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Ultra-deep sequencing of mixed virus populations

Wednesday 2nd April 2008 - 14:00 to 15:00
INI Seminar Room 1

The diversity of virus populations within single infected hosts presents a major difficulty for the natural immune response, vaccine design, and antiviral drug therapy. Recently developed ultra-deep sequencing technologies can be used for quantifying this diversity by direct sequencing of the mixed virus population. We present statistical and computational methods for the analysis of such sequence data. Inference of the population structure from observed reads is based on error correction, reconstruction of a minimal set of haplotypes that explain the data, and eventually estimation of haplotype frequencies. We demonstrate our approach by analyzing simulated data and by comparison to 165 sequences obtained from clonal Sanger sequencing of four independent, diverse HIV populations.

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University of Cambridge Research Councils UK
    Clay Mathematics Institute London Mathematical Society NM Rothschild and Sons