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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
agricultural and biological sciences
Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence
Genome Biology, Volume 9, No. 12, Article R171, Year 2008
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Description
Background: The malaria parasite Plasmodium falciparum exhibits abundant genetic diversity, and this diversity is key to its success as a pathogen. Previous efforts to study genetic diversity in P. falciparum have begun to elucidate the demographic history of the species, as well as patterns of population structure and patterns of linkage disequilibrium within its genome. Such studies will be greatly enhanced by new genomic tools and recent large-scale efforts to map genomic variation. To that end, we have developed a high throughput single nucleotide polymorphism (SNP) genotyping platform for P. falciparum. Results: Using an Affymetrix 3,000 SNP assay array, we found roughly half the assays (1,638) yielded high quality, 100% accurate genotyping calls for both major and minor SNP alleles. Genotype data from 76 global isolates confirm significant genetic differentiation among continental populations and varying levels of SNP diversity and linkage disequilibrium according to geographic location and local epidemiological factors. We further discovered that nonsynonymous and silent (synonymous or noncoding) SNPs differ with respect to within-population diversity, inter-population differentiation, and the degree to which allele frequencies are correlated between populations. Conclusions: The distinct population profile of nonsynonymous variants indicates that natural selection has a significant influence on genomic diversity in P. falciparum, and that many of these changes may reflect functional variants deserving of follow-up study. Our analysis demonstrates the potential for new high-throughput genotyping technologies to enhance studies of population structure, natural selection, and ultimately enable genome-wide association studies in P. falciparum to find genes underlying key phenotypic traits. © 2008 Neafsey et al.; licensee BioMed Central Ltd.
Available Materials
https://efashare.b-cdn.net/share/pmc/articles/PMC2646275/bin/gb-2008-9-12-r171-S1.pdf
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https://efashare.b-cdn.net/share/pmc/articles/PMC2646275/bin/gb-2008-9-12-r171-S3.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC2646275/bin/gb-2008-9-12-r171-S4.pdf
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https://efashare.b-cdn.net/share/pmc/articles/PMC2646275/bin/gb-2008-9-12-r171-S6.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC2646275/bin/gb-2008-9-12-r171-S7.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC2646275/bin/gb-2008-9-12-r171-S8.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC2646275/bin/gb-2008-9-12-r171-S9.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC2646275/bin/gb-2008-9-12-r171-S10.pdf
Authors & Co-Authors
Neafsey, Daniel E.
United States, Cambridge
Broad Institute
Schaffner, Stephen F.
United States, Cambridge
Broad Institute
Volkman, Sarah K.
United States, Boston
Harvard T.h. Chan School of Public Health
United States, Boston
Simmons University
Park, Daniel J.
United States, Cambridge
Broad Institute
Montgomery, Philip G.
United States, Cambridge
Broad Institute
Milner, Danny Arnold
United States, Boston
Harvard T.h. Chan School of Public Health
Lukens, Amanda K.
United States, Boston
Harvard T.h. Chan School of Public Health
Rosen, David M.
United States, Boston
Harvard T.h. Chan School of Public Health
Daniels, Rachel F.
United States, Cambridge
Broad Institute
Houde, Nathan
United States, Cambridge
Broad Institute
Cortese, Joseph F.
United States, Cambridge
Broad Institute
Tyndall, Erin
United States, Cambridge
Broad Institute
Gates, Casey
United States, Cambridge
Broad Institute
Stange-Thomann, Nicole
United States, Cambridge
Broad Institute
Sarr, Ousmane
Senegal, Dakar
Université Cheikh Anta Diop de Dakar
Ndiaye, Daouda F.
Senegal, Dakar
Université Cheikh Anta Diop de Dakar
Ndir, Oumar
Senegal, Dakar
Université Cheikh Anta Diop de Dakar
Mboup, Souleymane
Senegal, Dakar
Université Cheikh Anta Diop de Dakar
Ferreira, Marcelo Urbano
Brazil, Sao Paulo
Universidade de São Paulo
Moraes, Sandra L.
Brazil, Sao Paulo
Universidade de São Paulo
Dash, Aditya Prasad
India, New Delhi
National Institute of Malaria Research India
Chitnis, Chetan E.
Italy, Trieste
International Centre for Genetic Engineering and Biotechnology
Wiegand, Roger C.
United States, Cambridge
Broad Institute
Hartl, Daniel L.
United States, Cambridge
Harvard University
Birren, Bruce W.
United States, Cambridge
Broad Institute
Lander, Eric S.
United States, Cambridge
Broad Institute
Sabeti., Pardis C.
United States, Cambridge
Broad Institute
Wirth, Dyann F.
United States, Boston
Harvard T.h. Chan School of Public Health
Statistics
Citations: 125
Authors: 28
Affiliations: 8
Identifiers
Doi:
10.1186/gb-2008-9-12-r171
ISSN:
14747596
e-ISSN:
1474760X
Research Areas
Genetics And Genomics
Infectious Diseases
Study Design
Cross Sectional Study
Cohort Study