Genome Sequencing - On Special Offer.
(June 26th 2008) Kick-started by the Human Genome Project, sequencing methods have rapidly evolved, becoming faster and less expensive. In the latest announcement by Swedish scientists, a new approach has been presented that aims for $1000 genomes. Melanie Estrella reports.
In 1977, the first practical DNA sequencing method was described by the British biochemist, Frederick Sanger. But deciphering the A, C, T, G alphabet of nucleic acids was a slow and tedious venture, requiring bulky gels, radioactivity, and a time-consuming and often frustrating manual read out of the four-lane bar code. Sequencing a single gene was often enough to fill a whole PhD thesis!
Compare this to today's rapid, high-throughput procedures which are miniaturised and automatised, using a broad range of modern techniques, such as microarrays and PCR. Genomic data bases are now well stocked with more than 100 Gbp of genetic information. Complete genomes from more than 600 prokaryotes and 100 eukaryotes have so far been mapped, including mosquitoes, mice and man. Yet, although cohorts of scientists are busily sequencing their way through the genomes of every possible earthly creature, others are already planning to provide every human with access to their own individual genome.
One of these visionaries is the American geneticist, George Church, Professor at Harvard and MIT. In 2006, he launched the Personal Genome Project, publishing the entire genomes of volunteers on the internet, along with relevant physical and medical information, in order to investigate the possible risks/benefits of presenting freely accessible personal genetic charts. The project's long-term goal is to provide affordable genetic cards for everyone, allowing better personalized medical decisions. However, a prerequisite for this ambitious objective is to dramatically cut costs for DNA analysis, initiating the call for the "$1000 genome".
A Swedish research team lead by Sten Linnarsson from the Department of Medical Biochemistry and Biophysics at Stockholm's Karolinska Institute, is currently the closest to meeting this request. The Swedes have developed a sequencing method that they say would cost $960 when applied to an entire human genome, roughly one-tenth of today's charges, as calculated from the cost of crude reagents, that nowadays represent the most cost-limiting factor (
Nature Biotechnology, 2008, 26, 676-684).
The method developed by Linnarsson and colleagues, termed 'shotgun sequencing by hybridization', optimises the pre-existing 'sequencing by hybridisation' technique. It is based on hybridising a set of fluorescently labelled oligomer probes to genomic DNA fragments fixed on a microscope slide; subsequently the formation of perfect duplexes are monitored using a known reference genome and appropriate algorithms to reassemble the DNA sequences.
Linnarsson's team adjusted the hybridisation conditions for individual probes and employed a universal set of 582 tiling pentamer oligonucleotides to increase the probe stability and specificity. In addition, 200 bp long genomic DNA fragments were arranged in a defined order on a glass surface and duplicated by
in situ rolling circle amplification to further enhance the accuracy of the assembling process and signal sensitivity. Linnarsson's lab tested their sequencing approach for the 48.5-kbp genome of the bacteriophage λ, and the 4.6-Mbp genome of
E. coli. They correctly identified some 96% and 80% of the DNA sequences, respectively, which is much better than for the standard 'sequencing by hybridisation' method.
However, the new technique remains restricted to the resequencing of known DNA sequences. Linnarsson says that it is an application for mapping disease genes in large groups of patients, helping to track down individual variants in familiar sequences thereby fueling the development of new treatments.
Nevertheless, such breathtaking progress in sequencing technology ought to make us start thinking about the far-reaching consequences. Some day - perhaps very soon - it will be not lack of money, but rather ethical and political issues that will be decisive in determining when and under what circumstances we will be disclosing the secrets of our own DNA.
