting to sort him out. It’s important for this little guy.”

—Antonio Regalado

 - Antonio Regalado EDITOR Senior Editor, Biomedicine |218 stories I am the senior editor for biomedicine for MIT Technology Review. I look for stories about how technology is changing medicine and biomedical research. Before joining MIT Technology Review in July 2011, I lived in São Paulo, Brazil, where I wrote about science, technology, and politics in Latin America for Science and other publications. From 2000 to 2009, I was the science reporter at the Wall Street Journal and later a foreign correspondent

Credit: Illustration by Dadu Shin Tagged: Biomedicine, Google, DNA, EmTechMIT2015, genetics, genomics, gene editing, DNAnexus, Global Alliance for Genomics and Health


Here’s why the Internet of DNA is going to be the Next Big Thing in Fighting Disease Written by Stefan Wolf 11 months ago Posted: February 19, 2015 at 12:19 pm


SUPERHUMANS-SECRET WORLD OF HUMAN DNA #WAVEGENETICS OF BIOLOGICAL INTERNET #TRANSMIGRATION #DNA #OM | Yogini TrueKrishnaPriya | LinkedIn

We have the Internet of Things, why not DNA, right?

Let’s ponder over a scenario: Adam is a seven-year-old suffering from a disorder without a name. This very year, his physicians will begin sending his genetic information across the Internet to see if there’s anyone, anywhere, in the world who is like unto him.

If by some force majeure there is a match, it could make all the difference.

Adam is developmentally delayed, uses a walker, quips only a few words. Trouble is, he’s getting sicker. MRIs indicate that his cerebellum is diminishing. Thing is, his DNA goes through analysis by medical geneticists at a Children’s Hospital. Somewhere in the millions of As, Gs, Cs, and Ts is a mis-arrangement (these are the building blocks of DNA and RNA, you have heard of them in your biological studies-Adenine, Guanine, Cytosine, and Thymine), and maybe the clue to a treatment.

But unless they find a second child with the same symptoms, and DNA error akin to Adam’s, then there isn’t much his doctors can do to zero in on which mistake in Adam’s genetic code is the crucial one. The above scenario is based on a true story that I read in an article, but I shall not go into the details.


At the beginning of the year, programmers in Toronto began testing a system for trading genetic information with other hospitals. These facilities, in locations including Miami, Baltimore, and Cambridge, U.K., also treat children with so-described ¬Mendelian disorders (you do remember who Mendel was, the so-dubbed father if modern Genetics) , which are caused by an obscure mutation in a single gene. The system, called MatchMaker Exchange, represents something new: a way to automate the comparison of DNA from sick people around the world. I like the sound of that, but weary at the same time-I just hope the scientific value will not go ahead of itself to sacrifice even the slightest sense of decency or morality.


So who is This Guy Haussler?

One of the people behind this project is David Haussler, a bioinformatics expert based at the University of California, Santa Cruz. Haussler has to contend with the fact that genome sequencing is largely detached from our greatest tool for sharing information: the Internet.

That’s unfortunate because more than 200,000 people have already had their genomes sequenced (I want my genome sequenced then I can pay Google $25 to store my DNA, right? Wrong, no company is storing my DNA, what if they make a replica of me or sells my DNA for Research, or whatever, those are valid concerns, yeah?), a number certain to rise into the millions in years ahead.


Illumina's Bid to Beat Cancer with DNA Tests. --The unfolding calamity in genomics is that a great deal of life-saving information, though already collected, is inaccessible.

The next era of medicine is predicated on large-scale comparisons of these genomes, a task for which our good fellow Monsieur Haussler thinks scientists are poorly prepared, and the business opportunities are enormous according to me. “I can use my credit card anywhere in the world, but biomedical data just isn’t on the Internet,” he says. “It’s all incomplete and locked down.” Genomes often get moved around in hard drives and delivered under strict supervision.

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Global Alliance for Genomics and Health

Haussler is a founder and one of the technical leaders of the Global Alliance for Genomics and Health, a nonprofit organization formed in 2013 that compares itself to the W3C (the standards organization devoted to making sure the Web functions correctly).

Also known by its punning acronym, GA4GH, it’s gained a large membership; including major technology companies like Google (remember the $25 fee you have to pay to store your Genome).

Its products so far include protocols, application programming interfaces (APIs), and improved file formats for moving DNA around the Web. However, the real problems it is solving are mostly not technical. Instead, they are sociological: scientists are reluctant to share genetic data, and because of privacy rules, it’s considered legally risky to put people’s genomes on the Internet.

The interesting thing is that pressure is mounting to use technology to study tons of genomes at once and begin to compare that genetic information with medical records. This is because scientists think they’ll need to sort through a million genomes or more to solve cases—like Adam’s—that could involve a single rogue DNA letter, or to make discoveries about the genetics of common diseases that involve a complex combination of genes. At the moment, no single academic center currently has access to information that extensive, or the financial means to assemble it.

So the Internet of DNA is a pretty good idea. It could be like your email, with login details to track your Genome, how it is being accessed, and if so, is the ample compensation, that’s just my idea.



Haussler and others at the alliance are betting that part of the solution is a peer-to-peer computer network that can unite widely dispersed data, like how it works with bitcoin, I am thinking.

Their standards, for instance, would permit a researcher to send queries to other hospitals, which could choose what level of information they were willing to share and with whom. This control could ease privacy concerns. Adding a new level of complexity, the APIs could also call on databases to perform calculations—say, to reanalyze the genomes they store—and return answers, right?

I am worried that genomics is drifting away from the open approach that had made the genome project so potent and inspiring. If people’s DNA data is made more widely accessible, I hope, medicine may benefit from the same nature of “network effect” that’s propelled so many commercial aspects of the Web. The alternative is that this vital information will end up marooned in something like the disastrous hodgepodge of hospital record systems in the Kenyan Medical System.

One argument for quick action is that the amount of genome data is exploding. The largest labs can now sequence human genomes to a high refinement at the pace of two per hour, with that mind knowing that the first genome took about 13 years. Back-of-the-envelope calculations suggest that fast machines for DNA sequencing will be capable of producing 85 petabytes of data this year worldwide, twice that much in 2019, and so forth. For comparison, all the master copies of movies held by Netflix take up 2.6 petabytes of storage. (The Rise of the Quantified Self.)

“This is a technical question,” says Adam Berrey, CEO of Curoverse, a Boston startup that is using the alliance’s standards in developing open-source software for hospitals. “You have what will be exabytes of data around the world that nobody wants to move. So how do you query it all together, at once? The answer is instead of moving the data around, you move the questions around. No industry does that. It’s an insanely hard problem, but it has the potential to be transformative to human life.”

Currently scientists are broadly engaged in what is, in effect, a project to document every variation in every human gene and determine what the effects of those differences are.

Individual human beings differ at about three million DNA positions, or one in every 1,000 genetic letters. Most of these differences don’t matter, but the rest explain many things that do: heartbreaking disorders like Adam’s, for instance, or a higher than average chance of developing glaucoma, especially if you are African.

Thus, imagine that in the near future, you had the bad luck to develop cancer (the number is elevating in Kenya).

What could happen is a doctor might order DNA tests on your tumor, knowing that every cancer is propelled by specific mutations. If it were feasible to look up the experience of everyone else who shared your tumor’s particular mutations, as well as what drugs those people took and how long they lived, that doctor might have a good idea of how to treat you. “The limiting factor is not the technology,” says David Shaywitz, chief medical officer of DNAnexus, a bioinformatics company that hosts several large collections of gene data. “It’s whether people are willing.”

In the summer of 2014, Haussler’s alliance launched a basic search engine for DNA, which it calls Beacon. Currently, Beacon searches through about 20 databases of human genomes that were previously made public and have implemented the alliance’s protocols. Beacon offers only yes-or-no answers to a single type of question.

You can ask, for instance, “Do any of your genomes have a T at position 1,520,301 on chromosome 1?” “It’s really just the most basic question there is: have you ever seen this variant?” says Haussler. “Because if you did see something new, you might want to know, is this the first patient in the world that has this?” Beacon is already able to access the DNA of thousands of people, including hundreds of genomes put online by Google.

One of the co-founders of the Global Alliance is David Altshuler, who is now head of science at Vertex Pharmaceuticals but until recently was deputy chief of the MIT-Harvard Broad Institute, one of the largest academic DNA-sequencing centers in the United States.

Altshuler has his own reasons for wanting to connect massive amounts of genetic data. As an academic researcher, he hunted for the genetic causes of common diseases like diabetes. That work was carried out by comparing the DNA of afflicted and the non-afflicted, trying to spot the variations that materialize most often.

After burning through countless research grants utilizing this long, tedious way, geneticists realized there would be no easy answers, no common “diabetes genes” or “depression genes.” It turns out that common diseases aren’t caused by single, smoking-gun defects. Instead, a person’s risk, scientists have learned, is determined by a combination of hundreds, if not tens of thousands, of rare variations in the DNA code. Sometimes it kind of looked like they were playing “shoot-the-arrow” in the dark.

What are the concerns?

This has created a huge statistical migraine. Late summer saw a report listing 300 authors, Broad (remember MIT and Harvard) observed at the genes of 36,989 people with schizophrenia. We all know that schizophrenia is highly heritable ailment; the 108 gene regions identified by the scientists explained only a small percentage of a person’s susceptibility for the disease. Altshuler believes that enormous gene studies are still a good way to “break” these disturbed codes, but he thinks it will probably take millions of genomes to do it, I can think so, too, because the many there are, the greater the chances of finding the right pieces to complete the puzzle.

Sharing data no longer looks optional, if one is going by the quantified depiction, whether researchers are trying to unravel the causes of common diseases or ultra-rare ones. “There’s going to be an enormous change in how science is done, and it’s only because the signal-to-noise ratio necessitates it,” says Arthur Toga, a researcher who leads a consortium studying the science of Alzheimer’s at the University of Southern California. “You can’t get your result with just 10,000 patients—you are going to need more. Scientists will share now because they have to.” I hope this collaboration is replicated in Kenya and the greater African region.

Privacy, of course, is an obstacle to sharing. People’s DNA data is protected because it can identify them, like a fingerprint—and their medical records are locked, too. In some countries, exporting personal information for research is not permitted. But Haussler thinks a peer-to-peer network can sidestep some of these worries, since the data won’t move and access to it can be gated and armed.

More than half of Europeans and Americans say they’re comfortable with the idea of sharing their genomes, and some researchers believe patient consent forms should be dynamic, a bit like Facebook’s privacy controls, letting individuals decide what they’ll share and with whom—and then change their minds. “Our members want to be the ones to decide, but they aren’t that worried about privacy. They’re sick,” says Sharon Terry, head of the Genetic Alliance, a large patient advocacy organization. Privacy comes later when you are all feeling prim and proper, aye!



The risk of not getting data sharing right is that the genome revolution could sputter and fall of into oblivion of maladies and corporate profits. Some researchers say they are seeing signs that it’s happening already. Kym Boycott, head of the research team that sequenced Adam’s genome, says that when the group adopted sequencing as a research tool in 2010, it met with immediate success. Over two years, between 2011 and 2013, a network of Canadian geneticists uncovered the precise molecular causes of 146 conditions, solving 55 percent of their undiagnosed cases.

Nonetheless, the success rate appears to be tailing off, says ¬Boycott. Now it’s the tougher cases like Adam’s that are left, and they are getting solved only half as often as the others, a shiver just went down my spine. “We don’t have two patients with the same thing anymore. That’s why we need the exchange,” she says.

“We need more patients and systematic sharing to get the [success rate] back up.” In late January, when asked if MatchMaker Exchange had yielded any matches yet, she demurred, saying that it could be a matter of weeks before the software was fully operational. As for Adam, she said, “We are still waiting to sort him out. It’s important for this little guy.”

The unfolding calamity in genomics is that a great deal of life-saving information, though already available, is inaccessible. So the Internet of DNA provides an exciting new way to combat the onslaught of ‘weirdo’ and non-weirdo diseases. I just hope that vested interest doesn’t take the place of genuine concern for patients who seriously need help. Otherwise, hurrah for Science!


Chief News Editor: Sol Jose Vanzi
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