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Partnership aims to sequence 10,000 autistic genomes

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A research project launched today will blend the muscle of a huge Chinese genome sequencing center with the funding prowess and ambition of a high-profile American advocacy group, to create the world’s largest library of sequenced genomes from people with autism.

The American group Autism Speaks and Shenzhen-based BGI say in this press release that they plan to fully sequence 10,000 genomes in the next two years — genomes drawn mainly from families with two or more children with the poorly-understood disorder, which is marked by impaired communication and repetitive movements.

Most of the families are already participants in the Autism Genetic Resource Exchange, a US-based repository of DNA samples and relevant clinical and medical information from families with two or more children with autism. But researchers will also collect and sequence new samples from some 1,000 Chinese individuals, working with collaborators from Fudan University Medical School in Shanghai.

While a trove of papers have in recent years begun to tease out the genetic elements of autism, they have identified mutations in only about 15% of affected individuals. And while many studies have identified, for instance, point mutations and copy number variations — deletions or duplications of entire genes — few have systematically sequenced those portions of the vast three-billion-base-pair genome that do not code directly for proteins. It is suspected that abnormalities there may be responsible for some percentage of autism cases by, for example, altering the normal regulation of gene expression.


“There has been sequencing outside the coding regions [before], of course. But nothing at this scale,” says Andy Shih, the Vice President for Scientific Affairs at Autism Speaks. “That’s going to provide us not only with incremental advances but possibly with a transformative level of information.”

Shih said that his group chose the high-powered Chinese sequencing center both because of the quality of its work — which is regularly published in journals like Nature and Science — and because of its sheer sequencing muscle: it houses some 20% of the world’s sequencing capacity. “The fact that they are in a position to generate this highly valuable information in a very short period of time, for us, is crucial,” says Shih. “We see this as an opportunity to rapidly accelerate the pace of discovery.”

The project will begin with a pilot phase aiming to sequence 200 genomes by the end of the first quarter of 2012. Autism Speaks will contribute $200,000 initially to the sample collection effort in China, and $250,000 to the initial sequencing. This amounts, notes Shih, to “a tiny fraction” of the sequencing’s total costs, which, with the cost of sequencing an individual genome currently at $4,000 to $5,000, will come to $40 to $50 million. After the initial outlays, says Shih, AS will “work together” with BGI to deliver the rest of the funding.

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