Susana CampinoSarah AuburnKatja KivinenIssaka ZongoJean Bosco OuedraogoValentina ManganoAbdoulaye DjimdeOgobara K. DoumboSteven M. KiaraAlexis NzilaSteffen BorrmannKevin MarshPascal MichonIvo MuellerPeter SibaHongying JiangXin Zhuan SuChanaki AmaratungaDuong SocheatRick M. FairhurstMallika ImwongTimothy AndersonFrançois NostenNicholas J. WhiteRhian GwilliamPanos DeloukasBronwyn MacInnisChristopher I. NewboldKirk RockettTaane G. ClarkDominic P. KwiatkowskiWellcome Trust Sanger InstituteMenzies School of Health ResearchInstitut de Recherche en Sciences de la SantéUniversita degli Studi di Roma La SapienzaUniversity of Bamako Faculty of Medicine, Pharmacy and Odonto-StomatologyWellcome Trust Research Laboratories NairobiPapua New Guinea Institute of Medical ResearchDivine Word UniversityNational Institute of Allergy and Infectious DiseasesNational Center for Parasitology, Entomology and Malaria ControlMahidol UniversityTexas Biomedical Research InstituteShoklo Malaria Research UnitJohn Radcliffe HospitalWellcome Trust Centre for Human GeneticsLondon School of Hygiene & Tropical Medicine2018-05-032018-05-032011-06-13PLoS ONE. Vol.6, No.6 (2011)193262032-s2.0-79958084112https://repository.li.mahidol.ac.th/handle/20.500.14594/11306The 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.Mahidol UniversityAgricultural and Biological SciencesBiochemistry, Genetics and Molecular BiologyArticleSCOPUS10.1371/journal.pone.0020251