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Affymetrix, Partners HealthCare, Illumina, NHLBI, University of Pennsylvania, the Broad Institute, NimbleGen, DNAStar, Lumera, Plexera Bioscience, NuGEN, Kreatech

Affymetrix Expands Microarray Dx Pact With Partners HealthCare
Affymetrix this week said it has expanded a translational research alliance with Partners HealthCare and collaborators at Harvard University to include a contract array-manufacturing agreement, which will enable the companies to use custom chips made by Affy for lab-developed diagnostics.
Under the terms of the agreement, Affymetrix will create custom microarrays based on “recent discovery data” from Partners researchers. The arrays will be used to produce molecular diagnostics that will be validated and implemented in Partners HealthCare’s Clinical Laboratory Improvement Amendments-certified labs.
The team at Partners will begin focusing on array-based tests for hypertrophic cardiomyopathy, and will explore “many indications in a large number of diseases.”
Financial terms of the agreement were not released.

Illumina to Co-develop SNP Chip for Vascular Disease With NHLBI, Penn, and Broad
Illumina said this week it will develop a custom SNP microarray for the study of vascular diseases through a "multi-million dollar" collaboration with the Institute of Translational Medicine and Therapeutics at the University of Pennsylvania, the Broad Institute, and the National Heart, Lung, and Blood Institute's Candidate-gene Association Resource (CARe) Consortium.
The CARe consortium, initiated by the NHLBI in 2006, aims to create a resource for analyzing the association of phenotypes linked to diseases that are within the Institute's scope.
The IBC chip, named after the first letters of ITMAT, Broad, and CARe, will be used to analyze more than 55,000 SNPs in genes that have been selected for cardiovascular-related phenotypes.
Illumina said the collaborators will use the Illumina iSelect Custom Genotyping BeadChip to study the genetic diversity of pathways for around 2,100 genes that are linked to vascular conditions including hypertension, myocardial infarction, heart failure, stroke, insulin resistance, metabolic disorders, dyslipidemia, and inflammation. The iSelect BeadChip enables scientists to train their research on specific SNPS related to pathways or disease.
The company said that the study plans to analyze more than 120,000 samples from population studies and clinical trials for possible links to vascular disease.
"With Illumina's assistance, we worked together to build a comprehensive, focused vascular disease panel," said Joel Hirschhorn, coordinator of the Broad Institute's Metabolism Initiative. He said that the microarray will allow the researchers to “quickly genotype thousands of patients across thousands of genes to identify genetic risk factors underlying vascular diseases and other complex genetic traits."
Financial terms of the agreement were not released.

NimbleGen to Distribute DNAStar's New Gene-Expression Software
NimbleGen customers will receive a free trial of DNAStar’s latest gene-expression software as part of a new distribution agreement between the companies, DNAStar said last week.
Under terms of the agreement, NimbleGen customers will receive a free trial version of ArrayStar v.2.0 when they obtain either their chip data or product from NimbleGen.
DNAStar said ArrayStar is the first gene expression-analysis software product designed specifically for data files from NimbleGen microarrays.
The company said the software enables users to determine gene-expression levels, gene relationships and class discoveries, and it offers visualization capabilities such as heat maps, k-means clustering, and other statistical analysis options.
Financial terms of the agreement were not released.

Nanotech Shop Lumera Spins Out Proteomic Vendor Plexera Bioscience
Nanotechnology shop Lumera has spun out a company that will compete in the proteomics tools market, Lumera said last week.
The company, Plexera Bioscience, has become a wholly owned subsidiary of Lumera and will serve as the operations unit of Lumera's bioscience business that it started in 2006.
Plexera will focus on providing “tools, content, and methods to simplify and accelerate proteomic discovery for therapeutic antibodies as well as predictive biomarkers,” Lumera said.
Plexera’s products include the ProteomicProcessor, a “compact device for detecting and quantifying binding interactions in a label-free format utilizing surface plasmon resonance technology.”
The company also sells NanoCapture microarrays, which use “programmable hydrophobic and hydrophilic surface chemistries that result in minimal non-specific binding and high signal to noise ratios. They offer flexible surface chemistries for protein, nucleic acid, carbohydrate, and lipid immobilization in a flexible array density and flexible array spot size.”
Lumera board member Joseph Vallner, who was president and COO of Cell Genesys and CEO of the pharmaceutical company Capnia, will be chairman and CEO of the new division.
Tim Londergan, business director of Lumera’s Bioscience unit, has become president and COO of Plexera.
Lumera said it has hired investment bank Robert W. Baird & Co. to help it evaluate partnering and financing alternatives over the coming months.

NuGEN to Integrate Kreatech's ULS into New FL-Ovation Modules for Agilent Arrays
NuGen Technologies will integrate Kreatech’s Universal Linkage System into its FL-Ovation cDNA fluorescent module, NuGen said last week.
Under the non-exclusive agreement, Kreatech will supply NuGen with its ULS labeling system for one- and two-color microarray analysis.
NuGen will combine the new labeling module with its RNA aplification product line to provide a sample-preparation workflow for gene expression analysis projects performed with Agilent's DNA microarrays. 
NuGen said that by using only picograms of RNA, its systems allow small and degraded RNA samples to be amplified into micrograms of cDNA, which can then be “fragmented and labeled for same-day hybridization to Agilent DNA microarrays or used for direct qPCR.”
NuGen expects to start marketing the FL-Ovation cDNA modules this fall.
Financial terms of the agreement were not released.

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