A new study in The New England Journal of Medicine suggests that autism begins with changes in the brain that occur during pregnancy. (Shutterstock)

New research is offering evidence that autism is linked to differences in the brain that emerge during pregnancy.

A small study looking at brain tissue from children who had died finds that those with autism were missing important genetic markers within cells in multiple layers of the brain’s cortex. The finding suggests that something went awry during prenatal development, researchers report Thursday in The New England Journal of Medicine.

“Building a baby’s brain during pregnancy involves creating a cortex that contains six layers,” said study author Eric Courchesne of the University of California, San Diego. “This defect indicates that the crucial early developmental step of creating six distinct layers with specific types of brain cells — something that begins in prenatal life — had been disrupted.”

For the study, researchers examined brain tissue from 22 children — half of whom had autism and half did not — whose brains were donated to science after they died between the ages of 2 and 15.

Nearly all of the kids with autism had patches of abnormal cells in multiple layers of the cortex, they found. What’s more, areas of the brain associated with key difficulties for those with autism including language, communication, emotion and social functions appeared to be most affected.

Among the children with autism studied, some had intellectual disability and some did not, but similar issues were seen in the brains even in cases where symptoms had presented differently, the study found.

The findings could help explain why early intervention is often effective in young children with autism, researchers said. Since variances were found in patches rather than throughout the brain, kids who get therapy early on may be able to rewire connections to avoid the faulty spots, they said.

“If this new report of disorganized architecture in the brains of some children with autism is replicated, we can presume this reflects a process occurring long before birth. This reinforces the importance of early identification and intervention,” said Thomas Insel, director of the National Institute of Mental Health.

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