In the news

Following numerous tantalising announcements earlier in the year, US company Complete Genomics Inc. has now published the results of three complete genomes, which were sequenced for an average cost of $4,400 each using its third generation sequencing platform [Drmanac R et al. (2009) Science doi: 10.1126/science.1181498]. The company is one of the front runners in the race to achieve the coveted $1,000 genome, and previously announced that it “plans to sequence 10,000 human genomes in 2010” (see previous news). Although the current price-tag excludes the platform itself and any associated infrastructure, the consumables cost between $1,726 and $8,800 for these genomes, which were sequenced at a coverage ranging from 45- to 87-fold per genome respectively.

The individuals sequenced included two from the HapMap population – a Caucasian male and a Yoruban female – and an individual previously sequenced as part of the Personal Genome Project. The sequencing revealed around 2.9-4 million single nucleotide polymorphisms (SNPs) per genome, of which around 10-20% were novel, as well as 250-500 thousand short insertions and deletions.

The technology uses patterned nanoarrays upon which the DNA self-assembles, thus vastly increasing the sequence content per run relative to earlier technologies. Moreover, unlike second generation “sequencing by synthesis” methods, which sequentially sequence chains of DNA, this method independently sequences each base and therefore avoids accumulation of errors. Validation of one genome suggests an error rate of around one per hundred thousand basepairs, which translates into around 30 thousand errors per genome. Although this is still unsuitable for clinical use, where a high level of diagnostic accuracy is required, it is likely to be applicable both to research for whole-genome-wide association studies and in the direct-to-consumer genomics market.