DNA Jigsaw Puzzle

A new mathematical and statistical method allows the virus population in a diseased organism to be determined quickly and economically. Using this method, medicines and vaccines against diseases caused by viral infections could be developed and deployed in a more targeted way in the future.
Through their diversity resulting from continuous mutation, viruses easily develop drug resistance. This is also why the manufacture of a vaccine against HIV has been unsuccessful up to now. To bring both under control, the strains of virus present in the host must be known. A new method developed by researchers from Switzerland and America now promises help in identifying diverse virus populations.
The method is based on a next generation, high throughput DNA sequencing technique called pyrosequencing. Niko Beerenwinkel, Assistant Professor at the Department of Biosystems of ETH Zurich, explains that this involves a technique that has been in use since 2003, with which the sequencing can be carried out efficiently and economically. He is a co-author of a study published recently in the scientific journal PLoS Computational Biology, in which the researchers successfully identified the virus strains of four patients infected with the HIV virus.

Light signals identify structural elements

In their study, the scientists used the pyrosequencing technique to examine the DNA of HIV/AIDS viruses. As Beerenwinkel explains: “This involves determining the sequence of the DNA modules by synthesising the complementary DNA strand. Each newly incorporated base is recognised by a light signal. This method is reliable only for short DNA segments, but at the same time it can be highly parallelised, which ultimately leads to a very large number of short segments.”
The scientists now used a computer-assisted method which they had developed to combine together the DNA segments from the HIV samples to form virus strains. This involves piecing together matching DNA segments like a jigsaw puzzle to form the complete sequences of the various strains. Beerenwinkel explains that one does not know beforehand either how many or which strains the sample contains, or which DNA segments belong to the same strain.

Error rate minimized

But, according to Beerenwinkel, the disadvantage would be that the segments are very short and may conceal a high error rate. However, by using the mathematical and statistical error correction tools developed by the researchers, they were able to reduce the error rate with their method by a factor of 30, thus determining reliably the virus strains belonging to the DNA segments. This is shown by a comparison with conventional methods in which long DNA segments can be determined with high precision.
For this purpose they chose individual viruses at random from the population and used traditional methods to determine the sequence of the individual DNA structural elements. According to Beerenwinkel, this revealed that the results were very similar, but the pyrosequencing method works faster and more economically and – in contrast to conventional methods – enables entire virus populations to be identified more easily.
The method that has been developed allows the efficient use of new sequencing techniques with which the genetic diversity of the whole virus population of an infected patient can be determined. This can mean a big step forward for use of medicines to treat virus diseases and for vaccine development. This is because it could enable medicines to be used in a more targeted way, thus preventing the development of resistance. It could also facilitate the development of vaccines. — ScienceDaily (May 5, 2008)