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PacBio Explores Targeted Sequencing, Focusing on Complex Genomic Regions


NEW YORK (GenomeWeb) – Pacific Biosciences is making advances in the targeted sequencing space, including a partnership with Roche NimbleGen, the firm said this week. During a conference call discussing its 2015 first quarter results, CEO Mike Hunkapiller highlighted recent publications from customers who have turned to PacBio technology to target complex regions of the genome.

During the call, Hunkapiller also provided an update on the company's development agreement with Roche, saying that it expects to deliver a clinical sequencing system to Roche by the second half of next year. The most recent development milestone in the firms' pact has triggered a $10 million payment from Roche to PacBio.

PacBio has now earned half of the $40 million milestone revenue and the "pathway to the finish line is becoming more definite," Hunkapiller said. As planned, the company is on track to "deliver a product to Roche in the second half of next year."

Hunkapiller also noted that for the first time China's BGI has purchased a PacBio RS II system. He said that after an initial evaluation, BGI would likely "purchase additional units to integrate into its sequencing service business."

In addition, the firm said it no longer plans to provide updates on the number of instruments it has sold or installed during a quarter, due to competitive reasons. However, in a note following the earnings call, William Quirk, an analyst with Piper Jaffray, wrote that he estimated that the firm "validated" approximately 12 instruments and added another 12 orders to its pipeline, for an instrument backlog of 15.

Yesterday, PacBio also announced an agreement with RainDance Technologies to co-develop and commercialize technology that would create synthetic long reads around 100 kb in size that could be used for de novo whole-genome assembly.

Targeted sequencing

Hunkapiller said that PacBio last week partnered with Roche NimbleGen to develop a workflow using the NimbleGen SeqCap EZ enrichment technology to enrich DNA fragments up to 6 kb.

"This approach can provide a very comprehensive view of structural variants and haplotype information," Hunkapiller said.

The company also recently launched sample prep barcoding kits, "which allow customers to pool multiple samples onto a single SMRT cell," Hunkapiller said, "which can dramatically bring down the cost of sequencing large numbers of samples for applications like HLA typing."

He added that the product launch supports its goal of reducing the cost of sequencing on the RS II to "expand the use across a broader spectrum of applications."

Researchers at Baylor College of Medicine developed a method based on this approach using NimbleGen capture technology that they called PacBio-LITS, which they used to identify breakpoint junctions of low copy repeat-associated complex structural rearrangements on chromosome 17 in patients diagnosed with Potocki–Lupski syndrome. They published their work in BMC Genomics.

Similarly, a group from George Washington University developed a targeted sequencing method on the PacBio platform to search for biomarkers associated with ovarian hyperstimulation syndrome, and a group from Uppsala University used targeted sequencing on the RS II to search for mutations in the BCR-ABL1 gene fusion.

Customers sequencing more complex genomes

A sign that customers are turning to PacBio technology for increasingly complex projects is the rising consumable revenue and rising average annual consumable revenue per instrument, Hunkapiller said. In the first quarter, average consumable revenue per system was around $133,000. Total consumable revenues grew 69 percent in the quarter, to $4.3 million, he added.

"We have a long way to go on per-instrument usage," Hunkapiller said, adding that the company is seeing system usage rise at an increasing number of sites, "particularly as they get into more complicated genome projects, which require multiple SMRT cell runs per project," as opposed to microbial sequencing projects, which often need only one SMRT cell.

Hunkapiller said that going forward, increasing throughput will be key, which will bring down the cost. "We expect to get an increase of four-fold in throughput per dollar," he said, which will give the company a more competitive position in the human genome sequencing space.