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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
general
Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing
Nature, Volume 487, No. 7407, Year 2012
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Description
Malaria elimination strategies require surveillance of the parasite population for genetic changes that demand a public health response, such as new forms of drug resistance. Here we describe methods for the large-scale analysis of genetic variation in Plasmodium falciparum by deep sequencing of parasite DNA obtained from the blood of patients with malaria, either directly or after short-term culture. Analysis of 86,158 exonic single nucleotide polymorphisms that passed genotyping quality control in 227 samples from Africa, Asia and Oceania provides genome-wide estimates of allele frequency distribution, population structure and linkage disequilibrium. By comparing the genetic diversity of individual infections with that of the local parasite population, we derive a metric of within-host diversity that is related to the level of inbreeding in the population. An open-access web application has been established for the exploration of regional differences in allele frequency and of highly differentiated loci in the P.falciparum genome. © 2012 Macmillan Publishers Limited. All rights reserved.
Authors & Co-Authors
Manske, Heinrich Magnus
Unknown Affiliation
Miotto, Olivo
Unknown Affiliation
Campino, Susana G.
Unknown Affiliation
Auburn, Sarah A.
Unknown Affiliation
Almagro-Garcia, Jacob
Unknown Affiliation
Maslen, Gareth Ll
Unknown Affiliation
O'Brien, Jack
Unknown Affiliation
Djimde, Abdoulaye A.
Unknown Affiliation
Doumbo, Ogobara K.
Unknown Affiliation
Zongo, Issaka D.
Unknown Affiliation
Ouedraogo, Jean Bosco
Unknown Affiliation
Michon, Pascal A.
Unknown Affiliation
Mueller, Ivo
Unknown Affiliation
Siba, Peter Max
Unknown Affiliation
Nzila, Alexis M.
Unknown Affiliation
Borrmann, Steffen
Unknown Affiliation
Kiara, Steven M.
Unknown Affiliation
Marsh, Kevin
Unknown Affiliation
Jiang, Hongying
Unknown Affiliation
Su, Xinzhuan
Unknown Affiliation
Amaratunga, Chanaki
Unknown Affiliation
Fairhurst, Rick M.
Unknown Affiliation
Socheat, Duong
Unknown Affiliation
Nosten, François Henry
Unknown Affiliation
Imwong, Mallika
Unknown Affiliation
White, Nicholas J.
Unknown Affiliation
Sanders, Mandy J.
Unknown Affiliation
Anastasi, Elisa
Unknown Affiliation
Alcock, Dan
Unknown Affiliation
Drury, Eleanor
Unknown Affiliation
Oyola, Samuel O.
Unknown Affiliation
Quail, Michael A.
Unknown Affiliation
Turner, Daniel J.
Unknown Affiliation
Ruano-Rubio, Valentín
Unknown Affiliation
Jyothi, Dushyanth
Unknown Affiliation
Amenga-Etego, Lucas Naam Kayagre
Unknown Affiliation
Hubbart, Christina S.
Unknown Affiliation
Jeffreys, Anna E.
Unknown Affiliation
Rowlands, Kate
Unknown Affiliation
Sutherland, Colin J.
Unknown Affiliation
Roper, Cally
Unknown Affiliation
Mangano, Valentina Dianora
Unknown Affiliation
Modiano, David
Unknown Affiliation
Tan, John C.
Unknown Affiliation
Ferdig, Michael T.
Unknown Affiliation
Amambua-Ngwa, Alfred
Unknown Affiliation
Conway, David J.
Unknown Affiliation
Takala-Harrison, Shannon L.
Unknown Affiliation
Plowe, Christopher Vv
Unknown Affiliation
Rayner, Julian C.
Unknown Affiliation
Rockett, Kirk A.
Unknown Affiliation
Clark, Taane Gregory
Unknown Affiliation
Newbold, Chris I.
Unknown Affiliation
Berriman, Matthew
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MacInnis, Bronwyn L.
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Kwiatkowski, Dominic P.
Unknown Affiliation
Statistics
Citations: 455
Authors: 56
Affiliations: 20
Identifiers
Doi:
10.1038/nature11174
ISSN:
00280836
e-ISSN:
14764687
Research Areas
Genetics And Genomics
Health System And Policy
Infectious Diseases
Study Design
Cross Sectional Study