ArticleScientific reports2017
Overlap Extension Barcoding for the Next Generation Sequencing and Genotyping of Plasmodium falciparum in Individual Patients in Western Kenya.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
18 citing papers in PubMed.
- Schistosoma Species and Hybrid Genotyping With a Field Deployable Multi-Marker Amplicon Panel.Current protocols · 2026Article
- Molecular tools are crucial for malaria elimination.Molecular biology reports · 2024Review
- Whole Genome Sequencing Contributions and Challenges in Disease Reduction Focused on Malaria.Biology · 2022Review
- Comparative analysis of targeted next-generation sequencing for Plasmodium falciparum drug resistance markers.Scientific reports · 2022Article
- Effect of three years' seasonal malaria chemoprevention on molecular markers of resistance of Plasmodium falciparum to sulfadoxine-pyrimethamine and amodiaquine in Ouelessebougou, Mali.Malaria journal · 2022Article
- Potential Opportunities and Challenges of Deploying Next Generation Sequencing and CRISPR-Cas Systems to Support Diagnostics and Surveillance Towards Malaria Control and Elimination in Africa.Frontiers in cellular and infection microbiology · 2022Review
- Exposure to Diverse Plasmodium falciparum Genotypes Shapes the Risk of Symptomatic Malaria in Incident and Persistent Infections: A Longitudinal Molecular Epidemiologic Study in Kenya.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2021Article
- Antimalarial Drug Resistance and Implications for the WHO Global Technical Strategy.Current epidemiology reports · 2021Review
- High-resolution micro-epidemiology of parasite spatial and temporal dynamics in a high malaria transmission setting in Kenya.Nature communications · 2019Article
- Direct Estimation of Sensitivity ofThe American journal of tropical medicine and hygiene · 2019Article
- Applying next-generation sequencing to track falciparum malaria in sub-Saharan Africa.Malaria journal · 2019Review
- Deployment and utilization of next-generation sequencing of Plasmodium falciparum to guide anti-malarial drug policy decisions in sub-Saharan Africa: opportunities and challenges.Malaria journal · 2019Review
- Proof of concept: used malaria rapid diagnostic tests applied for parallel sequencing for surveillance of molecular markers of anti-malarial resistance in Bissau, Guinea-Bissau during 2014-2017.Malaria journal · 2019Article
- Longitudinal tracking and quantification of individual Plasmodium falciparum clones in complex infections.Scientific reports · 2019Article
- Article
- Molecular approaches to determine the multiplicity of Plasmodium infections.Malaria journal · 2018Review
- Malaria Epidemiology at the Clone Level.Trends in parasitology · 2017Review
- Development of amplicon deep sequencing markers and data analysis pipeline for genotyping multi-clonal malaria infections.BMC genomics · 2017Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Large-scale molecular epidemiologic studies of Plasmodium falciparum parasites have provided insights into parasite biology and transmission, can identify the spread of drug resistance, and are useful in assessing vaccine targets. The polyclonal nature infections in high transmission settings is problematic for traditional genotyping approaches. Next-generation sequencing (NGS) approaches to parasite genotyping allow sensitive detection of minority variants, disaggregation of complex parasite mixtures, and scalable processing of large samples sets. Therefore, we designed, validated, and applied to field parasites an approach that leverages sequencing of individually barcoded samples in a multiplex manner. We utilize variant barcodes, invariant linker sequences and modular template-specific primers to allow for the simultaneous generation of high-dimensional sequencing data of multiple gene targets. This modularity permits a cost-effective and reproducible way to query many genes at once. In mixtures of reference parasite genomes, we quantitatively detected unique haplotypes comprising as little as 2% of a polyclonal infection. We applied this genotyping approach to field-collected parasites collected in Western Kenya in order to simultaneously obtain parasites genotypes at three unlinked loci. In summary, we present a rapid, scalable, and flexible method for genotyping individual parasites that enables molecular epidemiologic studies of parasite evolution, population structure and transmission.
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