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

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 a...

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Main Authors:	Amambua-Ngwa, Alfred, Park, Daniel J., Volkman, Sarah K., Barnes, Kayla G., Bei, Amy K., Lukens, Amanda K., Sene, Papa, Van Tyne, Daria, Ndiaye, Daouda, Wirth, Dyann F., Conway, David J., Neafsey, Daniel E., Schaffner, Stephen F.
Format:	Online
Language:	English
Published:	Oxford University Press 2012
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3472499/

id	pubmed-3472499
recordtype	oai_dc
spelling	pubmed-34724992012-10-16 SNP Genotyping Identifies New Signatures of Selection in a Deep Sample of West African Plasmodium falciparum Malaria Parasites Amambua-Ngwa, Alfred Park, Daniel J. Volkman, Sarah K. Barnes, Kayla G. Bei, Amy K. Lukens, Amanda K. Sene, Papa Van Tyne, Daria Ndiaye, Daouda Wirth, Dyann F. Conway, David J. Neafsey, Daniel E. Schaffner, Stephen F. Letters 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. Oxford University Press 2012-11 2012-07-11 /pmc/articles/PMC3472499/ /pubmed/22688945 http://dx.doi.org/10.1093/molbev/mss151 Text en © The Author 2012. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Amambua-Ngwa, Alfred Park, Daniel J. Volkman, Sarah K. Barnes, Kayla G. Bei, Amy K. Lukens, Amanda K. Sene, Papa Van Tyne, Daria Ndiaye, Daouda Wirth, Dyann F. Conway, David J. Neafsey, Daniel E. Schaffner, Stephen F.
spellingShingle	Amambua-Ngwa, Alfred Park, Daniel J. Volkman, Sarah K. Barnes, Kayla G. Bei, Amy K. Lukens, Amanda K. Sene, Papa Van Tyne, Daria Ndiaye, Daouda Wirth, Dyann F. Conway, David J. Neafsey, Daniel E. Schaffner, Stephen F. SNP Genotyping Identifies New Signatures of Selection in a Deep Sample of West African Plasmodium falciparum Malaria Parasites
author_facet	Amambua-Ngwa, Alfred Park, Daniel J. Volkman, Sarah K. Barnes, Kayla G. Bei, Amy K. Lukens, Amanda K. Sene, Papa Van Tyne, Daria Ndiaye, Daouda Wirth, Dyann F. Conway, David J. Neafsey, Daniel E. Schaffner, Stephen F.
author_sort	Amambua-Ngwa, Alfred
title	SNP Genotyping Identifies New Signatures of Selection in a Deep Sample of West African Plasmodium falciparum Malaria Parasites
title_short	SNP Genotyping Identifies New Signatures of Selection in a Deep Sample of West African Plasmodium falciparum Malaria Parasites
title_full	SNP Genotyping Identifies New Signatures of Selection in a Deep Sample of West African Plasmodium falciparum Malaria Parasites
title_fullStr	SNP Genotyping Identifies New Signatures of Selection in a Deep Sample of West African Plasmodium falciparum Malaria Parasites
title_full_unstemmed	SNP Genotyping Identifies New Signatures of Selection in a Deep Sample of West African Plasmodium falciparum Malaria Parasites
title_sort	snp genotyping identifies new signatures of selection in a deep sample of west african plasmodium falciparum malaria parasites
description	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.
publisher	Oxford University Press
publishDate	2012
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3472499/
_version_	1611916598910648320

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

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