• White House pitches brain mapping project

    President Obama has proposed $100 million in federal funding to start an exhaustive brain mapping initiative. NBC's Robert Bazell reports.

    By Maggie Fox, Senior Writer, NBC News

    President Obama pitched a human brain research initiative on Tuesday that he likened to the Human Genome Project to map all the human DNA, and said it will not only help find cures for diseases such as Alzheimer’s and autism, but create jobs and drive economic growth.

    Obama proposed $100 million in federal funding to kick start the Brain Research through Advancing Innovative Neurotechnologies or BRAIN Initiative.

    “Imagine if we could reverse traumatic brain injury and PTSD for our wounded veterans coming home,” Obama said at an event unveiling the initiative at the White House.

    He said federal investment in basic research had led to completely unexpected inventions, from the Internet to GPS technology. “The Apollo project that put man on the moon gave us, eventually, CAT scans,” Obama said.

    He said the Human Genome Project, completed in 2003, had paid $140 for every dollar invested.

    “As humans we can identify galaxies light-years away, study particles smaller than an atom but we still haven’t unlocked the mystery of the 3 pounds of matter than sits between our ears,” Obama said.

    "Ideas are what power our economy. It’s what sets us apart. It’s what America has been all about," he added.

    "We have been a nation of dreamers and risk-takers; people who see what nobody else sees sooner than anybody else sees it.  We do innovation better than anybody else -- and that makes our economy stronger. When we invest in the best ideas before anybody else does, our businesses and our workers can make the best products and deliver the best services before anybody else."

    Obama said he’ll send the proposal to Congress next week as part of his budget request. Although Congress is working to slash the federal deficit, House Majority Leader Eric Cantor signalled an early willingness to pay for this one.

    “Mapping the human brain is exactly the type of research we should be funding, by reprioritizing the $250 million we currently spend on political and social science research into expanded medical research, including the expedited mapping of the human brain. It's great science,” Cantor said in a statement.

    It's not clear just what the initiative will do. Obama and collins said they'd appointed a "dream team" of experts to lay out the agenda -- they should report back before the end of the summer. They are led by neurobiologists Cori Bargmann of Rockefeller University and William Newsome of Stanford University.

    Allen Institute for Brain Research

    The brain's "emotion center", the amygdala, is highlighted in this 3-D representation of the human brain from the Allen Human Brain Atlas.

    “Investing in biomedical research is one of the wisest choices we can make as a nation,” National Institutes of Health director Dr. Francis Collins told the gathering. “The United States has been at the forefront of one medical breakthrough after another.”

    The public-private initiative, with money from groups such as the Howard Hughes Medical Institute and Microsoft co-founder Paul Allen's brain mapping project, aims to find a way to take pictures of the brain in action in real time.

    The $100 million funding will come from the National Institutes of Health, the Defense Advanced Research Projects Agency and the National Science Foundation, the White House said.

    “We want to understand the brain to know how we reason, how we memorize, how we learn, how we move, how our emotions work. These abilities define us, yet we hardly understand any of it," said Miyoung Chun, vice president of science programs at The Kavli Foundation, which is taking part in the initiative and which funds basic research in neuroscience and physics.

    The project has some big money and some big science to build on. Allen pumped another $300 million into his institute's brain mapping initiative a year ago, and has published freely available maps of the human and mouse brains. The Howard Hughes Medical Institute built a whole research campus devoted to brain science, called Janelia Farm, in Virginia.

    Arati Prabhakar, director of the Defense Advanced Research Projects Agency (DARPA) pointed to a project that allowed a quadriplegic woman to control a robot arm with her thoughts alone.

    "There is nothing like a project to inspire people to go to that next level," Collins told a telephone briefing.

    Not everybody is happy about a centralized, administration-led project. Michael Eisen, a biologist at the University of California at Berkeley, said earlier this year that grand projects in biology such as Project ENCODE for DNA analysis were emerging as the "greatest threat" to individual discovery-driven science.

    "It's one thing to fund neuroscience, another to have a centralized 10-year project to 'solve the brain,'" Eisen wrote in a Twitter update in February.

    President Barack Obama announces a new research initiative that he hopes will advance understanding of the human mind and will help revive middle class job growth.

     

    Related:

    This story was originally published on Tue Apr 2, 2013 6:00 AM EDT

  • Scientists demonstrate how hackers could unlock your genetic secrets

    Christine Cox / NBC News file

    Researchers say genetic genealogy databases can be leveraged to unlock more sensitive genetic information.

    By Alan Boyle, Science Editor, NBC News


    Researchers have shown that it's possible to link your identity to supposedly secret genetic information about your predisposition to diseases, merely by analyzing family-tree databases and other publicly available information.

    "It was quite surprising," said Yaniv Erlich, a genetic researcher at the Whitehead Institute for Biomedical Research. "When we got the first family, I was surprised. ... It's as if you opened a box that for a long time was locked."

    Erlich led the research team whose work is being published in this week's issue of the journal Science. The team's study already has led to a tightening of security measures for federally sponsored genetic databases.

    The security-cracking trick relies on the availability of genetic information linked to surnames in a variety of public family-tree databases. DNA samples from males can be tested to look at dozens of genetic markers on the Y-chromosome that change only rarely from generation to generation. If the markers from two individuals with the same surname are a close match, that's a tip-off that the two are closely related, even if they don't know each other.

    Tens of thousands of people (including yours truly) make that information public in hopes that someone else will match up with their results. The genealogical markers aren't linked to disease or other specific traits. But under the right circumstances, they could provide an opening for links with other, more sensitive genetic information.

    How the secrets were revealed
    Erlich and his colleagues conducted a three-step process to see how easy it'd be to use that opening. First, they analyzed anonymous Y-chromosome data from a public database for the 1000 Genomes Project, to come up with the DNA coding for markers that are used for genealogical purposes. Then they compared those markers against entries in the two largest family-tree databases, Ysearch and the Sorenson Molecular Genealogy Foundation.

    The researchers said their analysis projected a success rate of 12 percent for recovering the surnames of U.S. Caucasian males. Another 5 percent would theoretically be linked up with the wrong surnames. They said upper- to middle-class Caucasian males were easier to identify, presumably because they're more likely to participate in the family-tree databases.

    Once the surnames were identified, the third step was to look at other publicly available sources to go from the surname to a specific individual: Some genetic databases, for example, include information about the age and the state of residence of an anonymous participant, and even the number of children and their birth order. Those clues were added to information gleaned from other sources, ranging from public-record search engines to obituaries.

    The researchers linked five specific individuals in three separate families with supposedly anonymous genetic records. The process took three to seven hours for each family pedigree, the scientists said. Then they traced those three family-tree pedigrees to find other connections between relatives and sensitive genetic data. "In total, surname inference breached the privacy of nearly 50 individuals from these three pedigrees," the researchers wrote.

    "We show that if, for example, your Uncle Dave submitted his DNA to a genetic genealogy database, you could be identified," Melissa Gymrek, a member of the Erlich Lab and the Science paper's principal author, explained in a news release. "In fact, even your fourth cousin Patrick, whom you've never met, could identify you if his DNA is in the database, as long as he's paternally related to you."

    What is to be done with data?
    Erlich and his colleagues made a point not to reveal the identities of those individuals, and said they were not advocating a clampdown on the availability of genetic information.

    "Quite the opposite," Erlich said. "We found the gene for two devastating pediatric disorders by analyzing the data in public databases. Using these databases, we gave hope to these families and to other parents. We don't want to take away these databases. ... What we really want to do here is to have this really mature conversation about privacy — to tell people we cannot completely protect the privacy, but also to tell them about the benefits."

    For years, experts have worried that sensitive genetic data could be used to discriminate against patients, potential employees or would-be insurance customers. Such discrimination is illegal when it comes to employment or health insurance, but the law doesn't cover life insurance, disability insurance or long-term care insurance. Theoretically, an insurer could search through genetic records and turn you down because you have a genetic predisposition to, say, Alzheimer's disease. 

    In a Science policy paper, representatives of the National Human Genome Research Institute and the National Institute of General Medical Sciences at the National Institutes of Health said it was time to "re-examine how to balance the protection of research participants ... with the societal benefits likely to be gained through the enhanced research that broad data sharing facilitates."

    They said NIH "acted swiftly to mitigate future risks" by working with the NIGMS' genetic repository to shift the data about the age of study participants out of public view and into a controlled-access area of the database.

    "That reduces the risk," Erlich said. "It creates another fence."

    And what about the genealogical genetic data? Max Blankfeld, vice president for operations and marketing at Family Tree DNA, said his company has been dealing with privacy issues for more than a decade — and doesn't expect the latest research to lead to policy changes. Family Tree DNA has been running the Ysearch database as a free public resource for a decade, but does not force any of its more than 400,000 participants to use it.

    "People voluntarily post their information in that database, and therefore it has nothing really to do with the vast majority of the people who take the test and choose to have it protected by Family Tree DNA," Blankfeld said. "This data, we don't share with anyone."

    More about genetic ancestry:

    In addition to Erlich and Gymrek, the authors of "Identifying Personal Genomes by Surname Inference" include Amy McGuire, David Golan and Eran Halperin. The work was supported by the National Defense Science and Engineering Graduate Fellowship, the Edmond J. Safra Center for Bioinformatics at Tel Aviv University, and a gift from James and Cathleen Stone.

    The authors of the Science policy paper, "The Complexities of Genomic Identifiability," include Laura Rodriguez, Lisa Brooks and Erick Green of NHGRI and Judith Greenberg of NIGMS.

    Alan Boyle is NBCNews.com's science editor, and also the administrator of the Boyle Surname Project at Family Tree DNA.

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  • Black Death: Can the secrets of London's plague pits help fight modern diseases?

    Almost seven centuries ago, London was devastated by an apocalyptic plague that swept across Asia and continental Europe. Today, scientists are cracking the genome code for the disease using human teeth from skeletons excavated in the city.

    By Jim Maceda, NBC News

    LONDON -- They were the final resting place for victims of the Black Death, but London’s underground medieval plague pits are now unlocking the secrets of modern-day infectious diseases.

    The bodies of tens of thousands of Londoners were thrown into communal graves after one of the most devastating epidemics in human history swept through Europe in the 14th century.

    Between 1348 and 1351, the Black Death -- or bubonic plague -- killed up to three in five people as it spread rapidly through pre-industrial cities, unchecked by sanitation or modern medicine. That, and subsequent waves of the Yersinia pestis bacterium, claimed the lives of tens of millions of Europeans.

    WHO map: Spread of bubonic plague in Europe

    Direct descendants of the same plague still exist, killing about 2,000 people each year – although they are often now treatable with antibiotics.

    Earlier this month, a 7-year-old girl contracted a genetic variant of Black Death at a campground in Colorado.

    A Colorado girl who survived the bubonic plague is happy to be out of the hospital. KUSA's Cheryl Preheim reports.

    The girl, who was treated for the illness in a Denver hospital, is thought to have caught the disease in the same way as her medieval ancestors - from fleas living on rodent carcasses.

    Next month, a conference of forensic scientists will hear how an international team of experts - led by researchers based at McMaster University in Hamilton, Canada, and the University of Tubingen in Germany - sequenced the entire genome of the Black Death using DNA extracted from plague victims.

    The team used DNA from bodies buried at pits including one at East Smithfield, now underneath the heart of central London.

    It is the first time an ancient disease has been reconstructed, providing clues as to how it has evolved and whether it could strike again in future.

    The scientists hope their work heralds a new era of research into infectious disease.

    Additional reporting by Alastair Jamieson, NBC News

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