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The human brain is often called the most complex object in the universe, yet its basic architecture is created in just nine months, during pregnancy. Now scientists have taken a big step toward understanding how this happens. They've created a highly detailed map of the developing brain.

NPR's Jon Hamilton reports this map is already providing hints about the origins of brain disorders, including schizophrenia and autism.

JON HAMILTON, BYLINE: During pregnancy, the human brain grows from a single cell to more than 80 billion cells. And Ed Lein of the Allen Institute for Brain Science in Seattle says before we're born, these cells have to get organized in a way that will eventually let us think and feel and remember.

ED LEIN: We're talking about a remarkable process where we build a brain. The cells replicate. Different cells gain different properties, and these then give rise to the different structures and cell types of the brain.

HAMILTON: The process is controlled by our genes. So, Lein and a large team of researchers decided to use genetic techniques to create a map of a typical brain at about the midpoint of pregnancy. The unprecedented effort is described in the journal Nature. Researchers used brain tissue from aborted fetuses, which the Obama administration has authorized over the objections of abortion opponents. The project used tens of thousands of brain tissue samples. And researchers tested every sample to see which genes were turned on and off in that tiny bit of brain. Lein says this helped the team figure out which types of cells were present and what those cells were doing.

LEIN: What was quite unique here is that we sort of did this in a very standardized and high throughput way so that we were able to look at, effectively, all of the structures of the developing brain.

HAMILTON: Lein says the resulting map represents a huge leap forward and has already led to at least two important findings.

LEIN: The first is that many genes that are associated with brain disorders are turned on early in development, which suggests that these disorders may have their origin from these very early time points.

HAMILTON: In other words, in the womb, probably in the early stages of pregnancy. And Lein says the map tells researchers who study these disorders where in the brain they should be looking for signs of trouble. For example, he says, the map shows that genes associated with autism appear to be acting on a specific type of brain cell in an area called the neocortex.

LEIN: It tells us that we should be looking in the neocortex, that we should be looking at this particular type of cell in the neocortex and, furthermore, that we should probably be looking very early in the prenatal stages for the origin of autism.

HAMILTON: Lein says the second important finding from the mapping project is that the human brain is different from a mouse brain in ways researchers didn't know about before. He says these differences could explain why a number of brain drugs that work well in mice have failed badly in people. Tom Insel, who directs the National Institute of Mental Health, says the new map shows just how little scientists had known about the brain of a fetus.

THOMAS INSEL: It's an enormous surprise to us that the way that genes get expressed in the fetal brain doesn't look anything like what we would have expected from the adult brain. It's almost as if the fetal brain is a different organ altogether.

HAMILTON: Insel says that realization is already helping to explain the complex role that genes often play in brain disorders. For example, he says, researchers have been baffled by some genes linked to autism and schizophrenia because it's not clear how they are affecting an adult brain.

INSEL: But when you look at these new maps that we have of what's happening in the fetal brain, suddenly, much of this begins to make sense.

HAMILTON: The new map was funded with money from the federal economic stimulus package in 2009. The map is available to anyone who wants to use it. Jon Hamilton, NPR News.

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