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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
Characterization of within-host plasmodium falciparum diversity using next-generation sequence data
PLoS ONE, Volume 7, No. 2, Article e32891, Year 2012
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Description
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. © 2012 Auburn et al.
Available Materials
https://efashare.b-cdn.net/share/pmc/articles/PMC3290604/bin/pone.0032891.s001.tiff
https://efashare.b-cdn.net/share/pmc/articles/PMC3290604/bin/pone.0032891.s002.tiff
https://efashare.b-cdn.net/share/pmc/articles/PMC3290604/bin/pone.0032891.s003.tiff
Authors & Co-Authors
Auburn, Sarah A.
Unknown Affiliation
Campino, Susana G.
Unknown Affiliation
Miotto, Olivo
Unknown Affiliation
Djimde, Abdoulaye A.
Unknown Affiliation
Zongo, Issaka D.
Unknown Affiliation
Manske, Heinrich Magnus
Unknown Affiliation
Maslen, Gareth Ll
Unknown Affiliation
Mangano, Valentina Dianora
Unknown Affiliation
Alcock, Dan
Unknown Affiliation
MacInnis, Bronwyn L.
Unknown Affiliation
Rockett, Kirk A.
Unknown Affiliation
Clark, Taane Gregory
Unknown Affiliation
Doumbo, Ogobara K.
Unknown Affiliation
Ouedraogo, Jean Bosco
Unknown Affiliation
Kwiatkowski, Dominic P.
Unknown Affiliation
Statistics
Citations: 114
Authors: 15
Affiliations: 10
Identifiers
Doi:
10.1371/journal.pone.0032891
e-ISSN:
19326203
Research Areas
Genetics And Genomics
Study Design
Cross Sectional Study
Study Locations
Multi-countries