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Title: Population genetic analysis of plasmodium falciparum parasites using a customized illumina goldengate genotyping assay
Authors: 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. Fairhurst
Mallika 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
Wellcome Trust Sanger Institute
Menzies School of Health Research
Institut de Recherche en Sciences de la Santé
Universita degli Studi di Roma La Sapienza
University of Bamako Faculty of Medicine, Pharmacy and Odonto-Stomatology
Wellcome Trust Research Laboratories Nairobi
Papua New Guinea Institute of Medical Research
Divine Word University
National Institute of Allergy and Infectious Diseases
National Center for Parasitology, Entomology and Malaria Control
Mahidol University
Texas Biomedical Research Institute
Shoklo Malaria Research Unit
John Radcliffe Hospital
Wellcome Trust Centre for Human Genetics
London School of Hygiene & Tropical Medicine
Keywords: Agricultural and Biological Sciences;Biochemistry, Genetics and Molecular Biology
Issue Date: 13-Jun-2011
Citation: PLoS ONE. Vol.6, No.6 (2011)
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. © 2011 Campino et al.
ISSN: 19326203
Appears in Collections:Scopus 2011-2015

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