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New cost-effective means to reconstruct virus populations

Date:
May 12, 2008
Source:
Public Library of Science
Summary:
Researchers from the United States and Switzerland have developed mathematical and statistical tools for reconstructing viral populations using pyrosequencing, a novel and effective technique for sequencing DNA.
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Researchers from the United States and Switzerland have developed mathematical and statistical tools for reconstructing viral populations using pyrosequencing, a novel and effective technique for sequencing DNA.

The scientists knew that pyrosequencing reads are short and error-prone, and thus set out to improve upon this process. The new computational method they developed reduces the error rate and yields information faster and more efficiently. The method has been applied to four independent, diverse HIV-1 populations from drug-resistant patients and compared to 165 sequences obtained directly from clonal sequencing of the same samples.

"These new techniques produce results quite close to accepted techniques at a lower cost and potentially higher resolution," says Niko Beerenwinkel from ETH Zurich, one of the researchers.

Knowledge of the genetic structure of virus populations is critical for furthering biomedical research on disease progression, vaccine design, and drug resistance. The ability to better estimate the structure of virus populations holds great promise for new insights into viral evolution and disease control strategies.


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The above story is based on materials provided by Public Library of Science. Note: Materials may be edited for content and length.


Journal Reference:

  1. Nicholas Eriksson, Lior Pachter, Yumi Mitsuya, Soo-Yon Rhee, Chunlin Wang, Baback Gharizadeh, Mostafa Ronaghi, Robert W. Shafer, Niko Beerenwinkel. Viral Population Estimation Using Pyrosequencing. PLoS Computational Biology, 2008; 4 (5): e1000074 DOI: 10.1371/journal.pcbi.1000074

Cite This Page:

Public Library of Science. "New cost-effective means to reconstruct virus populations." ScienceDaily. ScienceDaily, 12 May 2008. <www.sciencedaily.com/releases/2008/05/080508222417.htm>.
Public Library of Science. (2008, May 12). New cost-effective means to reconstruct virus populations. ScienceDaily. Retrieved May 26, 2015 from www.sciencedaily.com/releases/2008/05/080508222417.htm
Public Library of Science. "New cost-effective means to reconstruct virus populations." ScienceDaily. www.sciencedaily.com/releases/2008/05/080508222417.htm (accessed May 26, 2015).

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