ArticleThe Journal of infectious diseases2022
Sensitive, Highly Multiplexed Sequencing of Microhaplotypes From the Plasmodium falciparum Heterozygome.
Article in The Journal of infectious diseases, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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Who cites it
56 citing papers in PubMed.
- Rapid multiplexed nanopore amplicon sequencing to distinguish Plasmodium falciparum recrudescence from new infection in antimalarial drug trials.Scientific reports · 2025Trial
- PvGAP: Development of a Globally Applicable, Highly Multiplexed Microhaplotype Amplicon Panel for Plasmodium vivax.The Journal of infectious diseases · 2026Article
- MalDeepSeq panel: A targeted ultra-deep sequencing approach to trace drug resistance markers in Plasmodium falciparum.Cell reports methods · 2026Article
- Spatiotemporal differentiation of Plasmodium vivax populations in the western Greater Mekong Subregion using a 22-SNP barcode.PLoS neglected tropical diseases · 2026Article
- Temporal trends inmedRxiv : the preprint server for health sciences · 2026Article
- Accuracy of Plasmodium falciparum genetic data for estimating parasite prevalence and malaria incidence in Uganda.Malaria journal · 2026Article
- Malaria-MOI: A flexible and scalable tool for predicting multiplicity of infection in malaria parasites.Genome medicine · 2026Article
- Target product profiles of laboratory and data analytical frameworks for genotyping to monitor antimalarial efficacy.PLOS global public health · 2026Article
- Molecular Surveillance of Malaria in Nigeria Reveals a Low Frequency of Antimalarial Resistance Markers and Clonal Expansion of Chloroquine-Sensitive Infections.Open forum infectious diseases · 2026Article
- The Portable Microhaplotype Object and Tools.bioRxiv : the preprint server for biology · 2025Article
- Accuracy of Plasmodium falciparum genetic data for estimating parasite prevalence and malaria incidence in Uganda.Research square · 2025Article
- Toward Setting Minimum and Optimal Data to Report for Malaria Molecular Surveillance with Targeted Sequencing: The "What" and "Why".The American journal of tropical medicine and hygiene · 2025Article
- Measuring changes ineLife · 2025Article
- Article
- Performance of molecular inversion probe DR23K and Paragon MADMalaria journal · 2025Article
- Var genes, strain hyperdiversity, and malaria transmission dynamics.Trends in parasitology · 2025Review
- Genetic surveillance reveals low but sustained malaria transmission with clonal replacement in Sao Tome and Principe.Communications medicine · 2025Article
- Potential and pitfalls of using identity-by-descent for malaria genomic surveillance.Trends in parasitology · 2025Review
- Sensitive and modular amplicon sequencing of Plasmodium falciparum diversity and resistance for research and public health.Scientific reports · 2025Article
- Sensitive and modular amplicon sequencing ofbioRxiv : the preprint server for biology · 2025Article
Corrections and comments
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Authors and funding
14 authors.
Funding
Abstract
backgroundTargeted next-generation sequencing offers the potential for consistent, deep coverage of information-rich genomic regions to characterize polyclonal Plasmodium falciparum infections. However, methods to identify and sequence these genomic regions are currently limited.
methodsA bioinformatic pipeline and multiplex methods were developed to identify and simultaneously sequence 100 targets and applied to dried blood spot (DBS) controls and field isolates from Mozambique. For comparison, whole-genome sequencing data were generated for the same controls.
resultsUsing publicly available genomes, 4465 high-diversity genomic regions suited for targeted sequencing were identified, representing the P. falciparum heterozygome. For this study, 93 microhaplotypes with high diversity (median expected heterozygosity = 0.7) were selected along with 7 drug resistance loci. The sequencing method achieved very high coverage (median 99%), specificity (99.8%), and sensitivity (90% for haplotypes with 5% within sample frequency in dried blood spots with 100 parasites/µL). In silico analyses revealed that microhaplotypes provided much higher resolution to discriminate related from unrelated polyclonal infections than biallelic single-nucleotide polymorphism barcodes.
conclusionsThe bioinformatic and laboratory methods outlined here provide a flexible tool for efficient, low-cost, high-throughput interrogation of the P. falciparum genome, and can be tailored to simultaneously address multiple questions of interest in various epidemiological settings.
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