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World's Geneticists Welcome Upcoming Release of Whole Autism Genomes

October 22, 2014

Autism Speaks previews MSSNG – a genomics program to change the future of autism with open science – at world’s largest genetics meeting

At this week’s annual meeting of the American Society of Human Genetics (ASHG2014), Autism Speaks scientists shared news of the upcoming public release of an initial 1,000 autism genomes. The conference, taking place in San Diego, is the world’s largest gathering of geneticists.

Renowned geneticist Stephen Scherer, director of the Autism Speaks genome project, made the announcement in a talk titled “Autism Speaks Ten Thousand Genomes (AUT10K): A roadmap for the complete genetic landscape of autism spectrum disorder.” Going forward, the project will be known as MSSNG (pronounced “missing”). The name’s deliberately omitted vowels stand for the missing answers that whole genome sequencing promises to deliver to advance understanding and treatment of autism.

“ASHG2014 is one of the most important annual events for those working in the field of human genetics,” says Autism Speaks Chief Science Officer Rob Ring. “It was a perfect venue to provide details on our newly branded MSSNG program.”

MSSNG involves a historic collaboration between Autism Speaks, Google and Toronto’s SickKids Hospital. It will provide open access to the whole genomes of 10,000 individuals with autism and their family members. MSSNG has already completed sequencing of more than 1,000 whole genomes and is using Google’s Cloud to store them in preparation for the launch of an open-access portal later this year. The MSSNG portal will also include powerful analytic tools that will enable the world’s researchers to process the information in this unprecedented database, Dr. Scherer told an enthusiastic audience.

“Through open science, this program will be changing the future of autism research,” Dr. Scherer says. “It will be an unprecedented database and a turnkey solution that researchers can use to rapidly test promising ideas.” Dr. Scherer also directs the McLaughlin Centre at the University of Toronto and the Centre for Applied Genomics at Toronto’s Hospital for Sick Children (SickKids).

Dr. Scherer adds that he was gratified by the positive feedback and many inquiries about MSSNG that he received following his talk. “We want to welcome the world’s research community to focus their eyes and minds on this unprecedented wealth of data,” he says.

Last year, Dr. Scherer and his co-authors, including Dr. Ring, published AUT10K’s inaugural report in the American Journal of Human Genetics. It focused on 32 families affected by autism. Through whole genome sequencing, the researchers identified autism-linked DNA changes in half of the families – more than doubling the success rate of standard genetic testing. Moreover, the sequencing identified medically relevant information for many of the participating families. (Discover magazine cited the study among its Top Science Stories of 2013.)

At this week’s genetics conference, Dr. Scherer’s presentation of Autism Speaks’ MSSNG program followed several days of presentations on the promise of whole genome sequencing to advance understanding of autism’s causes and treatments.

Whole genome sequencing moves far beyond conventional genetic testing, which looks only at protein-coding genes, or exons. Coding genes are directly involved in all body functions and structures. However, they make up just two percent of a person’s DNA.

The remaining 98 percent of human DNA was once considered “junk.” But it is now recognized as playing a role in controlling coding gene activity. In other words, a person’s whole genome is involved in ensuring that the right genes turn on at the right time and in the right place during development and throughout life.

In multiple presentations this week, researchers described whole genome sequencing of individuals with autism and their family members. In every study, whole genome sequencing found autism-associated DNA changes missed by conventional genetic tests.

Over the last 20 years, research has made clear that predisposition to autism is largely – but not wholly – genetic. Researchers have identified hundreds of autism-associated genes. However, conventional genetic testing identifies one or more of these genes in only 10 to 20 percent of individuals with autism spectrum disorder.

The looming question has been: Where is autism’s missing genetic “dark matter”? The consensus of multiple presentations at this week’s conference was that whole genome sequencing would reveal the bulk of genetic risk for autism, while also identifying subtypes of autism that may respond to tailored treatments.

Identifying the genes that contribute to autism is important, researchers say, to understand the disorder’s underlying biology. Autism risk genes also provide clues, or “targets,” for the development of individualized treatments.

Other ASHG2104 presentations on autism genome sequencing included:

* Mutation characteristics in families with two or more siblings with autism spectrum disorder

* The discovery of integrated gene networks for autism

* Increased complexity of the human genome revealed by single-molecule sequencing

* The landscape and clinical impact of cryptic structural variation in autism and related neuropsychiatric disorders.

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