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Helicos, DNAStar, BGI LifeTech, Genome BC, GATC Biotech, Link Technologies, Agilent, FujiFilm Dimatix, GINA, Beijing Genomics Institute, Monsanto, Divergence, National Institute for Agricultural Research, JGI, MIT, Penn State University

Helicos Reports $117,000 Revenues, $10.4M Net Loss in Q4
Helicos BioSciences this week reported its fourth-quarter and full-year 2007 earnings.
The company had $117,000 in revenues for the quarter, up from $159,000 during the year-ago quarter. For the full year, it recorded $582,000 in revenues, up from $159,000 in 2006. These revenues came from a National Human Genome Research Institute technology development grant.
Helicos President and COO Steve Lombardi said during a conference call this week that it would be “premature” to forecast company revenues for 2008. Instrument and reagent revenues will depend on the timing of revenue recognition, market condition, and customer feedback from initial placements, he said.
The first revenue recognition from instrument sales “is going to be at least in the second half of the year” according to Lombardi.
R&D expenses for the quarter were $6.8 million, up from $4.7 million during the fourth quarter of 2006. During 2007, R&D expenses totaled $27.8 million, up from $14.4 million in 2006, as the company doubled its headcount and prepared for the commercial launch of its instrument.
Helicos’ net loss for the quarter was $10.4 million, up from $7 million during the year-ago quarter, and $36.8 million for the year, up from $20.6 million.
As of Dec. 31, Helicos had $52.7 million in cash, cash equivalents, and short-term investments.
In 2008, Helicos expects to spend between $40 million and $50 million of its cash and will provide updates of its cash position throughout the year,
The company took $10 million from the $20 million senior secured credit facility from GE Healthcare Financial Services at the end of 2007, Lombardi reported.
He said it was not yet clear whether the company will need another round of financing this year, noting that it will depend on the number of orders, customer acceptance, and reagent sales.

BGI LifeTech to Distribute DNAStar’s Software in China
DNAStar of Madisoin, Wis., has signed on BGI Life Tech as distributor of its bioinformatics software in China, the company said this week.
Under the agreement, BGI LifeTech of Beijing will sell DNAStar’s Lasergene, ArrayStar, SeqMan genome assembler, and GenVision in China, including Hong Kong.
BGI LifeTech is a sequencing service provider and distributor of molecular biology products in China and Hong Kong. The company, a wholly owned subsidiary of the Beijing Genomics Institute, was founded in 2002 by Huanming Yang and three colleagues. 

Genome BC Receives $800K from Canadian Government
The Canadian government’s Western Economic Diversification division is making a four-year, CAN$800,000 ($805,000) investment in British Columbia’s Genome BC. The funding is intended to support Western Canadian genomics networks with multiple stakeholders.
With the new funding, Genome BC expects to create its own set of genomics networks — encompassing industry, provincial governments, universities, federal laboratories, and other research agencies — and to participate in other Western Canadian genomics networks led by Genome Prairie and Genome Alberta.
Canada has six genomics and proteomics networks funded through the central organization Genome Canada.

GATC Biotech Opens Stockholm Subsidiary
GATC Biotech said this week that it has opened a wholly owned subsidiary in Stockholm to provide sales and support services throughout Scandinavia.
The Constance, Germany-based DNA sequencing service provider said it established the new office in response to growing demand for its services. It noted that its employee base increased from 45 at the beginning of 2006 to 62 by the end of 2007, and its production capacity increased from 15.6 gigabases per year to 250 gigabases per year during that period.
In addition to traditional Sanger sequencing, GATC offers services using the Illumina Genome Analyzer, 454’s GS FLX, and Applied Biosystems’ SOLiD system.
Besides Germany and Sweden, the company already has offices in France and England.

Link Technologies Obtains Quality Certification for Oligo Manufacture
Link Technologies of Bellshill, Scotland, has been awarded ISO 9001:2000 quality certification for its oligonucleotide manufacturing facility, the company said this week.
The company also said it has finished construction of several new multi-purpose kilo-scale manufacturing laboratories.
Link Chairman Mick McLean said in a statement that “this ISO recognition gives us the official status necessary for partnering with the biggest and best in our industry. Combined with our significantly increased manufacturing capacity, we are now ideally equipped to work with companies developing therapeutic or diagnostic products at the forefront of the oligonucleotide industry.”
The new manufacturing facilities will be used for both custom and routine production.

Agilent to Use FujiFilm Inkjet Printing Technology in Upcoming Life Science Platform
Agilent Technologies will use inkjet technology from FujiFilm Dimatix in its life sciences applications to more efficiently target and analyze sequences of genetic material, FujiFilm said last week.
Under a collaboration, the companies are working together to incorporate the Dimatix Materials Cartridge into Agilent applications.
FujiFilm said its Shaped Piezo Silicon micro-electromechanical systems technique enables it to make printheads that are capable of jetting fluids with droplet sizes as small as 1 picoliter.
The precision and flexibility of the FujiFilm inkjet platform “figured prominently in our decision to base Agilent's SurePrint inkjet technology on FujiFilm Dimatix inkjet technologies, and also to use their products as the basis for a major new product platform we plan to launch later this year,” Bill Peck, senior engineer and a project manager for Agilent, said in a statement.
According to an Agilent spokesperson, the technology is used to synthesize oligos for “a wide range of catalog and custom products,” the main application being in situ synthesis of probes on glass wafers for DNA microarrays.
The technology also enables Agilent’s Oligo Library Synthesis products, custom mixtures of up to 55,000 oligos that can be used for genome partitioning, a product that is currently in early access use and is scheduled for commercial launch later this year.
In addition, the technology will be enable the launch of a million-feature microarray, also planned for later in the year.

House Passes Genetic Discrimination Bill Tucked into Mental Health Act
A broadly supported piece of legislation drafted to protect Americans from genetic discrimination in the workplace and by health insurance companies, but which has been held up for months by one senator, has passed in the US House of Representatives.
The Genetic Information Nondiscrimination Act passed in the House last week as a section of another bill, introduced by Representative Patrick Kennedy (D – RI), that would provide for equity of health insurance coverage for mental disorders and substance abuse-related disorders.
“Given that most mental health diseases are genetically linked, GINA is a natural addition” to the mental health bill, Rep. Louise Slaughter (D – NY) said in a statement.
GINA has been introduced in Congress several times over the past decade. Slaughter last year introduced the 2007 version of the bill, which passed overwhelmingly in the House, but Sen. Olympia Snowe’s Senate version stalled out when Sen. Tom Coburn (R – Okla.) used a tactic called a legislative “hold” on the bill.
In April of last year, GINA passed the house resoundingly, 420 to 3, and earlier versions had passed in the Senate by votes of 95 to 0 and 98 to 0.
But in September 2007, Sen. Coburn placed the hold on the bill, citing concerns about complications having to do with the definition of “genetic testing” and with the need for legal protections for employers.
The Kennedy-sponsored bill, the Paul Wellstone Mental Health and Addiction Equity Act of 2007, will now move on to the Senate.

Beijing Genomics Institute to Sequence Panda Genome
The Beijing Genomics Institute at Shenzhen announced last week that it is launching an International Giant Panda Genome Project.
Scientists at BGI-Shenzhen plan to sequence a panda to be selected from the Chengdu and Wolong breeding centers using high-throughput sequencing technology. They hope to have a draft genome sequence assembled within six months. The giant panda genome is roughly the same size as the human genome and contains some 20,000 to 30,000 genes.
The project is intended to provide new insights into panda ecology and evolution. This could shed light on the panda’s history, migration, and relationships to other animals, as well as information about panda fitness and diseases that may help protect the endangered animals. Eventually, the team plans to do panda transcriptome studies and studies on genetic variations in the panda population.
“[I]t is the first genome project to be undertaken specifically to gather information that will contribute to conservation efforts for an endangered species,” Oliver Ryder, an endangered species researcher at the San Diego Zoo who participated in a Panda Genome workshop held in Shenzhen earlier this year, said in a statement. “The giant panda is a global conservation symbol and deserving of such an effort.”
A BGI spokeswoman declined to specify whether the institute is going to use Illumina’s or ABI’s next-generation sequencing technology for the project.

Monsanto, Divergence Sequence Soybean Cyst Nematode Genome
Agricultural giant Monsanto and the nematode genomics company Divergence have completed a draft of the soybean cyst nematode genome, Heterodera glycines, the companies announced last week.
The SCN draft genome is the result of a collaboration between Monsanto and Divergence that began four years ago that is intended to develop strategies for controlling SCN. The draft genome, reportedly the first plant parasite nematode genome, was created using three-fold sequence coverage of the SCN genome. The companies anticipate that this genetic data will improve research on and, eventually, control of the pathogenic nematode.
Nematodes are microscopic roundworms, found in many environments, including sea water, fresh water, and soil. Some are involved in animal diseases such as heartworm in dogs and African river blindness in humans. Others are plant pathogens, affecting crops such as corn, cotton, strawberries, and bananas.
In particular, SCN depletes soybean yield by an estimated $1 billion each year. It affects growing soybean plants by entering their roots and pilfering precious nutrients.
“Sequencing the SCN genome is a tremendous step forward in our process of developing a product to help farmers protect their soybean crops against a devastating pest,” Monsanto Vice President of Biotechnology Steve Padgette said in a statement. “As global demand for soy protein increases, it is critical that companies evaluate and invest in novel approaches to combat this yield-robbing pest so farmers can get more yield out of every acre.”
The SCN draft genome will be made publicly available through the National Center for Biotechnology Information, subject to Monsanto and Divergence intellectual property rights, the firms said.

Fungal Symbiont Genome Sequence Hints at Secrets of Tree Relationships
An international research group has sequenced the largest fungal genome yet, revealing the genetics behind the fungus’ symbiotic relationships with its tree hosts.
Researchers at the National Institute for Agricultural Research in Nancy, France, the US Department of Energy’s Joint Genome Institute, and elsewhere sequenced the genome of a fungus called Laccaria bicolor, which has symbiotic relationships with a number of tree species.
The findings, published last week in Nature, reveal a complex genome with some features not previously seen in fungi. They also provide insight into the way L. bicolor draws nutrients from its host without damaging it.
For this study, researchers focused on L. bicolor, a symbiotic fungus commonly found in North American birch, fir, and pine forests. It frequently forms symbiotic relationships with poplar, a tree whose genome has also been sequenced.
The researchers sequenced the 65 million base pair L. bicolor genome at DOE’s JGI. They identified roughly 20,000 protein-coding genes, many belonging to expanded gene families. Some appear to have roles in processes such as protein-protein interactions and signal transduction, while others have yet-unknown functions.
They also used NimbleGen custom oligoarrays to see whether predicted L. bicolor genes were expressed, and where.
— Abbreviated version of an article from GenomeWeb Daily News by Andrea Anderson

Research Team Adds Gene Expression to Metagenomic Study of Marine Microbe Community
Scientists exploring a marine microbial community have developed a way to combine gene expression analysis with metagenomics, according to research published last week.
Researchers from the Massachusetts Institute of Technology and Pennsylvania State University used a combination of RNA amplification and next-generation sequencing to look at the gene expression and metagenomics of a marine, microbial community in the North Pacific.
Their work, published in the online edition of the Proceedings of the National Academy of Sciences last week, confirmed some previous findings, but also revealed some surprises — including widely expressed unknown or hypothetical genes.
Using a 454 GS 20 sequencer to capture both cDNA and genomic DNA, the researchers studied the sequence diversity by comparing all of the sequences to the National Center for Biotechnology Information’s nonredundant protein database.
To verify their results, they also used RT-qPCR and qPCR. In addition, throughout the study they calibrated and verified their broader microbial community results against Prochlorococcus, a well-characterized and highly abundant marine cyanobacterium for which genome and expression data were already available. Using Affymetrix custom-designed arrays of Prochlorococcus genes, they were also able to assess the amplification method in that organism before applying it to the larger microbial community.
— Abbreviated version of an article from GenomeWeb Daily News by Andrea Anderson

Elephant Shark Protocadherin Sequence Offers Peek Into Vertebrate Evolution
Researchers from Singapore and the US sequenced the protocadherin gene cluster of the elephant shark in order to piece together the history of jawed vertebrates.
Their results, published online last week in the Proceedings of the National Academy of Sciences, indicate that the elephant shark protocadherin cluster has undergone surprisingly little gene conversion and that jawed vertebrates have lost protocadherin subgroups through evolutionary history.
The elephant shark, also called the elephant fish or ghost shark, belongs to Chondrichthyes, a group of cartilaginous fishes — the oldest living jawed vertebrates — that also includes sharks, skates, and rays. The other living, jawed vertebrates belong to Osteichthyes, the bony vertebrates.

The Scan

Self-Reported Hearing Loss in Older Adults Begins Very Early in Life, Study Says

A JAMA Otolaryngology — Head & Neck Surgery study says polygenic risk scores associated with hearing loss in older adults is also associated with hearing decline in younger groups.

Genome-Wide Analysis Sheds Light on Genetics of ADHD

A genome-wide association study meta-analysis of attention-deficit hyperactivity disorder appearing in Nature Genetics links 76 genes to risk of having the disorder.

MicroRNA Cotargeting Linked to Lupus

A mouse-based study appearing in BMC Biology implicates two microRNAs with overlapping target sites in lupus.

Enzyme Involved in Lipid Metabolism Linked to Mutational Signatures

In Nature Genetics, a Wellcome Sanger Institute-led team found that APOBEC1 may contribute to the development of the SBS2 and SBS13 mutational signatures in the small intestine.