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Rare genetic variants linked to autism

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The search for the genetic underpinnings of autism spectrum disorder has just yielded a new set of clues. In the largest study to date, the Autism Genome Project consortium reports that people with autism have more copy number variants – segments of DNA that have been either duplicated or deleted – in their genes.

The results, published today in Nature, could eventually be used to develop quick diagnostic tests. The consortium was also able to group some of the affected genes into biochemical pathways. These pathways – some of which are clearly linked to brain function — may then become attractive targets for those who hope to develop drugs to treat the condition.

Autism is a complex disorder. Although the environment is thought to influence the risk of autism, genetics are known to play an important role.

The study included 996 people with autism and another 1,287 people without the disorder, to serve as controls. The researchers focused on rare genetic variants – a shift from previous approaches, which analyzed variants that are commonly seen in the population. (For more on rare variants, see ‘Hunt for genetic causes of diseases causes narrows targets’.)


They found that autistic people did not have more rare copy-number variants than those without the disorder, but their variants were more often found within genes rather than in the vast amount of DNA located between genes. Specifically, 20% more genes contained a rare copy-number variant in autistic participants in the study. And among genes previously linked to autism spectrum disorder or intellectual disability, 70% more of them contained a rare copy number variant.

Deletions in one region of the X-chromosome, called the DDX53-PTCHD1 locus, were associated with a three-fold higher risk of autism spectrum disorder.

Diagnostic tests based on the work will not be clearcut. Co-author Stephen Scherer of the Hospital for Sick Children in Toronto estimated that genetic clues to the disorder were present in only about ten percent of the families with an autistic member in the Canadian cohort of the study. And, the researchers noted, each patient carried their own unique assortment of copy number variations. Of nearly a thousand variants studied, the most prevalent was still only present in less than 1% of the participants with autism.

But a new test would nevertheless be welcome. At present, diagnosing autism can take months or longer – an agonizing wait for anxious parents that can delay the start of behavioural therapies. Early therapy has been shown in some cases to lessen the effects of the disorder.

Meanwhile, the hunt continues. The consortium has enrolled another 1,500 families, and hopes to use next-generation sequencing to sequence full genomes and exomes (the part of the genome that codes for RNA or protein).

Image: Ingram Publishing

Comments

  1. Report this comment

    Krister Gerdin said:

    Any connection to the genetic disorders of the MECP2 syndrome detected?

  2. Report this comment

    Paul said:

    While certain genetic alleles might affect the propensity to develop autism, if we accept the CDC’ Morbidity and Mortality Weekly statistics, the incidence of autism has increased some 10 fold in a generation. This can not be due to a generational change in genetics. Therefore we have environmental/infectious etiologies to consider. Seeing as a significant minority of parents of autistic children have stated that their child’s autism developed subsequent to a vaccine inoculation and considering these vaccines often contain preservatives designed to “kill cellular life”, this provides a very reasonable avenue for intense investigation. Or will we just call them the “refrigerator mothers” of the 21st century?

    Paul Maher, MD MPH

    http://healthjournalclub.blogspot.com/

  3. Report this comment

    Gene Clemson said:

    I would be interested to know if they can try to find the cause of autism rather than things to do early on to lessen the effects. As Paul said, something weird is going on which is causing such a huge increase in such a short amount of time.

  4. Report this comment

    Jessica said:

    I agree with Paul- it’s a wonder why we haven’t started looking into other causes more. The statistics showing the rapid increase of cases seem to speak for themselves here. Any updates on this discussion would be great to read.

  5. Report this comment

    Penny Stocks said:

    I have a brother also be autism, now a little better than before, how to treat?

  6. Report this comment

    Michael said:

    Just my 2 cents…

    cases of “Special childs” have indeed been really increasing over time. Is it because we really did not characterize mild autism as autism before? hence when we started characterizing autisms that is when we see the increased rate? The numbers are really quite alarming let’s hope we can find the real cause of autism, genetic or environmental this is something that needs to be addressed.

    Michael

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    Darrin Recton said:

    Wouldn’t it make more sense to use similar sized test and control groups? It seems to me, 996 autism cases against 1287 “control” cases would immediately lead to possible mistaken results evaluation. What is the standard size of similar tests? Interesting read, none the less.

  8. Report this comment

    Mr.M said:

    Well since alot of you think that they should focus more on the cause then to minimize symptoms of autism. Im quite sure there is ONE reason why they’re not focusing your way. MONEY, there would probably be more money to be made in treating autism then eradicating it. Company’s like Pfizer have no interest in curing everyone and.

    It’s a sad world but the truth.

    – Mr.M the cynic Psychic

  9. Report this comment

    filmes said:

    Is it because we really did not characterize mild autism as autism before? hence when we started characterizing autisms that is when we see the increased rate? The numbers are really quite alarming let’s hope we can find the real cause of autism, genetic or environmental And among genes previously linked to autism spectrum disorder or intellectual disability, 70% more of them contained a rare copy number variant.

  10. Report this comment

    avatar said:

    The statistics showing the rapid increase of cases seem to speak for themselves here

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