By Julia Karow
This article, originally published Jan. 13, has been updated with additional information from Complete Genomics' presentation at the JP Morgan Healthcare Conference.
Complete Genomics recorded $8 million to $9 million in preliminary revenue for its human genome sequencing service in 2010, and $25 million worth of total orders, and ended the year with about $69 million in cash on hand, according to a company executive.
At the end of 2010, the company had an order backlog of more than 1,000 genomes, not including a recent order of 615 genomes from the Institute of Systems Biology, plus another 1,000 genomes it expects to sequence for the National Cancer Institute as part of a multi-year contract (IS 9/7/2010).
While it sequenced more than 300 genomes in the fourth quarter of 2010, it expects to sequence more than 500 in the first quarter of this year, said CEO Cliff Reid during a presentation at the JP Morgan Healthcare Conference in San Francisco last week.
The firm's sequencing capacity is currently 400 human genomes per month, and it could double or triple to between 800 and 1,200 genomes per month by the end of the year "in response to market demand," he said.
This year, Complete Genomics plans to introduce a "long fragment read" technology that will allow it to distinguish between maternal and paternal chromosomes. This will enable scientists or doctors to distinguish whether a gene has several mutations in one copy, leaving the other one intact, or spread over both copies, Reid explained. "This is the only technology that will be commercially available that will enable a clinician to make that decision."
The same technology will also allow Complete to decrease its error rate from 10-5 to 10-7, or from 30,000 to 300 errors per genome, and to sequence genomes from fewer than 50 cells' worth of DNA. "These will be the first clinical-grade genomes ever made available to the clinical community," Reid said.
The company has also been able to sequence an increasing fraction of the human genome, using improved software: For the last 300 genomes it delivered, it covered 96 percent of the genome on average. By comparison, a recent analysis of two human genomes sequenced with the Illumina platform and assembled with the SOAPdenovo algorithm found that the coverage was slightly less than 84 percent of the reference genome (IS 1/4/2011).
"One of the misconceptions in the DNA sequencing industry is that it takes long reads to sequence a large fraction of the human genome," Reid said.
"I think this [96 percent coverage] is still a bit of a shocking result to the scientific community," he added, "but it demonstrates [that] good software, coupled with high-quality, inexpensive short reads, is the superior method for sequencing complete human genomes."
[ pagebreak ]
Currently, the firm has a turnaround time of about 83 days, which it plans to reduce to less than 60 days by the end of the year.
The company's focus will remain on complete human sequencing, he said, but it might add other services in that area, such as methylome sequencing, which he called a "very important adjunct to human genome sequencing in the cancer community."
Right now, the company has more than 35 customers, most of them academic centers. "Academia is the early adopter of new DNA sequencing technology, and it's been no exception for us," Reid said. "We see the research market being a wonderful entry market of a few billion dollars, but we see the clinical markets downstream being much more significant for our long-term growth."
Among current customers are a few pharma companies — notably Pfizer, Genentech, and Eli Lilly — but "these tend to be the research side of the pharmaceuticals industry," he said. "We're not yet at the clinical side of the pharmaceuticals industry."
But the company expects to sequence human genomes for clinical trials in the future, and to build a "leadership position" in clinical cancer sequencing.
Complete currently charges about $10,000 per genome, Reid said — at a consumables cost of "substantially less than" $1,000 per genome — which is still too high for clinical trials. "But we are inexorably driving the prices down and believe that the clinical trials market will be one of our bigger markets in the future," he said.
In terms of cancer sequencing, "we believe that all tumors will be sequenced in the future," he said, once the price has dropped to about $2,000 to $3,000 per sample. He provided no timeline for when Complete Genomics might be offering that price.
The firm also sees "great advantages" in opening additional human genome sequencing facilities around the world, he said, particularly in Asia, "to provide closer access of our technology to Asian markets." He provided no timeline for the firm's expansion plans.
Have topics you'd like to see covered in In Sequence? Email the editor at jkarow [at] genomeweb [.] com.