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International Consortium Finds New Genetic Clues in Autistic Families

An unprecedented collaboration between 120 genetic researchers at 50 institutions in 19 countries has identified components of the brain's glutamate chemical messenger system and a previously overlooked gene on chromosome 11 — as well as genetic variations on chromosome 15 — that may contribute to autism in several families.

The findings were published Feb.18 in an advance online publication of the journal Nature Genetic.

The Autism Genome Project Consortium, launched in 2002 and sponsored in part by the NIH, searched for genetic anomalies in over 11,000 families with more than one autistic member.

Figure

Nicky Gottlieb, who has Asperger syndrome, was featured in a documentary, "Todays Man." (For the review of the film, see Neurology Today, Mar. 6, page 44.)

The researchers combined two types of data to determine probable chromosomal involvement — linkage analysis, which tests whether specific genetic markers are located near a potential autism susceptibility gene; and chromosomal copy number variation (CNV), in which subtle abnormalities — submicroscopic insertions or deletions of genetic material — are examined.

The site on chromosome 11 most strongly linked to autism includes a gene for a protein that shuttles glutamate across synapses. Although detected previously, the linkage signal at this site was not considered significant.

Glutamate increases neuronal activity and plays an important role in early brain development, and prior research pointed to a role in autism (Neurology 2001;57:1618–1628). The new findings show stronger evidence of the role of sites controlling the activity of neurexins, molecules that build glutamate synapses, in autism and autism spectrum disorders (ASDs).

Submicroscopic deletions, doubling, tripling, or even multiplying of specific sequences of genetic material are not unusual or necessarily harmful in humans. However, these anomalies may increase the risk or even cause autism.

The autism consortium found variations in susceptibility locations on chromosome11, including deletion of the neurexin 1 gene.

“Neurexin 1 is a highly likely candidate,” said Joachim Hallmayer, MD, chair of the consortium's executive committee and an associate professor of psychiatry and behavioral science at Stanford University School of Medicine.

“The protein enables neurons to contact one another. We know neurexin 1 is involved at sites where the glutamate is released and that glutamate has been implicated in autism,” he told Neurology Today in a telephone interview.

“As for the chromosome 11 location, we think there is another susceptibility gene in there and we are actively pursuing it.”

Scientists contend there may be five or six major genes and perhaps as many as 30 others involved in the full range of ASDs.

ONGOING EXPLORATION

“Sample size plays an enormous role in the chance to find genes,” said Dr. Hallmayer. “This study is by far the largest ever conducted, in terms of both researchers and research subjects.”

Nonetheless, the results need to be followed up with more refined genetic maps to zero in on other possible candidate genes, he noted.

“In the families we studied there are variations in individual genes —changes in linkage. If you clean up the sample and eliminate families with submicroscopic copy number variations and rerun the analysis on the “clean” sample, it would have quite an impact on the findings,” he said, likely revealing more dramatic associations between anomalies and incidence of disorders.

“I would argue that in autism, many of the [genetic] changes are copy number variations that have yet to be identified. We have to get a much cleaner sample of genes, and mutations in other genes must be taken out. The problem is the small number of these families available for such studies.” Although the consortium is international, most families are white, he noted, adding, “It would be nice to have a broader racial mix.”

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Dr. Joachim Hallmayer: “Neurexin 1 is a highly likely candidate [gene for autism]. … We know neurexin 1 is involved at sites where the glutamate is released and that glutamate has been implicated in autism.”

The second phase will include 2,000 families with just one autistic child.

“Although substantial evidence suggests that up to 8 percent of individuals with autism have chromosomal abnormalities, standard tests miss many subtle chromosomal aberrations,” Dr. Hallmayer said. “Detection of these changes not only helps to identify candidate genes, but also improves linkage analysis by allowing us to separate chromosome abnormality-bearing families from those with other types of mutations.”

Yet even if the consortium scientists ultimately identify specific genes or mutations that might be targeted for correction with gene therapy or other techniques, potential treatment is still years away, Dr. Hallmayer noted.

LOOKING FORWARD

“Now we have a much better idea of just how heterogeneous autism really is,” commented Daniel Geschwind, MD, PhD, professor of neurology and psychiatry and the Gordon and Virginia MacDonald Distinguished Professor of Human Genetics at the David Geffen School of Medicine at the University of California-Los Angeles (UCLA), who also worked on the project.

Autism was once thought to result from one or perhaps several gene mutations (homogenous), however research with newer and more exact sampling and chromosome analysis techniques continues to reveal a much larger number of different (heterogenous) variations that result in, or increase the risk of, autism or ASD.

Dr. Geschwind, co-director of the UCLA Center for Autism Research and Treatment, said that combining linkage analysis and chromosomal copy number variation in such a large sample of families with autistic members will help researchers better understand the different subgroups of autistic patients.

Autism is associated with dysfunction in three core developmental areas: repetitive behaviors, social deficits, and language abnormalities, he noted.

“We've looked at language and social behavior, but we need to get much more powerful in our detection methods. This was an initial pass evaluating around ten thousand SNPs [single nucleotide polymorphisms] of DNA, but in our next study we'll be looking at anywhere from five hundred thousand to one million snips per individual,” he told Neurology Today in a telephone interview.

[SNPs are DNA sequence variations occurring when a single nucleotide — A, T, C, or G — in the genome (or other shared sequence) differs between members of a species, or between paired chromosomes in an individual.]

Dr. Geschwind said his team at UCLA has a paper in press at the American Journal of Psychiatry in which “much more power” was applied to detect genetic variations in a smaller cohort of autistic patients. The paper shows strong linkage with signals on chromosomes 11, 5, and 15, with the strongest on chromosome 11, just as in the Nature Genetics paper, he told Neurology Today.

“We have to think it in terms of ‘autisms’ instead of autism – there are just so many different variations,” he said. [Autism is considered a pervasive developmental disorder (PDD), which forms a group of disorders that also include Asperger disorder, PDD not otherwise specified, and Rett syndrome.]

Gerard Schellenberg, PhD, research professor of medicine and neurology at the University of Washington in Seattle, said he thinks researchers will eventually discover links between unique genetic variations and different manifestations of the disorder, including language acquisition, regression and non-regression of autism, and repetitive behaviors.

“This is a huge data set and it has enabled researchers to pool research and resources together to maximize their work,” he said. “It's pretty amazing to get all these researchers on the same page in the first place. There is still a lot of work to do. This isn't the end, but it's a major first step.”

ARTICLE IN BRIEF

An international autism research consortium searched for genetic anomalies in over 11,000 families with more than one autistic member, and found stronger evidence of the role of sites on chromosome 11 and 15 in controlling the activity of neurexins — molecules that build glutamate synapses — in autism and autism spectrum disorders.

INCIDENCE OF ASD ESTIMATED TO BE HIGHER

For decades, the best estimates of autism spectrum disorders (ASDs) put the incidence at between four and five cases per 10,000 children. However a report, released Feb. 9 by the Centers for Disease Control and Prevention (CDC), found incidence to be significantly higher, perhaps as high as one in 150 children (MMWR Surveill Summ 2007;56:29–40).

The first and largest summary of prevalence data on ASD in US communities found an average of 6.7 children out of 1,000 had ASD in six communities assessed in 2000, and an average of 6.6 children out of 1,000 had ASD in 14 communities included in a second 2002 study. Now recent studies from multiple countries, using current diagnostic criteria and conducted with different methods, have indicated that there is a range of ASD prevalence ranging between one in 500 to 166 children.

Asked how many children have ASD in the US, investigators said in a telebriefing that they were hesitant to give a statistic. But based on the estimate that one in 500 children with ASD – and that approximately 4 million children are born in the United States every year – they estimate that there are 560,000 children in the US with an ASD.

“Our estimates are becoming better and more consistent, though we can't yet tell if there is a true increase in ASDs or if the changes are the result of our better studies,” said CDC director Julie Gerberding, MD, in a news statement.

Overall, the 2000 study found ASD rates ranged from one in 222 children to one in 101 eight-year-old children in the six communities studied.

The 2002 study included approximately 10 percent of US eight-year-old children born in 1994 from 14 states — Alabama, Arizona, Arkansas, Colorado, Georgia, Maryland, Missouri, New Jersey, North Carolina, Pennsylvania, South Carolina, Utah, West Virginia, and Wisconsin. A total of 2,685 eight-year-olds were identified as having an ASD.

“It is extremely difficult to accurately estimate the number of children who have an ASD,” said Marshalyn Yeargin-Allsopp, MD, chief of CDC's autism program. “Medical records often do not provide such information, and identification is often made by schools or education specialists.”

The studies also focused on when parents and others first noted signs of developmental problems in children. The 2000 and 2002 studies found 51 percent to 88 percent of children with ASDs had documented developmental concerns before age 3 years, and fully half were diagnosed between ages 4.5 and 5.5 years. The most commonly documented problems were in language, followed by social development.

References

• The Autism Genome Project Consortium. Mapping autism risk loci using genetic linkage and chromosomal rearrangements. Nat Genet 2007;39:319–328. E-pub 2007 Feb. 18.
    • Purcell AE, Jeon OH, Pevsner J, et al. Postmortem brain abnormalities of the glutamate neurotransmitter system in autism. Neurology 2001; 57:1618–1628.
    • Van Naarden Braun K, Rice C, et al., for the Centers for Disease Control and Prevention. Evaluation of a methodology for a collaborative multiple source surveillance network for autism spectrum disorders—Autism and Developmental Disabilities Monitoring Network, 14 sites, United States, 2002. MMWR Surveill Summ 2007;56:29–40.