The vast array of behaviors that are seen in autism spectrum disorder seems to cover an even deeper range of genetic complexity just below the surface. And the largest genetic study of autistic children and their parents to date has located a host of new variations in autistic individuals.

By studying rare "copy number variations," which are individual errant insertions or deletions of DNA segments (each of which occur in less than one percent of the population), researchers discovered a new cluster of genes that are affected in some autistic individuals as well as a number of mutations that were present in autistic children but not their parents.

"We now really see how genetically complex autism is," says Rita Cantor, a professor in residence at the David Geffen School of Medicine at the University of California, Los Angeles, who studies human genetics and psychiatry and is a co-author of the new study, which was published online June 9 in Nature. (Scientific American is part of Nature Publishing Group.)

The researchers tested blood samples from 996 children in the U.S., Canada and Europe who had been diagnosed with autism. They compared genetic analyses of these samples with those from both parents (in 876 cases) as well as from 1,287 healthy children of European descent. The test scanned for about one million of the roughly 10 million gene variants in the human genome.

Results from the analysis confirmed previous findings of some copy number variants already associated with autism, but they also found a host of other genes (SHANK2, SYNGAP1, DLGAP2 and the X chromosome–linked DDX53-PTCHD1 locus) in which mutations seem to be linked to autism. The group also discovered that 5.7 percent of autistic children's variations were not present in either of their parents' DNA, suggesting that these copy errors stemmed from mutations in the egg and/or sperm.

Although "genomic rearrangements have been associated with autism for awhile," finding more of the novel changes is "quite exciting for the field," says Simon Gregory, an associate professor of medical genetics at Duke University's Center for Human Genetics, who was not involved in the study.

The new findings come from work by the Autism Genome Project Consortium, a collaboration of some 120 scientists working at more than 50 institutions in 19 countries, which is just one of many groups investigating the roots of autism.

Location, location, location
Human variation depends on a collection of random mutations across the genome, contributing to differences in appearance as well as behavior.

"While we're all walking around with copy number variants in our DNA, many of us don't have autism," Cantor notes. And rather than the total number of variations, she says, autism seems to be, in part, a result of "where the copy number variation hit." If a copy number variation disrupts certain genes, it is more likely to lead to autism.

"Autistic children have 20 percent more disruption of genes in copy number variants than children who do not have autism," Cantor explains. But the new study has underscored the variability in the copy number variants and genes that can be affected in autistic individuals.

About 10 to 15 percent of people with autism have a disorder linked to a known single-gene mutation, such as fragile X syndrome, or chromosomal alterations. But many more likely have a rare or unique collection of yet to be decoded genetic variations that have contributed to their condition.

"Now we see that perhaps the individual factors themselves are more rare than we expected," Cantor says.

Patterns in chaos

Given the rarity of each copy number variation and genetic glitch in the autism population, "it's going to be tough to suggest that any one of those individually can contribute to the development of the disorder," Gregory says.

He notes that because of the boggling number of potential factors, such as copy number variations, point mutations and epigenetic (inherited mutation) factors involved in autism, it will be important to find common pathways "because the mechanisms interrupting those pathways might be different among individuals."

Nevertheless, researchers are making progress in sorting disrupted genes and pathways. Many of the genes highlighted in the new study fall into certain categories, such as cellular signaling in the brain, which could play a role in the developmental disabilities common in autism.

The researchers also found that many of the disrupted genes in autistic children are the same as those found in children with diagnosed intellectual disability. The overlap is "not surprising," Gregory says, noting that genetic similarities make "biological sense" in terms of brain signaling and development.

"The lines drawn between different disorders are not related to the genes that predispose to the disorders," Cantor notes, explaining that two children can present very similar behavioral patterns but have vastly different sets of copy number variations—and vice versa. Formal disorder delineations have been based largely on behavior-based diagnoses, but the insight into genetic patterns behind these designations has shown the range of causes to be much more complex.

Constellation of factors
Twin studies have shown that identical twins (who share the same genes) are more likely to both suffer from the disorder than fraternal twins, which has demonstrated that "there's a large genetic component to the disorder," Cantor says. Research from other fields, however, is exploring other potential components, including possible epigenetic and environmental risk factors.

"This is so complex that it's not only what's going on in the one gene but the constellation of genes surrounding it—and maybe the environment," Cantor explains. "This, in some sense, is only the tip of the iceberg."

Researchers not involved in the work laud the study's size and scope as a means to obtain a fuller picture of genetic links for autism. "It is only through large genetic studies (such as this one) that we will be able to identify additional rare variants associated with this disorder," Dorothy Grice, an associate professor of clinical child psychiatry at Columbia University and New York State Psychiatric Institute, noted in an e-mail.

Despite the size of this study, the new genetic findings likely explain only about 3 percent of autism's genetic roots, researchers behind the new study noted.

And many scientists think that even larger studies are necessary: Cantor says a study 10 times bigger—sampling 10,000 children with autism and as many controls—would be required to see if the results replicate in a larger population as well as uncover new, rare genetic variations, which are almost certain to emerge. Using high-throughput sequencing of whole genomes will also be key in finding other kinds of genetic variation involved in autism, Grice explained.

Cure unknown
The increasingly apparent complexity of autism spectrum disorder means that targeting a single gene or point mutation for treatment, as is possible in some diseases, is unlikely to help many individuals.

"I think that treatments or drugs would have to address classes of problems, maybe not individual genes," Cantor says. Researchers will also need to start drilling deeper to study individual copy number variations and disrupted genes to understand how they might lead to autism, she notes.

But continued testing and larger genetic studies will likely help researchers establish a more complete map of the genetic errors that have led to cases of autism, which could eventually point the way toward treatment or cures. And some disorders associated with autism, such as fragile X and Rett syndrome, already have therapies under clinical investigation, Grice wrote.
In addition to possibly pointing the way to treatment, future research could lead to more technical diagnostics. "One day, when we know what the genes really are…we can get the child's DNA at birth" and test for possible genetic red flags, Cantor says.

Gregory, however, suggests that because genetic hallmarks of autism are turning out to be even rarer than previously thought, simple tests for key variations might not prove as useful as they are in other afflictions. He foresees "a whole cadre of tests," including genetic, genomic and epigenetic. Despite its difficulty, improving diagnosis is key, he notes, because "the earlier you can diagnose with autism" the better their final outcome.