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Illumina, Roche Holding, Geneservice, University of Oxford, Broad Institute, Gene-IT, SanAir Technologies, ABI, GE Healthcare, Qiagen

Illumina Says Improved Sequencer Enables Paired-End Reads, 50-Base Read Lengths
Illumina last week announced that it has met several technical milestones for the Illumina Genome Analyzer (formerly called the Solexa Genome Analyzer).
The company said that it has developed new methods for generating high-quality paired reads and the ability to increase the read length for the system to more than 50 bases, among other improvements.
Illumina said that paired-end reads are useful for a number of applications, including detection of genomic insertions, deletions, and chromosome rearrangements, as well as de novo sequencing and assembly of bacterial and mammalian genomes.
The increase in read length from approximately 25 to 30 bases to more than 50 bases enables “over 90 percent of the reads to be aligned to the human genome at high accuracy,” Illumina said.
The company said that it has also developed methods that enable “high levels of sample multiplexing” in a single channel, and improved methods to “routinely generate over a billion bases of high- quality raw data per flowcell.”
The company did not provide a timeline on when these features would be available in commercial versions of the Illumina Genome Analyzer.

GS 20 Sales Drive 12 Percent Revenue Growth for Roche Applied Science
Roche Holding said this week that sales for its Applied Science group, which markets the Genome Sequencer 20 and FLX from 454 Life Sciences, grew by 12 percent in 2006 to $509.5 million.
The company did not disclose sales figures for the 454 sequencing platform, but said in a statement that the growth rate “was driven primarily by the LightCycler 480 instrument and Genome Sequencer 20 system.”
The Applied Science group falls under Roche’s diagnostics unit, which brought in 2006 revenue of $7 billion, a 5 percent increase year over year.

Geneservice Buys Oxford Sequencing Shop to Offer Contract Services, Plans Expansion
Geneservice has acquired a sequencing facility located at the University of Oxford and will use it to perform contract research, the company said last week.
Cambridge, UK-based Geneservice said it will use the facility, which is part of Oxford’s Biochemistry Department, to offer DNA sample processing, genotyping, mRNA expression analysis, and microbial clone management.
Geneservice said the Biochemistry Department’s staff will remain at the lab but will become company employees.
Geneservice CEO Tom Weaver said in a statement that the company plans to expand the department and is planning to expand the lab “into new premises.” He did not elaborate.
Weaver said the company expects this agreement to be “the first of several similar alliances around the UK.”

Group Led by Broad Institute Finishes Early Draft of Horse Genome
Researchers led by the Broad Institute of MIT and Harvard have completed an initial draft of the horse genome, researchers affiliated with the Horse Genome Sequencing Project said last week.
The HGSP said it has completed a 6.8X coverage of the horse’s roughly 2.7 billion base pairs.
The HGSP also generated a map of genetic variations found in the genome using DNA samples from old and new breeds such as Andalusians, Arabians, Standardbreds, and Thoroughbreds.
The map is built from 1 million SNPs that the HGSP expects scientists to use for considering physical contributions from breed to breed and to assess disease susceptibility.
The sequencing began in 2006 and is a component of the Horse Genome Project, a 10-year international collaboration funded with $15 million from the National Human Genome Research Institute.
The HGSP said it plans to publish an analysis of the horse genome that will offer more information about its findings.

Illumina to Offer $350M in Convertible Notes; Will Use $202M to Repurchase Shares
Illumina plans to sell $350 million in convertible senior notes to help pay for corporate expenses, the company said this week.
The convertible senior notes will pay interest semiannually at a rate of 0.625 percent per year and are due in 2014. Illumina also granted the initial purchasers a 30-day option to purchase up to $50 million of additional notes to cover overallotments.
The offering is scheduled to close on Feb. 16, 2007.
Illumina estimates that the net proceeds from the offering will be around $341 million after deducting fees and expenses. The company said it expects to use around $202 million of the proceeds to purchase shares of its common stock in privately negotiated transactions.
Around $41 million of the proceeds will be used to fund convertible note hedge transactions and warrant transactions.
The company intends to use the balance of the net proceeds for other general corporate purposes, “which may include acquisitions and additional purchases of our common stock,” Illumina said in a statement.

Gene-IT Joins BioIT Alliance
DNA sequence analysis firm Gene-IT said this week that it has joined the BioIT Alliance, a group of biotech and IT companies working with Microsoft to advance biomedical information technology.
Gene-IT president and CEO Ronald Ranauro said the biomedical industry "has long needed more conceptual and technological advances along collaborative lines, and we feel that the Alliance is an excellent initiative in this direction."
Other BioIT Alliance members include Applied Biosystems, Thermo Fisher Scientific, Affymetrix, Agilent, and other biomedical informatics, tools, and services companies.

Environmental Mold-Testing Company SanAir Buys ABI 3130 Sequencer
Environmental-testing lab SanAir Technologies last week said it has purchased an Applied Biosystems' 3130 DNA sequencer for use in detecting environmentally harmful microorganisms.
The company, located near Richmond, Va., develops and performs tests for potentially harmful molds and bacteria. It said it plans to use the sequencer in addition to its current methods.
The purchase is the company’s first foray into DNA sequencing. SanAir president, Tom McGlynn, said in a statement that the company has “embarked on a dual approach in the identification of both bacteria and mold to the genus and species level. Not only do our degreed analysts use culture, sero-grouping and biochemical testing, they also employ DNA sequencing as the objective protocol for identification.”

ABI Licenses GE Healthcare's IP Covering Biomagnetic Isolation of DNA
GE Healthcare said last week that Applied Biosystems has licensed its patents covering biomagnetic isolation of nucleic acids.
Under the agreement, ABI has access to the magnetic separation IP to isolate and purify nucleic acids through the duration of the patents, GE Healthcare said.
This technology is used with DNA and RNA from lab and clinical samples. GE Healthcare said it offers higher yields and does not clog, which can be a drawback for filter-based isolation methods.
GE Healthcare said ABI plans to use the separation protocol with its MagMax isolation kits.
Financial terms of the agreement were not disclosed.

Qiagen Acquires Rights to RT-PCR for Use in IVDs
Qiagen said this week that it has acquired licenses from Roche and Ortho Clinical Diagnostics for the rights to use RT-PCR in in vitro diagnostics.
Qiagen said that the two separate agreements provide it with patent and marketing rights that were not covered by its original licensing agreements with Roche.
The agreements extend Qiagen’s technology portfolio to encompass “assay technologies and diagnostic tests using almost any basic PCR patent and real-time PCR patent rights related to reagents and methods for practicing PCR and real-time PCR for IVD,” the company said in a statement.
Qiagen said it now holds licenses for all of Roche’s RT-PCR patents and pending patent applications. The agreement with Roche also includes “additional enzyme patent rights, further PCR improvement patent rights, and pathogen specific patent rights,” the company said.
The license from Ortho Clinical Diagnostics covers patents related to a taq-polymerase antibody-mediated method used to accelerate the activation of PCR enzymes. The license gives Qiagen the right to use this so-called “Hot-Start” technology in the fields of research, applied testing, and IVDs.

The Scan

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Domestication Linked to Nervous System Genes in Inbred Mouse Strains

Researchers highlighted more than 300 positively selected genes in domesticated mice, including genes linked to nervous system function or behavior in Genome Biology.

ALS Genetic Testing May Be Informative Across Age Ranges, Study Finds

Researchers in the journal Brain identified clinically actionable variants in a significant subset of older ALS patients, prompting them to point to the potential benefits of broader test use.