Although recent advances in DNA-sequencing technologies have accelerated the analysis of genomes from various organisms, including humans, sequencing whole genomes is still a time-consuming and expensive process. Margulies and colleagues have now developed a quick and easy sequencing method by combining an emulsion system for DNA amplification and pyrophosphate-based sequencing (pyrosequencing) in picolitre-sized wells.

Large-scale sequencing projects are laborious — the cloning of DNA fragments into bacterial vectors and the amplification and purification of individual templates is followed by Sanger sequencing using fluorescence chain–terminating nucleotide analogues and either slab-gel or capillary electrophoresis. Driven by the desire to reduce time and cost, Margulies et al. have devised a scalable, highly parallel two-step sequencing approach. The first step involves shearing the genome and generating random libraries of 80–120 bp DNA fragments. Adapters are ligated to the fragments. These are bound to beads and captured in the droplets of an oil-emulsion mixture of a PCR reaction. PCR amplification in each droplet results in each bead carrying ten-million copies of a unique DNA template. In the second step, a modified pyrosequencing protocol is carried out, in which nucleotide incorporation is detected by the release of inorganic pyrophosphate and the generation of photons.

The reactions take place on a picolitre scale: the slides used contain approximately 1.6 million wells, with 480 wells mm−2 and a calculated well size of 75 pl. The authors chose the bacterial genomes of Mycoplasma genitalium and Streptococcus pneumoniae to test the throughput, accuracy and robustness of their approach and achieved consensus accuracies of roughly 99.9%.

As the authors indicate, this study points to a “mini-approach” for future high-throughtput functional studies, which shows that miniaturization is becoming the core theme of genomics research. What does the future hold for the de novo assembly of genomes that are more complex than bacteria? The development of new sequencing methods is probably required for complex mammalian genomes, and the authors have already started to work towards this goal.