Publication: Characterization of within-host Plasmodium falciparum diversity using next-generation sequence data.
Accepted Date
2012-02-07
Issued Date
2012
Copyright Date
2012
Resource Type
Language
eng
ISSN
1932-6203 (electronic)
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Mahidol University
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PLOS one
Bibliographic Citation
Auburn S, Campino S, Miotto O, Djimde AA, Zongo I, Manske M, et al. Characterization of within-host Plasmodium falciparum diversity using next-generation sequence data. PLoS One. 2012;7(2):e32891.
Suggested Citation
Auburn, Sarah, Campino, Susana, Miotto, Olivo, Djimde, Abdoulaye A., Zongo, Issaka, Manske, Magnus, Maslen, Gareth, Mangano, Valentina, Alcock, Daniel, MacInnis, Bronwyn, Rockett, Kirk A., Clark, Taane G., Doumbo, Ogobara K., Ouédraogo, Jean Bosco, Kwiatkowski, Dominic P. Characterization of within-host Plasmodium falciparum diversity using next-generation sequence data.. Auburn S, Campino S, Miotto O, Djimde AA, Zongo I, Manske M, et al. Characterization of within-host Plasmodium falciparum diversity using next-generation sequence data. PLoS One. 2012;7(2):e32891.. doi:10.1371/journal.pone.0032891 Retrieved from: https://repository.li.mahidol.ac.th/handle/123456789/744
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Title
Characterization of within-host Plasmodium falciparum diversity using next-generation sequence data.
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Abstract
Our understanding of the composition of multi-clonal malarial infections and the
epidemiological factors which shape their diversity remain poorly understood.
Traditionally within-host diversity has been defined in terms of the multiplicity
of infection (MOI) derived by PCR-based genotyping. Massively parallel, single
molecule sequencing technologies now enable individual read counts to be derived
on genome-wide datasets facilitating the development of new statistical
approaches to describe within-host diversity. In this class of measures the F(WS)
metric characterizes within-host diversity and its relationship to population
level diversity. Utilizing P. falciparum field isolates from patients in West
Africa we here explore the relationship between the traditional MOI and F(WS)
approaches. F(WS) statistics were derived from read count data at 86,158 SNPs in
64 samples sequenced on the Illumina GA platform. MOI estimates were derived by
PCR at the msp-1 and -2 loci. Significant correlations were observed between the
two measures, particularly with the msp-1 locus (P = 5.92×10(-5)). The F(WS)
metric should be more robust than the PCR-based approach owing to reduced
sensitivity to potential locus-specific artifacts. Furthermore the F(WS) metric
captures information on a range of parameters which influence out-crossing risk
including the number of clones (MOI), their relative proportions and genetic
divergence. This approach should provide novel insights into the factors which
correlate with, and shape within-host diversity.