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Genomic Health, Bristol-Myers Squibb, ImClone, Eastern Cooperative Oncology Group, SACGHS, Nanosphere, Genomic Standards Consortium, Nanogen

Genomic Health Advances Collaborations with Partners to Develop Diagnostics
In reporting its first-quarter earnings this week, Genomic Health announced that two abstracts describing initial results from collaborations with partners Bristol-Myers Squibb, ImClone, and Eastern Cooperative Oncology Group in Santa Fe have been accepted for presentation at the 2008 American Society of Clinical Oncology's annual meeting, taking place May 30 to June 3.
The first abstract is titled “Evaluation of tumor gene expression and KRAS mutations in formalin-fixed paraffin-embedded tumor tissue as predictors of response to cetuximab in metastatic colorectal cancer,” and the second abstract is titled “Predictive utility of progesterone receptor in multi-gene expression, and identifying benefit from adjuvant doxorubicin plus cyclophosphamide or docetaxel in an intergroup trial E2197.”
The partnership with Bristol-Meyers Squibb and ImClone is for the development of a genomic test to predict the likelihood of benefit from treatment with the metastatic colorectal cancer drug cetuximab, also known by the brand name Erbitux.
The second collaboration is an agreement with Eastern Cooperative Oncology Group in Santa Fe around identifying genes related to benefit from breast cancer treatment with docetaxel.
“These presentations reflect our early work and targeted therapies and we're enthusiastic about the future of this critical area of research and our own advancement,” the company said.
In addition, the company said last week that it had initiated a collaboration with Pfizer to develop a prognostic test for patients with renal carcinoma. “This is in the early stages of clinical development,” the company said.

SACGHS Issues Request for Priorities
Following the recent release of its recommendations on the oversight of genetic tests and its final report on pharmacogenomics, the HHS Secretary's Advisory Committee on Genetics, Health, and Society, has issued a public request to help it identify new priorities for the next four years.
“Members of the public who wish to suggest an issue are asked to submit a statement (approximately one paragraph in length) that: 1) describes a problem or policy challenge that needs exploration; and 2) proposes actions the Committee could take to address the issue,” the committee said in a request
The public's suggestions, along with submission of references or other background materials related to the topic, are due by May 16. SACGHS will discuss the suggested topics at its meeting on July 7- 8 in Washington, DC.
“At its upcoming meeting in July, the committee will review the results of the rankings and further narrow the number of issues to be considered,” Sarah Carr, SACGHS executive secretary, told Pharmacogenomics Reporter in an e-mail this week. “The Committee will determine its study priorities at the committee’s December 2008 meeting after a consideration of additional background information about the issues selected in July. The Committee will also consider the type of action needed for each issue, ranging from monitoring to in-depth study.”
According to SACGHS, it has fulfilled or is near fulfilling major projects, including issuing guidelines, crafting resolutions, and writing letters to the HHS Secretary, related to the 11 issues it had identified as priorities in the field of genomics research and of importance to public health.
The advisory committee is trying to set its priorities for the next four years, and thus, the issues suggested should take into consideration SACGHS' prior work, which can be reviewed here.
When making suggestions, the public should also take into account: The urgency and national importance of the issue; the extent to which the federal government has jurisdiction/authority over the issue; the need for federal guidance or regulation on this issue; whether the issue raises concerns that only the federal government can address; whether the issue raises moral or ethical concerns that warrant federal government involvement/leadership; whether the committee's policy advice on this issue would significantly benefit society; whether failure to address the issue would prolong any negative impact the issue may be having on society; whether sufficient data about the issue exist for the committee to develop informed policy advice; and whether another body is already addressing the issue or is better equipped to address it.

Nanosphere's Q1 Revenues Double on Verigene Uptake
Nanosphere reported this week that its first-quarter revenues more than doubled year over year on initial customer adoption of its Verigene system.
The Northbrook, Ill.-based molecular diagnostics firm brought in revenues of $576,016 for the three-month period ended March 31, compared to revenues of $269,903 in the first quarter of 2007. Product sales for the quarter were $303,404 compared to $46,645 in the comparable period of 2007, while grant and contract revenue increased to $272,612 from $223,258.
Nanosphere received US Food and Drug Administration clearance for its Verigene system and warfarin metabolism assay in September. It was the first time the FDA ever cleared a test to detect gene variants in patients that are sensitive to the anticoagulant. The firm also received FDA clearance for a hyper-coagulation assay the following month. 
“We anticipate that we will submit applications to the FDA for clearance of tests for cystic fibrosis, herpes, cervical cancer, respiratory illness, recurrent prostate cancer, and cardiovascular disease during the next 36 months, and we anticipate that we will submit two of such tests within 2008,” Nanosphere said in a filing with the US Securities and Exchange Commission this week.
Nanosphere posted a net loss of $8.7 million, or $.39 per share, flat with a loss of $8.7 million, or $9.37 per share, in the first quarter of 2007. Nanosphere was privately held at the time of Q1 2007. The firm went public in November, raising net proceeds of $102 million from the sale of 8,050,000 shares of common stock at $14 per share.
The company’s R&D expenses increased 18.4 percent year over year to $5.8 million from $4.9 million, while its SG&A costs rose 54.5 percent to $3.4 million from $2.2 million.
Nanosphere finished the quarter with $104.2 million in cash and cash equivalents.
Nanosphere said in the SEC filing that it believes its cash holdings are sufficient to meet its needs for “at least the next two to three years.”

Genomic Standards Consortium Issues Guidelines
The Genomic Standards Consortium has published a set of guidelines meant to improve the way researchers describe genomes and metagenomes.
The GSC, an international, open-membership group created in the fall of 2005, includes biologists, bioinformaticians, and computer scientists, as well as individuals affiliated with sequencing centers and organizations such as NCBI’s GenBank and the US Department of Energy’s Joint Genome Institute. In a perspectives article published in this month’s issue of Nature Biotechnology, the consortium outlines what it calls “minimum information about a genome sequence” or MIGS specifications
“There is great enthusiasm in the community for this project and we are already collecting MIGS-compliant reports,” lead author and GSC founder Dawn Field, a researcher at the UK’s Natural Environmental Research Council Center for Ecology and Hydrology, said in a statement. “We are a highly collaborative group and open to new participants joining the GSC at any time.”
The GSC hopes to standardize the way genomic and metagenomic data is collected, described, and stored. This includes providing information about everything from strain names, location or habitat from which the organism was isolated, to detailed information about the sequencing method, coverage, assembly methods, finishing, and so on.
The GSC also emphasize the need to create a consensus-based approach to genomics and metagenomics, to help researchers collect data quickly, share it with others, and integrate it with information already available to the genomics community.
To address such issues, the group has developed a freely available Genome Catalogue, or GCat, system intended to help users input data, view and search genome descriptions, and, ultimately, integrate ontological information. Genomic sequence data and initial annotations must be submitted to the International Sequence Database Collaboration, and MIGS contains only primary, curated information, the authors noted.
The MIGS specifications are just one of a set of “minimum information” standards being developed. In addition, other groups such as the Microarray and Gene Expression Data Society and the International Nucleotide Sequence Database Collaboration have also come up with genome information standards through the Minimum Information about a High-throughput Nucleotide Sequencing Experiment (MINSEQE) and the Genome Project Metadata initiative, respectively.
“With the rapid pace at which new genome sequences are appearing, the need to consider how best to ensure stewardship of these data for the long term has never been more pressing,” Field and her colleagues wrote. “Given the importance of the growing genome collection, the capital investment in its creation and the benefits of leveraging it value through diverse comparative analyses, every effort should be made to describe it as accurately and comprehensively as possible.”

Nanogen Posts Q1 Revenue Increase of 10.3 Percent; Loss Rises on Charges
Nanogen reported this week that its first-quarter revenues rose 10.3 percent but its net loss nearly doubled on a charge related to the extinguishment of debt.
The San Diego-based molecular diagnostics firm brought in total revenues of $10.7 million for the three-month period ended March 31, compared to revenues of $9.7 million in the first quarter of 2007. Its product sales increased 32.8 percent to $8.1 million from $6.1 million year over year, while license fees and royalty income increased to $1.8 million from $1.2 million. Its contracts and grant revenue dropped to $852,000 from $2.3 million.
Nanogen’s net loss for the quarter was $23 million, or $.31 per share, compared to a net loss of $11.9 million, or $.17 per share, for the first quarter of 2007. The most recent quarter’s results include a $2.9 million charge for a “warrant valuation adjustment” and a $10.2 million charge related to the extinguishment of certain debt.
The firm’s R&D costs declined 26.2 percent to $4.2 million from $6.5 million, while its SG&A expenses fell 5.6 percent to $8.7 million from $8.9 million.
"Our Q1 results clearly demonstrate that the restructuring plan, initiated in the fourth quarter, has substantially improved our financial performance,” Nanogen Chairman and CEO Howard Birndorf said in a statement. “Consistent with our prior guidance, we have achieved meaningful cost reductions while at the same time have experienced a 36 percent increase in product revenue from the prior quarter."
Nanogen said in September that it would sell its microarray business in an effort to focus on building its RT-PCR and point-of-care testing businesses and more rapidly achieve profitability. The firm began shutting down the microarray business in November.
“We will require additional financing to reach profitability and are currently working on financing alternatives,” Birndorf said during Nanogen's conference call this week.
He also said that the firm is discussing with Nasdaq a potential move from the Nasdaq Global Market to the Nasdaq Capital Market, which has less stringent listing requirements. “If approved this would provide additional time for our stock price to regain compliance with the $1 per share threshold without the need for a reverse split.”
In early December, Nasdaq notified Nanogen that it may delist NY’s stock from the market due to failure to maintain a minimum bid price for 30 days. At the time, Nanogen said that if its stock is delisted in May, it may transfer to the Nasdaq Capital Market, at which time it will receive another 180 days to comply with the minimum bid rule.
Birndorf said Monday that Nanogen cannot assure that Nasdaq will approve the switch, and if it does not, the firm may have to reconsider a reverse split of its stock.
Nanogen's shares were up 5.5 percent at $.42 per share in early Tuesday trade. The firm's stock has not closed a trading session above $1 since September.
It recently retained investment firm Cowen and Co. to assist it in reviewing options for its business, Birndorf noted.
Nanogen said that it expects its 2008 revenues to increase around 25 percent over its 2007 revenues of $38.2 million.

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