Data from: SNP genotyping identifies new signatures of selection in a deep sample of West African P. falciparum malaria parasites

Amambua-Ngwa A, Park DJ, Volkman SK, Barnes KG, Bei A, Lukens AK, Sene P, Van Tyne D, Ndiaye D, Wirth DF, Conway DJ, Neafsey DE, Schaffner SF

Date Published: June 12, 2012

DOI: http://dx.doi.org/10.5061/dryad.731f5

 

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Title senegambia_genotype_data
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Description Plasmodium falciparum isolates from Senegal and The Gambia, some DNA directly drawn and some from culture-adapted parasites; only single infections included. SNP calling was as described in (Van Tyne, et al. 2011): Parasite DNA was hybridized to a P. falciparum Affymetrix array containing 74,656 SNP markers and genotypes called using the BRLMM-P algorithm. SNPs were validated by comparing array genotypes with Sanger sequencing genotypes for 17 reference strains (Van Tyne, et al. 2011); perfect concordance was required, as was a minimum 80% call rate. Genomic positions and translations are based on the PlasmoDB v5.0 assembly and annotation.
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When using this data, please cite the original publication:

Amambua-Ngwa A, Park DJ, Volkman SK, Barnes KG, Bei A, Lukens AK, Sene P, Van Tyne D, Ndiaye D, Wirth DF, Conway DJ, Neafsey DE, Schaffner SF (2012) SNP genotyping identifies new signatures of selection in a deep sample of West African P. falciparum malaria parasites. Molecular Biology and Evolution 29(11): 3249-3253. http://dx.doi.org/10.1093/molbev/mss151

Additionally, please cite the Dryad data package:

Amambua-Ngwa A, Park DJ, Volkman SK, Barnes KG, Bei A, Lukens AK, Sene P, Van Tyne D, Ndiaye D, Wirth DF, Conway DJ, Neafsey DE, Schaffner SF (2012) Data from: SNP genotyping identifies new signatures of selection in a deep sample of West African P. falciparum malaria parasites. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.731f5
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