ArticlePloS one2011
Population genetic analysis of Plasmodium falciparum parasites using a customized Illumina GoldenGate genotyping assay.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed, 52 citations in OpenAlex.
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- Comparing newly developed SNP barcode panels with microsatellites to explore population genetics of malaria parasites in the Peruvian Amazon.Frontiers in genetics · 2024Article
- CRISPR-Cas13 in malaria parasite: Diagnosis and prospective gene function identification.Frontiers in microbiology · 2023Review
- Whole Genome Sequencing Contributions and Challenges in Disease Reduction Focused on Malaria.Biology · 2022Review
- Comparative Analysis of Plasmodium falciparum Genotyping via SNP Detection, Microsatellite Profiling, and Whole-Genome Sequencing.Antimicrobial agents and chemotherapy · 2022Article
- Genomic approaches for monitoring transmission dynamics of malaria: A case for malaria molecular surveillance in Sub-Saharan Africa.Frontiers in epidemiology · 2022Review
- A genotyping assay to determine geographic origin and transmission potential of Plasmodium falciparum malaria cases.Communications biology · 2021Article
- Advances and opportunities in malaria population genomics.Nature reviews. Genetics · 2021Review
- Diversify and Conquer: The Vaccine Escapism ofMicroorganisms · 2020Review
- Investigating the drivers of the spatio-temporal patterns of genetic differences between Plasmodium falciparum malaria infections in Kilifi County, Kenya.Scientific reports · 2019Article
- Strengthening Surveillance Systems for Malaria Elimination by Integrating Molecular and Genomic Data.Tropical medicine and infectious disease · 2019Review
- Genetic diversity and drug resistance surveillance of Plasmodium falciparum for malaria elimination: is there an ideal tool for resource-limited sub-Saharan Africa?Malaria journal · 2019Review
- Genome-Wide Analysis of Genetic Diversity inFrontiers in genetics · 2019Article
- Genetic Profiling Reveals High Allelic Diversity, Heterozygosity and Antigenic Diversity in the Clinical Isolates of theFrontiers in physiology · 2019Article
- Infectivity of Chronic Malaria Infections and Its Consequences for Control and Elimination.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2018Article
- Molecular approaches to determine the multiplicity of Plasmodium infections.Malaria journal · 2018Review
- Malaria Epidemiology at the Clone Level.Trends in parasitology · 2017Review
- Dual-strain genital herpes simplex virus type 2 (HSV-2) infection in the US, Peru, and 8 countries in sub-Saharan Africa: A nested cross-sectional viral genotyping study.PLoS medicine · 2017Article
- Quantifying connectivity between local Plasmodium falciparum malaria parasite populations using identity by descent.PLoS genetics · 2017Article
Corrections and comments
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Authors and funding
31 authors at 18 institutions in 10 countries.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.