In October 2008, Complete Genomics of Mountain View, California, said it would sell whole human genomes in 2009 for $5,000, but it released no supporting data. At the Advances in Genome Biology and Technology meeting in Marco Island, Florida, 2009 conference, the company revealed a human genome it said it had sequenced using nine machines for eight days over Christmas.
Complete Genomics’ says by June, 2009 its materials cost will be down to $1,000 per genome. The company aims to launch commercially that month, sequence 1,000 genomes this year and 20,000 human genomes next year. A few centres have now signed on for pilot projects in which Complete Genomics will sequence five genomes at $20,000 apiece.
The company’s chief executive, Clifford Reid, says it assembled 254 gigabases (254 billion base pairs) of data into a draft covering 92% of the genome of an anonymous man, and that it read each base an average of 91 times. Like many of the high-speed sequencing technologies currently in use — usually called ‘next-generation’ technologies, as opposed to the third generation still in development — Complete Genomics produces short reads of DNA. By sequencing each base many times, it aims to diminish the potential errors that could creep in when the short reads are assembled into longer pieces. Reid says that the technology is highly accurate, with less than one-third of a per cent chance of making an error in any given base. That’s comparable to the current generation of sequencers.
Stephen Turner, Pacific Biosciences of Menlo Park, unveiled a completed genome of the bacterium Escherichia coli, saying the company had covered each base an average of 38 times for an accuracy of greater than 99.9999%.
Pacific Biosciences uses a single-molecule technology with DNA polymerase, the enzyme used by cells to assemble DNA strands, that reads out the product of the sequencing reaction as it progresses. Although its current machines read 3 bases per second, it aims to produce entire human genomes in under three minutes by 2013. It has also promised to deliver longer read lengths; Turner says the average read length of the E. coli genome was 586 base pairs, with some as long as 2,805 base pairs — “higher than any other read length in production,” he says. Some scientists hope long read lengths will eliminate errors and allow them to see parts of the genome that are difficult to read.
Pacific Biosciences intends to launch commercially late next year. Meanwhile, current sequencing technologies — such as those sold by Illumina, based in San Diego; Applied Biosystems, from Foster City, California; and Roche, based in Basel, Switzerland — are pouring out data at an astonishing rate, delivering multiple human genomes’ worth of data in a single multi-day run. That rate continues to increase as prices drop; Illumina, for instance, said at the conference that its technology will be able to sequence human genomes for as little as $10,000 by the end of this year.