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Autism Genome Sequenced in Unprecedented Detail

First results from 10K Autism Genome Project go beyond discovery of new autism-linked genes to provide guidance for diagnosis and treatment
December 01, 2013

A “Top Ten Advances in Autism Research 2013” Selection
See all the year’s “Top Ten” here.

(Dec. 1, 2013) In July, investigators reported the success of the first sizable study to use whole genome sequencing to investigate autism. The study focused on 32 families affected by autism and identified autism-linked gene changes in half of them. This is more than doubled the success rate of standard genetic testing for autism, which looks at only 2 percent of a person’s DNA.

The study also identified several new autism-linked genes and provided important medical information to the participating families. This included some unexpected diagnoses for family members as well as personalized treatment guidance.

"Whole genome sequencing has shown its potential to fundamentally transform the future of medical care for people with autism," said study co-author and Autism Speaks Chief Science Officer Rob Ring.

The report, in the American Journal of Human Genetics, was the first from Autism Speaks’ “10K Autism Genome Project.” The project aims to sequence the complete genomes of 10,000 individuals in families affected by autism.  

As the project’s pilot study, this year’s historic report focused on 32 Canadian families enrolled in Autism Speaks Autism Genetic Resource Exchange.

Beyond standard gene sequencing
Standard genetic sequencing looks at the 2 percent of a person’s DNA that codes for proteins. The other 98 percent was once considered “junk DNA,” but is now recognized as vital for development and health.

In the new study, genome analysis identified four new autism-risk genes and eight suspected ones. It also found harmful de novo gene mutations in 15 of the affected children. De novo mutations aren’t carried by either parent but arise in germ cells or very early prenatal development. A growing body of research has linked this type of gene change to autism.

“The fact that we found notable genetic variants in half of the families reflects our new ability to apply genome sequencing to find those missed in other approaches,” says Stephen Scherer, the study’s senior author. “This could allow for earlier diagnosis and treatment, particularly among siblings of children with autism.” Dr. Scherer directs the Centre for Applied Genomics at the Hospital for Sick Children, in Toronto. 

Immediate benefit to families
In the process of discovering new autism-linked genes, the investigators were able to provide important medical information for several families.

Two of the newly identified autism genes, for example, were associated with difficult to diagnose syndromes that also affect multiple organ systems. “Families affected by these disorders often go through difficult medical odysseys trying to identify the cause of not only behavioral symptoms but also medical problems,” Dr. Scherer says. In the future, detection of this newly identified gene could speed diagnosis and appropriate medical care.

The researchers linked another of the newly identified autism genes with benign infant seizures. Because these seizures are generally harmless, the presence of this particular gene variation can reassure parents and physicians who might otherwise suspect a serious brain disorder.

Yet another newly discovered gene affected a brain pathway involved in Fragile X syndrome. As such, the family learned that their child might be a candidate for experimental medicines being developed for the disorder.

“This work has shown that whole genome sequencing can deliver clear and useful information for our families, while advancing our understanding of what causes autism,” says co-author Andy Shih, Autism Speaks senior vice president of scientific affairs. Other authors Duke University’s Yong-hui Jiang and Clara Lajonchere, Autism Speaks vice president of clinical programs. 

[Editor’s note: Discover magazine cited this study as one of its top science stories of 2013. More here.]