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Population genetic analysis of Plasmodium falciparum parasites using a customized Illumina GoldenGate genotyping assay

Campino, Susana, Auburn, Sarah, Kivinen, Katja, Zongo, Issaka, Ouedraogo, Jean-Bosco, Mangano, Valentina, Djimde, Abdoulaye, Doumbo, Ogobara K., Kiara, Steven M., Nzila, Alexis, Borrmann, Steffen, Marsh, Kevin, Michon, Pascal, Mueller, Ivo, Siba, Peter, Jiang, Hongying, Su, Xin-Zhuan, Amaratunga, Chanaki, Socheat, Duong, Anstey, Nicholas M. and et al. (2011). Population genetic analysis of Plasmodium falciparum parasites using a customized Illumina GoldenGate genotyping assay. PLoS One,6(6):e20251.

Document type: Journal Article
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Title Population genetic analysis of Plasmodium falciparum parasites using a customized Illumina GoldenGate genotyping assay
Author Campino, Susana
Auburn, Sarah
Kivinen, Katja
Zongo, Issaka
Ouedraogo, Jean-Bosco
Mangano, Valentina
Djimde, Abdoulaye
Doumbo, Ogobara K.
Kiara, Steven M.
Nzila, Alexis
Borrmann, Steffen
Marsh, Kevin
Michon, Pascal
Mueller, Ivo
Siba, Peter
Jiang, Hongying
Su, Xin-Zhuan
Amaratunga, Chanaki
Socheat, Duong
Anstey, Nicholas M.
et al.
Journal Name PLoS One
Publication Date 2011
Volume Number 6
Issue Number 6
ISSN 1932-6203   (check CDU catalogue open catalogue search in new window)
Start Page e20251
Total Pages 9
Place of Publication United States
Publisher Public Library of Science
HERDC Category C1 - Journal Article (DEST)
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.
DOI http://dx.doi.org/10.1371/journal.pone.0020251   (check subscription with CDU E-Gateway service for CDU Staff and Students  check subscription with CDU E-Gateway in new window)


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