By Julia Karow
In preparation for the commercial launch of its single-molecule real-time DNA sequencing system in the second half of this year, Pacific Biosciences has teamed up with almost a dozen companies who will develop sample-preparation and data-handling products, protocols, and services that are compatible with its platform.
The partner program, which currently has 11 members, is designed to "help customers rapidly and easily adopt" PacBio's platform for their research, according to the company. It involves firms that provide consumables, automation systems, complementary instrumentation, services, and supporting software and hardware.
Depending on the terms of the agreement, the firms will receive access to information and development tools, application programming interfaces, and protocols, and may co-develop or co-market products with PacBio.
Some of the solutions developed by the partners are expected to be available to PacBio's early-access customers, and the goal is to have most of them ready for the launch of the sequencing system later this year, according to Martha Trela, PacBio's vice president of marketing. The program "demonstrates our commitment to an open system and to developing an ecosystem to support our customers," she said.
On the sample-preparation side, PacBio has signed up Agilent Technologies, Fluidigm, and RainDance Technologies, which each provide targeted DNA enrichment products, as well as Caliper Life Sciences and NuGen Technologies, which offer sample-prep reagents and devices.
Agilent plans to develop target enrichment products that work with PacBio's platform. Agilent's SureSelect technology has "proven to be very effective" in making second-generation sequencing systems "more efficient," according to Fred Ernani, Agilent's senior product manager for emerging genomics applications, and "such efficiencies can also translate to technologies like that of PacBio's," he said.
Likewise, Fluidigm is working with PacBio "to ensure that Fluidigm's Access Array technology can be used as an upfront target enrichment platform for the PacBio sequencer," according to Martin Pieprzyk, product marketing manager for Fluidigm's next-generation sequencing products. Because the array can generate amplicons ranging in length from 200 bases to 10 kilobases, it can enable "multiple applications" on the sequencer, he said. No modifications to the Access Array system will likely be necessary to make it compatible with PacBio's instrument.
PacBio is exploring Caliper's LabChip XT, which is used to fractionate DNA and select specific fragment sizes, for use with its strobe sequencing workflow. The Caliper technology "will help us achieve tight fragment distributions critical for uniform loading of DNA sizes in excess of 6 kilobases," Donna Wilson Earley, PacBio's product manager for consumables, told In Sequence.
For data handling and analysis, the firm has formed alliances with Amazon Web Services, which offers cloud-based computing and storage; Geospiza and CLC Bio, which provide sequencing data analysis software; GenoLogics, which offers a laboratory information management system for sequencing; GenomeQuest, a provider of a sequence data management platform and service; and BioTeam, which offers consulting services for integrating computing and DNA sequencing platforms.
According to Edwin Hauw, PacBio's senior product manager for software and informatics, the company is working with informatics firms such as Geospiza and GenoLogics "to incorporate PacBio-specific workflow steps," for applications such as standard sequencing, circular consensus sequencing, and strobe sequencing. It is also working with these companies "to set up runs utilizing APIs, and to provide useful quality reports based on PacBio metrics," he said.
In addition, CLC Bio is adapting its CLC Genomics Workbench and Genomics Server products to support PacBio data, including "how to incorporate our strobe sequencing reads to improve assemblies and structural variation detection," he said.
BioTeam will help PacBio customers set up an appropriate IT infrastructure by providing computation and storage recommendations "that can keep up with the output of the SMRT system," according to Hauw.
What distinguishes the PacBio sequencing technology from other next-gen sequencing platforms is that "it is going to produce even more data faster," and will produce significantly longer reads, said Todd Smith, Geospiza's CTO. The company plans to adapt both its GeneSifter laboratory and analysis products for the PacBio sequencer.
Other vendors of sequencing systems also have software communities in place, efforts that are "improving all the time," Smith said. But partnering prior to the launch of its platform is probably going to pay off for PacBio. By the time its platform is fully commercialized and implemented by its customers, Smith predicted, "there is going to be a very robust collection of tools to use with the technology."
— Bernadette Toner contributed reporting to this article.