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Illumina, Mexican HapMap project, Affymetrix, Agilent, Kreatech, Genome Structural Variation Consortium, NimbleGen, ServiceXS, German Resource Center for Genome Research, Applied Microarrays, OGT

Mexico Genomics Initiative to use Illumina's BeadStation in SNP, Gene-Expression Studies
Illumina will provide its BeadStation to a large-scale genomics facility in Mexico City designed to continue and expand the work of the Mexican HapMap project, the company said this week.
The National Institute of Genomic Medicine (INMEGEN) will use the Illumina hardware with IBM bioinformatics in SNP-genotyping and gene-expression studies to “characterize the genetic variation of the Mexican population,” the company said.
The data collected on the genomes of Mexicans will be used to “incorporate genomics into methods of prevention, diagnosis, and treatment of disease, to enhance genomics training and research, to educate the public, and to make available advances in technology," INMEGEN Director Gerardo Jimenez-Sanchez said in a statement.
Illumina said INMEGEN has opened one lab, housing a genotyping and gene expression-analysis unit to be stocked with the BeadStation, as part of what will be a 40,000-square-foot facility.
INMEGEN researchers will use that lab to genotype and analyze samples from 1,200 individuals from six different Mexican states.
"Based upon results from the second phase of the Mexican HapMap Project, we will be able to lay the foundation necessary to improve and accelerate the development of clinical genomic medicine," Jimenez-Sanchez said.
The decision to play south of the border is a change of strategy of sorts for Illumina, which said as recently as 2005 that the shop had “no plans” to supply customers in Mexico with large-scale genomic needs (see BAN 8/3/2005).
After INMEGEN announced deals with Affymetrix and Applied Biosystems, Illumina CEO Jay Flatley said the company had “no plans to begin expanding its sales and marketing efforts into Central and South America at this time.”

European Consortium Using Affy Arrays to ID Mutations for Mental Retardation
A group of three European academic research institutes will use Affymetrix technology in an initiative aimed at identifying mutations in mentally retarded children, the company said this week.
The European Cytogenetic Research Initiative includes Affymetrix, the University of Tuebingen in Germany, the NHS Regional Genetics Laboratory in the UK, and the University of Nijmegen in the Netherlands, Affy said.
The three institutions will use Affy's microarrays to provide a high-resolution look at the human genome, "enabling researchers to better identify causative mutations, copy number variants, and loss of heterozygosity information," the company said.
University of Tuebingen's Olaf Riess said that by using the Affy microarrays, the collaborators "expect to find a much higher number of causal de novo deletions and amplifications than we could with the current gold-standard methods like karyotyping."
"Each year up to 30,000 children with learning difficulties will be tested in the UK alone using karyotyping and targeted FISH methods," said NHS' head of molecular cytogenetics, Dominic McMullan. But "these technologies are only helping to resolve five to ten percent of cases," McMullan added.

Agilent Licenses Kreatech's ULS Labeling Tech for Use With aCGH Platform
Agilent Technologies has licensed labeling technology from Kreatech for use with its formalin-fixed paraffin-embedded DNA tissue-extraction method, Agilent said this week.
Agilent said it will use Kreatech’s Universal Linkage System, which is a non-enzymatic direct-labeling methodology that has been optimized to be used with Agilent’s oligo comparative genomic hybridization microarrays.
There are around 400 million FFPE-preserved DNA samples in tissue banks that are “too degraded to use in microarray analysis techniques such as aCGH,” the company said. 
Having the capability to access degraded FFPE samples for microarray use offers “tremendous promise for cancer researchers,” Jay Kaufman, Agilent’s marketing director, said in a statement.
Financial terms of the agreement were not released.

Genome Structural Variation Consortium to Use NimbleGen Arrays To Create High-Res CNV Map
The Genome Structural Variation Consortium, an international group of applied genomics researchers from the US, UK, and Canada, has kicked off Phase 2 of an effort to create a high-resolution map of copy number variation linked to diseases in humans.
The consortium, which includes researchers from the Center for Applied Genomics at the Research Institute of the Hospital for Sick Children, the Wellcome Trust Sanger Institute, and from Brigham and Women's Hospital, said last week it will work with NimbleGen Systems to develop a comprehensive map of human CNVs and will focus on identifying genes involved in both rare and common diseases.
The consortium completed a first-generation draft of these CNVs in 2006. The group said in a statement that new technology, including "high-density microarrays and new computer algorithms," will enable it to develop a CNV map at a level 100-fold finer than that map.
The consortium said that it will use microarrays from NimbleGen that include 2.1 million features and will enable genome-wide detection of CNVs with 42 million probes.
"Our experiments will generate the highest resolution CNV catalogue of worldwide populations," said Stephen Scherer, senior scientist and director of TCAG at Toronto’s Hospital for Sick Children.
The group said it will use the new arrays to scan DNA from "dozens of individuals of diverse geographic background, in experiments designed to capture all CNVs with a frequency of five percent or greater in the world."
"Ultimately, the data generated from our Phase 2 studies will be important for disease association studies, cancer biomarker studies, and accurate interpretation of many genetic diagnostic tests," said Charles Lee, who is director of Cytogenetics at Brigham and Women's Hospital at Harvard Medical School.

ServiceXS Will Use Affy Arrays to Study Nutrigenomics for NuGo
Dutch genomics and proteomics outsourcing company ServiceXS will use microarrays designed by the European Nutrigenomics Organization and manufactured by Affymetrix to study nutrition and genomics for NuGo, ServiceXS said last week.
ServiceXS said the custom array, called the NuGo GeneChip, contains human or mouse genes that are considered relevant for nutrigenomics research.
Under the partnership, ServiceXS will use the GeneChips to conduct gene expression-profiling studies that look at the “interactions between nutrition and the genome that affect cell function” and human health.
Financial terms of the agreement were not released.

German Resource Center for Genome Research to Close its Doors
The German Resource Center for Genome Research said it is shutting down its services operations at the end of July, and that ImaGenes and Atlas Biolabs will take over “most” of its service offerings.
A reason for the closure was not given. RZPD said it will not take any orders after July 10.
The Berlin- and Heidelberg-based non-profit has been offering Affymetrix’ microarray services through Affy’s European distributor, NimbleGen, as well as a number of other genomics services.

Applied Microarrays Licenses OGT's Southern Array IP
Oxford Gene Technology has licensed its Southern array patents to Applied Microarrays, OGT said last week.
The IP comprises the fundamental patents enabling companies to manufacture and market oligonucleotide microarrays, and will allow Applied Microarrays to fabricate, market, and distribute the CodeLink line it acquired in May from GE Healthcare.
AMI, a new firm headed by a former Motorola Life Sciences researcher, also gets OEM rights to manufacture custom arrays for third parties under their own brand name. 
The license will remain valid for the patents’ lifetime. Financial details were not disclosed.