Credit: Technology Review

When little known start-up Complete Genomics announced last fall that it planned to offer a human genome sequencing service for $5000 a pop, the sequencing community responded with a mixture of excitement and skepticism. Everyone wanted to get their hands on that kind of sequencing capacity, but in a field littered with grand claims, no one was holding their breath. Now the company, based in Mountain View, CA, has released data on its first human genome assembly.

Researchers generated about 630 gigabytes of raw genome data, approximately 40 percent of which mapped to existing human genome sequence. Like other new sequencing technologies, Complete Genomics' process reads the sequence of very short pieces of DNA, which then must be computationally synthesized to create a whole genome. That data covered about 92 percent of the human genome--the remaining eight percent is likely made up of repetitive sequences of DNA, which have been notoriously difficult to sequence with newer technologies.

The company has already sent the raw data to the National Center for Biotechnology Information (NCBI), which runs a publicly accessible database. Complete Genomics' CEO Cliff Reid presented the research at a conference in Florida last night.

Complete Genomics' technology is centered on two innovations: a way to densely pack DNA, developed by Rade Drmanac, the company's chief scientific officer, and a method to randomly read DNA letters, based on sequencing technology developed at George Church's lab at Harvard. (For more on the technology, see "Five Thousand Bucks for Your Genome".)

The company has chosen an unusual business model: rather than selling instruments, as most sequencing companies have done, it plans to offer sequencing services through a commercial-scale genome center. At the conference, Reid emphasized the company's plans to focus solely on human genomes. According to an article from Bio-IT :

"We're a wholesaler of complete human genomes to the scientific community. We have no intention of writing NIH grants," said Reid, adding he planned to partner with genome centers such as the Broad, research centers such as the Institute for Systems Biology, and the direct-to-consumer companies. The five-year mission was to build ten genome centers around the world that would sequence 1 million genomes in that period. "We're trying to make sequencing completely ubiquitous."

So how much did this genome actually cost? "We're not giving out costs on all the gory details," Reid told Technology Review. "The first sequence we did cost about $4000 in materials, and we are on track to getting materials costs down to $1000 by the time we start service in June." That's the target materials cost to enable a $5000 commercial service.

A statement from the company reveals its big goals for the next few years:

In preparation for its service launch, Complete Genomics is rapidly scaling up its commercial genome center. It plans to sequence 1,000 genomes in the second half of 2009 and 20,000 genomes in 2010. To analyze the enormous amounts of data that will be created, it is also expanding its data center, which will house 5,000 processors and provide five petabytes (five million gigabytes) of disk storage by the end of 2009, and 60,000 processors and 30 petabytes of disk storage in 2010.