SNP Genotyping Identifies New Signatures of Selection in a Deep Sample of West African Plasmodium falciparum Malaria Parasites

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SNP Genotyping Identifies New Signatures of Selection in a Deep Sample of West African Plasmodium falciparum Malaria Parasites

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Title: SNP Genotyping Identifies New Signatures of Selection in a Deep Sample of West African Plasmodium falciparum Malaria Parasites
Author: Amambua-Ngwa, Alfred; Barnes, Kayla G.; Sene, Papa; Conway, David J.; Park, Daniel John; Volkman, Sarah; Bei, Amy Kristine; Lukens, Amanda Kathleen; Van Tyne, Daria Natalie; Ndiaye, Daouda; Wirth, Dyann Fergus; Neafsey, Daniel Edward; Schaffner, Stephen

Note: Order does not necessarily reflect citation order of authors.

Citation: Amambua-Ngwa, Alfred, Daniel John Park, Sarah Volkman, Kayla G. Barnes, Amy Kristine Bei, Amanda Kathleen Lukens, Papa Sene, et al. 2012. SNP genotyping identifies new signatures of selection in a deep sample of West African Plasmodium falciparum malaria parasites. Molecular Biology and Evolution 29(11): 3249-3253.
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Abstract: We used a high-density single-nucleotide polymorphism array to genotype 75 Plasmodium falciparum isolates recently collected from Senegal and The Gambia to search for signals of selection in this malaria endemic region. We found little geographic or temporal stratification of the genetic diversity among the sampled parasites. Through application of the iHS and REHH haplotype-based tests for positive selection, we found evidence of recent selective sweeps at a known drug resistance locus, at several known antigenic loci, and at several genomic regions not previously identified as sites of recent selection. We discuss the value of deep population-specific genomic analyses for identifying selection signals within sampled endemic populations of parasites, which may correspond to local selection pressures such as distinctive therapeutic regimes or mosquito vectors.
Published Version: doi:10.1093/molbev/mss151
Other Sources: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3472499/pdf/
Terms of Use: This article is made available under the terms and conditions applicable to Other Posted Material, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of-use#LAA
Citable link to this page: http://nrs.harvard.edu/urn-3:HUL.InstRepos:10589639
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