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Applied Biosystems, Applera, Kansas State University, NHGRI, NCI, NIMH, GWAS, PHAC, Whitney Lab, DNAStar, BioServe, Microchip Biotechnologies, University of Alberta, DNA2.0, Operon Biotechnologies, University of Georgia, JGI, Q Chip

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ABI to Support Third-Party Software Development for Next-Gen Sequencing
 
Applied Biosystems said this week that it has kicked off a program to help third-party software developers create bioinformatics tools for its SOLiD next-generation sequencing system.
 
ABI said it is expanding its so-called software development community to include sample data sets, data file formats, and data conversion tools for the SOLiD system. The company said that it has also dedicated resources to support bioinformatics developers that it expects to advance application development in several research areas, including whole-genome sequencing, chromatin immunoprecipitation, microbial sequencing, gene expression, microRNA discovery, digital karyotyping, epigenetic profiling, and detection of rare genetic variants.
 
ABI said it recently hosted a meeting for more than 40 researchers from 30 academic and commercial institutions “to provide input and share best practices with each other on their respective next-generation sequencing software development initiatives.”
 

 
Applera to Buy $600M of ABI Shares from Morgan Stanley
 
Applera said last week that it has signed an agreement to acquire $600 million worth of Applied Biosystems common stock from investment bank Morgan Stanley.
 
The accelerated purchase is part of Applera’s previously announced plans to buy back $1.2 billion worth of ABI shares over the next four to six quarters (see In Sequence 8/14/2007).
 
The number of shares repurchased is subject to a minimum and maximum based on the volume-weighted average daily price of ABI’s shares over the next approximately seven and a half months. The minimum number of shares will be delivered to the firm within roughly six weeks. Any additional shares will be delivered to Applera over the following six months.
 
Applera announced the share repurchase program in early August. On that same day, the firm said it had hired Morgan Stanley to advise the company as it considers restructuring its ABI and Celera groups, which are currently traded as tracking stocks under the parent firm.
 

 
Applera Obtains $100 Million Loan for General Corporate Purposes
 
Applera has obtained a $100 million unsecured term loan through its agent, the Bank of America, the company said last week.
 
Applera may use the loan, which it obtained on Aug. 27, on or before Oct. 26 for general corporate purposes, the company said in a filing with the US Securities and Exchange commission.
 
The company intends to use the proceeds from the loan, together with US cash reserves, funds from domestic operations, and other sources, to fund these repurchases.
 

 
Applied Biosystems Supports Genotyping Service Providers
 
Applied Biosystems will support certain genotyping providers that use its SNPlex genotyping system, the company said last month. The providers include the Chinese National Human Genome Center in China, DNAVision in Belgium, IntegraGen in France, Medical Solutions Geneservice in the UK, the University of California at Los Angeles DNA Sequencing and Genotyping Core Facility, and Vanderbilt University DNA Sequencing and Genotyping Facility.
 
These providers will offer high-throughput genotyping services on ABI’s SNPlex genotyping system, which consists of custom designed assays, universal core reagents, analysis software, and system documentation that are optimized for use on Applied Biosystems' CE platforms.
 
ABI is supporting the providers by granting technical and marketing support.
 

 
KansasStateUniversity Grants $1M for Sorghum Genomics
 
Kansans State University has funded a sorghum genomics project with $1 million, the university said last month.
 
The four-year Sorghum Translational Genomics program plans to study sorghum characteristics under the leadership of Frank White, a professor of plant pathology at Kansas State, as well as other researchers at Kansas State, scientists at Cornell University, Texas A&M University, and the US Department of Agriculture.
 
According to the program’s website, the researchers plan to sequence eight diverse sorghum strains to 4x to 8x coverage, focusing on 250 megabases of the sorghum genome that is thought to be expressed. They will align the sequence reads to the reference sorghum genome sequence and mine them for SNPs. They then plan to design a genotyping chip and use this to analyze 22 further sorghum strains. These form the parents of a set of crosses to result in twenty 200-line recombinant inbred sorghum mapping populations to be used for nested association mapping. The researchers will then use a second, much less dense genotyping assay to study at least 300 strains. Using phenotypic data, they will try to find genes that can be used to improve sorghum.
 
White told In Sequence by e-mail that his team is currently discussing which sequencing platform to use. “I think our initial efforts will use the Solexa/Illumina platform but we are not committed at this time for any one long term,” he said.
 
Kansas is the top sorghum producer in the US, which is the world´s largest cultivator of grain sorghum.
 

 
NHGRI Awards $30M for Genomic Centers of Excellence at Dana-Farber, Stanford
 
The National Human Genome Research Institute last month awarded around $30 million to the Dana-Farber Cancer Institute and Stanford University under its Centers of Excellence in Genomic Science program.
 
The five-year awards will provide around $16 million to Dana-Farber to create a new Center of Excellence and around $14 million for an existing center at Stanford.
 
NHGRI launched the Centers of Excellence in Genomic Science program in 2001. The initiative supports “multi-institution, interdisciplinary teams dedicated to making critical advances in genomic research,” NHGRI said.
 
The Stanford center, led by David Kingsley, is using the stickleback fish to explore the genomic underpinnings of vertebrate diversity. The Stanford team plans to crossbreed different strains of stickleback fish to produce a genome-wide map that can be used to search for genetic signatures related to adaptive changes in size, shape, body function, and behavior in fish populations worldwide.
 
Marc Vidal will lead the center at Dana-Farber, which plans to test the hypothesis that both human genetic variations and pathogens can influence cellular networks and cause disease.
 
The Dana-Farber researchers will analyze network-level disruption and protein-protein interactions in cells caused by particular viruses and will apply the knowledge gained from this exercise to genome-wide variation datasets for related human diseases.
 
The center’s goal is to develop guidelines for data integration and network prediction with the aim of developing better models to interpret genome-wide genetic variations in the context of human disease, NHGRI said.
 
In addition to the Dana-Farber and Stanford centers, the NHGRI’s Centers of Excellence program supports work at the Molecular Sciences Institute in Berkeley, Calif.; the California Institute of Technology; Harvard Medical School; Johns Hopkins University School of Medicine; Arizona State University; Yale University; and the University of Southern California, Los Angeles.
 

 
NCI Earmarks $2M in FY 2008 for Cancer Genome Atlas Data Analysis
 
The National Cancer Institute plans to award around $2 million in fiscal year 2008 to support new data analysis and visualization technologies for the Cancer Genome Atlas project.
 
In a request for applications published last week entitled “Advanced Genomic Data Analysis and Visualization Methods for the Cancer Genome Atlas (TCGA) Data,” NCI said that it plans to award between six and 10 grants to applications that “describe exploratory projects aimed at the development of highly innovative and novel advanced genomic data analysis methods and visualization technologies.”        
 

 
NHGRI, NIMH to Award $3.1M to 'Coordinating Center' for Epidemiological GWA Studies
 
The National Human Genome Research Institute and the National Institute of Mental Health have set aside $3.1 million to create a “coordinating center” to support a previously announced program that will investigate genetic variants associated with complex diseases by genome-wide association studies and other genetic studies.
 
In a request for applications released last month, NHGRI and NIMH said the coordinating center will serve as “a centralized resource to facilitate and support the investigation, in well-characterized population studies, of genetic variants identified as potentially causally associated with complex diseases in genome-wide association and other genetic studies, with the aim of widespread sharing of the resulting population-based descriptive and association data to accelerate the understanding of genes related to complex diseases.”
 
The coordinating center will work with three to five projects funded by the program “Epidemiologic Investigation of Putative Causal Genetic Variants – Study Investigators” to develop “criteria and methods for identifying highly-replicated, putative causal variants suitable for detailed epidemiologic pursuit within individual population studies,” the RFA said.
 
The institutes said they plan to award one four-year award of $3.1 million under the RFA. Letters of intent are due Oct. 19 and applications are due Nov. 19.
 

 
NIH Seeks to Balance Open Access and Privacy with GWAS Data-Sharing Policy
 
The National Institutes of Health last week issued a policy on sharing data obtained from NIH-funded genome-wide association studies.
 
The policy is designed to facilitate the research community's access to genotype-phenotype datasets from GWAS while ensuring the privacy of research participants.
 
“The potential for public benefit to be achieved through sharing GWAS data is significant. However, genotype and phenotype information generated about individuals, such as data related to the presence or risk of developing particular diseases or conditions and information regarding paternity or ancestry, may be sensitive,” NIH said in a notice last week. “Therefore, protecting the privacy of the research participants and the confidentiality of their data is critically important. Risks to individuals, groups, or communities should be balanced carefully with potential benefits of the knowledge to be gained through GWAS.”
 
The policy recommends that researchers deposit GWAS datasets in the Database of Genotypes and Phenotypes, or dbGaP, at the National Center for Biotechnology Information, which includes “multiple tiers” of data security to ensure privacy.
 
Further information about the data-sharing policy is available at NHGRI’s website and Office of Population Genomics page.
 

 
PHAC, Whitney Lab License DNAStar’s Lasergene Software
 
The Public Health Agency of Canada, based in Winnipeg, Manitoba, and the Whitney Laboratory for Marine Bioscience in St. Augustine, Fla., have licensed DNAStar’s Lasergene sequence analysis software.
 
Under the four-year site license, scientists anywhere on the Winnipeg campus of PHAC can use Lasergene.
 
Scientists at the Whitney Laboratory will be able to use the most current version of Lasergene for four years.
 
Lasergene is used to assemble and analyze DNA and protein sequences. The software provides researchers with analysis tools that can be used with traditional and next-generation sequence analysis projects and has been sold in over 65 countries worldwide, according to the company.
 

 
BioServe Moves into New Maryland Facility
 
BioServe has moved into a new facililty in Beltsville, Md., the company said last week.
 
The new 40,000-square-foot facility houses the company’s laboratories and offices as well as its repository of more than 600,000 DNA, tissue, and serum samples.
 
BioServe, which is based both in Beltsville and Hyderabad, India, develops diagnostic tests
and provides DNA methylation analysis services. The company offers a tissue bank of more than 600,000 human DNA, tissue, and serum samples that are linked to detailed clinical and demographic data from 140,000 consented and anonymized patients from four continents.
 

 
Microchip Biotechnologies Licenses Microfluidic Device Technology from University of Alberta
 
Microchip Biotechnologies has exclusively licensed a patent on manipulating beads on-chip from the University of Alberta, MBI said last month.
 
The technology, invented by Jed Harrison, a professor of chemistry, and protected by US Patent No. 6,432,290, allows trapping of beads on-chip, as well as packing and unpacking the trapping zones, which significantly extends the applications of microfluidic analysis systems, such as those used in biodefense and genomics industries.
 
MBI is developing nanofluidic sample preparation and analytical instrumentation for life sciences, applied sciences, and diagnostics markets.
 

 
Canadian Gov't to Help Create Biobank to Support CARTaGENE Project
 
The Canadian government said last month that it will help create a biobank to store and manage biological samples collected by the nation’s CARTaGENE research projects.
 
The biobank, which will be part of the P3G/CARTaGENE project, was developed by Genome Quebec and the Centre de santé et de services sociaux de Chicoutimi, a hospital center affiliated with the University of Montreal. GenVault of San Diego will implement the system and the technology for archieving and retrieving samples.
 
It will be responsible for collecting and managing biological samples from the 20,000 citizens of Quebec participating in the CARTaGENE project, as well as supporting other projects, according to GenVault, which has been hired to build the system for archiving and retrieving the samples.
 
The biobank, which will receive CA$9.6 million ($9 million) in government financing over three years, will be housed in the Centre de santé et de services sociaux de Chicoutimi. CA$2 million of this cash will be used to “adapt the premises needed to operate” and to support “quality jobs.”
 

 
DNA2.0, Operon Biotechnologies Pen Co-Marketing Alliance
 
Synthetic gene company DNA2.0 and oligonucleotide synthesis firm Operon Biotechnologies said last month they have formed a co-marketing alliance.
 
Terms of the deal call for Operon to co-market DNA2.0’s gene-synthesis services, while Operon’s oligos will become the “primary source” of the oligos that go into DNA2.0’s synthetic genes, the companies said.
 
The companies are betting that the alliance will increase DNA2.0's speed of synthesis and give Operon access to what the firms call “the fastest growing application area for oligonucleotides today.”
 

 
University of Georgia Scientists to Study Pine Gene Expression Using JGI Sequencing
 
Researchers at the University of Georgia Warnell School of Forestry and Natural Resources will analyze conifer gene expression under the Department of Energy’s Joint Genome Institute’s Community Sequencing Program, UGA said last month.
 
JGI will produce a comprehensive catalog of all the genes expressed as conifers grow, develop, and respond to their environments. By comparing genes expressed by different conifer species in similar tissues under similar conditions, the scientists want to identify the key genes controlling tree growth and development.
 
“Complete sequencing of a conifer genome is still a ways off since their genomes are typically enormous, but a complete catalog of expressed conifer genes would still be a watershed for our ability to study, predict, and understand how conifer genetics have contributed to the survival of these magnificent trees through hundreds of millions of years,” said Jeffrey Dean, a professor of forest biotechnology at UGA and the project leader, in a press release.
 
More than fifty research laboratories from around the world have pledged their support for the project.
 

 
PCR Reagent Startup Q Chip Raises $4M from Existing and New Investors
 
Q Chip, a spin-out of Cardiff University in Wales that makes bead-based reagents for DNA testing, has landed £2 million ($4 million) in new financing from previous and new investors, one of its backers said last month.
 
Biofusion, an intellectual property commercialization company that has agreements with Cardiff University and the University of Sheffield, said that it invested £125,000 in the funding round, raising its stake in Q Chip to 10 percent.
 
Other previous investors who backed Q Chip in this round included E-Synergy’s Early Growth Fund and John Moulton, managing partner of Alchemy Partners.
 
New investors include Forum des Entrepreneurs, an angel investor group based in Geneva; the Sustainable Technology Fund, based in London; and Finance Wales.
 
Earlier this year, Q Chip launched ReaX, a bead-based reagent kit for PCR sample prep. According to Biofusion, ReaX eliminates handling errors in PCR analysis and can reduce the time required for PCR set-up by up to 90 percent.

The Scan

Interfering With Invasive Mussels

The Chicago Tribune reports that researchers are studying whether RNA interference- or CRISPR-based approaches can combat invasive freshwater mussels.

Participation Analysis

A new study finds that women tend to participate less at scientific meetings but that some changes can lead to increased involvement, the Guardian reports.

Right Whales' Decline

A research study plans to use genetic analysis to gain insight into population decline among North American right whales, according to CBC.

Science Papers Tie Rare Mutations to Short Stature, Immunodeficiency; Present Single-Cell Transcriptomics Map

In Science this week: pair of mutations in one gene uncovered in brothers with short stature and immunodeficiency, and more.