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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
biochemistry, genetics and molecular biology
A genome-wide map of diversity in Plasmodium falciparum
Nature Genetics, Volume 39, No. 1, Year 2007
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Description
Genetic variation allows the malaria parasite Plasmodium falciparum to overcome chemotherapeutic agents, vaccines and vector control strategies and remain a leading cause of global morbidity and mortality. Here we describe an initial survey of genetic variation across the P. falciparum genome. We performed extensive sequencing of 16 geographically diverse parasites and identified 46,937 SNPs, demonstrating rich diversity among P. falciparum parasites (π = 1.16 × 10-3) and strong correlation with gene function. We identified multiple regions with signatures of selective sweeps in drug-resistant parasites, including a previously unidentified 160-kb region with extremely low polymorphism in pyrimethamine-resistant parasites. We further characterized 54 worldwide isolates by genotyping SNPs across 20 genomic regions. These data begin to define population structure among African, Asian and American groups and illustrate the degree of linkage disequilibrium, which extends over relatively short distances in African parasites but over longer distances in Asian parasites. We provide an initial map of genetic diversity in P. falciparum and demonstrate its potential utility in identifying genes subject to recent natural selection and in understanding the population genetics of this parasite. © 2006 Nature Publishing Group.
Authors & Co-Authors
Volkman, Sarah K.
United States, Boston
Harvard T.h. Chan School of Public Health
Sabeti., Pardis C.
United States, Cambridge
Broad Institute
DeCaprio, David
United States, Cambridge
Broad Institute
Neafsey, Daniel E.
United States, Cambridge
Broad Institute
Schaffner, Stephen F.
United States, Cambridge
Broad Institute
Milner, Danny Arnold
United States, Boston
Harvard T.h. Chan School of Public Health
Daily, Johanna Patricia
United States, Boston
Harvard T.h. Chan School of Public Health
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
Duraisingh, Manoj Theodore
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
Derr, Alan
United States, Cambridge
Broad Institute
Stange-Thomann, Nicole
United States, Cambridge
Broad Institute
Waggoner, Skye
United States, Cambridge
Broad Institute
Onofrio, Robert C.
United States, Cambridge
Broad Institute
Ziaugra, Liuda
United States, Cambridge
Broad Institute
Mauceli, Evan W.
United States, Cambridge
Broad Institute
Gnerre, Sante
United States, Cambridge
Broad Institute
Jaffe, David B.
United States, Cambridge
Broad Institute
Zainoun, Joanne
United States, Cambridge
Broad Institute
Wiegand, Roger C.
United States, Cambridge
Broad Institute
Birren, Bruce W.
United States, Cambridge
Broad Institute
Hartl, Daniel L.
United States, Cambridge
Harvard University
Galagan, James E.
United States, Cambridge
Broad Institute
Lander, Eric S.
United States, Cambridge
Broad Institute
United States, Cambridge
Massachusetts Institute of Technology
United States, Cambridge
Whitehead Institute
United States, Boston
Harvard Medical School
Wirth, Dyann F.
United States, Boston
Harvard T.h. Chan School of Public Health
United States, Cambridge
Broad Institute
Statistics
Citations: 316
Authors: 28
Affiliations: 7
Identifiers
Doi:
10.1038/ng1930
ISSN:
10614036
e-ISSN:
15461718
Research Areas
Genetics And Genomics
Infectious Diseases
Study Design
Cross Sectional Study
Study Approach
Quantitative
Study Locations
Multi-countries