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Nicholas Eriksson
University Seminar
Viral population estimation using pyrosequencing
November 14, 2006 10:00
Abstract:
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. In this talk, I'll present mathematical and statistical 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 which 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 EM algorithm. This is joint work with Lior Pachter, Soo-Yon Rhee, Yumi Mitsuya, Robert W. Shafer, and Niko Beerenwinkel.
If you have questions, or would like to meet the speaker, please contact Ponda at 4-1994 or pondabarnes@tti-c.org. For information on future TTI-C talks or events, please go to the TTI-C Events page.