Mapping the B Spot


Human Brain Atlas

allen-institute-for the brain



ALLEN Human Brain Atlas next training webinar is April 7, 2011.

The ALLEN Human Brain Atlas is a unique multi-modal atlas that integrates anatomic data (MRI,DTI, histology) and gene expression data (microarray, in situ hybridization).

The current release expands the scope and usability of the original release as described below:

  • Whole Brain Microarray Survey:
    • Data from two control brains, integrating MRI, histology and microarray data into a unified spatial framework.
    • Spatially mapped microarray data comprising approximately 1,000 samples covering cerebrum, cerebellum and brainstem in one brain, and the first approximately 450 samples from the cerebrum in a second brain.
  • ISH Data:
    • Data for one male and one female donor in the Subcortex Study characterizing 55 primarily glutamatergic and GABAergic genes in subcortical regions, and 10 anatomic marker genes through the hypothalamus.
    • An initial data set of disease-related genes in medial prefrontal cortex, ventral striatum, amygdala, hippocampus and visual cortex in a separate donor cohort.
  • New Tools:
    • Enhanced searches of the microarray data by anatomic region, probe or gene.
    • NeuroBlast search.
    • Options for comparing expression between structures or donors.

Additional data, additional brains, and more sophisticated visualization, navigation and mining tools will be available in subsequent releases.

The next data release of the Allen Human Brain Atlas will be on March 17, 2011.

Allen Institute for Brain Science
Downloadable archive files

The human brain is studied at the Allen Institute for Brain Science in Seattle, and the scientist is in a hurry: His specimen—this fragile cortex—is falling apart. Dying, the gray matter turns acidic and begins to eat away at itself; nucleic acids unravel, cell membranes dissolve. He takes a thin, sterilized knife and slices into the tissue with disconcerting ease.

The scientists here are mapping the brain. And while conventional brain maps describe distinct anatomical areas, like the frontal lobes and the hippocampus—many of which were first outlined in the 19th century—the Allen Brain Atlas seeks to describe the cortex at the level of specific genes and individual neurons. Slices of tissue containing billions of brain cells will be analyzed to see which snippets of DNA are turned on in each cell.

If the institute succeeds, its maps will help scientists decipher the function of the thousands of genes that help produce the human brain. (Although the Human Genome Project was completed more than five years ago, scientists still have little idea which genes are used to make the brain, let alone where in the brain they are expressed.) For the first time, it will be possible to understand how such a complex object is assembled from a basic four-letter code.

When the project is completed in 2012, at an expected cost of $55 million, its data sets will list the roughly 20,000 genes that, switched on in the exact right place at the exact right time, give rise to this self-aware tangle of neurons. And because the vast majority of mental illnesses and disorders, from schizophrenia to autism, have a significant genetic component, scientists at the institute hope that the atlas will eventually lead to new methods of diagnosis and more effective medical treatments. To map the brain is to map its afflictions.

This enterprise is unique in one other respect: scale. The whole brain is being mapped.

To achieve this, the Allen Institute reimagined the scientific process. There was no grand hypothesis, or even a semblance of theory. The researchers just wanted the data, and, given the amount needed, it quickly became apparent that the work couldn’t be done by hand. So, shortly after the institute was founded in 2003, Jones and his team started thinking about how to industrialize the experimental process. While modern science remains, for the most part, a field of artisans—scientists performing their own experiments at their own benches—the atlas required a high-throughput model, in which everything would be done on an efficient assembly line. Thanks to a team of new laboratory robots, what would have taken a thousand technicians several years can now be accomplished in less than 20 months.

The institute can produce more than a terabyte of data per day. (In comparison, the 3 billion base pairs in the human genome can fit in a text file that’s only 3 gigabytes.) And the project has another year to go.

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