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PacBio Eyes Clinical Diagnostic Market for Third-Gen Sequencing Platform

This article has been updated from a previous version to clarify the timeline for the expected performance of the SMRT technology.
 
NEW YORK (GenomeWeb News) — A Pacific Biosciences official said today that the firm has identified clinical diagnostics as a key market for the single-molecule real-time sequencing platform that it plans to launch commercially in 2010.
 
PacBio CEO Hugh Martin told investors at the UBS Global Life Sciences Conference that the firm has two key goals for the SMRT technology, which promises to sequence a human genome in 15 minutes within five years.
 
First, the firm hopes to stake a claim in the research sequencing market. Martin noted that this sector, long dominated by Applied Biosystems, is now “fragmented” due to competing next-gen platforms — creating an “opportunity to coalesce around a new standard.”
 
In addition, Martin said, PacBio has “a shot” at the clinical diagnostics market, where he said the technology’s long read lengths, low price, and quick turnaround time should give it an advantage over second-generation sequencing platforms from Roche/454, Illumina, and ABI. 
 
Martin acknowledged that PacBio’s instrument will be hitting the market several years after these systems, noting that it will need to “eclipse the performance” of its rivals — a goal that he is confident the company can meet.
 
PacBio expects its second-generation instrument to ultimately be able to generate more than 100 gigabases per hour. By contrast, Illumina and ABI are currently targeting tens of gigabases of data per run, and each run can take several days. The cycle time for the PacBio system is 30 minutes, Martin said, noting that this should be a benefit for the clinical market, where a run time of three days is “not acceptable.”
 
In addition, Martin said that the single-molecule sequencing system requires very little sample-prep time and “hardly any” reagents, which would bring the cost of a run to within several hundred dollars, rather than several thousand dollars per run for competing platforms.
 
Finally, Martin said that the read lengths for the PacBio system will be “significantly greater” than Sanger reads, and that the company is currently getting traces of around 500 base pairs — comparable to the upcoming version of the 454 FLX and much longer than the ABI and Illumina platforms, which are in the neighborhood of 30 base pairs.
 
This factor is expected to be one advantage in the clinical market, Martin said, noting that read length is a “big deal” for potential customers that the firm has spoken to so far, which include molecular diagnostic developers, pharmas, and biotechs as well as research groups.
 
As for the price of the instrument, Martin said that it could probably sell at “any price point” in the continuum of currently available sequencers, which range from around $400,000 for the Illumina system to $1.3 million for the Helicos platform. However, he said that the company is targeting the lower end of the scale because its market research indicates that $500,000 is a common price threshold for many potential customers, particularly in the research market.
 
PacBio currently has 12 prototype SMRT systems running in house, and is conducting a proof-of-principle sequencing project on the 5,386-base-pair phi X 174 bacteriophage.
 
Martin said that the company plans to release its specifications for the system by the end of the year and reiterated previous statements that the commercial rollout of the system will likely be in 2010.
 
He said that the company expects to launch an early-access program in the first half of next year that would allow customers to run their experiments on the prototype systems. PacBio would move those customers onto its production machines during the second half of 2009 and work with them to optimize the commercial system.
 
PacBio currently employs around 200 staffers, Martin said. The company, which has raised nearly $200 million in funding so far, including a $100 million round announced in July, currently has a burn rate of around $5 million per month as it works toward commercializing the system, he said.
 
Martin added that the company sees potential for the system “far beyond sequencing,” and noted that the technology was developed as a general platform for real-time single-molecule analysis, making it applicable to many molecules besides DNA.
 
For sequencing applications, PacBio places individual DNA polymerase molecules in nanoscale wells called zero-mode waveguides. The polymerase molecules capture fluorescently labeled nucleotides that emit a signal when they enter the active site of the enzyme. A laser at the bottom of the well captures this signal, which is ultimately translated into a base call.
 
However, Martin noted that other molecules can be placed in the wells other than DNA polymerase. As an example, he said that a research group in Tokyo is currently looking at using a ribosome in the waveguide in order to study protein synthesis in real time and another group at Harvard is considering adapting the system for protein-interaction studies.

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