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Completion of Allen Brain Atlas Hailed as 'Epoch-Making'

By Catherine Varmazis

Oct. 16, 2006 | Microsoft co-founder and philanthropist Paul G. Allen, founder of the Allen Institute for Brain Science (AIBS), announced the completion of the Allen Brain Atlas at a press conference on Capital Hill in Washington, D.C.

The Allen Brain Atlas is a Web-based, graphic 3-D database of the mouse brain that shows the location of expression sites of more than 21,000 genes at the cellular level. Because humans and mice share more than 90 percent of their genes, the completion of this database has important implications for research into neurological disorders that affect humans.

Francis Collins, director of the National Human Genome Research Institute, was among those attending the event. Also present were Sen. Ted Stevens of Alaska and Sen. Patty Murray of Washington, strong supporters of legislation for research and healthcare funding. Murray expressed the hope that the Atlas would be a catalyst for the understanding, diagnosis, and treatment of, among other conditions, traumatic brain injuries sustained by soldiers in combat.

In making the announcement, Allen said it was his fascination with the human brain that led to his funding this project. Coming from a software programming background, Allen said, "the more you learn about computers, the more you wonder how the human brain functions and solves problems like vision and speech understanding, in ways that no computer can do today."

Indeed, Allen has been described by Mark Boguski, founding director of the AIBS before moving to Novartis, as "a technologist and visionary who has always been interested in science and its applications." (See "Synapses in Seattle," Bio-IT World, Nov. 2003.)

Allen recalled assembling a group of experts, including top neuroscientists and geneticists, a few years ago and asking them what could be done that was not already being done to accelerate the field of neuroscience.  The answer to that question led to the launch, in 2003, with $100 million in seed money from Allen, of the Allen Brain Atlas. "I try to find projects like this and apply resources to problems that will have an impact worldwide," said Allen. "This database is online. Scientists from anywhere in the world can get online and within minutes be looking at genes of interest. We've seen fine structures in the mouse brain that have never been seen before."

AIBS chief scientific officer Allan Jones added that the Atlas was created by a multidisciplinary team of about 80 people - Ph.Ds in math and physics, neuroscientists, software engineers, and even an aeronautics engineer - working with "factory-like efficiency" on one mission.

The Atlas shows where each gene is expressed in a series of thin tissue sections spaced evenly throughout the brain. The completed database includes an enormous amount of data: the equivalent of 85 million photos, or 600 terabytes, or a quarter million microscope slides, said Jones. The powerful computational tools developed by the team are available to all researchers at no cost through an easy-to-use interface.

Despite the daunting scale of the project, chief operating officer Elaine Jones (no relation) noted proudly that the Atlas was completed on time and about 20 percent under budget.

The Gift of Time
Even before the formal launch of the Atlas, about 250 scientists from academia, biotechs, and the pharmaceutical industry were visiting it daily. Allan Jones finds that rewarding. "The nice thing about my job is I get to travel and talk to people who tell me how [the Atlas] has helped their project," he said. One scientist told him he was able to corroborate a hypothesis with a few mouse clicks using the Atlas - work that would have previously taken a lab technician a long time to corroborate. "We've done the experiment for them, so they can spend time furthering their research," said Jones. "We've given them the gift of time."

David Anderson, professor of biology at the California Institute of Technology and a member of the AIBS scientific advisory board, and also one of the scientists invited to Paul Allen's original meeting, said the Atlas had exceeded his wildest dreams.

To illustrate its significance, he asked listeners to imagine they were traveling on the space shuttle looking down on Earth, and that they had X-ray vision and could see beneath the surface. "You would be able to see where deposits of gold, silver, platinum, and oil are. You would not have to do any prospecting, but could go straight to mining." That's what the Brain Atlas does for scientists, he said. Before, Ph.D. students spent years prospecting. Now they can begin their work by mining the data.

Anderson compared the Allen Brain Atlas in scope and impact to the Human Genome Project. "It's an epoch-making discovery for neuroscience because genes implicated in a disease [such as epilepsy or Alzheimer's] can immediately be pinpointed in the brain." Conversely, he said, scientists can use the Atlas to narrow down the "field of suspects" for a gene by looking at the "neighborhoods" of the brain where they function.

Looking ahead to the next stage in the AIBS's development, Allan Jones pointed out that human brain disease affects everyone, either firsthand or through a relative suffering from Alzheimer's, for example. He noted that with one quadrillion communication points, the human brain is an enormously complex organ, but that "you can use a reductionist approach to understand" its workings.

And it is the human brain - the neocortex in particular - that will be the focus of the next stage of the AIBS's work. Anderson cited three specific goals:

  • Mine the data and create better tools
  • Collaborate with other institutions
  • Explore the human neocortex - the part that makes us uniquely human, and which constitutes 80 percent of our brain.

As a neuroscientist, Anderson looks forward to a database of the human brain that could show changes produced by conditions such as chronic stress or pain, drug addiction, and even learning disabilities.

Diseases such as Alzheimer's and Parkinson's, or epilepsy and autism, may also benefit from a 3-D database of the human brain. "It's up to us to mine this rich resource and discover the intellectual riches," said Anderson.

The AIBS will also seek collaborations and funding partnerships as it moves ahead. 

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