2005/07/31 by Marcel Margulies, Michael Egholm, William E. Altman +53 · 11 citations
Environmental Science · Biochemistry, Genetics and Molecular Biology · Immunology and Microbiology · #Bacteriophages and microbial interactions #Genomics and Phylogenetic Studies #Microbial infections and disease research #Sanger sequencing #DNA sequencing #Shotgun sequencing #Massive parallel sequencing #Pyrosequencing #Computational biology #Sequence assembly #Scalability #Computer science #Throughput #Metagenomics #Genome #Biology #DNA #Genetics #Gene #Database #Transcriptome
paper · pdf · doi:10.1038/nature03959
openalex publication_date 2005/07/31 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/04
The proliferation of large-scale DNA-sequencing projects in recent years has driven a search for alternative methods to reduce time and cost. Here we describe a scalable, highly parallel sequencing system with raw throughput significantly greater than that of state-of-the-art capillary electrophoresis instruments. The apparatus uses a novel fibre-optic slide of individual wells and is able to sequence 25 million bases, at 99% or better accuracy, in one four-hour run. To achieve an approximately 100-fold increase in throughput over current Sanger sequencing technology, we have developed an emulsion method for DNA amplification and an instrument for sequencing by synthesis using a pyrosequencing protocol optimized for solid support and picolitre-scale volumes. Here we show the utility, throughput, accuracy and robustness of this system by shotgun sequencing and de novo assembly of the Mycoplasma genitalium genome with 96% coverage at 99.96% accuracy in one run of the machine. The race is on for a big prize: the job of providing the world's DNA sequencing laboratories with the successor to the ‘Sanger-based’ technology that gave us the first wave of genome sequences. One technology in the frame is that produced by 454 Life Sciences Corporation of Branford, Connecticut. Today's technology reads 67,000 base pairs per hour; this new approach is 100 times faster, reading 6 million base pairs per hour. The improved performance results from using picolitre-sized chemical reactors, enhanced light-emitting sequencing chemistries and complex informatics. Further miniaturization of the system is planned. Such leaps in technology may one day make it possible to analyse an individual's genome before designing therapy: the ultimate in personalized medicine.