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New Beckman-Hopkins Partnership May Lead to Dxs Derived From Large-Scale Sequencing

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In one of the first indications that large-scale sequencing studies may lead to new diagnostic tests, Beckman Coulter said last week that it has obtained two options from Johns Hopkins University to license cancer mutations discovered in sequencing-service projects that its Agencourt Bioscience subsidiary has been conducting for the Johns Hopkins Kimmel Cancer Center since 2002.
 
Though next-generation sequencing is not used in the projects covered by the agreements, Agencourt is exploring new sequencing technologies for future targeted sequencing studies and is about to “very aggressive[ly]” launch its next-gen sequencing service, which uses instruments made by 454 and Applied Biosystems.
 
Under the first agreement, Beckman has the exclusive right to license mutations found in 200 genes linked to breast and colon cancer that were identified in a large-scale exon-sequencing study led by Hopkins researchers.
 
Agencourt provided sequencing services worth about $5 million for that study, which was published in Science last year (see GenomeWeb Daily News 9/12/2006). The researchers sequenced approximately 13,000 protein-coding genes in 11 breast cancers and 11 colorectal cancers, or about 465 megabases of DNA. A validation screen generated another 77 megabases of sequence data.
 
Last month, the researchers published a follow-up study in Science online that increased to more than 18,000 the number of genes analyzed in the 22 samples.
 
The second agreement covers ongoing sequencing services Agencourt is providing to JHU for six additional, undisclosed cancers, and gives Beckman the option to license any resulting cancer mutations that have diagnostic potential. Beckman and JHU declined to provide further information on these studies, their status, or their scale. Funding for the studies comes from a variety of private and public sources.
 
Agencourt has been providing sequencing services for JHU since 2002, starting with SAGE sequencing, and moving on to gene sequencing for SNP discovery. “The relationship has been going on for quite some time,” Erick Suh, director of genomic services at Agencourt, told In Sequence last week. “Finally, we decided to set more of a formal agreement, such that … we will have some licensing rights in return for the sequencing.”
 

“We have done a number of customer [next-gen sequencing service] projects, [so] we are comfortable now to get very aggressive and do an official launch” of the services.

The company is using traditional Sanger sequencing in these studies, but is investigating the use of next-gen technologies for future targeted sequencing projects, he said.
 
“I think in the near term, we will continue to use the Sanger sequencing, because we have got a benchmark for the quality, and the pipeline is set up,” Suh said. “But we will be evaluating the next-gen [technologies] for multiplexing and pooling, and we have already done some of those experiments,” he said.
 
The company, which owns a 454 Genome Sequencer FLX and installed an ABI SOLiD system last month, is in the process of launching next-generation sequencing services on these instruments.
 
On its recently updated website, it offers whole genome, transcriptome, RNA, and structural variation analyses by next-generation sequencing. “We have done a number of customer projects [so] we are comfortable now to get very aggressive and do an official launch” of next-gen services, according to Suh.
 
Beckman, if it chooses to license any of the cancer mutations from the Hopkins studies, wants to develop diagnostic tests for them that will run on a new molecular diagnostics instrument the company is currently developing, Mary Luthy, director of corporate communications at Beckman, told Biotech Transfer Week, a sister publication of In Sequence, last week. That new platform, called UniCel DxN, is scheduled for release in 2010.

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