Population genetic analysis of plasmodium falciparum parasites using a customized illumina goldengate genotyping assay

Susana Campino, Sarah Auburn, Katja Kivinen, Issaka Zongo, Jean Bosco Ouedraogo, Valentina Mangano, Abdoulaye Djimde, Ogobara K. Doumbo, Steven M. Kiara, Alexis Nzila, Steffen Borrmann, Kevin Marsh, Pascal Michon, Ivo Mueller, Peter Siba, Hongying Jiang, Xin Zhuan Su, Chanaki Amaratunga, Duong Socheat, Rick M. FairhurstMallika Imwong, Timothy Anderson, François Nosten, Nicholas J. White, Rhian Gwilliam, Panos Deloukas, Bronwyn MacInnis, Christopher I. Newbold, Kirk Rockett, Taane G. Clark, Dominic P. Kwiatkowski

Research output: Contribution to journalArticlepeer-review

36 Scopus citations

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.

Original languageEnglish (US)
Article numbere20251
JournalPloS one
Volume6
Issue number6
DOIs
StatePublished - 2011
Externally publishedYes

ASJC Scopus subject areas

  • General

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