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Sequenom, Nanopore, BioNanomatrix, Genetic Information Nondiscrimination Act, GATC Biotech, Celera, Atria Genetics, Mayo Clinic, Agilent, ABI, NIAID

Sequenom Licenses Nanopore Sequencing Technology from Harvard
Sequenom has exclusively licensed a readout technology for single DNA molecules that is based on simultaneous optical probing of multiple nanopores, the company said this week. Sequenom plans to develop the technology into a “third-generation” single-molecule nucleic acid analysis technology.
The technology, invented at Harvard University by Amit Meller, who is now an associate Professor at Boston University’s department of biomedical engineering , “should enable ultra-high throughput DNA analysis such as sequencing, genotyping, and RNA and epigenetic analysis on a whole genome scale,” according to the company.
Meller has been developing the technology under two advanced sequencing technology grants from the National Human Genome Research Institute (see GenomeWeb News, In Sequence’s sister publication, 8/8/2006).
Financial terms of the agreement include up-front fees, milestone payments, and royalties on future product sales.
“This technology should enable us to provide highly competitive large-scale genotyping, and RNA analysis and ultimately sequencing-based solutions to the market,” said Sequenom CEO Harry Stylli in a statement.
While the company plans to continue development of its MassArray genotyping technology, it also hopes to expand its market penetration “into the complementary whole genome analysis/single molecule sequencing markets with this potentially redefining nanopore technology,” according to Stylli.
“Near term we expect this nanopore technology to deliver large scale genotyping solutions and long term we believe it has the potential to provide a commercially viable, rapid, sub-thousand dollar human genome sequencing solution,” Stylli said.
“It is strategically important for Sequenom to be able to offer customers a cost-effective sequencing option and we do not believe the new second-generation sequencing methods will achieve the needed cost effectiveness," said Charles Cantor, Sequenom’s CSO, in a company statement.

BioNanomatrix Receives Nanofluidics Patent for Single-Molecule DNA Analysis
BioNanomatrix has received a patent for a “key element” of its whole-genome analyzer, the Philadelphia-based company said this week. The patent covers a new technique for integrating nanofluidic channels with sample delivery systems, enabling single molecules of DNA, RNA, or proteins to be separated from samples for direct imaging and analysis. The technology enables researchers to isolate and linearize several megabases of DNA for molecule-by-molecule haplotyping, mapping, and sequencing applications.
The company, a 2003 spin-out from Princeton University, has licensed the technology exclusively from Princeton, where it was developed by Han Cao, the firm’s chief scientific officer. It allows scientists to construct hundreds of thousands of enclosed, parallel nanofluidic channels on a surface, using a gradient-structured interface to guide the molecules into the nanoscale channels.
BioNanomatrix has developed this into the Nanoanalyzer, an integrated system with potential applications in diagnostics, personalized medicine, and biomedical research.

Leavitt Optimistic of GINA’s Passage by Year End Despite Holdouts
Despite a few holdouts in Congress blocking the passage of the embattled Genetic Information Nondiscrimination Act, the legislation is politically well-positioned for passage in this Congress, HHS Secretary Michael Leavitt assured participants at a conference on personalized medicine in Washington DC last week.
“We have reason to hope that the final bill can be worked out and passed in both chambers this year,” Leavitt said at the Personalized Medicine Coalition event “21st Century Medicine: Personalized and Evidence-Based.”
The bill has been passed by the House and is likely to be signed into law by President Bush, but Tom Coburn, a Republican Senator from Oklahoma, has placed a “hold” on it. The bill still needs to be considered by the Senate.
H.R. 493 would make it illegal for group health insurers to deny coverage to people based solely on a genetic predisposition to a specific disease, and would bar employers from using genetic information when making hiring, firing, job placement, or promotion decisions.
GINA was previously stalled in Congress for more than a decade. It was marked up in the House of Representatives for the first time in February, after being re-introduced on Jan. 16 by Representatives Louise Slaughter, a Democrat from New York, and Rep. Judy Biggert, a Republican from Illinois. Around 150 representatives co-sponsored the bill.
— Turna Ray, editor of Pharmacogenomics Reporter

GATC to Coordinate International Sepsis-Pathogen Dx Project
DNA sequencing company GATC Biotech said this week that it is coordinating an international effort to develop a microarray-based diagnostic test for bacterial and fungal pathogens that trigger sepsis.
GATC, based in Constance, Germany, said that it will function as the coordinating partner for the project, which includes the Fraunhofer Institute in Germany as well as the National University of Pusan and biotech company Gene In, both located in South Korea.
The German Federal Ministry of Education, Science, Research and Technology will fund part of the research, the company added.
The proposed sepsis diagnostic would “enable the immediate detection of organism-specific nucleic acid sequences, offering the advantage of reducing the time between sample collection and diagnosis, leading to a reduction in mortality rates,” the company said.

Celera to Buy Tissue Typing Company Atria Genetics for $33M
Celera said last week that it plans to acquire Atria Genetics of South San Francisco in a $33 million cash deal that is expected to add transplant-related sequencing-based testing to the company’s molecular diagnostics portfolio.
Celera expects the acquisition to close during its second fiscal quarter, which ends Dec. 31. The company expects the deal to be accretive to earnings by the second half of its 2008 fiscal year, which ends June 30, 2008.
Atria offers sequencing-based human leukocyte antigen testing to identify potential donors for bone marrow transplantations, Celera said. Since HLA genes are extremely variable, DNA sequencing represents the "gold standard" for their analysis. HLA testing, also referred to as tissue typing, is a key component in determining the compatibility between potential donors and recipients prior to transplantation.
The companies have an existing relationship: In 2004, Abbott Molecular began distributing Atria’s HLA sequencing-based tests through its alliance with Celera.
Celera’s president, Kathy Ordoñez, said the Atria acquisition “gives us direct access to this important niche market area of tissue typing in transplantation and the bone marrow registry markets.”
Celera said it will integrate Atria’s 13 employees into its ranks.

Mayo Clinic’s Minnesota Branch Lands $3M for Genomics Research
Two Minnesota foundations have awarded a total of $3 million to Mayo Clinic's Rochester branch for genomics research, the Mayo Clinic said last week.
The clinic will receive $2 million from the Curtis L. Carlson Family Foundation to endow the Carlson Family Professorship in Genomics Research and $1 million from the Nelson Family Foundation to establish the Nelson Family Genomics Research Fund.
Mayo Clinic also said it will toss another $3 million of its own funds into the genomics programs under a matching arrangement.
The foundations were created by Marilyn Carlson Nelson and her husband, Glen Nelson.

Agilent to License ABI's RT-PCR Thermal Cycler IP as Part of Settlement
Applied Biosystems and Agilent have settled their patent suit concerning real-time thermal cycler IP and have forged a licensing arrangement, ABI said last week.
Under the agreement, Agilent will license “certain Applera technology” relating to Agilent’s real-time thermal cycler instruments for research use, but not in vitro diagnostics. Agilent will also license Applera technology relating to Agilent’s PCR and real-time enzymes and kits.
The settlement lifts injunctions in Germany and the Netherlands, as well as pending cases in the US and France, and the settlement and agreement “fully resolve all pending disputes” between the companies.
The suit began in May when ABI parent Applera sued Stratagene, now part of Agilent, alleging that Stratagene's Mx3000P, Mx3005P, Mx4000P, and “certain related reagents” infringe ABI’s EU patent No. 0 872 562 B1.
Stratagene at the time claimed that ABI’s claims were “without merit” and said it intended to “vigorously defend these actions.”

NIAID, Partners Sequence Genome of Worm that Causes Elephantiasis, River Blindness
Researchers at the National Institute of Allergy and Infectious Disease, the J. Craig Venter Institute, Johns Hopkins University, and other partner institutions have completed a draft sequence of the genome of a parasitic worm that causes elephantiasis and river blindness and is common in South Asia and in Indonesia.
Brugia malayi is filarial nematode, which has four larval stages and moves through two host types, humans and mosquitoes.
The researchers sequenced roughly 90 Mb of the genome, and predicted around 11,500 protein coding genes in around 71 Mb of "robustly assembled sequence," according to a report in last week’s issue of Science.
The teams assembled scaffolds totaling around 71 Mb of data, and the researchers estimate the genome to be around 90 Mb to 95 Mb.
By comparing the Brugi malayi genome to that of the previously sequenced Caenorhabditis elegans genome, the researchers found that “despite these genes having maintained little conservation of local synteny during 350 million years of evolution, they largely remain in linkage on chromosomal units."
Analysis of the predicted proteome, the report suggests, should "offer a foundation for rational drug design" to combat the illnesses the worm causes.
While drugs are currently available to combat the worm, they "often must be taken for years, and the worms can cause massive immune reactions when they die," the authors wrote.
Also, current drugs are limited in that they "target the larvae only and do not completely kill the adult worms."

The Scan

Genetic Testing Approach Explores Origins of Blastocyst Aneuploidy

Investigators in AJHG distinguish between aneuploidy events related to meiotic missegregation in haploid cells and those involving post-zygotic mitotic errors and mosaicism.

Study Looks at Parent Uncertainties After Children's Severe Combined Immunodeficiency Diagnoses

A qualitative study in EJHG looks at personal, practical, scientific, and existential uncertainties in parents as their children go through SCID diagnoses, treatment, and post-treatment stages.

Antimicrobial Resistance Study Highlights Key Protein Domains

By screening diverse versions of an outer membrane porin protein in Vibrio cholerae, researchers in PLOS Genetics flagged protein domain regions influencing antimicrobial resistance.

Latent HIV Found in White Blood Cells of Individuals on Long-Term Treatments

Researchers in Nature Microbiology find HIV genetic material in monocyte white blood cells and in macrophages that differentiated from them in individuals on HIV-suppressive treatment.