Population Genetic Analysis of Plasmodium falciparum Parasites Using a Customized Illumina GoldenGate Genotyping Assay


Campino, S; Auburn, S; Kivinen, K; Zongo, I; Ouedraogo, JB; Mangano, V; Djimde, A; Doumbo, OK; Kiara, SM; Nzila, A; Borrmann, S; Marsh, K; Michon, P; Mueller, I; Siba, P; Jiang, HY; Su, XZ; Amaratunga, C; Socheat, D; Fairhurst, RM; Imwong, M; Anderson, T; Nosten, F; White, NJ; Gwilliam, R; Deloukas, P; MacInnis, B; Newbold, CI; Rockett, K; Clark, TG; Kwiatkowski, DP; (2011) Population Genetic Analysis of Plasmodium falciparum Parasites Using a Customized Illumina GoldenGate Genotyping Assay. PLoS One, 6 (6). ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0020251

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Abstract

The diversity in the Plasmodium falciparum genome can be used to explore parasite population dynamics, with practical applications to malaria control. The ability to identify the geographic origin and trace the migratory patterns of parasites with clinically important phenotypes such as drug resistance is particularly relevant. With increasing single-nucleotide polymorphism (SNP) discovery from ongoing Plasmodium genome sequencing projects, a demand for high SNP and sample throughput genotyping platforms for large-scale population genetic studies is required. Low parasitaemias and multiple clone infections present a number of challenges to genotyping P. falciparum. We addressed some of these issues using a custom 384-SNP Illumina GoldenGate assay on P. falciparum DNA from laboratory clones (long-term cultured adapted parasite clones), short-term cultured parasite isolates and clinical (non-cultured isolates) samples from East and West Africa, Southeast Asia and Oceania. Eighty percent of the SNPs (n = 306) produced reliable genotype calls on samples containing as little as 2 ng of total genomic DNA and on whole genome amplified DNA. Analysis of artificial mixtures of laboratory clones demonstrated high genotype calling specificity and moderate sensitivity to call minor frequency alleles. Clear resolution of geographically distinct populations was demonstrated using Principal Components Analysis (PCA), and global patterns of population genetic diversity were consistent with previous reports. These results validate the utility of the platform in performing population genetic studies of P. falciparum.

Item Type: Article
Keywords: MULTIPLE DISPLACEMENT AMPLIFICATION, ANTIMALARIAL-DRUG RESISTANCE, MALARIA, GENOME, DIVERSITY, MICROSATELLITE, IDENTIFICATION, SEQUENCE, PCR
Faculty and Department: Faculty of Epidemiology and Population Health > Dept of Infectious Disease Epidemiology
Faculty of Infectious and Tropical Diseases > Dept of Pathogen Molecular Biology
Research Centre: Malaria Centre
PubMed ID: 21673999
Web of Science ID: 291356400003
URI: http://researchonline.lshtm.ac.uk/id/eprint/540

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