ArticleMalaria journal2021
Optimization of whole-genome sequencing of Plasmodium falciparum from low-density dried blood spot samples.
Article in Malaria journal, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed.
- Efficacies of artemether-lumefantrine, artesunate-amodiaquine, dihydroartemisinin-piperaquine, and artesunate-pyronaridine for the treatment of uncomplicated Plasmodium falciparum malaria in children aged 6 months to 10 years in Uganda: a randomised, open-label, phase 4 clinical trial.The Lancet. Infectious diseases · 2026Trial
- Multiple local PfDHFR I164L haplotype expansions drive Plasmodium falciparum antifolate resistance in Uganda.Nature communications · 2026Article
- Challenges in Malaria Diagnosis and Treatment in Kinshasa Province, Democratic Republic of the Congo.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2026Article
- Population genomics of Plasmodium malariae from 4 African countries.JCI insight · 2026Article
- Development of an Oxford nanopore sequencing technology-based whole genome sequencing method for Plasmodium falciparum to support malaria molecular surveillance.Scientific reports · 2026Article
- Quantifying the Role of Importation on Sustained Malaria Transmission in a Low-to-Moderate Burden Region of Southwest Uganda.The Journal of infectious diseases · 2026Article
- Malaria control and the unexpected spread of diagnostic-resistantbioRxiv : the preprint server for biology · 2026Article
- Accuracy of Plasmodium falciparum genetic data for estimating parasite prevalence and malaria incidence in Uganda.Malaria journal · 2026Article
- Genomic Plasticity and Molecular Mechanisms of Antimalarial Drug Resistance in Plasmodium falciparum: Implications for Treatment Failure and Genomic Surveillance.BioMed research international · 2026Review
- Accuracy of Plasmodium falciparum genetic data for estimating parasite prevalence and malaria incidence in Uganda.Research square · 2025Article
- High prevalence and emerging positive association of kelch13 R622I and HRP2-based RDT negativity in Plasmodium falciparum in northern Ethiopia.PLoS pathogens · 2025Article
- High connectivity and low differentiation of Plasmodium falciparum parasite populations in a setting with high seasonal migration.Scientific reports · 2025Article
- Rising prevalence of Plasmodium falciparum Artemisinin partial resistance mutations in Ethiopia.Communications medicine · 2025Article
- High connectivity and low differentiation of Plasmodium falciparum parasite populations in a setting with high seasonal migration.Research square · 2025Article
- Artemisinin resistantmedRxiv : the preprint server for health sciences · 2025Article
- Genetic surveillance reveals low but sustained malaria transmission with clonal replacement in Sao Tome and Principe.Communications medicine · 2025Article
- Field evaluation of the Bioline Malaria Ag P.f/Pan rapid diagnostic test: causes of microscopy discordance and performance in Uganda.Malaria journal · 2025Article
- Geographical Heterogeneity in Antimalarial Resistance Markers Revealed by Genomic Surveillance in Angola, 2023.medRxiv : the preprint server for health sciences · 2025Article
- Assessment of Malaria Rapid Diagnostic Tests and Histidine-Rich Protein 2 Deletions among Asymptomatic Children and Adults in Bagamoyo, Tanzania.The American journal of tropical medicine and hygiene · 2025Article
- Sensitive and modular amplicon sequencing of Plasmodium falciparum diversity and resistance for research and public health.Scientific reports · 2025Article
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6 authors.
Funding
Abstract
backgroundWhole-genome sequencing (WGS) is becoming increasingly useful to study the biology, epidemiology, and ecology of malaria parasites. Despite ease of sampling, DNA extracted from dried blood spots (DBS) has a high ratio of human DNA compared to parasite DNA, which poses a challenge for downstream genetic analyses. The effects of multiple methods for DNA extraction, digestion of methylated DNA, and amplification were evaluated on the quality and fidelity of WGS data recovered from DBS.
methodsLow parasite density mock DBS samples were created, extracted either with Tween-Chelex or QIAamp, treated with or without McrBC, and amplified with one of three different amplification techniques (two sWGA primer sets and one rWGA). Extraction conditions were evaluated on performance of sequencing depth, percentiles of coverage, and expected SNP concordance.
resultsAt 100 parasites/μL, Chelex-Tween-McrBC samples had higher coverage (5 × depth = 93% genome) than QIAamp extracted samples (5 × depth = 76% genome). The two evaluated sWGA primer sets showed minor differences in overall genome coverage and SNP concordance, with a newly proposed combination of 20 primers showing a modest improvement in coverage over those previously published.
conclusionsOverall, Tween-Chelex extracted samples that were treated with McrBC digestion and are amplified using 6A10AD sWGA conditions had minimal dropout rate, higher percentages of coverage at higher depth, and more accurate SNP concordance than QiaAMP extracted samples. These findings extend the results of previously reported methods, making whole genome sequencing accessible to a larger number of low density samples that are commonly encountered in cross-sectional surveys.
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