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NimbleGen, FDA, CombiMatrix, Affy, Luminex, Genizon, Illumina, Affymetrix, Biacore, JPT, Mount Sinai School of Medicine

NimbleGen Says HD2 Chips Now in Early Access
NimbleGen Systems said this week that it has selected a number of limited access partners to work with the company’s second-generation NimbleChip HD2 microarrays, which contain 2 million probes.
NimbleGen’s chromatin immunoprecipitation (ChIP) products and services for human, mouse, rat, dog, Arabidopsis, and other organisms will be the first to be upgraded to the HD2 format, the company said.
Early access customers include the Yale Center for Genomics and Proteomics; the University of California, Davis’ Genome Center; and the Laboratory for Gene Regulation at the Ludwig Institute for Cancer Research at UC San Diego.
NimbleGen said that it was able to increase density because of the ongoing development of Texas Instruments’ Digital Micromirror Device, which the company uses in its Maskless Array Synthesis instruments to synthesize oligonucleotide probes on its standard arrays.
“We acheived this increase in feature content in the HD2 format by designing a new microarray manufacturing instrument that utilizes the newest generation Texas Instrument Digital Micromirror Device,” Emile Nuwaysir, the company’s vice president of business development, told BioArray News in an e-mail this week. “We also increased the overall size of the array on the slide, which increased the overall feature content.”
Nuwaysir added that NimbleGen will also apply the HD2 format to its comparative genomic hybridization, comparative genome sequencing, and gene-expression product lines.

FDA Seeks Meeting with CombiMatrix Over Constitutional Genetic Array Test
CombiMatrix said this week that the US Food and Drug Administration's Office of In Vitro Diagnostic Device Evaluation and Safety has asked to speak with it about its Constitutional Genetic Array Test.
CombiMatrix said the FDA wants to "discuss" the company's "plans to market [the] CGAT in September." CombiMatrix said that it plans to meet with the FDA in the “near future.”
Last month CombiMatrix Molecular Diagnostics said it will launch its first molecular diagnostic service in the US in August. The service will use the CGAT, which “can genetically identify more than 50 common genetic disorders,” including developmental disorders. The service is already sold in Europe through Paris-based Array Genomics.
CMDX said it's in the "final phases" of internal human and clinical validation.
In March, CMDX and Array Genomics said they will co-develop and co-market a series of comparative genomic hybridization microarrays for diagnosing genetic anomalies associated with mental retardation.
Matt Watson, CEO of CMDX, said in June that the firm is "actively developing further tests based on both our oligo and BAC capabilities that augment our microarray portfolio and over the next three quarters, we have plans to launch three to five additional products into the molecular diagnostics market."

Affy, Luminex Rejoin Nasdaq Biotech Index
Affymetrix, Caliper, and Luminex  are among five firms added back to the Nasdaq Biotechnology Index after an interim review in May removed them, the exchange said last week.
Nasdaq said in a statement that the "sole purpose" of the review was "to include some companies that were removed from the Index during the May semi-annual re-ranking due to sector classification assigned by the Industry Classification Benchmark."
In May, Accelrys, Affymetrix, Caliper Life Sciences, and Luminex were among nine firms dropped from the index due to a change in their ICB classification.  
"As a result of ICB's recent sector evaluation, five securities will be added back into the Index as their sector classification has been changed to biotechnology or pharmaceutical," Nasdaq said last week. "In addition to qualifying for this sector, companies being added back met all other continued eligibility criteria."
The change became effective on July 24.

Genizon Begins Offering SNP-Genotyping Services on Illumina Platform
Genizon BioSciences said last week that it has begun providing SNP-genotyping and statistical-analysis services on Illumina’s platform.
Research and commercial partners of the Montreal-based company now have access to eight Illumina BeadArray instruments, custom Illumina Infinium chips, and GoldenGate marker sets, Genizon said.
John Hooper, president and CEO of Genizon, said in a statement that the biomarker discovery firm, which has been using the tools in-house and with collaborators, saw the opportunity to set up a SNP-genotyping and genetic-analysis service as “a natural extension” for the company.
Genizon also performs genetic analysis with its own platform, GeneSys. The system is capable of genotyping as many as 100 million genotypes per day.
All services will be performed at Genizon's GLP-compliant facilities.

Affymetrix Deploys Brooks MEDIC MES Solution at Singapore Plant
Brooks Software, a division of Brooks Automation, said this week that Affymetrix will employ its MEDIC MES software for its manufacturing facility in Singapore.
Affymetrix will use the Brooks MEDIC suite to automate, track, and trace all manufacturing-related activities, including work-in-process, quality and equipment engineering, the company said.
Robert Ragusa, senior vice president of global operations at Affymetrix, said in a statement that the company "supports a GMP-compliant environment and is currently deploying Brooks’ manufacturing applications in [its] facilities around the world."
Financial details were not discussed. In January, Greg Schiffman, Affy’s chief financial officer, said that the Singapore plant would be operational by the second half of this year.
"The Singapore plant is roughly double the size of our current array manufacturing plant, and [it] provides us with significant space [that] we can grow into over coming years," he said at the time (see BAN 1/31/2006).

CombiMatrix Says Q2 Revenues Decline 3.5 Percent
CombiMatrix last week said that second-quarter revenue declined 3.5 percent as R&D spending doubled and net losses narrowed slightly.
Total receipts for the three months ended June 30 declined to $1.79 million from $1.85 million in the year-ago period.
Revenues from government contracts fell 55 percent to $574,000 from $1.3 million, year over year. Receipts from product sales more than doubled to $1.2 million from $567,000 and service contracts quintupled to $60,000 from $9,000, the company said.
CombiMatrix excused the drop in government contracts by saying that the second quarter of 2005 had an "anomalously high level of activity" under its Department of Defense biological threat detection contract.
The Acacia unit said net losses shrank slightly to $3.4 million versus $3.7 million in the year-ago period. The current quarter's loss included non-cash stock compensation, patent amortization, and depreciation charges totaling $971,000 versus $541,000 in the comparable 2005 period.
R&D spending in the period increased to $2.2 million from $1.2 million year over year. This increase was due "primarily" to developments ongoing at the CombiMatrix Molecular Diagnostics division.
CombiMatrix reported $10 million in cash, cash equivalents, and short-term investments as of June 30.

Biacore Reports 80-Percent Decline in Q2 Profits

Biacore said last week that despite a 21-percent jump in sales for the second quarter, profits dropped 80 percent as a tax credit had affected Q2 2005 earnings, and costs in the current period increased.
For the quarter ended June 30, sales rose 21 percent to SEK 162 million ($22.1 million) from SEK 133 million a year ago. Sales in Europe and the US rose 33 percent and 48 percent, respectively, but Asia-Pacific sales declined by 50 percent.
Biacore, which is set to be acquired by GE Healthcare, posted second-quarter net income of SEK 23 million, or SEK 2.38 per share, versus SEK 113 million, or SEK 11.62 per share, during the same period last year. The company said contributing to the decline in profits this quarter was a SEK 97 million tax credit included in net income for the second quarter 2005 (see BAN 6/20/2006).
R&D spending declined to SEK 26 million from SEK 27 million in the second quarter of 2005.
The company modified its forecast for the full-year 2006. Biacore said it expects 2006 sales to increase "at a somewhat higher rate than in 2005 with operating income growing faster than sales."
As of June 30, Biacore had SEK 181.6 million in cash and cash equivalents.

JPT, Mount SinaiSchool of Medicine Biomarker-Discovery Alliance
JPT Peptide Technologies, a wholly owned subsidiary of Jerin, and Mount Sinai School of Medicine this week announced a partnership to discover and validate peptide biomarkers for use in developing immune monitoring tools and immune therapies for patients suffering from food allergies.
This collaboration pairs MSSM's ability to identify food allergens with JPT's PepStar peptide-microarray platform in order to understand the B-cell epitope response of certain populations.
"Our experience has shown the use of peptide microarrays to be a highly efficient and cost-effective tool for the systematic screening of the B-cell response of complex patient populations,” Hugh Sampson, director of the Jaffe Food Allergy Institute at MSSM, said in a statement.

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.