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Allen Institute Team Releases Human Brain Atlas Data

By Andrea Anderson

NEW YORK (GenomeWeb News) – Researchers from the Allen Institute for Brain Science announced yesterday that they have developed an online resource bringing together genetic and anatomical information for sites throughout the human brain.

As part of the Allen Human Brain Atlas effort, the team characterized two adult human brains, profiling gene expression, histological patterns, and more at about 1,000 sites in each. By compiling this information and making it available to other researchers, those involved in the project hope to stimulate and support future studies on everything from normal brain function to brain injury, disease, mental illness, and related drug development.

"[T]his is data that individual labs could not have generated, due in part to the difficulty of acquiring fresh human brain tissue and the millions of dollars that went into developing unique machinery and technology to handle this kind of large-scale human tissue project," Allen Institute for Brain Science CEO Allan Jones told GenomeWeb Daily News in an e-mail message. "That said, the data is incredibly powerful for a wide range of research initiatives in all areas of neuroscience."

For each of the brains, he explained, the team defined about 1,000 anatomical sites using laser capture micro-dissection and other methods. They then used Agilent 60-mer microarrays to do gene expression profiling for samples from each of the sites. Brain samples were also characterized with magnetic resonance imaging, diffusion tensor imaging, and in situ hybridization.

"Upon collection of the brain we first get an MRI of the entire intact brain to serve as a 'scaffolding' framework on which we ultimately hang the detailed gene expression data," Jones explained in an e-mail. "For each brain, we manually determine the anatomic location, then painstakingly dissect the [approximately] 1,000 samples from these regions and extract total RNA for microarray analysis."

From their initial analyses of the data, researchers found that some 82 percent of genes are expressed in the brain — information that's expected to help in teasing apart the genetic pathways and biological processes at work in brain regions.

Because they found that gene expression patterns in the two brains were 94 percent similar to one another, those involved in the effort say their findings should have a wide range of applications for those studying normal brain function as well researchers interested in understanding and treating injuries or diseases that affect the brain.

"Understanding how our genes are used in our brains will help scientists and the medical community better understand and discover new treatments for the full spectrum of brain diseases and disorders, from mental illness and drug addiction, to Alzheimer's and Parkinson's diseases, multiple sclerosis, autism, and more," Jones said in a statement.

The Brain Atlas is eventually expected to house information on 10 human brains, Jones said, noting that the team plans to incorporate genomic information for the donors down the road.

"We ultimately plan on sequencing the genomes from the donors and hope to make this information available to scientists in a way that preserves confidentiality," he said.

Data from the brain mapping effort — including searchable gene expression data for genes in known brain-related pathways — is being made available as a public resource through the Allen Human Brain Atlas web site.