HealthLawProf Blog

Editor: Katharine Van Tassel
Concordia University School of Law

Thursday, November 30, 2006

Allen Brain Atlas

WOW!  The NewsHour has a terrific segment last night on the Allen Brain Atlas, a new tool for medical research, that "provides a three-dimensional catalog of all the genes active in the brain and has revealed clues to diseases such as Alzheimer's, Parkinson's and Lou Gehrig's, as well as conditions such as autism."  You can access the information at  Here is a brief excerpt from last night's show discussing how the Allen Brain Atlas was created.

SUSAN DENTZER: The ideal would be to have an atlas of genes expressed throughout the entire human brain, but that would require dissecting a live brain, an ethical and physical impossibility.

So scientists at the Allen Institute settled for the next best thing: an atlas of the brains of special laboratory-bred, genetically identical mice. It may be surprising, but 90 percent of a mouse's genes are identical to a human's. Assembling the Atlas required the work of nearly 100 scientists, engineers, mathematicians and information experts.

ALLAN JONES: We've got individual microscope slides. Each one of them is bar-coded so we can track all of the information. And there, as you can see here, there are very thin slices of mouse brain on each of these slides.

SUSAN DENTZER: They began by literally slicing apart the brains of several thousand mice. Each slice, just 25 microns thick, or about one-sixth of a human hair, was subjected to special chemical probes to detect the presence of specific genes.

Under sophisticated microscopes, the mouse brain cells with specific genes switched on look like this. Special cameras captured thousands of these images.

ALLAN JONES: We've generated over 600 terabytes of raw data, raw picture data. To put that in context, that would fill over 20,000 iPods.

SUSAN DENTZER: The digital images of the mouse brain cells with genes switched on were assembled into a giant database.

ALLAN JONES: We've assembled a large cluster of computers, which simply grind away and process this information and put it into this three-dimensional framework.

SUSAN DENTZER: The end product is this 3-D catalog. It's freely accessible to all on the Web site Users can easily click on a brain section and see which genes are active there.

DR. SUSAN SWEDO, National Institute of Mental Health: It is exactly like having a Google for the mouse brain now.

SUSAN DENTZER: One researcher who's used the Allen Brain Atlas is Dr. Susan Swedo. She oversees autism research at the National Institute of Mental Health.

DR. SUSAN SWEDO: To be able to go online and just map various areas of the brain and what genes are being expressed in that area is phenomenal. I, in five minutes, was able to do what used to take a graduate student four years for one tiny, little nerve cell connection, and now they have it for the entire brain.

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