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Keygene, Illumina, VCU, TGen, Spectrumedix, Qiagen, JGI, Cogenics, Epigenomics

Keygene Buys Illumina Analyzer and Upgrades its 454 Sequencer
Keygene said this week that it has purchased a 454 GS FLX sequencer from Roche and an Illumina Genome Analyzer.
The company upgraded to the GS FLX from a GS 20 and bought the Illumina hardware to "further develop its array of innovative DNA sequence-based applications."
Keygene said it has been using the GS 20 for almost two years. Last year, the company signed a co-marketing collaboration with Roche to market plant genetics applications it developed using the 454 sequencer.
The company has developed a range of applications based on the 454 technology, including a method for detecting mutations in mutagenized plant libraries called KeyPoint and a technology called CRoPS (complexity reduction of polymorphic sequences) that uses the 454 system to sequence the fragments generated by its Amplified Fragment Length Polymorphism technology [see In Sequence 01-23-07].
The company said this week that it will use the higher-throughput GS FLX to serve its customers' sequencing needs and to support its internal mutation screening and polymorphisms discovery applications.
Keygene said it will use the Illumina analyzer for transcript mapping and for further developing its AFLP method for whole-genome mapping.
Financial terms of the deals were not released.

VCU Buys Sequencers from Illumina and 454, Hires New Genomics Staff
Virginia Commonwealth University said last week that it has purchased a 454 GS FLX sequencer from Roche and an Illumina 1G Genetic Analyzer.
VCU said it has also recruited Yuan Gao from Harvard, who had been working with George Church on next-generation sequencing technologies, and Maria Rivera from the University of California, Los Angeles, whose research focuses on applying comparative genomics.
The sequencers will be used by researchers in VCU’s Center for the Study of Biological Complexity. According to VCU, Gao’s lab will use the Illumina machine for high-throughput genome sequencing, gene-expression profiling, and the Personal Genome Project, in collaboration with Church’s lab at Harvard. 
Rivera will use the technology for her research on the origin of eukaryotes, VCU said.
CSBC Director Gregory Buck in a statement that the new sequencing tools will bring the center’s sequencing costs down to “a fraction” of previous projects.
Buck said the center spent four years and more than $2 million on its recent sequence of the 10-megabase Cryptosporidium hominis genome. Now, he said, “we could reproduce that effort in two weeks for a cost well south of $100,000.”
Financial terms of the deals were not released.

TGen Opens Pathogen Genomics Facility
The Translational Genomics Research Institute and Northern Arizona University last week opened TGen North, a new pathogen genomics and biodefense research facility in Flagstaff, Ariz.
The facility has been operational a year as a “virtual lab,” TGen said. Last week’s opening marked its move to a 4,500-square-foot permanent facility.
TGen North researchers will use a range of genomic technologies to develop diagnostics for infectious diseases. It includes three research centers: the Center for Public Health and Clinical Pathogens, the Center for Dangerous Pathogens, and the Center for Pathogen Bioinformatics.
The facility’s initial research activities are focused on common infectious diseases like influenza, hospital infections like drug-resistant staphylococcus, and several bioterrorism agents, including tularemia and plague.
TGen North has access to Biosafety Level 3 facilities on the NAU campus as well as the genomic research capabilities of TGen’s Phoenix headquarters.

Transgenomic Picks up Spectrumedix CE Assets Following Company’s Closure
Spectrumedix, a maker of high-throughput capillary-electrophoresis tools, closed its doors last month, according to Transgenomic, a Spectrumedix distributor.
To make up for the resulting supply problems created by the dissolution, which occurred March 9, Transgenomic said it has purchased certain assets from the company along with a license to a gel patent it needs to make consumables for the Spectrumedix systems.
Transgenomic said it will continue to offer service and support to Spectrumedix customers in the US and elsewhere. The company said Spectrumedix-made tools are used in comparative genome scanning, SNP genotyping, heterozygote identification, fragment sizing, PCR quality testing, and custom assay development.
Transgenomic CEO Craig Tuttle said the company has been “concerned” about the supply of consumables and spare parts to its customers in Europe, and said this series of moves “clarifies the situation” for former Spectrumedix customers as well.
Financial terms of the deal were not released.

Illumina to Close Connecticut BeadExpress Facility, Will Consolidate in San Diego
Illumina plans to close its manufacturing operations in Wallingford, Conn., and fold some of the assets from the space into its San Diego facilities, the company said last week.
The Wallingford site was originally established in connection with the acquisition of CyVera, and has helped Illumina develop and manufacture its BeadXpress system analysis platform, which debuted last month.
Illumina CEO Jay Flatley said that Illumina decided to consolidate the facility after its recent acquisition of Solexa enabled the company to evaluate “all of our operations.” He said that combining the operations “will provide us with efficiencies from both the manufacturing and development perspective.”
It was not immediately clear whether the step would result in layoffs.
Flatley said Illumina will concentrate its R&D and manufacturing work in San Diego and in its facility in Little Chesterford, UK.
The company said it will incur roughly $2 million in incremental charges related to the consolidation, and expects that the move will be complete over the course of 2007.

Qiagen to Buy eGene in $34M Cash and Stock Deal
Qiagen said last week that it will buy the sample-separation technology company eGene in a cash and stock deal valued at around $34 million.
Qiagen offered $.65 cash and .0416 of its common shares for each share of eGene’s stock.
eGene, which is based in Irvine, Calif., sells the HAD-GT12 Genetic Analyzer, a multi-channel sample separation and analysis solution that includes software and a range of consumable cartridges.
Qiagen CEO Peer Schatz said eGene’s products will combine with Qiagen’s sample and assay technologies for molecular diagnostics and clinical research applications.
Qiagen said it expects the acquisition will contribute revenues of around $2 million in the second half of this year and revenues of $7 million to $9 million in 2008. After 2008, Qiagen expects the eGene division to “grow rapidly” and to make a “significant” contribution to profits.
Qiagen said it will incur a one-time charge of $.01 on earnings per share in the third quarter of 2007 and an overall reduction in EPS of $0.1 for the second half of 2007.
Both companies’ boards have approved the deal, which is expected to close in the third quarter of this year.

Report: JGI Looking to Expand in Walnut Creek
The Bay Area’s Contra Costa Times reported last week that the Department of Energy’s Joint Genome Institute is planning to add another 22,000 square feet to its facility in Walnut Creek, Calif.
JGI currently rents about 60,000 square feet in the Shadelands Business Park and employs 240 workers, approximately twice the staff it had when it first moved into the facility in 1999, the paper reported.
The expansion depends on a congressional appropriations bill and approval by the president, according to the report.

Cogenics, Epigenomics Pen Co-Marketing Pact
Cogenics and Epigenomics have signed a co-marketing agreement for DNA methylation, Cogenics’ parent company Clinical Data said last week.
Under the deal, Cogenics will market Epigenomics' services for genome-wide DNA methylation analysis, bisulfite sequencing, and PCR, which are performed in Epigenomics’ facilities in Germany.
Also under the deal, the companies will offer regulated DNA methylation analyses in Cogenics’ US labs. Epigenomics will promote these services through its Clinical Solutions segment. 
Robert Bondaryk, senior vice president and general manager of Cogenics, said the pact expands the company’s biomarker offerings to include DNA methylation for disease diagnosis, prognosis, and drug response prediction.

The Scan

UK Pilot Study Suggests Digital Pathway May Expand BRCA Testing in Breast Cancer

A randomized pilot study in the Journal of Medical Genetics points to similar outcomes for breast cancer patients receiving germline BRCA testing through fully digital or partially digital testing pathways.

Survey Sees Genetic Literacy on the Rise, Though Further Education Needed

Survey participants appear to have higher genetic familiarity, knowledge, and skills compared to 2013, though 'room for improvement' remains, an AJHG paper finds.

Study Reveals Molecular, Clinical Features in Colorectal Cancer Cases Involving Multiple Primary Tumors

Researchers compare mismatch repair, microsatellite instability, and tumor mutation burden patterns in synchronous multiple- or single primary colorectal cancers.

FarGen Phase One Sequences Exomes of Nearly 500 From Faroe Islands

The analysis in the European Journal of Human Genetics finds few rare variants and limited geographic structure among Faroese individuals.