September 21, 2003
Paul Allen Brain Atlas To Map All Brain Genes In Mouse

Paul Allen is ponying up $100 million dollars to map all the genes that are activated in mouse brain cells in 3 to 5 years.

Microsoft co-founder Paul Allen has donated $100 million to launch a private research organization in Seattle devoted to deciphering the links between our genes and our brain.

Dr. Thomas Insel, director of the National Institute of Mental Health, says that approximately 6,000 genes are thought to be expressed only in brain with many more that are expressed in the brain and also in other parts of the body as well.

Insel and his team at the NIH have been working on a gene map of the mouse brain since 1999 and hope to soon publish the location of several hundred genes. Allen's project, Insel noted, is on a much larger scale aiming to identify 10,000 genes a year.

Note that Allen is therefore accelerating work on identifying genes active in the brain by at least an order magnitude over that of the NIMH Brain Molecular Anatomy Project.

While the anatomy project can analyze 600 to 800 genes a year, Dr. Boguski's team is shooting for about 10,000 genes a year.

This work will make it easier to find the equivalent genes that control human brain development and on-going operation.

Because mice and humans have 99 percent of the same genes, scientists hope the map of the mouse brain will provide a template for comparison with the human brain.

Insel says these genes would all have been identified over the next couple of decades but that Allen's money is going to compress the amount of time to discover them down to only a few years. Well then hurray for Paul Allen!

Once all the genes which are expressed in the brain are identified the bigger job of figuring out how each affects the brain will still remain to be done.

It's like opening a box filled with parts to build two tables and there are 30,000 parts and no instructions. There is no map," says Mark Boguski, a longtime genomics researcher who is the senior director of the Allen Brain Atlas team. "We have to figure out which are for the brain, and then we have to figure out how they are put together or what they do."

Still, just by knowing which genes are expressed in the brain the next step will be able to be done much more quickly. Just being able to compare people with different genetic variations for brain genes will lead to the much more rapid identification of genetic variations that affect intelligence, personality type, tendencies toward specific forms of behavior, and susceptibility to a large assortment of neurological and mental disorders such as Alzheimer's Disease, Parkinson's Disease, depression, and anxiety.

This first effort by the Allen Institute for Brain Science is known as the Allen Brain Atlas project.

The first endeavor of the Allen Institute for Brain Science is the Allen Brain Atlas project, the planning for which has been underway for two years. For decades, scientists have been eager for an intense, focused effort to develop a compendium of information that could serve as a foundation for general brain research. Instead of researching genes one at a time, the Allen Brain Atlas project will give scientists an unprecedented view of that portion of the genome that is active in the brain.

From the Allen Brain Atlas web site:

Why build a brain atlas?
The human brain has been an object of mystery and wonder since antiquity. It defines who we are as a species and as individuals—our emotions, thoughts and desires—and controls many of the body’s essential, but unconscious functions, such as breathing and heart rate.

Our understanding of how the brain is organized and how it works is still in the very early stages. Basic processes of memory and cognition remain a mystery. While it is estimated that the human brain contains a trillion different nerve cells or neurons, capable of making up to a thousand different connections each, scientists don’t know how many subtypes of neurons exist, how they are linked up in circuits, or how they work.

Despite more than a century of research, classical neuroanatomists still cannot agree on the boundaries of different brain regions or even their names. In some regions of the brain, there is such fundamental disagreement about mapping regional boundaries that it is almost like comparing maps of Western Europe from 100 years ago to today. An accurate, definitive map is of utmost importance if we want to develop new therapies for neurological disorders such as Alzheimer’s, schizophrenia, depression, and addiction, or simply to understand the essence of what makes us human.

This project demonstrates the value of "Big Science" funding in molecular biology and genetics to achieve major goals. Note that DNA double helix co-discoverer James Watson is serving as one of Allen's advisors on this Brain Atlas project. Watson is advocating a Manhattan Project style effort to map all the genes expressed in each type of cancer in order to rapidly develop far more effective treatments for cancer. Watson thinks his proposed project could be done for a few hundred millions of dollars. We are at the point where the instrumentation and techniques for doing DNA sequencing and gene expression measurement with gene arrays have gotten fast enough that such ambitious projects can be done within a few years to provide substantial benefits fairly rapidly.

Share |      Randall Parker, 2003 September 21 04:40 PM  Biotech Advance Rates

Don Mitchell said at September 25, 2003 6:30 PM:

Hello Randall,

Your article on Allen Mind Atlas was crisp with the best detail of any I have found yet.

I'm a knowledge research and development effort .

If you have any information that I could obtain from you regarding how to approach the key players of the research institute, I would be much obliged.

I and my lawyer are attempting to establish network opportunities with the players.

Thank you.


Laura Common said at October 5, 2003 12:34 PM:

This is great. Please keep up your coverage of this important subject.

Hansen Wang said at January 10, 2004 6:49 PM:

Allen Brain Atlas is realy exciting.

Richard Sarabi said at July 27, 2004 10:46 PM:

Knowing how the Brain works is one of the most important aspects of human biology and may save our species.I think the Government should chip in 10% of the Annual defense budget toward this goal.But bush and his crew would never imagine such a thing.Paul Allen is doing a wonderful thing!

John said at November 2, 2005 8:46 AM:

great article. Should also check out for higher resolution brain images and brain atlases of both primate and mouse.

Peter said at May 8, 2006 8:08 PM:

Here's some interesting information over the Allen Brain Atlas:

Mark Seibold said at November 29, 2006 7:44 PM:

Dear Paul

I just saw the Lehrer news hour report about your brain atlas project. I must say that this is very impressive to say the least. I have been active in providing community service public astronomy and for schools to enlighten minds.

I will look forward to hearing more as your project develops,

best regards,


Jim McGhee said at August 13, 2008 2:52 PM:

I have ALS (LOU GEHRIG'S disease). I appreciate hearing about these developments and any other news or additional links that would provide me updates about what is going on with in research that could affect treatment for my disease. Thank you for adding any new information or new links as you see them. Jim

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