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ABI, Agilent, NJMRC, Gen-Probe, Digene, Qiagen, Sigma-Aldrich, Affymetrix, HealthCare, Illumina, Veridex, Becton Dickinson

ABI to Accelerate Launch of Sequencer, Posts 7 Percent Revenue Gain for Q4
Applied Biosystems this week said that it is accelerating by at least three months the formal launch of its SOLiD next-generation DNA sequencer.
The company also said that fiscal fourth-quarter revenues rose 7 percent as R&D spending surged 15.6 percent and profit grew 14.5 percent. 
Tony White, CEO of ABI parent Applera, said that “based on positive [early-access] customer feedback and progress in our manufacturing process” of the SOLiD system “we are accelerating plans to expand production and commence a full commercial release in October.”
The company had originally planned to launch the tool early next year.
Total receipts for the three months ended June 30 increased to $557 million from $523 million year over year.
Revenue from the company’s DNA-sequencing segment ticked up around 1 percent to $139 million; real-time PCR and applied genomics sales rose 13 percent to $193 million; mass spectrometry revenue increased 9 percent to $146 million; core PCR and DNA-synthesis sales slipped 7 percent to $48 million; while “other” sales grew 9 percent to $32 million. 
R&D spending rose to $53.5 million from $46.3 million in the year-ago period. That increase was due to investments made in developing the SOLiD instrument, the company said. 
ABI’s profit for the fourth quarter increased to $87.8 million, or $.42 per share, from $76.7 million, or $.41 per share.
For full-year 2007, ABI had revenues of $2.09 billion, an increase of roughly 10% over fiscal 2006 revenues of $1.91 billion.
ABI said it expects “mid- to high-single-digit growth” overall for fiscal 2008, with increased revenue for both products and consumables.

Agilent Signs On Distributors for Asia-Pacific Region;
Inks Systems Biology Training Pact with NJMRC
Agilent has hired five new distributors and added two new service providers in Asia-Pacific markets, the company said this week.
Agilent said it has landed distribution agreements for its Bioanalyzer products and its GeneSpring software in Indonesia, India, Korea, Hong Kong, China, and Australia, and has added certified service providers in China and India.
Distributors include Imperial Life-Sciences, Korea Biomics, LnC Bio, Pacific Laboratory Products, and Research Biolabs. Service providers include Shanghai Bio in China and Genotypic Technology in India.
Chris Tan, Agilent’s director of genomics for the Asia Pacific region, said the area is a “strategic focus” for the company because it “has experienced double-digit growth for the last five years.”
Agilent said it plans to continue to hunt for more service provider collaborations in the region, Tan added.
Financial terms of the agreements were not released.
In a separate collaboration announced last week, Agilent Technologies and the National Jewish Medical and Research Center said they will provide educational training focused on systems biology applications.
The training programs, which will be open to the public, include e-seminars, classroom courses, and hands-on instruction on life-science hardware, the company said.
Agilent will provide a 6410 triple quadrupole liquid chromatography/mass spectrometer; a 6510 quadrupole time-of-flight LC/MS with HPLC chip technology; a 6210 TOF LC/MS with electrospray ionization; a 6340 ion trap LC/MS with HPLC chip technology; several 1200 Series HPLCs, including the Rapid Resolution LC system; a 2100 Bioanalyzer; a DNA microarray scanner with analysis software; GeneSpring GX and MS software for statistical analysis of array and mass spectrometry data; SpectrumMill software for analysis of peptides and proteins; and proteomics LC columns, including macroporous reverse phase columns for separating intact proteins and MARS immunodepletion columns for isolation of plasma proteins.
"Agilent's integrated collection of mass spectrometers, DNA microarrays, and informatics software allows us to teach coherent, comprehensive 'omics' techniques in our lab," said Nichole Reisdorph, assistant professor of immunology and director of the National Jewish mass spectrometry facility. Reisdorph will lead the training programs, Agilent said.
Reisdorph said the collaboration will allow NJMRC students to study systems biology and the “amazing answers that are now available via modern tools and techniques” without having to “combine disjointed platforms from many vendors.”
The courses include the new "Hands-on Metabolomics and Proteomics Workshop" to be held Aug. 27-31, as well as database-searching and clinical-proteomics programs.

California Court Dismisses Gen-Probe Suit Against Digene, but
Third Wave Says US District Court Takes its Side in Markman Hearing
A California court has dismissed a complaint Gen-Probe filed against Digene last year over a 2005 agreement between Gen-Probe and Roche, Digene said this week.
However, in a separate case, the US District Court for the Western District of Wisconsin agreed with Third Wave Technologies’ definitions for each of the disputed patent claims in an IP infringement suit filed against Digene, Third Wave said this week.
Gen-Probe filed the complaint in a San Diego County court in December 2006 to counter claims by Digene that its agreement concerning human papillomavirus-related materials with Roche was not legal because Gen-Probe was not part of a pre-existing cross-license agreement between Digene and Roche.
In its decision, the court also gave Gen-Probe “no option to re-file” the complaint or amend it, Digene said.
Digene claims that Gen-Probe was not a party to the 1990 cross-license agreement between Roche’s predecessor, called Institut Pasteur, and Digene’s predecessor, Life Technologies, that would grant it access to the HPV-related technology, and turned to that argument when it filed to have Gen-Probe’s claims dismissed from the San Diego Court in March. 
Digene has one HPV test that has received US Food and Drug Administration approval, and Gen-Probe is in the process of developing one.
Digene said the court decided that there is “no actual controversy between Digene and Gen-Probe.”
A separate ongoing proceeding promises to keep the HPV matter in play for now, however, as a New York-based arbitration panel last week agreed to allow Gen-Probe to join a proceeding between Digene and Roche. 
Last week, Digene said it filed for the arbitration in December 2006 claiming that Roche had transferred to Gen-Probe human papillomavirus products under “the guise of a supply and purchase agreement.”
Michael Watts, Gen-Probe’s senior director of investor relations and corporate communications, told BioCommerce Week sister publication GenomeWeb Daily News that the company filed the proceeding in December 2006 as “a parallel proceeding in case we weren’t included in the arbitration proceedings with Digene and Roche.”
“That’s really the dispute that we wanted to be a part of,” Watts added, saying that Digene requested that Gen-Probe not be included in the arbitration.
The San Diego County case “was for a summary judgment that our agreement in Roche was in fact valid,” Watts said.
Digene CEO Daryl Faulkner said in a statement his company is “very pleased with this result, and with the termination of this litigation.”
Separately, a US District Court in Wisconsin issued a claims construction opinion and order in a patent infringement case between Digene and Third Wave. According to Third Wave, the court “agreed with each and every of Third Wave’s definitions for the disputed claims terms.”
The firms have been embroiled in a suit filed by Digene and a countersuit filed by Third Wave over Digene’s patent covering its human papillomavirus molecular diagnostic test (see BioCommerce Week 4/11/2007).
Third Wave said that it plans to file a motion for summary judgment of non-infringement and invalidity in September.
“We believe the order reinforces the narrow scope of the asserted patent claims and Third Wave’s position that we do not infringe,” Kevin Conroy, president and CEO of Third Wave, said in a statement. “Today’s Markman order also strengthens our view that Digene’s suit was brought in an attempt to impede competition in the HPV testing market.”

Qiagen Nears Completion of Digene Acquisition; Signs on to
Distribute JCSG’s Protein Crystallization Screens
Qiagen this week said that its offer to buy all of Digene's outstanding shares expired on Friday night, and that it plans to continue with the acquisition by accepting tendered shares making up more than 90 percent of Digene's stock.
Qiagen said it will complete the $1.6 billion deal, without the approval of Digene's stockholders, after the acceptance of the shares.
Last week, Qiagen said that its shareholders approved the deal and that it had cleared US federal regulators' Hart-Scott-Rodino antitrust deadline.
The company expects the merger to be completed either next month or in September.
In a separate announcement last week, Qiagen said that it will distribute protein crystallization screens developed by the Joint Center for Structural Genomics.
Terms of Qiagen’s agreement with JCSG call for the company to distribute the new screens, known as the JCSG Core Suites I-IV. The company said these screens resulted from JCSG’s analysis of more than 500,000 high-throughput crystallization experiments.
"These new screens are the result of mining the vast database of crystallization experiments performed by the JCSG,” said Qiagen’s global business director of proteins Kai te Kaat.
JCSG is one of the Protein Structure Initiative’s Genomics Production Centers, and is funded by the National Institute for General Medical Sciences.
JCSG principal investigator Ian Wilson said the supplier agreement with Qiagen “enables the fruits of the NIH Protein Structure Initiative to become available to all structural biologists and allow them the opportunity to enhance their own individual success rates in protein crystallization."

Sigma-Aldrich’s Q2 Revenues Rise 13.2 Percent
Sigma-Aldrich this week reported second-quarter revenues of $507.5 million, a 13.2 percent increase over revenues of $448.5 million in the second quarter last year.
The firm’s Research Essentials unit generated revenue of $95.9 million, the Research Specialties unit had revenues of $185.6 million, the Research Biotech unit had revenues of $72.8 million, and the SAFC unit had revenues of $153.2 million.
Sigma-Aldrich posted net income of $79.7 million, or $.60 per share, compared with net income of $70.3 million, or $.52 per share, in the comparable period a year ago.
Its R&D expenses increased to $14.5 million from $13.4 million year over year.
Sigma finished the quarter with $190.1 million in cash and cash equivalents.

Affymetrix Expands Translational Research Alliance with Partners HealthCare;
CHOP to Use Affy’s New SNP Chip in Studies
Affymetrix said this week that 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.”
In a separate announcement this week, Affy said the Children's Hospital of Philadelphia will use Affymetrix’s newly released Genome-Wide Human SNP Array 6.0 in whole-genome studies aiming to identify genes responsible for cardiovascular, metabolic, and central nervous system disorders.
CHOP researchers will initially run studies on DNA taken from 7,000 individuals and plan to increase the genome-wide studies with outside collaborators. Affy’s 6.0 SNP array, launched in May, measures 1.8 million markers for genetic variations, the company said.
Hakon Hakonarson, director of CHOP’s Center for Applied Genomics, said the Affy array allows researchers to genotype “more markers at a lower cost per sample,” and it increases the chance of finding genes that are linked to diseases or to adverse drug responses.
“The results from these projects will open the door to new genetic studies and help us extend current collaborations with other investigators around the world," Hakonarson said.
Financial terms of both agreements were not released.

Illumina to Develop Custom Vascular SNP Array for Collaborators
Illumina this week said that 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 for 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 blood pressure issues, 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.

J&J’s Veridex Gets FDA OK to Sell Breast Cancer Metastasis Assay
Johnson & Johnson subsidiary Veridex said last week that the US Food and Drug Administration has cleared its RT-PCR breast cancer assay that detects the spread of breast cancer in the lymph nodes.
Detecting breast cancer in the lymph nodes may offer faster and more accurate diagnoses of the spread of the disease, thereby potentially reducing the need for additional surgeries, Veridex said.
The intra-operative test, called the GeneSearch Breast Lymph Node assay, uses real time reverse transcriptase polymerase chain reaction technology with tissue extracted from a sentinel lymph node tissue sample to detect genes indicating metastasis of breast cells in the lymph node.
Conducted on Cepheid’s SmartCycler system, the test can generate results in 35 to 40 minutes compared with the two or three days for standard tissue pathology, Veridex said.
Veridex also said the GeneSearch enables surgeons to test up to 50 percent of the sentinel node, as opposed to only 5 percent typically examined under a microscope.
The test, which the company said correctly identified 95.6 percent of patients who had metastases in their lymph nodes in clinical trials of 300 women, also can be used to make real-time decisions in the operating room about whether to remove a lymph node, and could prevent the need for a second operation in as many as 5,200 breast cancer patients in the US per year.

BD Board Authorizes Dividend, Share Repurchase
Becton Dickinson’s board of directors this week declared a quarterly dividend of $.245 per share, which will be payable on Sept. 28 to holders of record on Sept. 7.
The board also authorized the repurchase of up to 10 million BD common shares. The authorization is in addition to the roughly 1.6 million shares that remained available as of June 30 under a 10 million-share repurchase authorized in November 2005.

The Scan

Study Points to Tuberculosis Protection by Gaucher Disease Mutation

A mutation linked to Gaucher disease in the Ashkenazi Jewish population appears to boost Mycobacterium tuberculosis resistance in a zebrafish model of the lysosomal storage condition, a new PNAS study finds.

SpliceVault Portal Provides Look at RNA Splicing Changes Linked to Genetic Variants

The portal, described in Nature Genetics, houses variant-related messenger RNA splicing insights drawn from RNA sequencing data in nearly 335,700 samples — a set known as the 300K-RNA resource.

Automated Sequencing Pipeline Appears to Allow Rapid SARS-CoV-2 Lineage Detection in Nevada Study

Researchers in the Journal of Molecular Diagnostics describe and assess a Clear Labs Dx automated workflow, sequencing, and bioinformatic analysis method for quickly identifying SARS-CoV-2 lineages.

UK Team Presents Genetic, Epigenetic Sequencing Method

Using enzymatic DNA preparation steps, researchers in Nature Biotechnology develop a strategy for sequencing DNA, along with 5-methylcytosine and 5-hydroxymethylcytosine, on existing sequencers.