In the month since it presented human genome-sequencing data for the first time at the Advances in Genome Biology and Technology conference, Complete Genomics has been optimizing its technology, has signed up more than half a dozen early collaborators, and has been preparing to launch its service in late June.
At AGBT last month, the company showed results from analyzing a HapMap sample, which it sequenced in December 2008 in nine 8-day machine runs, each generating about 70 gigabases of sequence data (see In Sequence 2/10/2009). So far, the firm has shipped the dataset to about 40 interested users for analysis, Complete Genomics Chief Scientific Officer Rade Drmanac told In Sequence last week.
By the time the service launches, the firm plans to increase the throughput to 200 gigabases per run, and expand it to 600 gigabases "or even more" by the end of the year, Drmanac said during a talk at the Cambridge Healthtech Institute Next-Generation Sequencing meeting in San Diego last week.
For the HapMap sample, the company was unable to call SNPs in about 8 percent of the genome, including 6 percent that contained repeats and 2 percent of mostly AT-rich regions that had low coverage, but Drmanac said the problem of coverage bias "has been fixed now."
Company researchers are currently working on "different types" of human genome sequencing projects to gain more experience and to lower the materials cost from a recent $4,000 to less than $1,000 for the June launch, he said.
This cost reduction would help the company deliver the $5,000 human genomes that it has promised it will start offering at launch. Customers will need to order an as-yet undetermined minimum number of genomes to receive this price, Complete Genomics Vice President of Marketing Jennifer Turcotte told In Sequence last week.
Complete Genomics currently has a small number of early-access customers for whom it sequences five human genomes for $100,000, but the company is now at capacity for these pilot-type projects and is already discussing larger projects for the second half of the year with some customers, according to Turcotte.
So far, the firm has signed up more than half a dozen early collaborators, including the Institute for Systems Biology, the Broad Institute, and a couple of unnamed pharmaceutical companies, and plans to deliver the first set of genomes to them in April or May.
Details about its sequencing service will be available in late May or early June, according to Turcotte. Besides human genome sequencing, transcriptome sequencing is "definitely on our roadmap," she said, although it will likely not be among the first offerings.
Complete Genomics is targeting research organizations and pharma companies as customers initially, but Turcotte mentioned that the company has been approached by direct-to-consumer personal genomics firms and is considering offering its services to these companies in the future.
"We are looking longer-term how to be a channel for these personal-genomics companies, but that is not a 2009 goal," mainly due to regulatory requirements, she said.
Part of the plan to serve these firms would be to have Complete Genomics' genome center CLIA-certified, she said — a "roadmap item" that the company is considering for late 2009 or early 2010. "We really want to wait to see how the DTC market unfolds before we make firm plans," she added.
With the exception of Knome, most DTC genomics companies, which include 23andMe, Navigenics, DNADirect, and others, currently provide SNP array-based information to their customers, but several have said their long-term goal is to switch to sequencing-based genotyping.