title: Population genetic analysis of Plasmodium falciparum parasites using a customized Illumina GoldenGate genotyping assay.
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.
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, United Kingdom. sc11@sanger.ac.uk
authors.forename: Susana
authors.initials: S
authors.lastname: Campino
authors.forename: Sarah
authors.initials: S
authors.lastname: Auburn
authors.forename: Katja
authors.initials: K
authors.lastname: Kivinen
authors.forename: Issaka
authors.initials: I
authors.lastname: Zongo
authors.forename: Jean-Bosco
authors.initials: JB
authors.lastname: Ouedraogo
authors.forename: Valentina
authors.initials: V
authors.lastname: Mangano
authors.forename: Abdoulaye
authors.initials: A
authors.lastname: Djimde
authors.forename: Ogobara K
authors.initials: OK
authors.lastname: Doumbo
authors.forename: Steven M
authors.initials: SM
authors.lastname: Kiara
authors.forename: Alexis
authors.initials: A
authors.lastname: Nzila
authors.forename: Steffen
authors.initials: S
authors.lastname: Borrmann
authors.forename: Kevin
authors.initials: K
authors.lastname: Marsh
authors.forename: Pascal
authors.initials: P
authors.lastname: Michon
authors.forename: Ivo
authors.initials: I
authors.lastname: Mueller
authors.forename: Peter
authors.initials: P
authors.lastname: Siba
authors.forename: Hongying
authors.initials: H
authors.lastname: Jiang
authors.forename: Xin-Zhuan
authors.initials: XZ
authors.lastname: Su
authors.forename: Chanaki
authors.initials: C
authors.lastname: Amaratunga
authors.forename: Duong
authors.initials: D
authors.lastname: Socheat
authors.forename: Rick M
authors.initials: RM
authors.lastname: Fairhurst
authors.forename: Mallika
authors.initials: M
authors.lastname: Imwong
authors.forename: Timothy
authors.initials: T
authors.lastname: Anderson
authors.forename: François
authors.initials: F
authors.lastname: Nosten
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: White
authors.forename: Rhian
authors.initials: R
authors.lastname: Gwilliam
authors.forename: Panos
authors.initials: P
authors.lastname: Deloukas
authors.forename: Bronwyn
authors.initials: B
authors.lastname: MacInnis
authors.forename: Christopher I
authors.initials: CI
authors.lastname: Newbold
authors.forename: Kirk
authors.initials: K
authors.lastname: Rockett
authors.forename: Taane G
authors.initials: TG
authors.lastname: Clark
authors.forename: Dominic P
authors.initials: DP
authors.lastname: Kwiatkowski
mesh_terms: D019976:Cloning, Organism; D046508:Culture Techniques; D016054:DNA, Protozoan / Q000235:genetics / Q000302:isolation & purification; D056426:Genetic Loci / Q000235:genetics; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D007753:Laboratories; D016778:Malaria, Falciparum; D010963:Plasmodium falciparum / Q000235:genetics* / Q000254:growth & development / Q000302:isolation & purification* / Q000502:physiology; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D013997:Time Factors
chemical_list: D016054:DNA, Protozoan