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Illumina, Agilix, CombiMatrix, Ciphergen Biosystems, Beckman Coulter, Bioinformatics, Genencor International, Rosetta Biosoftware


Illumina Lands $1.2M Phase 2 NCI Grant to Develop Immunoassays


Illumina of San Diego has been awarded a $1.2 million Phase 2 research grant from the National Cancer Institute to develop an immunoassay system using its bead-based array technology, the company said this week.

Illumina is planning to use this grant, which is being funded through the NCI’s Innovative Molecular Analysis Technologies (IMAT) program, to further develop its fiber optic-based bead array technology as a tool for measuring and characterizing proteins, as well as their post-translational modifications.

This grant follows the successful completion of a Phase 1 feasibility study. The Phase 2 research will involve the development of an immunoassay designed to identify and evaluate defects in lymphoid system homeostasis and the immune response to cancer.

The company is collaborating on this research with Christopher Goodnow, a professor of molecular medicine at the Australian National University’s John Curtin School for Medical Research and a pioneer in the use of mouse models for the study of the immune system.


Agilix Signs Service Agreement with SAIC


Universal array startup Agilix of New Haven, Conn., has snagged what it calls “a strategic services agreement” with Science Applications International Corporation (SAIC), Agilix said this week.

SAIC, a $5.9 billion research and engineering company, will develop high-throughput applications of Agilix’ “Fixed address analysis of sequence tags” (FAAST) transcription analysis system, the universal array technology for whole genome transcript analysis; as well as its ZeptoLabeling proteomics technology.

“Agilix’s development team can now access engineering skills and technologies available only to companies like SAIC,” said Agilix president and CEO Martin Mattessich.

SAIC also participated in Agilix’s recent Series B financing, in which the company raised $28 million.


CombiMatrix Captures $6.4 M in 2001 Revenues: Joint Venture with Marubeni Japan


Semiconductor protein chip maker CombiMatrix, a subsidiary of Newport Beach, Calif., company Acacia Research, garnered $6.4 million in revenues for 2001, and $456,000 in revenues for the fourth quarter, the parent company said last week. Additionally, Combi- Matrix received $4.9 million in revenues during the quarter from its agreements with NASA and Roche Diagnostics, which are being recorded as deferred until after December, 31, 2001 pursuant to agreements with these organizations.

Of the recorded Q4 revenues, $91,000 came from US Defense Department Grants. CombiMatrix currently has two SBIR grants from the Department of Defense, and last month was awarded a Phase I grant from the National Institutes of Health to further develop its protein chips.

During the quarter, CombiMatrix formed a joint venture with Japanese trading company Marubeni Japan to develop and license its biochip technology in the Japanese pharmaceutical and biotech arena. Marubeni has a minority stake in the venture.

For the quarter, parent company Acacia Research lost a total of $5.2 million, vs. $14.2 million for the previous year’s period.


Ciphergen Teams Up with Beckman Coulter to Automate Protein Chip Tech


Ciphergen Biosystems will collaborate with Beckman Coulter to combine its SELDI protein chip biomarker system with Beckman’s Biomek 2000 system, the companies announced last week.

The resulting “turnkey” platform for proteomics research will be marketed to industry, academia, and government institutes, the companies said.

“We are happy that we can now make these solutions available broadly through this alliance with Beckman Coulter,” William Rich, president and CEO of Ciphergen, said in a statement. The firms said their alliance hopes to speed sample throughput five-fold and improve reproducibility.

Financial terms of the agreement were not disclosed.


Papers Sought: Bioinformatics to Publish Special Section on Microarray Data Analysis


The Journal Bioinformatics is looking for papers on microarray data analysis algorithms and techniques. The section is being organized by Colin Campbell of the University of Bristol, and Shayan Mukherjee of MIT, and will feature papers on common microarray analysis techniques such as cluster analysis, classification, feature selection, regression, sample complexity; determination of network structures, and feature dependencies.

“However, we also welcome papers from researchers interested in analytical methods beyond machine learning (e.g. statistics) which may include techniques for evaluating the effect of noise, imputing missing values, discovering outliers, scoring features, etc.,” Campbell wrote in an e-mail posting on the section. “We welcome case studies in which the techniques described above are applied to new datasets, illustrating practical problems and the successful use of these methods.”

The submission deadline is April 30, 2002. For more details, go to


Genencor License Rosetta’s Resolver


Genencor International has licensed Rosetta Biosoftware''s Resolver gene-expression data-analysis system, Rosetta said this week. Neither financial nor duration details of the deal were disclosed.

The Resolver system, considered the Rolls Royce of gene-expression analysis, was developed by Rosetta Biosoftware and exclusively distributed by Agilent Technologies.

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.