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Beijing Genomics Institute Shenzhen, Saudi Biosciences, CLC Bio, 23andMe, Ancestry.com, Broad Institute, Duke University, Eurofins, Operon, NIH, Zygem, Commonwealth Biotechnologies, 5 Prime, International Rice Research Institute, eGenomics, Invitrogen

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BGI Shenzhen, Saudi Biosciences, CLC Bio Sequence Arab’s Genome
 
Saudi Biosciences, Beijing Genomics Institute Shenzhen, and CLC Bio said this week that they have used Illumina’s Genome Analyzer to sequence and analyze the genome of an Arab individual, which they claim to be the first such genome ever sequenced.
 
The study is part of a larger project to sequence 100 Arab human genomes at high resolution by the end of 2010, with the aim to map unique genetic variations of the Arab population.
 
Saudi Biosciences said it launched the project earlier this year and fostered the collaboration with BGI and CLC Bio. The project used CLC Bio’s software to assemble and analyze the genome.
 
The partners have not released the data but are planning to make it available after publishing the study.
 

 
23andMe Slashes Price of Service By 60 Percent; Partners with Ancestry.com
 
23andMe said this week that it has reduced the price for its personal genotyping service by 60 percent, to $399, from $999.
 
The company said the price cut is related to “technological advancements” made by Illumina. Genotyping services will now be run on a new Illumina Beadchip, called HumanHap550-Quad+, which can analyze four samples.
 
23andMe also said it has added a broader range of SNPs and rare mutations to the new chip, thus “providing more relevant data on published associations, as well as maternal and paternal ancestry.”
 
The firm has also added social networking and community features to its offering.
 
By lowering the price for its service, the company said in a statement, it hopes to “broaden the opportunity for people to participate” in 23andWe, the firm’s research division.
 
Separately, 23andMe said this week that it has partnered with Ancestry.com to provide genetic information to Ancestry.com’s DNA customers.
 
Users of the Ancestry.com DNA service will now have access to the same ancestral content available through the 23andMe website.
 
Ancestry.com has access to over 7 billion names in 26,000 databases, and includes more than 7 million user-submitted family trees, which enables customers to “trace their roots and connect with distant cousins,” 23andMe said.
 

 
Broad Institute Gains Additional $400M Endowment to Transition to 'Permanent' Status
 
The Broad Institute of Harvard and MIT said last week that philanthropists Eli and Edythe Broad have committed an additional $400 million to the institute, bringing its total endowment to $600 million.
 
The interdisciplinary institute, which includes more than 1,200 researchers from both MIT and Harvard, was created in 2004 as a “venture experiment” with a $100 million commitment from the Broads. The philanthropists doubled that gift the following year.
 
The institute said last week that the additional funding will allow it to transform itself into a “permanent biomedical research organization aimed at transforming medicine.”
 
The $600 million total gift, the largest such commitment for biomedical research in the world, according to the institute, will help it “transition to a permanent non-profit organization, with both universities continuing to help govern it.”
 
Eli Broad said in a statement that the institute’s “unique collaborative model for scientific research has resulted in remarkable accomplishments in a very short period of time.”
 
He added that despite the size of the gift — the largest his foundation has ever made — “it is only a fraction of what will be needed to unlock the enormous promise of biomedical research at MIT and Harvard.”
 
The Broad Institute said that the organization hopes to see the endowment grow to $1 billion through investment and additional contributions.
 

 
Rare Variants Seen as Next Frontier in Untangling Genetic Differences in HIV Response
 
Researchers are starting to look beyond common variants in an effort to understand the genetics behind individual differences in response to HIV exposure, infection, and treatment.
 
Speaking at the Genomics of Common Diseases meeting at the Broad Institute in Cambridge, Mass., last weekend, David Goldstein, director of Duke University’s Center for Population Genomics and Pharmacogenetics, outlined strategies for mining the genome for rare but highly penetrant variants influencing host HIV response. By re-sequencing extreme populations — such as those who appear resistant to HIV infection — Goldstein hopes to uncover rare variants that round out the roster of host genes mediating HIV infection.
 
Although several common variants have been implicated in host HIV response, these variants explain a relatively small amount of the actual individual variation observed in patients. That suggests that the genetic variation influencing individuals’ control of HIV is likely more complex than previously imagined, Goldstein explained.
 
Having cast their nets for common variants using genome-wide association studies in typical populations, researchers are now beginning to fish in somewhat murkier waters, looking for rare genetic variants with strong effects on HIV response.
 
Taking a cue from genetic studies of traits, Goldstein noted that re-sequencing individuals with extreme phenotypes may be the most promising strategy for accessing this rare genetic diversity. He proposed using a case control of a thousand or so hemophilia patients who were exposed to HIV in the late 1970s and early 1980s but did not contract HIV.
 
By genome-wide re-sequencing on these exposed-but-uninfected patients, Goldstein suggested that it should be possible to identify rare genes that explain much more of the variation behind HIV resistance and other host differences. That, in turn, may uncover candidate genes that can be tested in larger studies of more general populations.
 
— Abridged version of an article from GenomeWeb Daily News by Andrea Anderson
 

 
Eurofins, Operon in Legal Tussle over Investment in Genomics Venture
 
Eurofins and Operon Holdings are engaged in a legal dispute over Operon’s financial obligations to the Eurofins Genomics venture that was formed through a combination of certain of their businesses in November 2007 (see In Sequence 12/11/2007).
 
Eurofins Genomics was formed through a combination of Eurofins’ subsidiaries MWG Biotech and Medigenomix with Operon Biotechnologies. Under an agreement between Eurofins and Operon Holdings, Eurofins Ventures was obligated to provide $10 million in funding to the venture, while Operon was to contribute $5 million in cash.
 
Eurofins, headquartered in Breda, The Netherlands, filed suit in the US District Court for the District of Delaware on Aug. 1 against Operon Holdings and two executives of the firm for allegedly failing to make a required $1.3 million payment to the Eurofins Genomics venture. The Dutch firm said that since Operon officials subsequently “refused to provide Eurofins Ventures with assurances that it intended to pay the undisputed amount due under the contribution agreement and related documents,” it exercised its rights to satisfy the payment through the issuance of a portion of Operon’s shares in the venture.
 
According to Operon’s motion to dismiss the case, filed on Aug. 22, Eurofins’ letter stated that because of the reduced stake in the venture, Operon was no longer entitled to representation on the Eurofins Genomics board. Operon’s CEO Patrick Weiss is on the board of the venture, pursuant to the contribution agreement.
 
Eurofins asked the court to declare that the dispute between the firms is arbitrable, according to terms of the contribution agreement — or, if it decides the dispute isn’t arbitrable, then it asked the court for “substantive relief” for Operon’s alleged breach of contract.
 
However, Operon argues that the court should dismiss Eurofins’ complaint “because there is no ripe, actual controversy concerning the arbitrability of any dispute between the parties.” According to its filing, Operon said the court could not rule on the matter because a contractually mandated 60-day negotiation period has yet to expire, and Eurofins filed its suit midway through that period.
 
“Eurofins seeks to avoid this condition precedent to arbitration by claiming that Operon has unequivocally refused to arbitrate any aspect of the parties’ dispute,” Operon stated in its motion to dismiss. “This allegation is inaccurate, and Eurofins’ attempt to obtain a declaratory judgment on arbitrability is premature.”
 
Furthermore, Operon disclosed that prior to being contacted by Eurofins in late June about its financial obligations, Eurofins Genomics was notified that it was in default on debt payments to Eurofins Finance, a Eurofins affiliate that committed to loan up to $20 million to the venture. Eurofins Finance demanded a payment of over $14 million from the venture on June 11, according to Operon.
 
In a July 10 letter to Eurofins, Operon discussed what it viewed as the misuse of its $5 million capital contribution to the venture, and the alleged failure by Eurofins to allow Eurofins Genomics to use available resources to service its debt.
 
Operon also alleged in its filing that Eurofins has misused statements made at a settlement conference between the firms at the end of July and has misrepresented what was said at the meeting. In addition to seeking a dismissal of the case, Operon said that the two executives who are named as defendents, Weiss and James Hudson, “may themselves have claims to be asserted against Eurofins.”
 
Eurofins has until Oct. 2 to respond to Operon’s motion to dismiss the case.
 

 
NIH Commercialization Assistance Program Aimed at SBIR Awardees
 
The National Institutes of Health said last week that it has renewed a program aimed to help small life sciences businesses that have been recent or current Small Business Innovation Research Phase II awardees move their products or services toward the market.
 
The Commercialization Assistance Program, now in its fifth year, will last until June 2009.
 
The CAP program is designed to help small and promising life science companies develop commercial businesses and develop their products for the market. Through a contract with the Larta Institute of Los Angeles, the CAP will provide participants with individualized assistance in reaching their goals.
 
The ten-month program will offer two tracks: the Commercialization Training Track, or CTT, and the Accelerator Commercialization Track, or ACT.
 
The CTT is aimed at providing training and mentoring from industry and investment professionals, and the ACT is geared toward helping participants achieve clear and specific near-term objectives and plans, using experts with current market experience.
 
All NIH SBIR awardees that have a Phase II award that is active or that was active in the past five years are eligible for the program.
 
The deadline for applications for the program is Sept. 26. More information is available here.
 

 
CBI to Evaluate Zygem's DNA Extraction Technology
 
Zygem said last week that Commonwealth Biotechnologies will evaluate how Zygem’s forensicGEM DNA extraction technology works in CBI's forensic operations.
 
Under the collaboration, CBI is integrating the kits into its Fairfax Identity Laboratories, which analyze forensic samples and develop enhanced forensic testing procedures.
 
Zygem’s forensicGEM kits use a proprietary enzyme to extract DNA from samples and use a single closed-tube system, an approach that the company said “simplifies laboratory workflow, minimizes error, reduces the risk of contamination, and ensures sample integrity, while also reducing costs.”
 
The kits are formulated for DNA extraction from “a range of different crime sample types without the need for further purification,” the company said.
 

 
5 Prime Gives $500K of Technology and Reagents to International Rice Institute
 
The German life sciences company 5 Prime has donated $500,000 worth of molecular biology technologies and reagents to the International Rice Research Institute in the Philippines, the company said last week.
 
The IRRI plans to use the donation, which includes technologies and reagents for DNA isolation, amplification, and molecular analysis, to develop rice strains that are cheaper and easier to cultivate than current strains. The institute is focused chiefly on developing drought-resistant strains for cultivation in rain-fed lowlands that are vulnerable to drought.
 
IRRI, founded in 1960 by the Ford and Rockefeller Foundations along with the Philippine government, is next to the University of the Philippines.
 
5 Prime offers products for use in research including nucleic acid purification, genomic DNA, RNA, PCR, real-time PCR and RT-PCR, and molecular biology reagents.
 

 
EGenomics Receives Patent On Sequencing-Based Platform to Control Hospital-Acquired Infections
 
EGenomics said last week that it has been awarded a patent that covers “key elements” of its sequencing-based warning system for controlling hospital-acquired infections.
 
The patent, US Patent No. 7,449,808 entitled "System and Method for Tracking and Controlling Infections," covers a system that "fingerprints" infectious bacteria using automated DNA sequencing, stores the DNA sequences in a central database, and analyzes the results using proprietary algorithms.
 
The system differentiates clusters of related strains in order to identify a source or transmission vector. It can also identify when strains are not related. The platform includes a proprietary library of over 6,000 analyzed S. aureus strains as well as other infectious organisms.
 
According to the company, the platform allows hospitals to monitor the spread of specific pathogens. It is currently used in surveillance programs at Beth Israel Medical Center in New York, Beth Israel Medical Center Newark, St. Barnabas Health Care System, and the VA Medical Center East Orange.
 

 
Invitrogen Licenses Amplification Patents to Qiagen and Others
 
Invitrogen said last week that it had non-exclusively licensed its patents covering the random prime amplification of nucleic acids to Qiagen, New England Biolabs, and Kirkegaard & Perry Laboratories.
 

The patents cover methods and kits used for “substantially” amplifying nucleic acids, Invitrogen said. The technology is used in common lab techniques, such as random prime labeling reactions, first-strand cDNA synthesis, and whole-genome amplification.

The Scan

Dropped Charges

The US Justice Department has dropped visa fraud charges against five Chinese researchers, according to the Wall Street Journal.

More Kids

The Associated Press says Moderna is expanding its SARS-CoV-2 vaccine study to included additional children and may include even younger children.

PNAS Papers on Rat Clues to Human Migration, Thyroid Cancer, PolyG-DS

In PNAS this week: ancient rat genome analysis gives hints to human migrations, WDR77 gene mutations in thyroid cancer, and more.

Purnell Choppin Dies

Purnell Choppin, a virologist who led the Howard Hughes Medical Institute, has died at 91, according to the Washington Post.