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Invitrogen, Applied Biosystems, Life Technologies, Children’s Hospital Boston, Geospiza, Illumina, GenoLogics, 1000 Genomes Project, Fluidigm, NHGRI, ClinSeq, Source BioScience, VWR, ZyGem, RIKEN Advanced Science Institute, Genetics and Public Policy Cent

EU Authorities Clear Invitrogen, ABI Merger; New Firm to Join S&P Index
Invitrogen and Applied Biosystems said last week that European Union regulators have cleared their proposed $6.7 billion merger.
The deal already cleared US antitrust hurdles and is expected to close on Nov. 21, the firms said. The combined company will be called Life Technologies.
ABI stockholders have until the end of business on Nov. 19 to elect whether they will receive all cash, all stock, or a mix of the two in consideration for their shares.
Standard & Poor’s said this week that Life Technologies will replace Applied Biosystems in the S&P 500 Index.

Children’s Hospital Boston to Analyze SOLiD Data with Geospiza Software
The molecular genetics core facility of Children’s Hospital Boston and Harvard Medical School will use Geospiza’s FinchLab to manage its SOLiD-based sequencing operations, the Seattle-based bioinformatics firm said this week.
FinchLab is a web-based system designed to help researchers with data analysis and lab management across multiple platforms, including capillary electrophoresis-based sequencing and second-generation sequencing instruments, said Geospiza.
"We were looking for a way to provide access to our sequencing data through one location," said Hal Schneider, laboratory supervisor of the core facility, in a statement. He said that FinchLab “not only met our basic requirements, but also provided a whole package — from taking care of the server operations, tracking the samples, and then completing the alignments and essential analysis for SOLiD with a simple data distribution method."

Illumina to Use GenoLogics Data Management System with Genome Analyzer
GenoLogics said last week that Illumina has selected its Geneus lab and data management system to be used in combination with Illumina’s Genome Analyzer.
GenoLogics said that the collaboration would provide customers with a “clear path to obtain an end-to-end lab and data management solution for next-generation sequencing as well as a single system for enabling cross-genomics experiments.”
Victoria, BC-based GenoLogics said that Geneus supports both the Genome Analyzer and Illumina’s iScan data workflows for multiple genomics applications.
“The comprehensive way in which we are working with GenoLogics is a new approach for us, taking our partnership to a whole new level by integrating Genome Analyzer workflows into Geneus, in addition to integrating other Illumina platforms,” Omoshile Clement, senior product manager of informatics for Illumina, said in a statement.

1000 Genomes Project to Release Data Within Months as Pilot Phase Nears Completion
The 1000 Genomes Project collaborators plan to begin releasing data early next year and expect to finish sequencing 1,200 human genomes by around the end of 2009, project representative David Altshuler said last week at the American Society of Human Genetics meeting in Philadelphia.
The team expects to begin official releasing data starting in January 2009, following a pilot data release this December, said Altshuler, an associate professor of genetics and medicine at Harvard Medical School and a lead investigator for the project. After January, new data will likely be released quarterly, he said.
Begun in January, the three 1000 Genomes pilot projects are nearing completion, Altshuler said. The aim to achieve low coverage of 180 individuals, high coverage of two parent-offspring trios, and targeted sequencing of 1,000 genes in approximately 1,000 individuals. Those efforts seem to be generating high-quality data and have already uncovered new genetic variants, he added.
“We declared the pilot project very much a success at this point,” Altschuler told reporters at a press briefing last week.
So far, the international project has generated 3.8 terabases of data. In September and October, Altshuler said, the team deposited as much data each week as was present in GenBank when the effort began. In 2009, the project is expected to increase that dramatically, producing a petabyte of data.
Along with the sequencing effort itself, Altshuler emphasized a need for developing shared data formats for different stages of the analysis. In the absence of standard formats or a clear framework for such analysis, he added, efforts to decipher the genetic information would be delayed. Consequently, team members are working to develop draft formats to aid this analysis.
The goal of the 1000 Genomes Project is to uncover the genetic variants that are present at a frequency of 1 percent or more in the human genome.
The effort may also help researchers impute new information for the more than 100,000 genotyped genomes currently available. While that has not been shown for rare variants, Altshuler explained, it is possible that it could add value to the multitude of samples already scanned with chips.
But beyond the direct implications for the 1000 Genomes Project, the effort has spurred researchers to pioneer and evaluate methods that benefit other research efforts as well. For instance, researchers have been working with high-throughput sequencing technologies, and have developed new approaches to exchange and analyze data, such as discovering SNPs and CNVs.
Former National Human Genome Research Institute director Francis Collins noted at the press briefing that while the project itself is not aimed at linking genotypes to phenotypes, “It will be the engine of many follow-up studies.”
— By Andrea Anderson; originally published on GenomeWeb Daily News

Fluidigm's Q3 Revenues, Net Loss Rise
Fluidigm said this week that its third-quarter revenues increased 124 percent over the comparable period of 2007, while its net loss grew 51 percent year over year.
The South San Francisco, Calif.-based firm said its total revenues were $4.6 million, compared to nearly $2.1 million for the third quarter of 2007. Its product revenue, which consists of sales of integrated fluid circuits, instruments, software, reagents, and services, tripled to $4.2 million from $1.4 million.
Fluidigm said that sales volume for its BioMark system, which is used for gene expression analysis, genotyping, and digital PCR applications, doubled compared to the second quarter of this year. The company also launched this past summer its 96.96 Dynamic Array that can perform 9,216 simultaneous experiments.
Fluidigm’s net loss for the quarter was $8.9 million, compared to $5.9 million for Q3 2007. The firm did not report its loss per share as it is still privately held.
The company had filed for an initial public offering earlier this year and was expected to float on the Nasdaq exchange in September at a price of between $14 and $16 per share. However, the ongoing financial crisis has led the firm to ditch its IPO in late September.
Fluidigm acknowledged that it is not customary for a privately held firm to publicly report its financials. However, “we felt an obligation to update the financial world after we had promoted our company and its business prospects during our IPO roadshow,” said Fluidigm President and CEO Gajus Worthington. “We do not plan to disclose our financial data regularly.”
The company recently launched its first product for next-generation sequencing applications (see feature article, in this issue).

NHGRI Researcher Provides ClinSeq Update at ASHG Meeting
The National Human Genome Research Institute’s ClinSeq initiative is making headway and appealing to potential volunteers, according to NHGRI researcher Leslie Biesecker.
Biesecker described the progress on the initiative last week at the American Society of Human Genetics meeting in Philadelphia.
NHGRI launched ClinSeq last year as part of an effort to move into translational genomics by bringing together information about human genomes and clinical data using a large number of subjects. Biesecker explained that the study will enable scientists to connect genotypes with phenotypes and more.
The goal of the ClinSeq project is to gather phenotypes for 1,000 unrelated individuals diagnosed with a range of atherosclerotic conditions. Initially, the team plans to sequence 400 candidate genes for each individual, sort them by their genotypes, and validate the results and return information to participants.
Enrollment for the project began in January 2007, and volunteers have been rolling in since then, Biesecker said. “We cannot keep up with the demand from volunteers who want to participate in a whole-genome sequencing study.”
So far, the ClinSeq team has identified thousands of new, non-exon variants. But the large amount of data being generated is presenting new issues for researchers. “Using this data will be a big challenge,” Biesecker said.
Even so, the team is working to provide feedback to participants about their research results. Whereas clinical geneticists are used to operating in a rare-variant, single-gene space, Biesecker said, larger studies such as ClinSeq require a different approach.
He and his team are addressing that challenge by looking for genes for which associations are most certain and providing information about these variants to participants. They then move to less certain associations and continue providing feedback until participants tell them they are no longer interested. In so doing, the team also hopes to start defining the line at which participants no longer wish to receive feedback about the research.
“There are a lot of strongly held opinions about where that line is, but there’s no data,” Biesecker said.
Based on the initial results from the project, Biesecker added, it is possible to consent subjects for whole-genome studies, sift out clinically relevant results, and provide information to participants.
In the future, Biesecker said, ClinSeq intends to move from exon sequencing to whole-genome sequencing. In addition, researchers plan to begin enrolling participants from a variety of different backgrounds — 97 percent of the current participants are of European descent — and to incorporate reams of other data ranging from coronary calcium scores to blood pressure scores and clinical chemistry.
— By Andrea Anderson; originally published on GenomeWeb Daily News

Illumina to Seek FDA Clearance, CLIA Certification in '09
Illumina hopes to have a diagnostic assay cleared by the US Food and Drug Administration and opepn a Clinical Laboratory Improvement Act-compliant laboratory operational by the middle of next year, according to a company official.
Greg Heath, senior vice president and general manager of the diagnostics business unit, told analysts at the San Diego firm’s annual Analyst Day Nov. 6 that the company will submit a test that runs on the digital microbead-based BeadXpress reader to the FDA in the first quarter of 2009.
“We expect FDA approval shortly thereafter; it could move into the second half of ’09, depending on how long the FDA takes with their clock,” he said.
Heath did not specifically discuss the targeted indication of the company’s first test, but said that “oncology is the sweet spot of growth in molecular diagnostics,” and he discussed ongoing research programs in ovarian and gastric cancer.
Health also said that Illumina will seek CLIA certification by the end of the second quarter. The company hopes to offer not only BeadXpress-based assays but also sequencing and array-based services.
According to Health, the CLIA lab is “essential” for rolling out Illumina’s pipeline of oncology tests. “Because of a long regulatory pathway, we want to be able to offer laboratory-developed tests earlier” through the lab, he said.
CEO Jay Flatley told GenomeWeb Daily News that Illumina also could offer array-based services through the lab, such as for its consumer genetics partners, 23andMe and Decode Genetics.
Illumina used to perform array-based services for 23andMe, but 23andMe switched to using Laboratory Corporation of America’s CLIA-compliant lab earlier this year after receiving warning letters from regulators in New York and California to stop marketing genetic tests directly to consumers. One of the reasons cited by regulators was that the consumer genomics firms were not licensed in these states to provide laboratory services.
— By Justin Petrone; originally published on GenomeWeb Daily News

Source BioScience Opens Genomic Services Facility at UCL
Source BioScience said this week that it has opened a new DNA sequencing and genotyping facility at University College London.
The company said that it is collaborating with the UCL Genetics Institute to offer sequencing and genotyping services across UCL for an initial period of three years.
Source BioScience currently operates a central reference laboratory in Nottingham and has additional service facilities in Cambridge and Oxford.
The new facility at UCL, which includes second-gen sequencing, “extends the company’s reach as it continues to build on its expertise in the DNA sequencing arena and further expands the network of core DNA sequencing facilities embedded in leading academic and research institutions,” according to Source BioScience.
Steve Humphries, director of UGI, said in a statement that Source BioScience is the institute’s first commercial partner.
“A key step in achieving the vision for the development of Genetics at UCL was the establishment of a commercial collaboration to service the existing sequencing and genotyping needs within UCL whilst also providing access to next-generation technologies to accommodate future service needs,” Humphries said.

VWR to Distribute ZyGem's DNA Extraction Products
New Zealand-based ZyGem said this week that lab supply firm VWR International will exclusively distribute ZyGem’s DNA extraction products to the life science research, forensics, diagnostics, agriculture, and animal health markets in North and South America.
ZyGem’s technology uses a thermophilic enzyme to extract DNA from samples in a single closed-tube system. The firm said that its approach can significantly reduce the time and cost of DNA extractions while simplifying laboratory workflow, minimizing error, and reducing the risk of contamination.
“We believe this technology is transforming and expect that greater access to our DNA extraction kits will facilitate the growing use of genetic analyses in diverse applications,” ZyGEM CEO Paul Kinnon said in a statement.

Researchers Sequence New Termite Gut Microbe
A team of Japanese researchers reported last week that they have sequenced the genome of a yet-uncultured bacterial endosymbiont that lives inside a protist called Pseudotrichonympha grassii, a single-celled organism found in the gut of termites.
In a paper appearing online last week in Science, a team of researchers led by Moriya Ohkuma at Japan’s RIKEN Advanced Science Institute described isolating a single P. grassii cell and collecting the bacteria inside. They used whole-genome amplification to prepare the DNA for sequencing and came up with the genome sequence for a bacterial species known as CfPt1-2, which accounts for an estimated 70 percent of the bacterial cells found in the termite Coptotermes formosanus.
“This highly evolved symbiotic system probably underlies the ability of the worldwide pest termite Coptotermes to use wood as its sole food,” Ohkuma and colleagues wrote.
Among the organisms in the termite’s gut, P. grassii cells help the termite break down wood particles. Each of these single-celled protists, in turn, contains roughly 100,000 CfPt1-2 cells, a bacterial phylotype in the Bacteroidales order.
For this paper, Ohkuma and his team used whole-genome amplification to sequence the 1,114,206 basepair genome CfPt1-2 — contained in a single circular chromosome — as well as four circular plasmids. Earlier this year, the team sequenced the genome of another termite gut bacteria, Rs-D17, using a similar approach (see In Sequence 4/15/2008).
The researchers determined that the CfPt1-2 genome houses 758 putative protein-coding genes, 38 transfer RNA genes, and four ribosomal RNA genes. Their subsequent analysis revealed that CfPt1-2 had more DNA repair and recombination genes than other intracellular symbionts that have been characterized to date.
When they turned their attention to metabolic pathways, the team uncovered several genes involved in nitrogen fixation. That was surprising, the authors noted, since no other species in this phyla have been shown capable of nitrogen fixation. Based on their subsequent analysis, they suggested that CfPt1-2 is likely responsible for the bulk of nitrogen fixation occurring in termite guts.

GPPC Survey Finds Most Americans Would Participate in Large-scale Genomic Cohort Study
A survey made public last week suggests that a majority of people in the US may be willing to participate in large-scale, long-term genomic studies.
More than four in five Americans say that they support the idea of a nationwide study of how genes interact with environmental and lifestyle factors, and three out of five say they would agree to participate in such a study, according to the survey, released last week by the Genetics and Public Policy Center at Johns Hopkins University.
The survey included responses from 4,695 US adults from diverse racial and geographic backgrounds. It asked respondents about their views on, and willingness to participate in, a large cohort study for genetics, the environment, and lifestyle that is national in scope and could be used much in the way that the Framingham Heart Study has been used for many purposes.
Such a study would collect DNA and other samples from at least 500,000 people who represent the US population, and then follow them over many years to find out how their particular genomes interact with lifestyle and environmental factors in ways that affect their health.
“Our survey found that widespread support exists in the general public for a large, genetic cohort study. What’s more, we found little variation in that support among different demographic groups,” said David Kaufman, a project director at the GPPC and a lead author of the paper on the survey, which was funded by the National Human Genome Research Institute.

Evonik Licenses Integrated Genomics' Bioinformatics Platform
Integrated Genomics said last week that it has licensed its Ergo bioinformatics platform to Evonik Industries for use in optimizing production strains and finding new methods for high-yield production of specialty chemicals.
Integrated Genomics said that the Ergo platform is optimized for analysis of microorganisms and integrates biological data from genomics, biochemistry, gene expression studies, genetics, and literature. It contains data on more than 1,500 genomes in various stages of completion, the Chicago-based firm said.

Thomas Haas, director of Evonik's Science-to-Business Center for biotechnology in Marl, Germany, said Evonik expects the Ergo platform to “assist us in developing new production strains for higher and more cost-effective production of biological compounds.”

The Scan

Genes Linked to White-Tailed Jackrabbits' Winter Coat Color Change

Climate change, the researchers noted in Science, may lead to camouflage mismatch and increase predation of white-tailed jackrabbits.

Adenine Base Editor Targets SCID Mutation in New Study

Researchers from the University of California, Los Angeles, report in Cell that adenine base editing was able to produce functional T lymphocytes in a model of severe combined immune deficiency.

Researchers Find Gene Affecting Alkaline Sensitivity in Plants

Researchers from the Chinese Academy of Science have found a locus affecting alkaline-salinity sensitivity, which could aid in efforts to improve crop productivity, as they report in Science.

International Team Proposes Checklist for Returning Genomic Research Results

Researchers in the European Journal of Human Genetics present a checklist to guide the return of genomic research results to study participants.