Publication: Population genetic analysis of Plasmodium falciparum parasites using a customized Illumina GoldenGate genotyping assay.
Accepted Date
2011-04-28
Issued Date
2011
Copyright Date
2011
Resource Type
Language
eng
ISSN
1932-6203 (electronic)
Rights
Mahidol University
Rights Holder(s)
PLos ONE
Bibliographic Citation
Campino S, Auburn S, Kivinen K, Zongo I, Ouedraogo JB, Mangano V, et al. Population genetic analysis of Plasmodium falciparum parasites using a customized Illumina GoldenGate genotyping assay. PLoS One. 2011;6(6):e20251
Suggested Citation
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, Chanaki Amaratunga, Socheat, Duong, Fairhurst, Rick M., Mallika Imwong, มัลลิกา อิ่มวงศ์, Anderson, Timothy, Nosten, Francois, White, Nicholas J., Gwilliam, Rhian, Deloukas, Panos, MacInnis, Bronwyn, Newbold, Christopher I., Rockett, Kirk, Clark, Taane G., Kwiatkowski, Dominic P. 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, et al. Population genetic analysis of Plasmodium falciparum parasites using a customized Illumina GoldenGate genotyping assay. PLoS One. 2011;6(6):e20251. Retrieved from: https://repository.li.mahidol.ac.th/handle/20.500.14594/644
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Title
Population genetic analysis of Plasmodium falciparum parasites using a customized Illumina GoldenGate genotyping assay.
Author(s)
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
Chanaki Amaratunga
Socheat, Duong
Fairhurst, Rick M.
Mallika Imwong
มัลลิกา อิ่มวงศ์
Anderson, Timothy
Nosten, Francois
White, Nicholas J.
Gwilliam, Rhian
Deloukas, Panos
MacInnis, Bronwyn
Newbold, Christopher I.
Rockett, Kirk
Clark, Taane G.
Kwiatkowski, Dominic P.
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
Chanaki Amaratunga
Socheat, Duong
Fairhurst, Rick M.
Mallika Imwong
มัลลิกา อิ่มวงศ์
Anderson, Timothy
Nosten, Francois
White, Nicholas J.
Gwilliam, Rhian
Deloukas, Panos
MacInnis, Bronwyn
Newbold, Christopher I.
Rockett, Kirk
Clark, Taane G.
Kwiatkowski, Dominic P.
Editor(s)
Corresponding Author(s)
Other Contributor(s)
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.