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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
Population genetic analysis of plasmodium falciparum parasites using a customized illumina goldengate genotyping assay
PLoS ONE, Volume 6, No. 6, Article e20251, Year 2011
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Description
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. © 2011 Campino et al.
Available Materials
https://efashare.b-cdn.net/share/pmc/articles/PMC3108946/bin/pone.0020251.s001.tif
https://efashare.b-cdn.net/share/pmc/articles/PMC3108946/bin/pone.0020251.s002.tif
https://efashare.b-cdn.net/share/pmc/articles/PMC3108946/bin/pone.0020251.s003.docx
https://efashare.b-cdn.net/share/pmc/articles/PMC3108946/bin/pone.0020251.s004.xlsx
https://efashare.b-cdn.net/share/pmc/articles/PMC3108946/bin/pone.0020251.s005.docx
https://efashare.b-cdn.net/share/pmc/articles/PMC3108946/bin/pone.0020251.s006.docx
Authors & Co-Authors
Campino, Susana G.
Unknown Affiliation
Auburn, Sarah A.
Unknown Affiliation
Kivinen, Katja J.
Unknown Affiliation
Zongo, Issaka D.
Unknown Affiliation
Ouedraogo, Jean Bosco
Unknown Affiliation
Mangano, Valentina Dianora
Unknown Affiliation
Djimde, Abdoulaye A.
Unknown Affiliation
Doumbo, Ogobara K.
Unknown Affiliation
Kiara, Steven M.
Unknown Affiliation
Nzila, Alexis M.
Unknown Affiliation
Borrmann, Steffen
Unknown Affiliation
Marsh, Kevin
Unknown Affiliation
Michon, Pascal A.
Unknown Affiliation
Mueller, Ivo
Unknown Affiliation
Siba, Peter Max
Unknown Affiliation
Jiang, Hongying
Unknown Affiliation
Su, Xinzhuan
Unknown Affiliation
Amaratunga, Chanaki
Unknown Affiliation
Socheat, Duong
Unknown Affiliation
Fairhurst, Rick M.
Unknown Affiliation
Imwong, Mallika
Unknown Affiliation
Anderson, Timothy J.C.
Unknown Affiliation
Nosten, François Henry
Unknown Affiliation
White, Nicholas J.
Unknown Affiliation
Gwilliam, Rhian G.
Unknown Affiliation
Deloukas, Panos
Unknown Affiliation
MacInnis, Bronwyn L.
Unknown Affiliation
Newbold, Chris I.
Unknown Affiliation
Rockett, Kirk A.
Unknown Affiliation
Clark, Taane Gregory
Unknown Affiliation
Kwiatkowski, Dominic P.
Unknown Affiliation
Statistics
Citations: 49
Authors: 31
Affiliations: 18
Identifiers
Doi:
10.1371/journal.pone.0020251
e-ISSN:
19326203
Research Areas
Genetics And Genomics
Infectious Diseases
Study Design
Cross Sectional Study
Study Locations
Multi-countries