Next-generation sequencing opens gate to new insights

New findings about drug resistance have been obtained through the sequencing of the genomes of pathogenic microorganisms, and in particular their drug-resistant strains. The sequencing of complete or partial viral genomes from clinical samples has given us some idea of the course of an infection over time, the response to treatments, and indications of possible strategies for the future development of drugs.

The electrophoresis-based Sanger method is currently the most popular sequencing technology. It was the foundation stone of the human genome project.

With the Sanger technique it became possible to sequence not only complete genomes, but also fragments of genomes, for example for clone verification or for the detection of mutations in the genome that may be related to the development of illnesses.

The method has been steadily perfected over the past 10 years. During this period sequencing costs have fallen by around 90 per cent while, at the same time, the throughput of a modern automated sequencer has increased tenfold.

Nevertheless, this standard method will probably reach its physical limits within the foreseeable future.
If sequencing is ever to become a constituent part of individualised diagnosis and preventive medicine – and the potential is certainly there – the costs must be reduced still further. The international planning target is $1000 for a complete human genome.

New sequencing techniques are also of interest to the pharmaceutical sector, for example in research on drug resistance and the pathogenicity of bacteria, for identifying human DNA variations, establishing the onset of drug resistance in HIV or HCV, producing tumour profiles as a guide to cancer treatments or for differentiating the modes of action of antibiotics.

A whole range of research institutes and companies are now working on technologies designed to lower costs and increase throughput. While most of these are still in their development phase, some are already usable and suitable, to a greater or lesser extent, for resequencing and/or de novo sequencing (see box).

First to the market

The method developed by the US company 454 Life Sciences was the first of these techniques to be launched on the market.

Roche’s ultrafast Genome Sequencer 20 System was developed on the basis of this method and is distributed by Roche Diagnostics.

Roche and 454 are working together on the further development of this system. Introduced to the market in end of 2005, it already found its use in a widespread range of applications eg, tumour research, Mammoth- and Neanderthal sequencing, the Marine Census project, and many more.

The Genome Sequencer 20 system can perform sequencing runs up to 60 times faster than conventional commercially available platforms. The technology on which the system is based was developed by 454 Life Sciences.

The system’s hallmark is a the proprietary PicoTiterPlate, which allows the Genome Sequencer 20 System to sequence over 20 million bases within a five hour run. The method is fast thanks to a high degree of parallelisation: the entire process sequences thousands of DNA molecules simultaneously.

The role of sequencing in Life Science research will change dramatically over the next few years. The attempts to obtain new high-throughput sequencing technologies are ultimately aimed at lowering costs sufficiently to allow personalised genome sequencing.

The US$1000 genome is the eventual goal of these attempts. To this end, the hardware will need to be improved in the field of bioinformatics in order to keep pace with the huge data volumes and new applications in the future.

Discovery and development

New applications are gradually opening up, thanks to the new-generation sequencing technologies, and particularly their use in the medical field and the discovery and development of drugs.

The determination of disease-relevant exons within a population, the exploration of viral quasi-species in patients in relation to the course over time and drug use and the search for genome changes of pathogens in relation to drug resistance or changes in virulence are just some of the possibilities.

In each case, doors will open up to new developments and the solution of previously unaddressed problems. 

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Dr Burkhard Ziebolz is with Roche Diagnostics, Mannheim, Germany.

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