Charles Darwin University

CDU eSpace
Institutional Repository

 
CDU Staff and Student only
 

Characterization of within-host Plasmodium falciparum diversity using next-generation sequence data

Auburn, Sarah, Campino, Susana, Miotto, Olivo, Djimde, Abdoulaye, Zongo, Issaka, Manske, Magnus, Maslen, Gareth, Mangano, Valentina, Alcock, Daniel, MacInnis, Bronwyn, Rockett, Kirk, Clark, Taane, Doumbo, Ogobara, Ouedraogo, Jean and Kwiatkowski, Dominic (2012). Characterization of within-host Plasmodium falciparum diversity using next-generation sequence data. PLoS One,7(2):e32891.

Document type: Journal Article
Attached Files (Some files may be inaccessible until you login with your CDU eSpace credentials)
Name Description MIMEType Size Downloads
Download this reading Auburn_38322.pdf Published version application/pdf 176.14KB 78
Reading the attached file works best in Firefox, Chrome and IE 9 or later.

IRMA ID bsmithxPUB62
Title Characterization of within-host Plasmodium falciparum diversity using next-generation sequence data
Author Auburn, Sarah
Campino, Susana
Miotto, Olivo
Djimde, Abdoulaye
Zongo, Issaka
Manske, Magnus
Maslen, Gareth
Mangano, Valentina
Alcock, Daniel
MacInnis, Bronwyn
Rockett, Kirk
Clark, Taane
Doumbo, Ogobara
Ouedraogo, Jean
Kwiatkowski, Dominic
Journal Name PLoS One
Publication Date 2012
Volume Number 7
Issue Number 2
ISSN 1932-6203   (check CDU catalogue open catalogue search in new window)
Scopus ID 2-s2.0-84857678104
Start Page e32891
Total Pages 6
Place of Publication United States
Publisher Public Library of Science
HERDC Category C1 - Journal Article (DIISR)
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 FWS 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 FWS approaches. FWS 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 FWS metric should be more robust than the PCR-based approach owing to reduced sensitivity to potential locus-specific artifacts. Furthermore the FWS 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.
DOI http://dx.doi.org/10.1371/journal.pone.0032891   (check subscription with CDU E-Gateway service for CDU Staff and Students  check subscription with CDU E-Gateway in new window)


© copyright

Every reasonable effort has been made to ensure that permission has been obtained for items included in CDU eSpace. If you believe that your rights have been infringed by this repository, please contact digitisation@cdu.edu.au.

 
Versions
Version Filter Type
Access Statistics: 34 Abstract Views, 78 File Downloads  -  Detailed Statistics
Created: Fri, 17 Jan 2014, 01:27:50 CST