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Knome, BGI, NHGRI, OpenHelix, CLC bio, Danish Agency for Science Technology and Innovation, Genome Corp., Slater Technology Fund, JGI, Applera, ABI, European Research Area Network on Plant Genomics

Knome and BGI Win First Two Customers for Personal Sequencing Service
Knome and the Beijing Genomics Institute said this week that they have won their first two customers for the personal genome sequencing service they offer and have “initiated the process” of sequencing their genomes.
The partners expect to complete sequencing these clients, who chose to remain anonymous, “in the coming months,” according to a statement.
Knome, based in Cambridge, Mass., offers personal genome sequencing to a limited number of individuals this year for a price of at least $350,000, which includes sequencing and data analysis.

NHGRI Awards OpenHelix $1M to Develop Genomics Training Portal
OpenHelix of Seattle said this week that the National Human Genome Research Institute has awarded it a $1 million Small Business Innovation Research grant to develop an online training portal for genomics resources.
The company said that it expects the tools will “greatly reduce the amount of time necessary to locate and use the vast genomics and bioinformatics resources available to scholars and scientists.”
Many genomics and bioinformatics resources are currently “underutilized,” according to the company, because researchers are not aware of their existence. In addition, these tools all use different navigation methods and documentation, which can make it difficult for researchers to use them, OpenHelix said.

CLC bio, Danish Researchers to Develop Next-Gen Sequencing Software
CLC bio said last week it will work with researchers at several Danish institutes to develop user-friendly software designed to handle data from next-generation sequencing technologies.
The company said it has established the Seqnet network, which will initially operate for three years, using $3 million from the Danish Agency for Science Technology and Innovation.
Roald Forsberg, senior scientific officer at CLC bio, said in a statement that the company will work with its partners to develop graphical user interfaces, algorithms, and high-performance computing solutions. Forsberg said new platforms from 454 Life Sciences, Illumina, and Applied Biosystems have “given rise to a plethora of novel applications for DNA sequencing” and “dramatically increased the ambitions of existing projects.”
The other Seqnet partners include the Department of Life Sciences at Aalborg University, the Faculty of Agricultural Sciences at Aarhus University, the Department of Biology at the University of Copenhagen, the University of Southern Denmark, and the Aalborg University Hospital.
The company said that it plans to develop a “significant amount of new or optimized bioinformatics algorithms” that will be used to help analyze sequencing data from corporate, public, and private research groups.

Genome Corp. Raises $250,000 In Additional Funds
Genome Corp. has raised $250,000 in additional funding from a state-backed venture fund, the Providence, RI-based startup said this week.
The Slater Technology Fund invested a similar amount in the company last September, bringing its total investment in Genome Corp. to $500,000.
Genome Corp. plans to make Sanger dideoxy sequencing faster and cheaper, and to focus on human genome sequencing services.

JGI Releases Soybean Genome to Aid Bioenergy Research
The US Department of Energy’s Joint Genome Institute said last week that it is making the preliminary soybean genome freely available to researchers.
Eddy Rubin, director of the JGI, announced the move, an effort to facilitate and stimulate bioenergy research, at the Plant and Animal Genome Conference in San Diego last week.
The DOE’s interest in the soybean, Glycine max, stems from the plant’s role as the main source of biodiesel, a renewable, alternative fuel.
The agency said that having detailed knowledge of soybean genetics could lead to the development of soybeans even better suited for producing bioenergy.
DOE scientists, along with researchers at Stanford University, the University of Missouri-Columbia, Iowa State University, and Purdue University, have been sequencing the soybean genome using Sanger technology. The current, preliminary assembly, GlymaO, is expected to be replaced by a chromosome-scale Glyma1 assembly by the end of 2008.
The soybean genome project began in mid-2006 and is supported by the US Department of Agriculture and the National Science Foundation.
Preliminary soybean genome information is available online here.

Applera Declares Quarterly Dividend for ABI Shareholders
Applera’s board of directors has declared a quarterly dividend of $.0425 per share of Applied Biosystems stock, the firm announced last week.
The dividend is payable on April 1 to shareholders of record as of the close of business on March 3.

Pan-Euro Plant Genomics to Get $22.3M Boost for Collaborative Research
A European plant genomics initiative backed by €15 million ($22.3 million) in new funding from nine different nations has put out a call for collaborative research proposals that will advance the field by integrating new technologies in new studies.
The European Research Area Network on Plant Genomics, or ERA-PG, recently launched its second call, which is focused on driving genomics-based technology forward and creating “a strong and competitive European bioeconomy,” ERA-PG said earlier this month.
ERA-PG was conceived as a pan-European funding collaboration in 2004 under the European Framework Programme 6 ERA-Net plan, and in 2006 issued its first call for applications to be supported by a total available budget of €35 million. That program aimed to satisfy different research interests, and covered 29 projects in Germany, UK, Spain, Italy, France, Denmark, The Netherlands, Finland, Norway, Flanders, and Portugal.
Funders contributing to this program will include: Austria’s Federal Ministry for Science and Research; Belgium’s Flemish Government; Finland’s Academy of Finland; Germany’s German Research Foundation; Israel’s Ministry of Agriculture and Rural Development; Portugal’s Foundation for Science and Technology; and the Netherlands Genomics Initiative and Netherlands Organization for Scientific Research. Canada’s Genome Canada may participate, although its involvement has not been confirmed.
The group said its ambition is to support a “broad and inclusive” range of studies, including applying genomics-based technologies to pursue questions that are relevant to the bio-economy it hopes to help cultivate.
The group said it expects to fund projects for up to three years, but some exceptions may be made for projects requiring four years.
Applications for funding are due on Apr. 2, 2008. More information about the programs and guidelines can be found here.

The Scan

Lung Cancer Response to Checkpoint Inhibitors Reflected in Circulating Tumor DNA

In non-small cell lung cancer patients, researchers find in JCO Precision Oncology that survival benefits after immune checkpoint blockade coincide with a dip in ctDNA levels.

Study Reviews Family, Provider Responses to Rapid Whole-Genome Sequencing Follow-up

Investigators identified in the European Journal of Human Genetics variable follow-up practices after rapid whole-genome sequencing.

BMI-Related Variants Show Age-Related Stability in UK Biobank Participants

Researchers followed body mass index variant stability with genomic structural equation modeling and genome-wide association studies of 40- to 72-year olds in PLOS Genetics.

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.