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ABI, US Department of Defense, SuperArray, Sigma-Aldrich, Bio-Rad, Beckman Coulter, Qiagen, Biomatrica, ITN, Sequenom, MDS Nordion, Ottawa Heart Institute

ABI Ships Next-Gen Sequencers to Early-Access Institutions
Applied Biosystems said this week that it has shipped its SOLiD next-generation sequencer to Stanford University and other research institutions through an early-access program, and said it is developing new applications for the system through collaborations with other academic institutions.
The company did not say which other institutions have plans to buy the system, which uses oligonucleotide ligation and detection for high-throughput DNA analysis.
The SOLiD system differs from polymerase sequencing approaches in that it uses stepwise ligation, ABI said. The company said the technology has applications in whole-genome sequencing, medical sequencing, genotyping, gene expression, and small RNA discovery.
ABI acquired the technology for the SOLiD system from Agencourt Personal Genomics last year. Since that time, the company said it has increased sample throughput five-fold, and has increased the base read length 66 percent.
ABI said it is developing new applications for the system through collaborations with Stanford, the Broad Institute, the Wellcome Trust Sanger Institute, Baylor College of Medicine, the Joint Genome Institute, the University of Queensland, and Washington University, "among others.”
The system offers 2-base encoding, which interrogates each base twice in order to reduce sequencing errors, and can generate more than a gigabase of useable data per run, ABI said.
Mark Stevenson, president for ABI’s molecular and cell biology division, said in a statement that the SOLiD system has "the best commercial viability among more than 40 next-generation sequencing technologies we evaluated," and that the company will continue its development collaborations to refine the system and develop new applications.
Arend Sidow, an associate professor at Stanford School of Medicine, has used the system to analyze 282 megabases of aligned sequence data, and used it to help create a high-resolution map of nucleosome positioning in C. elegans.
George Weinstock, a director at the Human Genome Sequencing Center at the Baylor College of Medicine, said in a statement that when he used the ABI system to resequence the genome of a strain of E. coli for validation assembly it identified a large duplication that was missed in earlier Sanger sequencing runs.
Weinstock said the SOLiD system "will enable us to generate highly accurate sequence data for infectious disease pathogens and other microbes."
More information on the launch can be found in this week’s issue In Sequence, a BioCommerce Week sister publication.

US Department of Defense Cancels ABI Contract
The US Department of Defense has terminated a pathogen-identification technology contract with Applied Biosystems because the company and the US Air Force could not agree on the best route for commercializing the product, ABI said last week.
The DOD awarded ABI a $24.5 million contract last August to develop a prototype system that would identify infectious diseases for epidemiological and biosecurity purposes.
ABI said on Friday that it had successfully completed all technical milestones for the contract, but that it was unable to agree with the USAF on “an approach for further development and commercialization of an instrument” based on an ABI prototype.
ABI said it anticipates “no material financial impact” from the cancellation of the contract and expects to continue developing pathogen-detection technology for biosecurity applications.

SuperArray Licenses ABI’s PCR Technologies
SuperArray Bioscience has licensed PCR and real-time PCR technologies from Applied Biosystems to develop and market PCR and related reagents, SuperArray said this week.
Under the non-exclusive agreement, SuperArray said it will market reagents and assay kits for PCR and real-time PCR that use ABI’s SYBR Green and probe-based methods, and will develop real-time PCR reagents and technologies that it will market to researchers.  
SuperArray President Li Shen said in a statement that the combination of qRT-PCR with SuperArray’s coverage of human, mouse, and rat genes will help researchers “unveil important biomolecular networks of genes.”
Financial terms of the agreement were not released.

Sigma-Aldrich Launches AQUA Peptide Partnership Program
Sigma-Aldrich this week said that proteomic researchers ordering custom absolute quantitation peptides from the company will be invited to join its newly formed AQUA Peptide Partnership Program.
In addition, AQUA peptide sequences will be added to Sigma-Aldrich's growing AQUA Peptide Library, and contributors will receive partnership pricing on their custom orders, the company said.
The AQUA Peptide Library, initially developed in collaboration with the Protein Quantitation Consortium, will contain hundreds of AQUA Peptides, Sigma said.
Sigma-Aldrich said the AQUA initiative “enables focused, quantitative mass spectrometric studies” of protein biomarkers and amino acids.
The company said the technique also allows researchers to use mass spectrometry to validate gene silencing at the protein level.
The program is a response to “the need within the proteomics community for a sizable library of stable-isotope labeled tryptic peptides,” Jennifer Williams, Sigma-Aldrich’s quantitative proteomics product manager, said in a statement.

Bio-Rad, Beckman Coulter Expand Immunodiagnostics Alliance
Bio-Rad Laboratories and Beckman Coulter have extended by eight years an alliance to develop and manufacture immunodiagnostic products that test for viral and infectious disease, Bio-Rad said last week.
Under the new agreement, Bio-Rad said it will develop new blood-based immunoassays, including tests for hepatitis B and HIV, for Beckman’s UniCel and Access systems.
The company said some of these assays will test for chronic hepatitis or active infection, and that it plans to develop a next-generation HIV assay to detect the virus.
Financial terms of the extended agreement were not disclosed.

Credit Agency Raises Beckman Coulter Outlook
Credit-rating firm Fitch Ratings last week raised its outlook for Beckman Coulter to “stable” from “negative,” largely in response to Beckman’s decision to step away from a bidding war with Inverness Medical Innovations over the firms' intent to acquire Biosite.
Fitch had lowered Beckman's credit rating in late March, just after Beckman disclosed its intent to buy the diagnostics company for $85 a share.
But Fitch’s analysts said Beckman showed “financial discipline by walking away from the transaction” as the price rose with Inverness’ rival offers.  
Fitch also said that it is “concerned” with the company’s recent shareholder payout dividend and stock buybacks.

Qiagen to Distribute Biomatrica’s DNA-Storage Technology
Qiagen said last week that it will market and distribute Biomatrica’s room temperature DNA-storage technology.
Under the agreement, Qiagen will pay Biomatrica an up-front fee, followed by development milestone payments, commission, and royalties.
Biomatrica’s sample-storage system uses its SampleMatrix technology, which forms a protective seal around biomolecules. The samples are accessed through rehydration, the company said.
Biomatrica also offers sample-management software that can be used in low- and high-throughput research, and with biobanks.
Qiagen said the SampleMatrix technology is “highly synergistic” with its own sample-prep technology and is usable with its PCR-based genotyping and molecular testing products, and for comparative genomic studies.
The company said it expects to expand the exclusive agreement in the future to include Biomatrica’s technology to stabilize, ship, and store DNA molecules in blood and buccal-swab samples.
Financial details of the agreement were not released.

ITN to Use Sequenom’s MassArray for Gene-Expression Projects
The Immune Tolerance Network will use Sequenom’s MassArray technology and services for quantitative gene expression projects, the company said last week.
The ITN, based out of the University of California, San Francisco, is a collaboration focused on developing, implementing, and soliciting assays and clinical strategies for tolerance studies of kidney, liver, and islet transplants, autoimmune diseases, allergy, and asthma.
Funding for the ITN comes from the National Institute of Allergy and Infectious Diseases and the National Institute of Diabetes and Digestive and Kidney Diseases.
Financial terms of the agreement were not released.

MDS Nordion, Ottawa Heart Institute to Open Molecular ImagingCenter of Excellence
MDS Nordion, a unit of MDS, said this week that it is collaborating with the University of Ottawa Heart Institute to create a molecular imaging center of excellence focused on cardiovascular research.
The center is set to open later this year on the heart institute’s campus and will feature MDS Nordion’s molecular imaging technologies. The firm expects to invest $2.2 million in the new center.
MDS Nordion also said that it will offer molecular imaging services to large pharmaceutical companies.

The Scan

Genetic Risk Factors for Hypertension Can Help Identify Those at Risk for Cardiovascular Disease

Genetically predicted high blood pressure risk is also associated with increased cardiovascular disease risk, a new JAMA Cardiology study says.

Circulating Tumor DNA Linked to Post-Treatment Relapse in Breast Cancer

Post-treatment detection of circulating tumor DNA may identify breast cancer patients who are more likely to relapse, a new JCO Precision Oncology study finds.

Genetics Influence Level of Depression Tied to Trauma Exposure, Study Finds

Researchers examine the interplay of trauma, genetics, and major depressive disorder in JAMA Psychiatry.

UCLA Team Reports Cost-Effective Liquid Biopsy Approach for Cancer Detection

The researchers report in Nature Communications that their liquid biopsy approach has high specificity in detecting all- and early-stage cancers.