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Roche, NimbleGen, Applied Biosystems, NCGR, NHGRI, Biofortis, NCRR, BP, Synthetic Genomics, Illumina

Roche to Acquire NimbleGen for $272.5M, Eyes Additional Genomic Vendors
Less than a month after acquiring 454 Life Sciences for $152 million, Roche said this week it plans to acquire NimbleGen Systems for $272.5 million.
Noting that NimbleGen’s arrays complement Roche’s ongoing genomics campaigns, Roche Diagnostics CEO Severin Schwan said the deal is part of the company’s strategy to gain ground in the genomics research market by “extending our activities into the microarray segment.”
NimbleGen, a private company based in Madison, Wisc., in March filed with the US Securities and Exchange Commission for an initial public offering of stock but had not set a specific date or opening share price.
Roche said the acquisition, which would make NimbleGen a division of Roche Applied Science, which is part of Roche Diagnostics, still depends on approval from NimbleGen’s shareholders. 454 is part of the same division.
NimbleGen offers products and services for genomic hybridization, chromatin immunoprecipitation arrays, comparative genome sequencing, and expression analysis.
The array systems from NimbleGen are “highly synergistic and will complement the existing Roche portfolio of innovative genomic research tools such as the LightCycler qPCR systems and the high-throughput sequencing systems from the recently acquired company 454 Life Sciences," Roche said in a statement.
Roche said NimbleGen has plans to expand its product line “in the near future” to include higher-density arrays, integrated instrument systems, and related reagents and consumables for advanced genome analysis.
In its filing with the SEC, NimbleGen said that 2006 revenues from microarray sales and grants grew 43 percent to $13.5 million, from $9.5 million in 2005.
NimbleGen in October licensed nucleic acid microrarray technology from Affymetrix, and in January it struck a licensing and supply deal with Oxford Gene Technology for oligonucleotide array IP.
Having access to Roche’s international sales and distribution network “will accelerate and broaden our high-density DNA microarray business,” said NimbleGen CEO Stan Rose in a statement, adding that the merger also will enhance the companies' “new technologies focused on targeted DNA sequencing.”
Roche said it expects to retain NimbleGen’s 140 employees and keep NimbleGen’s facilities in Madison; Reykjavik, Iceland; and in Waldkraiburg, Germany. The company expects the deal to close in the third quarter.
Separately, a news report quoted a Roche spokesperson as saying that the company continues to screen the market for genomic-research tools companies, though no deal is currently in the pipeline.
“Genomic research tools are key for the future of any major pharma group,” a Roche spokesperson was quoted by Thomson Financial News as saying. “These tools help our understanding of genetic causes of disease and predisposition factors, and also help in identifying potential drug targets and thus offer a great potential for pipeline development.”

ABI Opens Application Support Center in Foster City
Applied Biosystems has opened an application support center at its research and development headquarters in Foster City, Calif., the company said this week.
The 10,000 square-foot facility will showcase the company’s instrumentation and software and will offer training courses and applications support for its life-science customers.
The center houses ABI technologies for DNA sequencing, fragment analysis, human identification, and real-time PCR applications, including ABI’s SOLiD high-throughput DNA sequencing system. It includes a fully staffed laboratory as well as classrooms.
The company said it offers training and application support through 20 centers around the world.
"We envision this center as providing an environment for collaborating with our customers, developing new applications, and providing comprehensive training on our technologies, all in an effort to address their most difficult research challenges and ultimately to advance their science," said Mark Stevenson, president for ABI’s molecular and cell biology division, in a company statement.

NCGR Lays Off One-Third of Staff as Focus Shifts From Informatics to Sequencing
The National Center for Genome Resources has laid off around one-third of its staff as it shifts its focus from bioinformatics and software development to DNA sequencing, In Sequence sister publication GenomeWeb Daily News reported last week.
NCGR CEO Stephen Kingsmore announced the plans to his staff two weeks ago, and the lay-offs took place two days later, according to people familiar with the event.
The lay-offs consisted almost entirely of software engineers on the bioinformatics side of the business, including Scott Wolff, director of software engineering. Remaining staffers include business-operation employees and a handful of informatics researchers who will contribute to NCGR’s DNA sequencing work.
Also, Bill Beavis, chief science officer and second in command at the Santa Fe, NM, lab, will leave NCGR to become a professor of plant genomics at Iowa State University, his alma mater, according to an official at the school. His tenure begins in mid-August.
“We were told that were having trouble winning [government] grants, and our PIs thought it would be best if we [abandoned] the cyberinfrastructure/bioinformatics/software-engineering type of business model, and that we should put all our efforts into the sequencing model,” according to one laid-off researcher, who asked to remain anonymous because he does not want to jeopardize future employment.
Specifically, NCGR recently learned that it had not won a grant under the National Science Foundation’s $50 million Plant Science Cyberinfrastructure Collaborative program, the researcher said, noting that since “all of our eggs were in that one basket … we’re not going to be able to support everyone.”
The NSF said it does not comment on pending awards.
According to this individual, Kingsmore told his staff that because the NCGR has had difficulty obtaining “significant” government grants in general over the past few years that it would be in NCGR’s best interest “to get away from that whole software-engineering thing and become a sequencing center.”
It was not immediately clear if the NCGR plans to hire sequencing staff to replace the informatics employees.
According to income tax returns filed with the Internal Revenue Service, NCGR’s revenue from government grants grew 38 percent to $3.6 million between 2003 and 2004, and 11 percent to $4 million in 2005, the most recent time for which figures are available.
According to the documents, Kingsmore received $326,986 in salary and benefits in 2005. Around 28 percent of this total figure went to “fundraising” responsibilities, 16 percent went to “program services,” and around 56 percent went to “management and general.”
Last week’s move fortifies plans NCGR disclosed in January to create a sequencing center with the New Mexico Institute of Mining and Technology. At that time the NCGR had secured $600,000 from the state to buy its first sequencer for the center, called the New Mexico Genome Sequencing Center. The center is seeking another $1.1 million in federal funds.
“Everybody [at NCGR] who was kept has something to do with sequencing,” another former employee said.
This source, who also asked to remain anonymous because he does not want to endanger future employment, said that the only informatics component that will remain at NCGR will be related to genome assembly and databasing.
The source also said that Kingsmore “is looking” to hire a chief financial officer in order to free him up to do more PI work.
When reached earlier this week, Kingsmore declined to comment. He could not be reached for comment today. Repeated telephone calls to other NCGR executives went repeatedly to voicemail.

NHGRI Using Biofortis' Labmatrix for ClinSeq Study
The National Human Genome Research Institute is using Biofortis’ Labmatrix data-management software in its ClinSeq sequencing program, which intends to sequence the genomes of 1,000 human subjects and to continue research with these subjects over time in the clinical setting, Biofortis said last week.
Biofortis said the NHGRI is using Labmatrix to “manage and integrate patient, sample tracking, and genetic data.”
NHGRI has already been using Labmatrix as its central database in its intramural research programs, Biofortis CEO Ethel Rubin told In Sequence sister publication BioInform last week.
Financial terms of the agreement were not released.

NCRR to Award $20M in FY ’08 Under High-End Instrument Grant Program
The National Center for Research Resources at the National Institutes of Health plans to award $20 million in fiscal year 2008 under it High-End Instrumentation Grant Program, according to a funding announcement issued last week.
The program is intended to support the purchase of “a single major item of equipment to be used for biomedical research that costs at least $750,000,” with a maximum award of $2,000,000, the NIH said.
Instruments in this category include, but are not limited to, structural and functional imaging systems, macromolecular NMR spectrometers, high-resolution mass spectrometers, cryoelectron microscopes, and supercomputers.
Yale University was recently awarded $1 million to purchase new sequencing technology under the HEI program [see In Sequence 06-12-07]
Applications should show “a clear need for the instrumentation by projects supported by multiple NIH peer reviewed research grants,” NIH said, and must demonstrate that these projects will require at least 75 percent of the total usage of the instrument.
NCRR has earmarked around $20 million in fiscal 2008 to fund between 10 and 15 one-year awards. The anticipated start date is July 1, 2008.

BP Buys Stake in Synthetic Genomics as Part of Bioenergy Deal to Study Hydrocarbon Flora
Synthetic Genomics has formed a “long-term” research and development partnership with petroleum firm BP to identify alternative energy sources from subsurface hydrocarbons, the company said last week.
The oil company has also made an undisclosed equity investment in the privately held biotech, and the two companies intend to jointly commercialize technologies developed under the partnership, Synthetic Genomics said.
The research will focus first on microbial communities found in hydrocarbon formations such as oil, natural gas, coal, and shale, Synthetic Genomics said.
Synthetic Genomics will perform genomic sequencing and cell-culture studies of the microbial populations living in these environments. The company, founded in 2005 by Craig Venter to create an organism from synthetically crafted and oriented genes, aims to “discover and/or design new genomes that will code for new types of cells with desired properties for bioenergy or specific chemical production.”
Once the basic science research phases are complete, BP and Synthetic Genomics will seek to jointly commercialize the technologies developed, Synthetic Genomics said.
Venter said in a statement that Synthetic Genomics hopes the collaboration “will achieve a new and better understanding of the subsurface hydrocarbon bioconversion process, which we are confident will yield substantial cleaner energy sources."
Tony Meggs, BP’s group vice president of technology, said the partnership “could lead to an unprecedented understanding of the microbial activity in the subsurface; and eventually to the development of more environmentally friendly and efficient energy production and recovery techniques."
"We believe that one of the most promising solutions to producing cleaner fuels will be found through genomic-driven advances," Venter added.  

Illumina Marks 75th Order for Genome Analyzer; Broad Installs 16 of Planned 20
Illumina said last week that it has received more than 75 orders for its Genome Analyzer, and that the Broad Institute has so far installed 16 Genome Analyzers out of a ”near term goal of” 20.
An Illumina spokeswoman would not disclose how many of the ordered instruments have been installed, or how many customers have ordered more than one system.
At the end of January, 454 Life Sciences said it had an installed base of more than 60 Genome Sequencer instruments.

NHGRI Offers Access to Cancer Sequencing Data
The National Human Genome Research Institute said last week that it is granting access to datasets from cancer sequencing projects through open-access and controlled-access programs.
Researchers will be able to access controlled information from the Medical Sequencing Program by downloading individual-level genotype and assembled DNA-sequence data, NHGRI said.
Most of the data in the open category are available through the National Cancer Institute’s Center for Bioinformatics. DNA sequences may be accessed through the National Center for Biotechnology Information’s trace archive.
NHGRI also said it plans to announce procedures for accessing individual-level data for the Cancer Genome Atlas program separately. 

NHGRI’s Medical Sequencing Program also is supporting investigations of other diseases besides cancer, and data from those studies may be found in the NCBI’s Genotype and Phenotype database.

The Scan

Y Chromosome Study Reveals Details on Timing of Human Settlement in Americas

A Y chromosome-based analysis suggests South America may have first been settled more than 18,000 years ago, according to a new PLOS One study.

New Insights Into TP53-Driven Cancer

Researchers examine in Nature how TP53 mutations arise and spark tumor development.

Mapping Single-Cell Genomic, Transcriptomic Landscapes of Colorectal Cancer

In Genome Medicine, researchers present a map of single-cell genomic and transcriptomic landscapes of primary and metastatic colorectal cancer.

Expanded Genetic Testing Uncovers Hereditary Cancer Risk in Significant Subset of Cancer Patients

In Genome Medicine, researchers found pathogenic or likely pathogenic hereditary cancer risk variants in close to 17 percent of the 17,523 patients profiled with expanded germline genetic testing.