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Emory Scientists to Pair NimbleGen Arrays With Illumina Sequencer in New Autism Study

Using an experimental design made possible by the advent of next-generation sequencers, a team of scientists at Emory University School of Medicine in Atlanta will use new NimbleGen microarrays and Illumina’s Genome Analyzer in a three-pronged study to identify genetic variants associated with autism.
According to principal investigator Michael Zwick, the group will use a $3 million grant from the Simons Foundation to seek genetic explanations for why males have much higher autism rates than females.
Researchers will use NimbleGen’s 2.1-million-feature microarrays for copy number variation studies, the Genome Analyzer for Solexa sequencing, and a new DNA isolation technique developed at Emory’s department of genetics and featured in an upcoming issue of Nature Methods. The isolation technique is performed on the NimbleGen platform.
The pairing of arrays with sequencing matches the kind of approach that vendors of these technologies have advocated. Both Illumina and Roche — which acquired 454 Life Sciences and NimbleGen this year — see array and sequencing platforms as complementary to one another.
Zwick and fellow Emory investigators Stephen Warren and Bradford Coffee will use all three approaches to survey the X chromosome, which could be linked to autism.
“Autism exhibits a four-to-one male-to-female excess among affected individuals,” Zwick told BioArray News this week. “It seemed reasonable to us that genetic variation on the X chromosome might account for this sex bias, as much as it does in mental retardation.”
According to Zwick, the high-density genome coverage of NimbleGen’s 2.1-million feature arrays plus the recent launch of the Genome Analyzer have created a perfect technology environment in which to test the hypothesis. “In the past, technological limitations have precluded the systematic identification of X-linked genetic variation that may contribute to autism susceptibility,” he said.
Zwick said work on the project is expected to commence immediately. The group plans to use the three technologies to detect variation in 330 families that have two or more boys with autism. “The basic design is that we are going to contrast the fathers with the sons so that we can do a case control framework in that sense,” he said.
“The notion is that rare variants can be studied even though they may be unique to a certain family, and if you find the same gene in different families it can clue you in to the idea that the gene might be the location where there could be multiple variants related to the disease,” said Zwick.

“I think we can handle the informatics challenges. Our group is sufficiently quantitative and quantitational.”

Stephen Warren, who is the PI for the entire project, will use the NimbleGen arrays to scan the X chromosome, Zwick said. Zwick will be responsible for resequencing the coding portion of all the genes on the X chromosome using the Genome Analyzer and the group’s novel array-based method of target DNA isolation. Bradford Coffee will also characterize the epigenetic state of all the gene promoters on the X chromosome that appear to be affected.
The goal “is to definitely rule in or out the role of the X chromosome in autism,” according to Zwick.
The Emory researchers will perform data extraction and analysis across the different platforms on a thousand-node computational cluster. Zwick said the research team felt it would be more effective to rely on its own computational biology skills than solely using the vendors’ software. He has an ongoing collaborative relationship with NimbleGen, which includes the early access to the 2.1-million-feature chips, and the group may borrow some source code to handle the “huge bioinformatics challenge” of sifting through the combined data from the arrays and the sequencing platform.
“The bottom line is that you have to build a substantial data infrastructure to handle and analyze the data,” Zwick said. “I think we can handle the informatics challenges. Our group is sufficiently quantitative and quantitational.”
Zwick is also no stranger to the Illumina sequencer, having used it previously in the genomics group at the US Department of Defense.
“I have had a lot of experience with these next-generation sequencers and in general I think this is the way technology is moving,” he said. “There are substantial bioinformatics challenges but in the history of genetics, finding variation has been limiting. With sequencing, you can get a more comprehensive look at variation at a cost dramatically less than just a few years ago.”

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