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Helicos BioSciences, Invitrogen, NIH, Qiagen, Biotage, Mars, US Department of Agriculture, Roche, GenomeQuest, Invitrogen, Royal DSM, Zygem

Helicos Ships Instrument to Stanford University
Helicos BioSciences said this week that it has shipped a Helicos Genetic Analysis System to Stanford University, the company’s second shipment to a customer site.
Helicos said in August that it had received an order from a US cancer research center that will use the instrument for research into cancer stem cell biology (see In Sequence 8/5/2008). A company spokesperson told In Sequence this week that this order came from Stanford University.
The company shipped its first sequencing instrument to genomic services provider Expression Analysis earlier this year.

Qiagen Acquires Biotage Pyrosequencing Tech for MDx Applications
Qiagen said last week that it has acquired the Biosystems business of Biotage, which includes pyrosequencing technology that will be used for molecular diagnostic applications, for approximately $53 million in cash and milestone payments of up to around $7 million over the next four years.
The Biosystems unit sells real-time sequence detection systems called PyroMark MD, PyroMark ID, and PyroMark Q24. It said that the systems offer “significant advantages” over other sequence analysis technologies in short-length sequence detection and quantification.
Qiagen said that the technology can be applied to epigenetic research, molecular diagnostics, and multiplex analysis in genetic and pathogen detection. The firm noted that pyrosequencing is the only technology that has been shown to perform absolute and direct quantification of methylation patterns. It also said that unlike other PCR-based multiplex assays, the technology can detect both known and unknown genetic variants in DNA target regions.
Qiagen said that it would optimize its existing assays for use on Pyromark, and will develop new molecular diagnostics and research tests for the platform.
"Pyrosequencing technologies are excellent complements to our portfolio of current and future molecular testing solutions, including our modular processing platform QIAsymphony", Qiagen CEO Peer Schatz said in a statement.
Qiagen said that in connection with this acquisition, it has purchased the remaining 17.5 percent of the outstanding stock of Corbett Life Sciences, which it acquired for up to $135 million earlier this year.
All of Biotage Biosystems’ employees will join Qiagen, and Uppsala, Sweden-based Biotage will provide certain administrative services for Qiagen over the next 12 months.
Qiagen said that it expects to incur a one-time charge of $.02 per share in the fourth quarter related to the acquisition. It expects the Biosystems business to add $2.5 million in sales for the remaining three months of 2008 and around $15 million in 2009.
In 2003, Biotage licensed to 454 Life Sciences, now part of Roche, the rights to certain massively parallel formats of the pyrosequencing technology, which became the base for that firm’s next-generation sequencing platform. At that time, Roche gained the exclusive rights to use the technology for five years for whole-genome applications.
A Roche spokesperson told In Sequence’s sister publication GenomeWeb Daily News that Roche has since obtained exclusive rights to the technology for the entire life of the patent.
"The acquisition does therefore not affect our ability to address applications in any field, including diagnostics, for high-throughput sequencing," the spokesperson said.
He also said that Biotage's Pyromark instrument is currently being used for low-throughput molecular tests, and those assays provide "orders of magnitude fewer reads" than the Roche 454 GS FLX platform.

Invitrogen Files Formal Merger Notification with EU Authorities
Invitrogen has filed a formal notification with the European Commission regarding its pending $6.7 billion acquisition of Applied Biosystems, the firm said this week.
The commission has 25 business days following the notification to respond to the filing, said Invitrogen. US regulatory authorities have already cleared the merger.
Invitrogen and ABI will hold a special meeting of shareholders on Oct. 16 to vote on the proposed deal. The firms expect to close the deal next month.

NIH Names 27 New Centers for National Children's Study; Recruiting Starts in January
The National Institutes of Health last week kicked off the next phase of a long-term study of genes and the environment, which will study 100,000 children around the country, by naming 27 research centers that will receive funding in 2008.
The National Children’s Study will collect genetic and environmental data from children, from before they are born until age 21, from 105 locations around the country. The NCS will begin recruiting for its pilot study at the beginning of 2009, and will collect information about genetic and environmental factors linked to a wide variety of diseases including autism, cerebral palsy, learning disabilities, birth defects, diabetes, asthma, and obesity.
NIH has now named 36 centers that will collect information from 72 locations. Eventually, 40 centers will be involved. The study will be run by the Eunice Kennedy Shriver National Institute of Child Health and Human Development and the National Institute of Environmental Health Sciences, and will include efforts and coordination with the Centers for Disease Control and Prevention and the Environmental Protection Agency.
The study will involve recruiting pregnant women, or women who could become pregnant, from a range of ethnic and socio-economic backgrounds, and follow the effects of genetic and environmental influences on their children.
“The advantage of a long-term study of development is that it will yield important health information at virtually every phase of the life cycle,” NIH Director Elias Zerhouni said in a statement. While it will eventually “provide greater understanding of adult disorders,” he said, in the near future, “we expect it to provide insight into the disorders of birth and infancy.”
Calling the NCS a “representative sample” of US children, NICHD Director Duane Alexander explained that it will include children “from rural, urban, and suburban areas, from all income and educational levels, and from all racial groups.”
The centers NIH has named for 2008 support include: Arkansas Children’s Hospital Research Institute; Baylor College of Medicine; Brown University; Emory University; Johns Hopkins University; Maine Medical Center; Michigan State University; Mount Sinai School of Medicine; Northwestern University; Saint Louis University School of Public Health; Tulane University School of Public Health and Tropical Medicine, Center for Applied Environmental Public Health; University of Arizona; University of California, Irvine; University of California, Los Angeles; University of Colorado; University of Iowa; University of Louisville; University of Miami; University of North Carolina at Chapel Hill, Carolina Population Center; University of Texas health Science Center San Antonio; University of Texas Southwestern Medical Center at Dallas; University of Utah School of Medicine, Department of Pediatrics; Vanderbilt University Medical Center; and Yale University.
NIH did not immediately release the funding numbers for the individual NCS centers. Last year, the NCS study partners received a total of $69 million.

Cacao Plants Show Unexpected Genetic Diversity
Cacao plants are far more genetically diverse than anticipated, new research suggests.
Researchers from Mars, the chocolate company; the US Department of Agriculture’s Agricultural Research Service; and agricultural institutions in France, Brazil, and Ecuador genotyped roughly a thousand wild and cultivated cocoa plants, Theobroma l. cacao. Their results, appearing online last week in PLoS ONE, suggest that the current T. cacao classification scheme is genetically inaccurate.
To date, the plants have been classified into two main cacao sub-species. But researchers say there are actually ten genetically distinct T. cacao groups. By mapping the geographic distribution of these groups, the team also began exploring T. cacao’s origin and diversification. Overall, they say, such genetic insights may eventually help boost the productivity of cacao crops.
To date, cacao plants have been classified into two main sub-species groups called cacao, commonly known as Criollo, and sphaeorocarpum, known as Forastero. Other cultivars have also been described, including Trinitario, a Criollo-Forastero hybrid first grown in Trinidad.
But these groups do not accurately reflect the genetic differences and diversity in cacao plants, the researchers found. They genotyped 106 microsatellites markers in 1,241 plant samples, including wild T. cacao samples collected in Peru, Brazil, Colombia, Ecuador, French Guiana, and Central America over nearly 70 years as well as cultivated clones from these and other locations.
Instead of identifying two main genetic groups, the researchers found ten genetic clusters, which they classified as Marañon, Curaray, Criollo, Iquitos, Nanay, Contamana, Amelonado, Purús, Nacional, and Guiana.
Based on their results, the authors urged those studying T. cacao genetics and/or curating cacao collections to adopt a new classification scheme that reflects the genetic clusters identified in the paper in order to manage the crop more effectively.
Earlier this year, researchers from the USDA-ARS, Mars, and IBM announced that they were launching a project to sequence the cacao genome.

Roche Expanding German Diagnostics Facility
Roche said last week that it is investing 215 million Swiss francs ($191.7 million) in expanding its research, development, and production operations in Germany for its Applied Science and Professional Diagnostics businesses.
The money will be used to construct a multi-purpose building for Roche Diagnostics in Penzberg, near Munich, the firm said. From around mid-2010, the complex is expected to manufacture products ranging from biotech constituents for immunodiagnostics and life sciences research through immunodiagnostic test kits, which are used on Roche’s Cobas and Elecsys instruments.
The firm said that the expansion of production capacity for its Applied Science business is a reaction to “the sustained growth in demand for research reagents, including LightCycler real-time PCR systems.”

GenomeQuest, Invitrogen Make Sequence Analysis and Management Software Interoperable
GenomeQuest said last week that its sequencing data handling platform will now operate with Invitrogen’s sequence analysis software.
The Westborough, Mass.-based company said that it has worked with Invitrogen to interconnect its GenomeQuest 5.0 platform with the Invitrogen Vector NTI Advance software.
The GenomeQuest platform now interoperates with the Vector NTI Advance Versions 9 and 10, and it also will operate with the upcoming Version 11, the company said.
GenomeQuest 5.0 users will be able to select sequences of interest and send them to the Vector NTI Advance software for analysis including DNA assembly, multiple sequence alignment, protein analysis, and recombinant molecule construction.
Vector users also will be able to choose sequences and send them to the GenomeQuest platform for advanced searching, which includes a collection of over 225 million sequences, and the information could then be exported back to the Vector software for analysis.

Royal DSM, Collaborators Sequence Penicillium Genome
Netherlands-based life sciences and materials sciences company Royal DSM and collaborators from seven international research groups have sequenced the genome of the penicillin-producing fungus Penicillium chrysogenum.
Because P. chrysogenum is used for the industrial production of penicillin, the results are expected to have implications for improving antibiotic production methods. The team also used microarrays to compare the transcriptomes of the strain that was sequenced with another “high-producing” penicillin strain to find genes that are ramped up or down in conjunction with penicillin production. The work appeared online last week in Nature Biotechnology.
Penicillin was discovered by Sir Alexander Fleming some 80 years ago from the fungus Penicillium notatum, now known as P. chrysogenum. It produces several beta-lactam type antibiotics, including penicillin and related compounds. With time, systematic improvements in Penicillium strains by mutagenesis and selection have led to the large-scale production methods for beta-lactam antibiotics, the authors noted. But current strains are all believed to be derived from one natural strain isolated from cantaloupe during World War II.
For the latest project, which started about four years ago, the researchers sequenced the 32.2-megabase P. chrysogenum Wisconsin54-1255 genome to nearly ten times coverage using whole-genome random sequencing. They also sequenced the 32-kilobase mitochondrial genome. They found that the P. chrysogenum genome contains 13,653 different genes, while the mitochondrial genome contains 17 open reading frames.
Based on their subsequent analysis, the researchers estimated that more than half of the P. chrysogenum genome is compromised of protein-coding sequences. Of these, 5,329 could be assigned to functional protein classes designating proteins involved in metabolism, energy, cellular transport, and protein fate.
A phylogenetic analysis suggested that P. chrysogenum was closely related to Aspergillus species (including Aspergillus niger, a species whose genome was sequenced by DSM last year), but distantly related to two other Penicillium species, P. marneffei and P. stipitatum. The researchers also pinpointed P. chrysogenum-specific genes.
“Despite the massive improvements already achieved in classical strain improvement, our results indicate that further improvement of penicillin production remains a possibility,” the authors wrote. They noted that the newly available genome sequence will help to unravel the genetic changes that have accompanied the strain improvements achieved so far by classical methods.

Zygem Licenses DNA Purification Technology from WaikatoLink
Zygem said last week that it has obtained exclusive worldwide rights from WaikatoLink, the technology transfer unit of the University of Waikato, for a DNA contaminant removal method.
The technology allows users to remove DNA contaminations from samples that are to be used in DNA-based diagnostic tests and analyses, including tests where contamination from a single molecule would result in failure.
The new approach has similar properties to the enzyme DNAse1, but Zygem claims the new technology “achieves this in a simpler and more efficient manner.”

Zygem plans to make the nucleic acid sequestering technology available to customers shortly.

The Scan

Study Reveals Details of SARS-CoV-2 Spread Across Brazil

A genomic analysis in Nature Microbiology explores how SARS-CoV-2 spread into, across, and from Brazil.

New Study Highlights Utility of Mutation Testing in Anaplastic Thyroid Cancer

Genetic mutations in BRAF and RAS are associated with patient outcomes in anaplastic thyroid carcinoma, a new JCO Precision Oncology study reports.

Study Points to Increased Risk of Dangerous Blood Clots in COVID-19 Patients

An analysis in JAMA Internal Medicine finds that even mild COVID-19 increases risk of venous thromboembolism.

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.