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NimbleGen, BioMicro Systems, AutoGenomics, Illumina, Affymetrix, Expression Analysis, Agencourt, Novartis, Epigenomics

NimbleGen Will Help Upstream Validate Biomarkers
NimbleGen will help Upstream Biosciences validate biomarkers, Upstream said this week.
Under the agreement, NimbleGen will provide lab services including its whole-genome chromatin immunoprecipitation arrays to validate in silico binding-site predictions, Upstream said.
Upstream said it has filed five patents that would cover the use of genetic variations in certain regions that mark "various" cancers.
The NimbleGen studies will use samples of prostate and liver cancer to validate these proprietary markers," Upstream said.

BioMicro Systems to Manufacture Hybridization Tools for NimbleGen
BioMicro Systems will manufacture customized hybridization instruments for NimbleGen’s NimbleChip microarrays under a non-exclusive agreement, BioMicro said this week.
BioMicro Systems, based in Salt Lake City, Utah, said it will make NimbleGen-branded hybridization tools and custom hybridization chambers for NimbleGen under the OEM agreement.
Financial terms of the agreement were not released.

AutoGenomics Pockets $12M in VC Cash; Will Expand Manufacturing, S&M
AutoGenomics has hauled in $12 million through a Series C round of private-equity financing from non-institutional investors, the company said last week.
President Fareed Kureshy said in a statement that the company will use the cash to “extend our test application menu, expand manufacturing, and increase our sales and marketing efforts” for its Infiniti film-based microarray system.
The assays are designed to help diagnose clotting disorder thrombophilia.
Kureshy said the company does not expect to require more funding for continued growth because its coagulation Factor II and V in vitro diagnostic tests and its analyzer were recently cleared by the US Food and Drug Administration (see BAN 2/13/2007).

Neuroscience Microarray Consortium Installs Affy and Illumina Array Tools at Yale, TGen
A National Institutes of Health-led group of research facilities has installed Illumina and Affymetrix array tools to support collaborative neuroscience whole genome association studies, the group said last week.
The group, Neuroscience Microarray Consortium, has centers at the University of California, Los Angeles; Duke University; Yale University; and the Translational Genomics Research Institute.
“These high-throughput genotyping services will ultimately make a dramatic impact in clinical care of neurological disorders,” NMC chairman and TGen neurogenomics director Dietrich Stephan said in a statement.
Stephan told BioArray News sister publication GenomeWeb Daily News that the NMC is working with roughly $25 million in NIH funding. He said the group bought an Illumina BeadLab 1000 in late 2006, and that the system is “up and running” at Yale, and that TGen’s lab in Phoenix is running an Affy Human Mapping 500K Array Set.
As many as 10,000 researchers will have access to the hardware for whole-genome studies, particularly researchers studying genes linked to neurological disorders.
The consortium member institutions each offer different services, the NMC said: TGen offers expression profiling and SNP-genotyping using Affy’s Gene Chips; Yale offers genotyping using both Affy and Illumina services; UCLA uses the Affy platform; and Duke contributes LCM services.

Affymetrix Validates Agencourt’s AMPure System for Use with SNP Array 5.0
Agencourt Bioscience said last week that Affymetrix has validated its PCR target-preparation system for use with its new SNP Array 5.0.
Lynn Doucette-Stamm, Agencourt’s vice president of business development, said the validation is confirmation that its AMPure system is “adaptable to manual and automated methods for SNP genotyping applications."
The purification system is based on Solid Phase Reversible Immobilization, which is used with automated purification methods on Beckman Coulter’s lab workstations, Agencourt said.
Agencourt, a Beckman Coulter subsidiary, said Affy’s Genome-Wide Human SNP Array 5.0 is currently being used to study autism, bipolar disease, cancer, diabetes, and heart disease.

Expression Analysis to Use NuGen's FFPE Tool in Gene-Expression Services
Expression Analysis said last week it will offer gene expression-profiling services using NuGen’s WT-Ovation system with formalin fixed, paraffin-embedded tissues.
Expression Analysis said the deal, which will rely on its whole transcriptome-amplification technology, gives it exclusive rights to use NuGen’s system until it is commercially launched. Expression Analysis CEO Steve McPhail said that profiling generally uses fresh samples because “RNA samples isolated from FFPE blocks are usually so degraded that expression profiling is impossible.”
McPhail said the NuGen system can generate useful targets from such samples. Expression Analysis said it recently helped to optimize the WT-Ovation and validated it using RNA specimens from FFPE tissues that were stored over varying lengths of time.
Financial terms of the agreement were not released.

Novartis Licenses Its Evanescent Resonance Detection Tech to SRU Biosystems
SRU Biosystems said last week that Novartis has granted it an exclusive license to evanescent resonance technology, a detection platform that enhances the sensitivity of fluorescence-based assays for drug discovery and diagnostics. SRU now has the right to use ER technology for drug discovery, as well as all supporting intellectual property rights, the company said.
Owen Dempsey, president and CEO of SRU Biosystems, said in a statement that the technology could be incorporated into standard microarray slides and microtiter plates and is compatible with existing infrastructure and commercial equipment on the market.
According to SRU, ER technology enables researchers to measure gene expression from very small samples that include less than one nanogram of RNA, an attribute that the company claims will give the technology a boost over traditional microarrays, which it said require much more RNA for gene-expression profiling.

After 'Challenging' '06, Epigenomics Refocuses On DNA Methylation-Based Dxs
Epigenomics, trying to recover from a year in which it lost a significant revenue-generating partner, has streamlined its product-development plans for its DNA-methylation-based screening products, and seeks to strike up “multiple non-exclusive partnerships,” the company said last week.
The company made its remarks in a statement reporting its 2006 financial results, which showed that revenues plummeted 63 percent as R&D spending ticked up 7 percent and net losses rose 75 percent.
Epigenomics’ new CEO, Geert Nygaard, said in the statement that he is “convinced that Epigenomics’ DNA-methylation technology is ideally positioned to fill the large unmet need in early cancer diagnosis. … ”
He said the company, which called 2006 a "challenging" year," is “focusing all our strength, expertise and resources” on developing its colorectal cancer diagnostic and on finding new partnerships to commercialize its screening pipeline.  
The German diagnostics company hopes to launch a colorectal cancer test “via a reference lab” some time in 2008.
As for the financials, total receipts for the year ended Dec. 31, 2006, dropped to €3.5 million ($4.7 million), from €9.6 million in 2005.
The company said contributing to decline in receipts was a one-time “multi-million-euro milestone payment” connected to the termination of its four-year biomarker alliance with Roche Diagnostics in December, and fewer new business collaborations.
Roche abandoned the alliance with Epigenomics because it said the colorectal cancer screening data Epigenomics had presented at the time “did not meet Roche criteria for development as in vitro tests.”
The companies had agreed in 2003 to employ Epigenomics’ DNA-methylation technology to develop cancer drugs and diagnostics and prognostic tools for colon, breast and prostate cancer. Roche backed out of the colon and breast cancer development alliances at the beginning of 2006.
The company said that in spite of losing the Roche partnership, it plans to build on some successes it had during the year, including out-licensing patent families under deals with Qiagen and Affymetrix.
The company said it has now been granted 61 patents.
Revenue for 2007 will depend on R&D spending and partnerships, but it is expected to be “similar to 2006,” the company said.
R&D spending increased to €8.7 million from €8.1 million year over year.
Epigenomics said it shifted 2006 R&D resources toward its prostate cancer classification program and the development of a proprietary tissue-testing diagnostic program in 2006.  
In 2007, the company said it intends to focus its resources on development of its colorectal cancer screening test.
The company said net loss increased to €15.4 million from €8.8 million a year ago.

Epigenomics said it had around €17.3 million in cash, cash equivalents, and marketable securities as of Dec. 31.

The Scan

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.

Team Presents Cattle Genotype-Tissue Expression Atlas

Using RNA sequences representing thousands of cattle samples, researchers looked at relationships between cattle genotype and tissue expression in Nature Genetics.

Researchers Map Recombination in Khoe-San Population

With whole-genome sequences for dozens of individuals from the Nama population, researchers saw in Genome Biology fine-scale recombination patterns that clustered outside of other populations.

Myotonic Dystrophy Repeat Detected in Family Genome Sequencing Analysis

While sequencing individuals from a multi-generation family, researchers identified a myotonic dystrophy type 2-related short tandem repeat in the European Journal of Human Genetics.