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1.
Nucleic Acids Res ; 42(14): e115, 2014 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-24972832

RESUMO

Next-generation sequencing (NGS) technologies enable new insights into the diversity of virus populations within their hosts. Diversity estimation is currently restricted to single-nucleotide variants or to local fragments of no more than a few hundred nucleotides defined by the length of sequence reads. To study complex heterogeneous virus populations comprehensively, novel methods are required that allow for complete reconstruction of the individual viral haplotypes. Here, we show that assembly of whole viral genomes of ∼8600 nucleotides length is feasible from mixtures of heterogeneous HIV-1 strains derived from defined combinations of cloned virus strains and from clinical samples of an HIV-1 superinfected individual. Haplotype reconstruction was achieved using optimized experimental protocols and computational methods for amplification, sequencing and assembly. We comparatively assessed the performance of the three NGS platforms 454 Life Sciences/Roche, Illumina and Pacific Biosciences for this task. Our results prove and delineate the feasibility of NGS-based full-length viral haplotype reconstruction and provide new tools for studying evolution and pathogenesis of viruses.


Assuntos
Variação Genética , HIV-1/genética , Haplótipos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Genoma Viral , Infecções por HIV/virologia , Humanos
2.
Artigo em Inglês | MEDLINE | ID: mdl-26355517

RESUMO

This paper presents a new computational technique for the identification of HIV haplotypes. HIV tends to generate many potentially drug-resistant mutants within the HIV-infected patient and being able to identify these different mutants is important for efficient drug administration. With the view of identifying the mutants, we aim at analyzing short deep sequencing data called reads. From a statistical perspective, the analysis of such data can be regarded as a nonstandard clustering problem due to missing pairwise similarity measures between non-overlapping reads. To overcome this problem we propagate a Dirichlet Process Mixture Model by sequentially updating the prior information from successive local analyses. The model is verified using both simulated and real sequencing data.


Assuntos
Biologia Computacional/métodos , Infecções por HIV/virologia , HIV-1/genética , Haplótipos/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Análise de Sequência de DNA/métodos
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