ArticleMolecular ecology resources2022
Design and implementation of multiplexed amplicon sequencing panels to serve genomic epidemiology of infectious disease: A malaria case study.
Article in Molecular ecology resources, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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Who cites it
58 citing papers in PubMed, 71 citations in OpenAlex.
- Rapid multiplexed nanopore amplicon sequencing to distinguish Plasmodium falciparum recrudescence from new infection in antimalarial drug trials.Scientific reports · 2025Trial
- Microhaplotype deep sequencing assays to capture Plasmodium vivax infection lineages.Nature communications · 2025Trial
- Anti-sporozoite monoclonal antibody for malaria prevention: secondary efficacy outcome of a phase 2 randomized trial.Nature medicine · 2025Trial
- Sickle cell haemoglobin status shapes malaria parasite genotype in asymptomatic infections.Nature microbiology · 2026Article
- Genetic Evidence of Cross-Border Plasmodium vivax Spread in a Malaria Pre-elimination Region of South Asia.The Journal of infectious diseases · 2026Article
- 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
- Genotypic analysis of Plasmodium falciparum malaria parasites in a clinical trial of RTS,S vaccination in combination with seasonal malaria chemoprevention.Malaria journal · 2026Article
- Integrated evaluation of antibody responses to mosquitoes and mosquito-borne pathogens using highly multiplexed serology.Science advances · 2026Article
- UnderstandingiScience · 2026Article
- Continental-scale genomic surveillance of Plasmodium falciparum malaria across sub-Saharan Africa with rapid nanopore sequencing.Nature communications · 2026Article
- Classification of outcomes in antimalarial therapeutic efficacy studies with Aster.Antimicrobial agents and chemotherapy · 2026Article
- PvGTSeq and PvCRiSP: Two amplicon-based targeted sequencing panels for Plasmodium vivax.PLoS neglected tropical diseases · 2026Article
- Temporal trends inmedRxiv : the preprint server for health sciences · 2026Article
- SIMPLseq: a high-sensitivity Plasmodium falciparum genotyping and PCR contamination tracking tool.Malaria journal · 2026Article
- Complexity of Infection andmedRxiv : the preprint server for health sciences · 2026Article
- Haplotype diversity ofFrontiers in parasitology · 2026Article
- Article
- 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
- Amplicon-based DNA sequencing to characterize Duffy antigen polymorphisms and analysis of Duffy blood system and glucose-6-phosphate dehydrogenase deficiency in Mauritania.PLoS neglected tropical diseases · 2025Article
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Authors and funding
22 authors at 8 institutions in 6 countries.
Funding
Abstract
Multiplexed PCR amplicon sequencing (AmpSeq) is an increasingly popular application for cost-effective monitoring of threatened species and managed wildlife populations, and shows strong potential for the genomic epidemiology of infectious disease. AmpSeq data from infectious microbes can inform disease control in multiple ways, such as by measuring drug resistance marker prevalence, distinguishing imported from local cases, and determining the effectiveness of therapeutics. We describe the design and comparative evaluation of two new AmpSeq assays for Plasmodium falciparum malaria parasites: a four-locus panel ("4CAST") composed of highly diverse antigens, and a 129-locus panel ("AMPLseq") composed of drug resistance markers, highly diverse loci for inferring relatedness, and a locus to detect Plasmodium vivax co-infection. We explore the performance of each panel in various public health use cases with in silico simulations as well as empirical experiments. The 4CAST panel appears highly suitable for evaluating the number of distinct parasite strains within samples (complexity of infection), showing strong performance across a wide range of parasitaemia levels without a DNA pre-amplification step. For relatedness inference, the larger AMPLseq panel performs similarly to two existing panels of comparable size, despite differences in the data and approach used for designing each panel. Finally, we describe an R package (paneljudge) that facilitates the design and comparative evaluation of genetic panels for relatedness estimation, and we provide general guidance on the design and implementation of AmpSeq panels for the genomic epidemiology of infectious disease.
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Registered trials
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