Academic Journal
Viral population estimation using pyrosequencing.
| العنوان: | Viral population estimation using pyrosequencing. |
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| المؤلفون: | Nicholas Eriksson, Lior Pachter, Yumi Mitsuya, Soo-Yon Rhee, Chunlin Wang, Baback Gharizadeh, Mostafa Ronaghi, Robert W Shafer, Niko Beerenwinkel |
| المصدر: | PLoS Computational Biology, Vol 4, Iss 4, p e1000074 (2008) |
| بيانات النشر: | Public Library of Science (PLoS), 2008. |
| سنة النشر: | 2008 |
| المجموعة: | LCC:Biology (General) |
| مصطلحات موضوعية: | Biology (General), QH301-705.5 |
| الوصف: | The diversity of virus populations within single infected hosts presents a major difficulty for the natural immune response as well as for vaccine design and antiviral drug therapy. Recently developed pyrophosphate-based sequencing technologies (pyrosequencing) can be used for quantifying this diversity by ultra-deep sequencing of virus samples. We present computational methods for the analysis of such sequence data and apply these techniques to pyrosequencing data obtained from HIV populations within patients harboring drug-resistant virus strains. Our main result is the estimation of the population structure of the sample from the pyrosequencing reads. This inference is based on a statistical approach to error correction, followed by a combinatorial algorithm for constructing a minimal set of haplotypes that explain the data. Using this set of explaining haplotypes, we apply a statistical model to infer the frequencies of the haplotypes in the population via an expectation-maximization (EM) algorithm. We demonstrate that pyrosequencing reads allow for effective population reconstruction by extensive simulations and by comparison to 165 sequences obtained directly from clonal sequencing of four independent, diverse HIV populations. Thus, pyrosequencing can be used for cost-effective estimation of the structure of virus populations, promising new insights into viral evolutionary dynamics and disease control strategies. |
| نوع الوثيقة: | article |
| وصف الملف: | electronic resource |
| اللغة: | English |
| تدمد: | 1553-734X 1553-7358 |
| Relation: | http://europepmc.org/articles/PMC2323617?pdf=render; https://doaj.org/toc/1553-734X; https://doaj.org/toc/1553-7358 |
| DOI: | 10.1371/journal.pcbi.1000074 |
| URL الوصول: | https://doaj.org/article/2c802e0d512a44e39c176e49fa56e6ca |
| رقم الانضمام: | edsdoj.2c802e0d512a44e39c176e49fa56e6ca |
| قاعدة البيانات: | Directory of Open Access Journals |
Full Text Finder | تدمد: | 1553734X 15537358 |
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| DOI: | 10.1371/journal.pcbi.1000074 |