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Tackling the Whole Autism Genome: Insights for Diagnosis & Care

Early results from Autism Speaks “10K Autism Genome Project” show promise for improving diagnosis and personalizing treatments
July 11, 2013

For the first time, researchers have analyzed the entire DNA sequence (whole genome) of individuals affected by autism and their families. In doing so, they were able to link autism symptoms to specific genetic changes in half the families studied. This more than doubles the success rate of standard genetic testing, which identifies autism-related gene changes just 20 percent of the time.

The researchers also went beyond merely identifying new autism genes to show how whole genome sequencing can guide diagnosis and treatment of autism and related medical conditions.

The study appears today in the American Journal of Human Genetics. It’s the first to come out of Autism Speaks “10K Autism Genome Project.” The project’s goal is the whole genome sequencing of 10,000 individuals in families affected by autism. As the project’s pilot study, today’s report included 32 Canadian families participating in Autism Speaks Autism Genetic Resource Exchange (AGRE).

“This pilot study has shown that whole genome sequencing can deliver clear and useful information for our families, while advancing our understanding of what causes autism,” says Autism Speaks Vice President for Scientific Affairs Andy Shih. Dr. Shih oversees the 10K Autism Genome Project, a collaboration with the Chinese genome-sequencing giant BGI.

"From diagnosis to treatment to prevention, whole genome sequencing efforts like these hold the potential to fundamentally transform the future of medical care for people with autism," adds Autism Speaks Chief Science Officer Rob Ring.

Drs. Ring and Shih are co-authors of the study, along with Autism Speaks Vice President of Clinical Programs Clara Lajonchere and Duke University’s Yong-hui Jiang. The study was led by Stephen Scherer, director of the Centre for Applied Genomics at the Hospital for Sick Children (SickKids), in Toronto. Dr. Scherer also directs the University of Toronto’s McLaughlin Centre for genomic medicine.

Moving beyond standard genetic sequencing
Standard genetic sequencing looks at the tiny portion of a person’s DNA that spells out instructions for making proteins. By contrast, whole genome sequencing analyzes genes in a more comprehensive manner by including the other 98 percent of a person’s DNA blueprint. Once considered “junk,” this portion of the genome is now recognized as vital for development and function.

In addition to finding and confirming known and suspected autism genes, the study identified four new autism genes and eight candidate autism genes. Several families had combinations of autism-related gene changes.

“The fact that we found notable genetic variants in 50 percent of the families reflects our new ability to apply genome sequencing to find spontaneous, or de novo, as well as inherited genetic variants often missed in other approaches,” Dr. Scherer notes. “It could also allow for earlier diagnosis of autism, particularly among siblings of children with autism.”

Providing vital information to families
Indeed, the study’s medical team is providing useful information to several of the families participating in the study. This includes:

* Alerting undiagnosed family members that they carry newly identified autism-risk genes and encouraging them to receive thorough evaluation and care.

* Alerting members of one family that they carry a newly identified gene change affecting the brain pathway involved in Fragile X syndrome. This family may benefit from medicines currently being evaluated for treating the social withdrawal associated with this syndrome.

* Alerting another family that several members carry an autism gene associated with CHARGE syndrome. A rare disorder, CHARGE involves developmental problems affecting the eyes, ears, heart and brain. In this instance, the newly identified gene has the potential to speed diagnosis and care of a difficult to identify syndrome.

* Reassuring news for a family carrying a newly identified gene associated with autism and infant seizures. Because these seizures are generally harmless, the information can reassure parents and physicians who might otherwise suspect a serious brain disorder.

“Whole genome sequencing offers the promise of being the ultimate tool to advance understanding of the genetic architecture of autism,” Dr. Scherer concludes. “In the future, results from whole genome sequencing could speed the diagnostic path and highlight molecular targets for pharmacological intervention, paving the way for individualized treatments in autism.”

Also see Guidance on Genetic Testing for Younger Sibling of Child with Autism in the "Got Questions?" blog.


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