September 26, 2006
Allen Genetic Brain Atlas Completed

A 3 dimensional map of gene activity in mouse brains shows whether each gene is active in each part of the brain.

The completion of the Allen Institute for Brain Science's inaugural project signals a remarkable leap forward in one of the last frontiers of medical science -- the brain.

The Institute today announced the completion of the groundbreaking Allen Brain Atlas, a Web-based, three-dimensional map of gene expression in the mouse brain. Detailing more than 21,000 genes at the cellular level, the Atlas provides scientists with a level of data previously not available.

Since humans share more than 90 percent of their genes with mice, the Atlas offers profound opportunity to further understanding of human disorders and diseases such as Alzheimer's, Parkinson's, epilepsy, schizophrenia, autism and addiction. About 26 percent of American adults -- close to 58 million people -- suffer from a diagnosable mental disorder in a given year.

Many human brain diseases have mouse equivalents developed using genetic engineering on lab mice. As the cost of measuring gene activity drops a logical next step would be to repeat this work using mice which have a variety of brain disorders.

You can access the Brain Atlas for free online.

"This project is an unprecedented union of neuroscience and genomics," said philanthropist and Microsoft co-founder Paul G. Allen, who provided $100 million in seed money to launch the Allen Institute for Brain Science and its first project, the Allen Brain Atlas, in 2003. "The comprehensive information provided by the Atlas will help lead scientists to new insights and propel the field of neuroscience forward dramatically."

Publicly available at no cost, the map shows which genes are active -- or "expressed" -- within the brain and which regions and cells they are expressed in, thereby linking them to particular brain functions.

The brain uses most of the genome.

The project has already led to several significant new findings about the brain. It reveals that 80 percent of genes are turned on in the brain, much higher than the 60 to 70 percent scientists previously believed.

It indicates that very few genes are turned on in only one region of the brain -- paving the way for additional insight about the benefits and potential side effects of drug treatments. And it shows the location of genes associated with specific functions, providing scientists with valuable information about regional brain activity.

Many brain scientists use the Atlas.

Even before its announced completion, the Atlas was receiving more than 4 million hits monthly and being accessed by approximately 250 scientists on any given work day. Users are not required to provide information about their work, but anecdotal evidence indicates that the Atlas is already assisting research projects.

"I use it around the clock, night and day. My whole lab does," said Stanford University neurobiology professor Ben A. Barres, who is using the Atlas to confirm his team's findings about glial cells, a type of non-neuronal cell within the nervous system.

"It's completely essential. It's saved us years and years of work, maybe decades. We could never have done all this, either financially or in terms of the amount of labor and time. It was just so incredibly generous of Mr. Allen to do this, and I think it's hard to even overstate what the payoff is going to be for research."

Slides of brain slices labelled with DNA probes were read by computers to measure gene activity in brain cross sections.

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.

The development of gene array chips and other technologies for measuring many parts of a biological system at once look set to continue to accelerate the rate at which scientists can collect information from cells and organisms. The Brain Atlas couldn't have been developed 10 years ago. 10 years from now we'll have still more orders of magnitude improvement in the ability to measure and collect data on the activites inside cells and organisms.

A map of gene activity in the human brain neocortex is next up for the Allen Institute.

The next project, Jones said, will be to develop a digital, three-dimensional, interactive map of the genes at work in a human brain's neocortex, the outer layer that is the seat of higher thought and emotion, using brains from cadavers as well as tissue removed during brain surgeries.

We are coming to the end of the dark ages of how the human brain works.

Share |      Randall Parker, 2006 September 26 07:37 PM  Brain Genetics

John said at October 1, 2006 9:01 AM:

this link has interesting info on the allen brain atlas:

neubrain said at October 29, 2006 12:07 PM:

Common misconceptions about the Allen Brain Atlas:

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