Wednesday, September 27, 2006

A Genetic Map of the Brain

This new "atlas" reveals the expression pattern in the brain of every gene in the mouse genome.

By Emily Singer

A three-dimensional reconstruction of the mouse brain, with the expression pattern of two different genes marked in yellow and turquoise dots. (Credit: Allen Institute for Brain Science)

A massive genetic map of the mouse brain was released yesterday, providing an invaluable new tool for understanding neural disease, memory, and other thought processes.

Initiated in 2003, with a $100-million grant from Microsoft cofounder Paul Allen, the database--which is freely available on the Web--provides a neural map of the expression of the approximately 21,000 genes in the mouse genome.

Having access to this information, pieces of which would have taken months or years for individual neuroscientists to generate, will radically speed up research in the neurosciences, shedding light on the genetic basis of diseases such as autism and multiple sclerosis, and providing new targets for drugs.

"There's never been anything like it before," says Ben Barres, a neuroscientist at Stanford University who served as an advisor for the project. "It's an incredible gift."

The idea for the project came four years ago, when Allen gathered several prominent neuroscientists and geneticists to ask what could be done to accelerate brain research. The result was the Allen Brain Atlas. "The human genome project describes the 'what'--what are the genes?" says Allen Jones, chief scientific officer at the Allen Institute for Brain Science, a nonprofit research institute in Seattle, WA, that did the work. "The atlas describes the 'where'--where in the brain are these genes turned on?"

The resulting database will help researchers understand a wide range of problems in neuroscience, from neurological diseases to learning and memory and the fundamental processes of emotion and consciousness, says David Anderson, a neuroscientist at the California Institute of Technology, and a scientific advisor on the project.

Researchers at the Allen Institute created the database using a process known as in-situ hybridization. A mouse brain is sliced into thin layers and then labeled with a DNA "probe" that binds only to a single gene, highlighting the expression pattern for that gene.

In-situ maps were made for every gene in the mouse genome, then loaded into a massive database. To complete the entire database, researchers processed 170 genes per day, and produced some 1,000 gigabytes of data each day. The finished atlas cost about $41 million to produce.

While human and mouse brains look somewhat different, they share many of the same basic anatomical structures and about 90 percent of their genes. Scientists studying particular genes or brain functions can search the new database to find out where in the brain a particular gene of interest is expressed, or which genes are expressed in the brain area involved in, say, fear or the region of the brain that's lost in Parkinson's disease.