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Pacific Biosciences, LightSpeed Genomics, Affymetrix, NSF, Cold Spring Harbor Laboratory, 454 Life Sciences, Roche Diagnostics, University of Miami

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Pacific Biosciences Publishes Papers in PNAS, Journal of Applied Physics; Re-Launches Website
 
Researchers at Pacific Biosciences published an article in the Proceedings of the National Academy of Sciences last week and another one in the Journal of Applied Physics this week that outline parts of its sequencing technology.
 
In the PNAS study, the scientists showed that individual DNA polymerase molecules immobilized in nanostructures called zero-mode waveguides in high-density arrays were able to synthesize thousands of bases of DNA.
 
These results “support the application of immobilized single DNA polymerase in ZMW arrays for long-read-length DNA sequencing,” the authors write.
 
On its recently relaunched website, Pacific provides a description of its single-molecule real-time SMRT sequencing technology.
 
According to the description, DNA sequencing is performed on chips, each containing several thousand ZMWs, holes tens of nanometers in diameter with a detection volume of 20 zeptoliters.
 
Within each of these chambers, a single DNA polymerase molecule is attached to the bottom surface. Scientists then add phospholinked nucleotides at high concentrations, each type labeled with a different fluorophore. 
 
When the polymerase incorporates a nucleotide, it emits fluorescent light that can be detected. The polymerase then cleaves off the fluorophore, which diffuses out of the detection volume, and the process repeats at a speed of tens of nucleotides per seconds.
 
“Researchers at Pacific Biosciences have demonstrated this approach has the capability to produce reads thousands of nucleotides in length,” according to the website.
 

 
LightSpeed Genomics to Develop High-Speed DNA Sequencer
 
LightSpeed Genomics, based in Sunnyvale, Calif., is developing a high-speed DNA sequencing platform that “will allow human genome sequencing to be performed more quickly and less expensively than ever before,” according to the company’s website.
 
LightSpeed founder and CEO Josh Ryu told In Sequence this week that the company is currently in stealth mode and not yet ready to talk about its plans. Ryu, who holds a PhD from the Massachusetts Institute of Technology, is a former Affymetrix staff scientist. Stanley Hong, a former colleague of Ryu from MIT, is a co-founder and chief technology officer of the company.
 
According to a press release from the Kauffman Foundation last week, LightSpeed was “spun out of a research program” at MIT. Bo Fishback, another company co-founder, recently became vice president of entrepreneurship at the Kauffman Foundation (see Paired Ends in this issue).
 
Formerly called Solametrix, LightSpeed Genomics received an undisclosed amount of funding from Rockhill Partners and other angel investors in March 2007.
 

 
Affymetrix Says New Products Will Include Sequencing Technology
 
Affymetrix said last week that it plans to incorporate its next-generation sequencing technology into several products.
 
During the company’s fourth-quarter earnings call last week, Affymetrix CEO Stephen Fodor reiterated that the company will first apply its array-based next-generation sequencing technology to screen approximately 1,100 individuals — an “extended human diversity panel” — for 12.5 million markers currently found in the dbSNP database. The company wants to use the resulting database and its sequencing technology to design next-generation genotyping products, he said.
 
These products “will include whole-genome applications of the sequencing method as well as targeted genotyping applications of this sequencing method,” he said. He added that they will fit on the company’s GCS 3000 instrument, though “we can package these in many different types of formats.”
 
Fodor said Affymetrix has plans “for some new presentations of this technology, both from a sequencing perspective and from an instrumentation perspective” that it will make public later this year.
 
The company previously said that it plans to use enzymes and reagents for its sequencing technology from USB, which Affy acquired for approximately $75 million in cash last week.
 
Affymetrix reported fourth-quarter revenues of $107.6 million, a 3.3 percent increase over revenues of $104.2 million in the fourth quarter of 2006.
 
It posted a net income of $12.8 million, or $.17 per share, 47 percent higher than in the year-ago fourth quarter.
 
The firm’s R&D spending dropped 10.2 percent year over year to $17.6 million from $19.6 million.
 
Affymetrix finished the year with cash and cash equivalents of $288.6 million.
 

 
NSF Awards $50M to Five Institutes Under Computational Plant Biology Initiative
 
The National Science Foundation said last week it has granted $50 million to create a national cyberinfrastructure center for plant biology that will employ genomics and genetics sciences, along with biological and computational science.   
 
The University of Arizona's BIO5 Institute will lead the so-called iPlant Collaborative, and will be joined by researchers at Cold Spring Harbor Laboratory, Arizona State University, the University of North Carolina at Wilmington, and Purdue University.
 
The NSF said in a statement that the initiative will rely on information generated through the National Plant Genome Initiative, "enabling more breadth and depth of research in every aspect of plant science."
 
The research will include interdisciplinary science, “for instance, plant genome experts working side-by-side with mathematicians and statisticians to interpret the results of innovative microarray scans of genomic mutations,” CSHL said in a statement.
 
The five-year iPlant Collaborative potentially renewable for a second five years and a total of $100 million, NSF said.
 

 
Cold Spring Harbor, 454 Life Sciences Partner to Study Tasmanian Devil Disease
 
Roche subsidiary 454 Life Sciences is collaborating with researchers at Cold Spring Harbor Laboratory to sequence parts of the genome of the Tasmanian devil.
 
The CSHL project, led by Tasmanian native Elizabeth Murchison, a post-doctoral researcher, aims to understand the genetics of a fatal cancer ravaging wild Tasmanian devil populations. The team presented its research plan to visiting Tasmanian government officials last week. 
 
“Our efforts to sequence the devil’s genome mark the first time anyone has attempted to use the technology for exploring this particular type of cancer biology,” CSHL Research Director David Spector said in a statement. “When we have a complete view of the devil tumor genes, scientists will be able to identify the cancer-causing genes, which may lead to the development of therapies and vaccines.”
 
The CSHL group is using several approaches to try to identify the devil tumor’s tissue of origin and to understand how it is controlled by specific oncogenes or tumor suppressor genes. They also hope to use miRNA analysis to compare the tumor with the animal’s normal tissues.
 
The team is currently sequencing full-length cDNAs from one animal’s tumor and host tissue in an effort to map all the genes expressed in the tumor using 454 Life Sciences’ sequencing technology. They also hope to eventually establish a cDNA library so they can compare gene expression in several tumors, an approach that will help them determine whether the disease is evolving.
 
454 Life Sciences is contributing personnel and expertise to the studies. CSHL researchers are currently isolating devil tumor RNA and sending it to the company’s lab for analysis.
 
—Abridged version of an article from GenomeWeb Daily News by Andrea Anderson
 

 
Roche Diagnostics' Q4 Revenues Rise 8.4 Percent; MDx Sales Dip in 2007
 
Roche reported last week that its diagnostics division had fourth-quarter 2007 revenues of 2.5 billion Swiss francs ($2.3 billion), an 8.4-percent gain on revenues of CHF 2.3 billion in the fourth quarter of 2006.
 
Roche reported strong growth for its Professional Diagnostics and Applied Science businesses, while sales for its molecular diagnostics products slipped 2 percent to CHF 1.15 billion for the year.
 
Sales for the Applied Science business rose 11 percent year over year to CHF 692 million. That business has been boosted by the acquisitions over the past year of 454 Life Sciences, BioVeris, and NimbleGen Systems.
 
Roche said the key growth drivers in Applied Science were its LightCycler 480 instrument; the Genome Sequencer FLX; and research reagents.
 

 
Florida Pumps $80M into Miami Human Genomics Institute
 
The state of Florida has pledged $80 million to the Miami Institute for Human Genomics at the University of Miami as part of an effort to make the university’s downtown campus “an internationally renowned scientific research powerhouse,” the university said last week.
 
The institute, which opened in November 2007 and is part of the Miller School of Medicine, is focused on genomic studies of diseases and will research Alzheimer’s and Parkinson’s disease, multiple sclerosis, macular degeneration, and cardiovascular and other common diseases.
 
IHG is supported by an initial $37 million in federal funds and an undisclosed amount from the Miller School. According to MIHG Director Margaret Pericak-Vance, much of the federal funding came from grants from the National Institutes of Health that the institute’s researchers brought with them from their previous research posts.
 
The institute also houses a Center for Genome Technology and the Morris K. Udall Parkinson Disease Research Center of Excellence.

The Scan

Billions for Antivirals

The US is putting $3.2 billion toward a program to develop antivirals to treat COVID-19 in its early stages, the Wall Street Journal reports.

NFT of the Web

Tim Berners-Lee, who developed the World Wide Web, is auctioning its original source code as a non-fungible token, Reuters reports.

23andMe on the Nasdaq

23andMe's shares rose more than 20 percent following its merger with a special purpose acquisition company, as GenomeWeb has reported.

Science Papers Present GWAS of Brain Structure, System for Controlled Gene Transfer

In Science this week: genome-wide association study ties variants to white matter stricture in the brain, and more.