By Monica Heger
Complete Genomics is in the midst of developing both second- and third-generation versions of its sequencing system that will increase the throughput eventually to 80 genomes per day per instrument.
CEO Cliff Reid said during a presentation at the Morgan Stanley Global Healthcare conference in New York last week that the company plans to roll out its second generation of instruments in the second quarter of 2012, and third-generation instruments by 2015, possibly earlier.
"The instruments we're running today in our lab are on their way to being obsolete by next year," Reid said in his presentation, which was webcast.
The second-gen instruments, which Reid initially discussed during an earnings call earlier this year (IS 5/10/2011), will have an initial capacity of six genomes per day and an eventual capacity of 10 genomes per day. These instruments will be based on the same optical technology that the current systems use, and the increased capacity will be achieved by building a "faster architecture," he said.
Among the improvements for the system, the company is doubling the density of its DNA nanoballs, which will increase imaging density from 2 pixels per piece of DNA to 1 pixel per piece of DNA. It is also continually making improvements to its sample-prep protocols and computing.
Additionally, the company is developing a third-generation instrument, with a planned launch of 2015, that will be able to sequence 80 genomes per day. Reid said that this improvement will be accomplished through an entirely new optics technology.
Specifically, Fairchild Imaging, now part of BAE Systems, recently launched a new scientific complementary metal-oxide semiconductor camera that Complete Genomics plans to use in its third-gen instruments, Reid said. To support the camera, Complete Genomics is undergoing a two-year development process to build the necessary optics "to get the photons into these lightning-fast cameras" and the fluidics that can "feed enough DNA into the cameras to keep them running," Reid said.
Currently, Complete Genomics is operating 24 machines in its Mountain View, Calif., headquarters, which can each produce one genome per day. By the end of the year, capacity will be upped to one and a half genomes per day per instrument.
However, there is space for about 50 machines, Reid said, and once the newest instruments are rolled out and the headquarters is filled to capacity, the company will be able to sequence 1 million genomes per year.
The total market for whole human genome sequencing has increased five-fold each of the last two years, said Reid. Two years ago, around 500 whole human genomes were sequenced at labs around the world. Last year that increased to about 3,000, and he estimated that by the end of this year, researchers will place orders for 15,000 genomes.
"We're seeing the uptake happen at a pretty hefty clip," Reid said. He did not provide an update on the company's order backlog in his presentation beyond what the co company said in early August: that it had booked 5,700 genomes since the beginning of the year and plans to ship a total of 4,000 genomes in 2011 (IS 8/9/2011).
Reid noted that despite the fact that Illumina and Life Technologies continue to sell increasing numbers of instruments to researchers, owning a sequencing machine does not preclude labs from outsourcing sequencing services.
Of Complete Genomics' 80 customers, 70 of them operate at least one sequencing instrument, said Reid.
"The outsourced service is a complement, not a substitute, for operating instruments," he said. "Small, quick-turnaround projects are done in house," while "big projects that require huge infrastructure are outsourced. … That's a stable model going forward."
As sequencing technology matures and becomes more widespread, and as prices come down, Reid anticipates that several "grades" of genomes at different price scales would emerge, including a research-grade genome, a high-quality research grade genome, and a clinical-grade genome.
He said that the company currently delivers a research-grade genome, which is 40-fold coverage, and that prices for that would continue to drop from a current level of around $5,000 per genome. For orders of 50 or more it is charging $4,000 per genome.
Additionally, Complete recently began offering a higher-quality research genome at 80-fold coverage, which is particularly useful for cancer genomes, he said, though he did not provide pricing information.
Reid reiterated the company's plans to launch its "long fragment read" technology to early-access customers this year, and commercially next year, which will enable the sequencing of 100,000 base pair fragments and allow for whole-genome haplotyping.
That technology will truly enable clinical-grade genomes, said Reid, which will be priced higher than research-grade genomes.
At the UBS Global Life Sciences conference today in New York, Complete's chief financial officer Ajay Bansal said that even as sequencing costs drop, prices for clinical genomes will remain higher than for research genomes because of the extra interpretation and data analysis required.
He maintained that the company will still be able to make a profit even as the price falls to $1,000 per genome. He noted that the company is working on process improvements that will eventually drive internal costs to around $100 per genome, not including sample-prep or labor costs.
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