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NCI, FDA, Solexa, NHGRI, Gene Logic, Roche, SystemsX, AIM, ABI, VisiGen, Genomic Health, Affy, Imperial College London, CeMines, Ciphergen

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NCI RFA Offers $3M for Developing Molecular Technologies

The National Cancer Institute has allocated nearly $3 million for research on developing cancer-relevant molecular technologies, according to a request for applications published on the National Institutes of Health web site.

NCI said it expects to award between 10 and 15 new and/or competing continuation grants for periods up to two or three years, depending on the award mechanism.

The institute will consider proposals that involve methods and tools to enable research, including instrumentation, techniques, and devices. Molecular technologies are distinct from resources such as databases, individual reagents, therapeutic agents, and tissue repositories, which are not included under this initiative.

The receipt dates for intents are Jan. 23 and April 26. The applications must be received by Feb. 22 and May 26.

More details are available under the title "Innovative Technologies for Molecular Analysis of Cancer" here.


FDA Issues Draft Guidance for Pathogen-Detection IVDs

The US Food and Drug Administration released last week a draft guidance for industry on the types of information the agency would consider during the premarket review of nucleic acid-based in vitro devices that detect exposure to pathogens.

The draft document, which represents the FDA's current thinking on nucleic acid-based in vitro diagnostic devices, comes at a time when the US government and many companies are actively engaged in developing microarrays and diagnostics tools to detect and manage such pathogenic diseases as bird flu and anthrax.

The FDA acknowledged the recommendations are "purposefully" general as they are intended to be a "framework" for the types of data that should be addressed in the premarket review of these devices.

The 26-page document, which can be found here (pdf), outlines its recommendations under four headings: Risks to Health, Device Descriptive Characteristics, Performance, and Labeling.

The section on risks recommends providing sufficient detail to indicate the device has been designed to reduce errors in performance or in interpreting test results. Device characteristics seeks information on the patient population to be tested, targeted disease and organism, testing methods, reagent components, instruments to be used, and safety aspects.

Under performance, the recommendations specify data indicating reliability, diagnostic accuracy, and reproducibility. Finally, labeling requests information on how specimens were collected and the types of collection devices used.

The guidance document is intended to offer the "least burdensome" approach, the FDA said. The agency invites comments and suggestions regarding the recommendations outlined in the draft document within 90 days.


Solexa, Releasing New Sequencer, Plans to Sequence Human Genome in '06

Solexa will use its newly launched Genome Analysis System to sequence an entire human genome next year and to make the data publicly available, the company said this week.

Solexa said it will choose the DNA from a set of anonymous samples recently used in the International Haplotype Mapping Project. The company said the project will enable researchers to compare its results with other publicly available data.

"In sequencing a human genome, our aim is to demonstrate the performance of the Solexa Genome Analysis System," David Bentley, chief scientist of Solexa, said in a statement.

Solexa said it will release sequence data at "regular intervals" in 2006 "so that researchers can objectively assess the output of the Solexa Genome Analysis System in comparison with previously validated, high-quality genetic data already in the public domain."

Solexa disclosed its plans to sequence the human genome on the day it launched its Genome Analysis System. The tool comprises the Solexa 1G Genetic Analyzer, the Solexa Cluster Station and associated reagents, consumables, and software, and is designed to generate more than 1 billion bases of sequence per run.

CEO John West reiterated earlier comments that the company "expect[s]" to begin accepting orders and ship initial production units during the second quarter of next year.


NHGRI to Publish Six RFAs for Genome Sequencing

The National Human Genome Research Institute plans to issue six requests for applications for projects focusing on genome sequencing technologies, the National Institutes of Health said last week.

The amounts allocated for the awards will be available once the RFAs are published, NHGRI said.

The research scope for these RFAs will be the same as the ones issued in 2004 on near-term technology development for genome sequencing and on revolutionary genome sequencing technologies. NHGRI committed $8 million in fiscal year 2004 and $5 million in fiscal year 2005 to fund four to 10 grants for near-term technology projects. For projects on revolutionary technologies, the NHGRI committed $6 million in fiscal year 2004 and $5 million in fiscal year 2005 to fund three to 10 awards.

The receipt date for intents will be Jan. 17 and applications must be submitted by Feb. 17.

More information can be found here.


Gene Logic Pens Drug-Repositioning Deal With Roche; Stands to Pocket Royalties, Milestones

Gene Logic has penned a "drug-repositioning" alliance with Roche in an effort to help the Swiss drug giant identify alternative development paths for "multiple" candidate compounds, the company said last week.

The Roche drugs Gene Logic will reevaluate under its Drug Repositioning Program have all passed Phase I human trials but were discontinued in Phase II or Phase III trials.

Gene Logic stands to receive success-based milestone payments for each drug candidate Roche returns to clinical development, and could pocket royalties for each marketed drug, the company said.

The agreement also gives Gene Logic the option to receive an exclusive license to any drug candidate that Roche chooses not to pursue. In this case, Roche, not Gene Logic, will receive success-based milestone and royalties.

The news comes three months after Gene Logic said it would help Pfizer, the world's biggest drug maker by revenue, reposition its stalled candidates.

Gene Logic's Drug Repositioning Program, which the company outlined in March, aims to find alternative development paths for drug candidates with good safety records that have been shelved by drug makers in Phase II or Phase III clinical trials.

Gene Logic said it can complete "initial repositioning testing and analysis" in less than a year and "potentially" return drug candidates "expediently" to clinical testing.


Roche to Invest $1.6M in Diabetes Biomarker-Discovery Research with SystemsX

Roche announced this week a three-year research partnership with SystemsX, the Swiss Initiative in Systems Biology, to develop diabetes drugs and identify biomarkers.

Roche will finance 2.1 million Swiss francs ($1.6 million) for the duration of the project.

In a statement, Roche called the project a "holistic" approach.

A team of 15 scientists from Roche and SystemsX's Competence Center for Systems Physiology and Metabolic Diseases will be joined by researchers from the Swiss Federal Institute of Technology in Zurich and University of Zurich.


AIM Develops Protein Biomarker-based Cancer Dx

Advanced Ideas in Medicine has developed a blood test to diagnose and detect cancer, the company said last week.

The tests are designed to identify a series of blood protein biomarkers that could help diagnose cancers such as prostate, colorectal, breast, lung, and ovarian.

The former principals of Predictive Diagnostics launched Advanced Ideas in Medicine as a diagnostics company in July 2005.


As Expected, ABI Completes Equity Investment in VisiGen

Applied Biosystems said last week that it has completed its equity investment in VisiGen Biotechnologies.

ABI announced its plans to invest in the company, which is developing next-generation sequencing technology, in October. ABI has also entered into a scientific collaboration with VisiGen.

Financial terms of the transaction was not disclosed, although ABI's investment hinged on a follow-on investment from VisGen shareholder SeqWright.

SeqWright announced that it had made a second equity investment, of an undisclosed amount, in November.


Study: Genomic Health's Oncotype Dx
Useful in Predicting Loco-regional Recurrence

Genomic Health said last week that a new analysis of 1,674 patients from previous clinical trials shows that the same recurrence score from its Oncotype Dx breast cancer recurrence test is also a "significant predictor of local or regional recurrence in tamoxifen-treated patients."

According to the company, the study found Oncotype's score to be a significant predictor of loco-regional recurrence in trials involving 895 tamoxifen-treated patients with lymph node-negative, estrogen receptor-positive breast cancer. The results were independent of age, clinical tumor size, and tumor grade. The researchers also saw significant associations between the recurrence score and loco-regional recurrence in the placebo-treated and chemotherapy plus tamoxifen-treated patient groups, Genomic Health added.

The study on National Surgical Adjuvant Breast and Bowel Project trials B-14 and B-20 was conducted by researchers from the NSABP, Genomic Health, and the Aultman Health Foundation, and was presented at the 28th Annual San Antonio Breast Cancer Symposium.


Affy Partners with Imperial College London, MRC to Genotype Heart Disease, Diabetes, and Cancer

Affymetrix said this week that researchers at Imperial College London and the UK's Medical Research Council will use the company's GeneChip technology to study the genetic variations associated with cancer, cardiovascular disease, and diabetes.

The researchers will use Affy arrays to perform genotyping and gene-expression experiments. Affymetrix did not disclose which of its GeneChips the UK researchers will use.

Affymetrix said that the collaboration is part of its translational medicine program, an initiative designed to "accelerate clinical research and improve patient care by helping to bring more effective personalized tests and therapies to market faster."

Financial terms of the agreement were not provided.


CeMines Puts Research Tools Business on the Block as Clinical Market Beckons

CeMines is putting on the block its research tools business and related inventory of polyclonal antibodies, cDNA, and mRNA, the company said this week.

"Our decision is based on the company's final preparations to enter global clinical markets, beginning in Europe, with our CellCorrect product family of high-accuracy molecular diagnostic tests for cancer detection," said Roger Attick, president and CEO of CeMines, in a statement.

As reported in Pharmacogenomics Reporter sister publication GenomeWeb News on Sept. 27, the company's Estonian subsidiary filed for CE Mark registration for its CellCorrect product family, a gene expression-based lung cancer diagnostic tool.

The company has already received multiple offers from selected prospective buyers and is actively reviewing pro forma bids, CeMines said. The company expects to make a final decision before the end of this year, but declined to comment on pricing or specific proposals.

According to the company, CeMines entered the research tools business in 2001. The business includes associated trademarks and a multinational customer base.


Ciphergen to Develop Breast Cancer Diagnostics

Ciphergen Biosystems said last week that it is developing breast cancer diagnostics based on a "series of discoveries" that have been made using the company's SELDI technology.

Ciphergen cited a study by researchers at the Johns Hopkins School of Medicine, published in Clinical Chemistry in 2002, that detailed the discovery of three serum biomarkers that can improve the detection of breast cancer.

"Two out of the three markers have since been identified and validated in further studies that were published this month," the company said in a statement. The markers are named C3a and BC1.

Ciphergen said it plans to expand upon these studies in a collaboration with the University of College London and UCL BioMedica that will analyze samples collected from 200,000 women with breast and ovarian cancer.

Ciphergen did not provide a timeline for the development program.

Filed under

The Scan

Review of Approval Process

Stat News reports the Department for Health and Human Services' Office of the Inspector General is to investigate FDA's approval of Biogen's Alzheimer's disease drug.

Not Quite Right

A new analysis has found hundreds of studies with incorrect nucleotide sequences reported in their methods, according to Nature News.

CRISPR and mRNA Together

Time magazine reports on the use of mRNA to deliver CRISPR machinery.

Nature Papers Present Smartphone Platform for DNA Diagnosis of Malaria, Mouse Lines for Epigenomic Editing

In Nature this week: a low-cost tool to detect infectious diseases like malaria, and more.