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PacBio to Expand Apps, Offer Partners Early Access

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Pacific Biosciences plans to focus on cancer and infectious diseases as initial application areas for its single-molecule real-time sequencing platform, noting that these areas are best suited to take advantage of the system's long reads and short cycle time.

In preparation for the full commercial launch of its instrument during the second half of 2010, the company has begun to build a sales force, and to scale up in the areas of manufacturing and operations.

PacBio is also working on additional applications for its SMRT analysis platform, to be introduced over time, including methylation sequencing, direct RNA sequencing, and protein translation.

The firm further disclosed that it is collaborating with six early-access customers, including Monsanto and the Scripps Institute, on a variety of sequencing projects. It will soon finalize the list of institutions that will receive an early commercial version of its SMRT sequencer during the first half of next year, which will likely include Monsanto and large academic genome centers.

At the UBS Global Life Sciences conference in September, PacBio CEO Hugh Martin said that the platform's long reads — expected to be at least 1,500 bases at launch next year — are especially sought after by cancer researchers, and its short run time of 15 minutes makes it attractive for infectious disease applications that require a fast answer.

At the moment, Martin said, the company has six collaborations underway that cover a variety of sequencing projects, including candidate variant discovery, agricultural biology, medical sequencing for cancer, and infectious diseases. Collaborators include three genome centers, two academic centers, and Monsanto, an investor in PacBio's last funding round.

Also among the collaborators is Nicholas Schork's team at the Scripps Institute in San Diego, which uses PacBio data to study drug-resistant bacteria, according to PacBio Vice President of Marketing Martha Trela.

— Julia Karow

Sequencing Notes

Helicos BioSciences has demonstrated that its platform can be used to directly sequence single molecules of RNA without prior conversion to cDNA, a capability the company says could have advantages for analyzing small amounts of RNA or short RNAs and for providing unbiased sampling of transcriptomes. The paper was published in Nature this fall.

SAIC-Frederick and Roche Applied Science will collaborate to test Roche's sequence capture and sequencing technologies for use in research projects for the National Cancer Institute. SAIC-Frederick will use the NimbleGen Sequence Capture technology and the Genome Sequencer FLX in cancer genomics studies.

Datapoint

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Life Technologies and co-plaintiffs filed suit against Illumina, claiming that it infringes three of Life's DNA amplification patents. Illumina has countersued.

Funded grants

$500,000/FY 2009
Epigenetic markings in developing and diseased prefrontal neurons
Grantee: Schahram Akbarian, University of
Massachusetts Medical School
Began: Sep. 30, 2009; Ends: Aug. 31, 2001

This project will "combine two of the most innovative approaches in the field of neurosciences as it pertains to epigenetics, by selectively sorting neuronal chromatin followed by massively parallel sequencing of immunprecipitates (ChIP-seq) to obtain insight into the epigenomic landscape of prefrontal neurons," the abstract says.

$562,181/FY 2009
Controlling large DNA fragments during nanopore sequencing
Grantee: Mark Akeson, University of California, Santa Cruz
Began: Sep. 22, 2009; Ends: Jun. 30, 2011

This grant will allow Akeson to "test how efficiently nanopores can control and process long DNA templates (up to 2500 nt in length) as they are catalytically modified by DNA polymerases," according to the abstract. Goals of the project include limiting DNA replication to template strands captured individually and more.

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