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TGen, Affymetrix, Illumina, Fluidigm, Genotypic, Agilent, NHGRI, Caltech, Agendia, NanoInk

TGen, Partners to Use Affy Chips to Study Age-Related Hearing Loss
Researchers at the Translational Genomics Research Institute and the House Ear Institute have begun a study that will use Affymetrix GeneChips to identify the genes and genetic interactions involved in presbycusis, or age-related hearing loss, TGen said last week.
The researchers will use Affy’s 500K SNP chips to study nearly 2,000 patient samples collected at the Hereditary Deafness Laboratory at the University of Antwerp, Belgium. A short-term goal of the study is to create a screening chip to identify variations in specific genes that lead to presbycusis, TGen said.
"This study will serve as a foundation for gene discoveries in other complex diseases and provides the groundwork for early diagnosis and treatment of age-related hearing loss," said Rick Friedman, principal investigator of the study at the House Ear Institute, in a statement.

Affy Restates Earnings, Clears Nasdaq Noncompliance and Investor Default
Affymetrix last week said it has filed its restated financial results dating back to 1997 with the Securities and Exchange Commission.
“The company is now current in its SEC reporting obligations and, as a result, expects that the previously disclosed Nasdaq delisting action will be terminated and believes that the previously disclosed notice of default under the company's indenture has been cured,” Affy said in a statement. 
Affy said the adjustments increased previously reported basic and diluted net income per common share by $.13 and $.12, respectively, for the year ended Dec. 31, 2005, and decreased basic and diluted net income per common share by $.03 for the year ended Dec. 31, 2003.
As BioArray News reported last month, Affymetrix said it planned to restate its financial results as far back as 1997 after an internal review into its stock-option granting practices turned up “certain documentation lapses” (see BAN 8/15/2006).
“The review identified certain documentation lapses but did not find any pattern or practice of inappropriately identifying grant dates with hindsight in order to provide ‘discounted’ or ‘in-the-money’ grants,” Affy said in a statement on Aug. 10. The company granted the options between 1997 and 1999.

Illumina to Develop Bovine BeadChip, Plans to Market It in Early 2007
Illumina said last month that it plans to develop a new multi-sample bovine BeadChip and sell it early next year.
SNP content will be developed with scientists at the US Department of Agriculture’s Agricultural Research Service, the University of Missouri-Columbia, and the University of Alberta.
The array content will be based on data from the draft sequence of the cow genome and recent genome assembly done at the Baylor College of Medicine. The partners will use the SNP markers to map quantitative trait loci and to selectively breed cattle, Illumina said.
Illumina plans to offer the bovine BeadChip as a new product in early 2007 as a standard catalog array after it analyzes the initial batch of samples.
“The bovine chip is being developed initially as a custom iSelect chip but will then be offered as a standalone product. The chips can be run either by us as a service or by customers on their BeadStations,” Illumina CEO Jay Flatley told BioArray News in an e-mail last week.
According to Illumina, the researchers will select the SNPs after using Illumina’s Infinium assay to genotype more than 10,000 cattle samples representing at least 10 different breeds.

Fluidigm’s Singapore Manufacturing Facility Ready Ahead of Schedule
Fluidigm last week said that its manufacturing facility in Singapore has begun working at full process ahead of schedule.
The facility, which opened its doors less than one year ago, was to reach this level by the end of 2006, a Fluidigm spokesperson said.
The facility manufactures BioMark dynamic arrays, among other products, which are integrated fluidic circuits that are designed to increase qPCR efficiency. Fluidigm will sell these products to study genetic and protein biomarkers.
Other chips currently being developed “address multi-step processes on a nanovolume scale, including synthesis of imaging probes used in positron emission tomography and the preparation of nucleic acids for analysis,” Fluidigm said in a statement.

Genotypic to Provide Agilent-Based Gene-Expression Services in India
Agilent Technologies last month said Indian bioinformatics company Genotypic will provide gene expression-analysis and consulting services in that country.
Genotypic, based in Bangalore, is an authorized Agilent distributor.

NHGRI Gives Caltech $18M to Create New Genomic Science COE
The National Human Genome Research Institute last month announced $54 million in grants to establish a new Center of Excellence in Genomic Science and continue supporting two existing CEGSs.
The NHGRI will give the California Institute of Technology $18 million over five years to create a CEGS. It will be called the Center for In Toto Genomic Analysis of Vertebrate Development.
The NHGRI will also give the two existing centers $18 million apiece over the next five years. They are the Microscale Life Sciences Center at the University of Washington and the Yale Center of Excellence in Genomic Science.
The Center will initially develop and test its technologies in zebrafish embryos and eventually move on to bird embryos. Ultimately, the team plans to produce a "digital" fish and a "digital" bird that will be available online.
The University of Washington's CEGS, led by Deirdre Meldrum, will try to develop miniaturized, automated systems to detect and analyze the differences between healthy cells and diseased cells at the level of an individual cell.
Meantime, Yale’s CEGS will be led by Michael Snyder and will continue trying to develop new technologies for identifying functional elements within the human genome.
The CEGS has already created new genomic tiling arrays that can identify transcribed sequences, transcription-factor binding sites, DNA replication timing and DNA sequence variation on a large scale. It now hopes to “improve these … technologies, as well as explore new methods and approaches, including protein microarrays, with the goal of using these tools in an integrated fashion to analyze the regulatory steps involved in inflammation,” NHGRI said.

Agendia Acquires ISO Accreditation for CupPrint Dx Service
The Dutch Accreditation Council has granted Agendia the ISO/IEC 17025:2005 accreditation for its CupPrint service, which is carried out at the company's laboratory facilities in Amsterdam, Agendia said this week.
Agendia received ISO17025 accreditation for its MammaPrint breast cancer prognostic in Sept. 2005. Both of the tests have also been CE Marked.
According to Agendia, CupPrint is intended for patients with a Cancer of Unknown Primary, and aids physicians in assessing the origin of the primary tumor, which then guides treatment.

NanoInk Awarded $735K to Develop Nanoarray Fabrication Method
NanoInk said last month that it has been awarded a $735,000 Phase II Small Business Innovation Research grant from the National Human Genome Research Institute to develop a patterning methodology based on its Dip Pen Nanolithography technology to generate sub-micron sized features on solid surfaces.
NanoInk will also develop a nanoarray fabrication platform consisting of a DPN arrayer, parallel multipen arrays with integrated microfluidic inking systems and appropriate pen and surface modification chemistry to allow patterning with a variety of biomolecules, the firm added.

The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

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.