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Short Reads: Mar 24, 2009

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Life Tech Plans to Launch SOLiD 4 in Early 2010

Life Technologies plans to release a new version of its Applied Biosystems SOLiD sequencing platform — tentatively called SOLiD 4 — early next year, In Sequence has learned.

A Life Tech spokesperson told In Sequence last week that the company is not yet disclosing the features of SOLiD 4, "other than to say that we will continue to pursue our advantages in providing the most accurate data via our two-base encoding, and the most throughput via improved bead density and other imaging techniques."

The planned SOLiD update was reported in a research note by Leerink Swann analyst Isaac Ro last week. In his note, he mentioned that in a meeting, Life Tech "management also stated that a new version of [the SOLiD] platform is due to be released in February 2010 and should offer further cost reductions."


Life Technologies Cuts Staff at Foster City

Life Technologies has cut 75 positions at Applied Biosystems' facilities in Foster City, Calif., and will cut a further 40 employees in the summer, according to a notice posted on the website of California's Employment Development Department.

The first group of cuts occurred in January, according to the website. Such job cuts are not unexpected in the wake of the roughly $5 billion merger of Invitrogen and ABI to form Life Technologies. Invitrogen said in October that it expects $80 million in synergies, mostly from cost savings, in the first year after closing the deal.

"The company stated that part of those synergies would be achieved through corporate overhead reductions, which unfortunately does include the elimination of redundant positions between the two legacy companies," the firm said in a statement to In Sequence's sister publication, GenomeWeb Daily News, last week. "Life Technologies cannot confirm the number or timing of those workforce reductions," it added.

The firm has already closed ABI's corporate offices in Norwalk, Conn., as part of efforts to eliminate redundant operations.

Life Technologies employs around 9,500 people worldwide.


JCVI Starts New Sorcerer II Expedition; Plans to Test Life Tech's Single-Molecule Sequencer

The J. Craig Venter Institute said last week that it is launching a new Sorcerer II Expedition, called the J. Robert Beyster and Life Technologies 2009-2010 Research Voyage.

On the two-year voyage, a team of scientists led by Craig Venter will sample microbial diversity in the Baltic, Mediterranean, and Black Seas — areas of interest because they are isolated from the major oceans and expected to contain unique microbial communities.

Sorcerer II left the port of San Diego last week. From there it will travel south along the Mexican coast, through the Panama Canal, to Florida, Bermuda, and the Azores before landing at Plymouth, UK. From there, the ship will head to Stockholm, Sweden. Baltic Sea sampling is scheduled for this summer, while Mediterranean and Black Sea samples are to be collected in 2010.

During the sampling phases of the journey, researchers collect between 200 and 400 liters of water every 200 miles or so. This water is filtered to catch microorganisms of various sizes, which are then frozen and shipped to JCVI laboratories in Maryland and California for genomic DNA analysis.

Some of the samples will be analyzed using "new innovative technologies, such as single-molecule DNA sequencing" from Life Technologies, Greg Lucier, the company's chairman and CEO, said in a statement (see article in this issue).

Venter noted in the same statement that Sorcerer II expeditions so far have turned up roughly 20 million new genes and thousands of previously unidentified protein families.

"[W]e are excited to now sample in new environments on this journey to the Baltic, Black, and Mediterranean [seas]," Venter said. "We are confident that this voyage will yield important insights into the microbial universe there and will add to the growing catalogue of microbes and genes my team has been compiling through the Sorcerer II Expedition."

The trip is funded by the Beyster Family Foundation Fund of the San Diego Foundation along with matching grants from Life Technologies and anonymous donors. The anticipated cost of the voyage was not disclosed.


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BioNanomatrix Gets $2.1M Grant to Develop Single Molecule Analyzer

BioNanomatrix has received a Phase II grant in the amount of nearly $2.1 million from the National Human Genome Research Institute to support further development of the firm's single-molecule nanoscale whole-genome analyzer.

The 30-month Small Business Innovation Research award was made under the BioEngineering Nanotechnology Initiative, which is intended to support the development of nanotechnologies for biomedicine applications. The newest grant follows completion of a similar Phase I grant for initial development of the technology.

"BioNanomatrix's nanoscale technology is intended to allow researchers to directly image and analyze very long, individual intact strands of DNA at the single-molecule level with very high resolution, yielding a great deal of genomic information that is not currently accessible," said BioNanomatrix President and CEO Michael Boyce-Jacino in a statement. "We believe our technology has the potential to increase the utility of whole-genome imaging and analysis for a wide range of research and diagnostic applications, and we are delighted at NHGRI's renewed vote of confidence in the potential of our program."

Philadelphia-based BioNanomatrix also is working with Complete Genomics on a DNA sequencer that they hope will achieve the "$100 genome." The firms received $8.8 million in funding from the National Institute of Standards and Technology in October 2007 to support efforts to combine BioNanomatrix's nanofluidic DNA imaging device and Complete Genomics' sequencing chemistry.


Life Technologies, Nanosys in Quantum Dot Licensing Deal

Life Technologies and Nanosys have entered into a cross-licensing deal to share rights to intellectual property covering fluorescent nanocrystals, also called quantum dots.

The firms said that the deal is expected to result in the development of new tools to detect counterfeit products worldwide. The firms said that between them they have over 270 patents and patent applications, including 84 issued US patents, for using fluorescent nanocrystals.

"Life Technologies' quantum dots are currently being used in life science research and pathology, but there are vast opportunities to use them in a wide variety of applications," Paul Grossman, senior VP of corporate development and strategy for Life Technologies, said in a statement. "Our new partnership with Nanosys will allow both companies to expand the opportunities for our combined technologies, and further the reach of Life Technologies into the applied markets."

The firms estimated that the global counterfeit good trade, excluding counterfeit money, is around $1 trillion annually. They said that the quantum dot technology will enable manufacturers to trace the source of their materials and manage and track product shipments.

Financial and further terms of the licensing agreement were not disclosed.

In 2005, Invitrogen, now a division of Life Technologies, purchased Quantum Dot, a firm that makes QDot semiconductor nanocrystals. Invitrogen said at the time that the particles demonstrate unique optical properties, such as photostability, narrow emission spectra, and brightness, and can be used in a wide range of applications in life-science research, including gene expression and proteomics. The company also plans to use quantum dots for the single-molecule sequencing platform it is developing (see article in this issue).


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NHGRI Awards Grant to Geospiza-HDF Collaboration

Genetic analysis software developer Geospiza and the HDF Group, a not-for-profit, open-source organization aimed at supporting the hierarchical data format, or HDF, said last week that they have received a Phase II Small Business Technology Transfer grant from the National Human Genome Research Institute.

Geospiza and the HDF Group are collaborating to develop scalable bioinformatics technologies based on a version of the HDF5 format called "BioHDF." These technologies are intended to support various high-throughput sequencing applications such as digital gene expression, small RNA, copy number variation, and re-sequencing analyses.

By combining their experience in genetic analysis and scalable scientific data technologies, the collaborators plan to tackle data management issues related to existing and future DNA sequencing platforms. In particular, the partners intend to create new data organization, storage, analysis, and access technologies, reduce space requirements, and enable computational access to data supporting high-performance computing.

"It is clear that second- and third-generation sequencing technologies will continue to push the limits of computing technology," Geospiza Founder and Chief Scientific Officer Todd Smith said in a statement. "BioHDF will give us the needed foundation to rapidly provide innovative solutions to our customers and to the community as new opportunities to advance science emerge."


Pressure Bio Lands SBIR Contract

Pressure BioSciences has been awarded a grant of $110,000 from the National Institutes of Health for its pressure cycling technology, the company said last week.

The Small Business Innovation Research grant, from the National Institute on Allergy and Infectious Diseases, funds development of sample preparation technology using pressure for microbiome studies and for clinical diagnostics. The company said that the research calls for PCT to be used to prepare all of the samples for the study.

If PCT is successful in those studies, the company said, it hopes to reel in a Phase II grant, which would likely be for around $1 million over two years.

"This SBIR grant will help fund the development of novel, PCT-based sample preparation methods for an important NIH initiative," PBI VP of Marketing Nate Lawrence said in a statement.

If the PCT-based methods help in improving microbial analysis, Lawrence said, "We believe that PCT products could be adopted by many laboratories involved in the Human Microbiome Project, as well as others working in the area of microbe detection and analysis. We further believe that the development of rapid, PCT-based microbiological sample preparation methods could potentially open up significant clinical and research market opportunities for PBI."


Cofactor Genomics to Donate 700 Mb of Sequencing for Classroom Project

Sequencing service provider Cofactor Genomics is donating a free 700-megabase sequencing project, using either the Illumina Genome Analyzer or the SOLiD 3 platform, for a science classroom.

The St. Louis-based company said on its website that it will ask course organizers for a one-page proposal, including an explanation of how their project could be used as an "effective teaching aid" in their class.

Cofactor plans to choose the winning project in May. The award will include experimental design, sample QC, library construction, sequencing, and computational analysis.


Ambry Genetics Offers NimbleGen Sequence Capture for Illumina, 454 Platforms

Ambry Genetics said last week that it is now offering a Roche/NimbleGen sequence capture service for the Illumina Genome Analyzer or Roche/454 GS FLX sequencing platforms.

Customers can choose between custom 385K or pre-designed 2.1M NimbleGen arrays, and can request sequencing of the enriched material by Ambry on its Illumina GA II.

Ambry Genetics, based in Aliso Viejo, Calif., is a CAP-accredited, CLIA-certified commercial clinical laboratory that was founded in 2000.


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Affymetrix Transfers Ownership of CLIA Lab to Navigenics

Affymetrix recently decided to hand over ownership of its Clinical Laboratory Improvement Amendments-compliant lab to direct-to-customer genetic-testing firm Navigenics as part of a strategy to refocus on being a platform provider.

The move comes as an increasing number of drug makers outsource their molecular diagnostic research needs to CLIA labs.

An Affymetrix spokesperson told In Sequence's sister publication BioArray News last week that Affy transferred ownership of its 10,000-square-foot Clinical Services Lab in Sacramento, Calif., to Redwoods Shores, Calif.-based Navigenics earlier this year.

Navigenics' DTC service uses a custom version of Affy's SNP 6.0 genotyping array, and the two firms have close ties. Navigenics' Chief Operating Officer Sean George was formerly vice president of marketing at Affy; General Counsel Stephen Moore previously held the same position at Affy; and board member Sue Siegel, who is now managing the firm, was formerly president at Affy.

The lab was CLIA compliant in April 2007 when Affy began to offer clinical trial and patient testing via gene expression monitoring, genotyping, chromosomal copy-number analysis, and other molecular diagnostics.

According to the Affy spokeperson, in selling ACSL to Navigenics, the Santa Clara-based array vendor wanted to return its focus to its "core business objective of being an enabler for the broad adoption of microarrays across all genetic analysis markets, including CLIA lab services, to help all individuals benefit from understanding their own DNA.

For its part, Navigenics decided to acquire the clinical lab because the company has seen an increase in the volume of orders for its genetic screening service, according to Vance Vanier, Navigenics' chief medical officer.

The increase in testing volume may be attributed to the launch of a cheaper service offering, a marketing partnerships with a physicians group called MDVIP, and a research collaboration with The Scripps Translational Science Institute, Affymetrix, and Microsoft to genetically screen 10,000 participants.

By Justin Petrone; originally published on GenomeWeb Daily News


Enzymatics Gets ISO Certifications

Molecular biology enzymes manufacturer Enzymatics said last week that it has received ISO 13485:2003 and 9001:2000 standards certification from TÜV SÜD America.

The Beverly, Mass.-based firm makes proteins that are used for research and diagnostics purposes with a focus on nucleic acid detection technologies. It provides enzymes and buffer solutions for the Polonator, a low-cost sequencing system developed by George Church's group at Harvard Medical School and sold by the Dover unit of Danaher-Motion.

ISO 13485:2003 is a globally recognized standard that specifies requirements for a quality management system and is intended to facilitate harmonized medical device regulatory requirements for quality management systems. ISO 9001:2000 shares significant overlap with 13485:2003, while including a focus on continuous improvement and customer satisfaction, said Enzymatics.


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NY State Regulating DTC Genomics Firms as Labs

Despite claims by direct-to-consumer genomics companies that they should not be regulated as clinical laboratories because they provide educational information about genetic risk, the New York State Department of Health is regulating such facilities as laboratories, according to a state health official.

"We believe it's consistent to say that these entities that will obtain raw data from the analytical testing facility, and generate a report that would go to the ordering practitioner, are a laboratory," Ann Willey, director of the New York State Department of Health Office of Laboratory Policy, said at a meeting of the HHS Secretary's Advisory Committee on Genetics, Health, and Society last week in Washington, DC.

"We consider these data-management facilities no different than laboratories," Willey added in her presentation updating the advisory committee on New York's stance on DTC consumer genomics firms.

Willey's comments come nearly one year after the New York State Department of Health sent letters to 23 consumer genomics and genetic testing firms saying they must obtain a permit and that a state-licensed physician must order the tests.

Regulation of DTC consumer genomics firms is a new and evolving area for state and federal regulation. Most states have limited or no guidelines on DTC marketing of genetic tests. The US Food and Drug Administration has said it is watching the burgeoning industry closely, but has yet to issue federal guidance on the sector.

New York State regulations for laboratories operating within the state are considered within the industry to be more stringent than CLIA. According to industry observers, New York regulators' thinking on DTC genetic testing can have broad impact on the regulations in other states. To date, however, the state's Department of Health has not disclosed much detail regarding its thinking in this area.

In the absence of federal guidelines on DTC genetic testing, many consumer genomics companies have argued that they should not be regulated as providers of medical tests because the genetic risk information they sell to consumers is for education only and not meant to be used to make medical decisions.

However, one of these shops, 23andMe, recently began to include BRCA testing in its offering — a test that most physicians believe carries serious clinical implications. Another consumer genomics firm, Navigenics, began marketing a version of its service to doctors in an effort to incorporate genetic risk data into individuals' annual physical exams.

Currently, New York State law requires that all laboratories testing human specimens must first obtain a permit in order to operate in the state. The law also states that labs can only order tests at the request of a state-licensed physician, who is not employed or financially compensated by the company that will perform the test.

Several of the consumer genomics firms working in states that allow DTC marketing of genetic tests employ physicians licensed in that state to order tests for their customers. This practice violates anti-kickback statues in New York restricting labs from offering physicians who order tests monetary payments or other kinds of incentives.

Willey also stressed during her talk that New York's statutes governing how labs may test human specimens also apply to companies collecting samples within the state's geographic borders.

This has implications for 23andMe's highly publicized "spit party" last year, in which the company collected saliva samples from celebrities in order to raise awareness of its genetic-screening service.

"We have told 23andMe repeatedly that without a NY license, any samples collected in the state have to be destroyed. We've been assured that this has been done," Willey said. "Of course, we've not confirmed that the samples have been incinerated."

By Turna Ray; originally published on GenomeWeb Daily News


'Footprint' Approach Maps Regulatory Protein Binding

A team of researchers from the University of Washington has developed a technique for mapping regulatory protein occupancy across the genome, without prior knowledge of the specific proteins involved.

The approach, which they dubbed "digital genomic footprinting," relies on a combination of DNase I cleavage and high-throughput sequencing. The team applied its genomic footprinting approach to the model organism Saccharomyces cerevisiae, identifying thousands of proposed protein binding regions in the genome.

The research, which appeared online last week in Nature Methods, suggests that digital genomic footprinting can be used — along with gene expression data and information from chromatin immunoprecipitation experiments — to characterize regulatory protein functions and binding patterns.

"Whereas ChIP requires that each DNA-binding protein first be interrogated by genome-wide location analysis, and can be carried out for only one protein at a time, DNase I footprinting addresses all factors simultaneously in their native state and detects regions of direct binding with nucleotide precision," the authors explained.

The researchers argued that the digital genomic footprinting approach could be applied to a variety of cellular conditions — for instance, to look at how regulatory protein occupancy in the genome changes with different growth conditions or cell cycle stages.

In addition, they noted, digital genomic footprinting should prove useful not only for expanding researchers' understanding of well-studied genomes but also as a "powerful tool for annotation of the genomes of diverse organisms, about which little is known beyond the genome sequence itself."

The Scan

Push Toward Approval

The Wall Street Journal reports the US Food and Drug Administration is under pressure to grant full approval to SARS-CoV-2 vaccines.

Deer Exposure

About 40 percent of deer in a handful of US states carry antibodies to SARS-CoV-2, according to Nature News.

Millions But Not Enough

NPR reports the US is set to send 110 million SARS-CoV-2 vaccine doses abroad, but that billions are needed.

PNAS Papers on CRISPR-Edited Cancer Models, Multiple Sclerosis Neuroinflammation, Parasitic Wasps

In PNAS this week: gene-editing approach for developing cancer models, role of extracellular proteins in multiple sclerosis, and more.