ArticleScientific reports2019
An analysis of large structural variation in global Plasmodium falciparum isolates identifies a novel duplication of the chloroquine resistance associated gene.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 22 citations in OpenAlex.
- Article
- Global-scale population genetic analysis of Plasmodium falciparum identifies region-specific patterns of malaria parasite adaptation.Nature communications · 2026Article
- Replication stress increases de novo CNVs across the malaria parasite genome.Nucleic acids research · 2026Article
- Replication stress increases de novo CNVs across the malaria parasite genome.bioRxiv : the preprint server for biology · 2025Article
- Pooled, Long-read Sequencing for Structural Variant Characterization in Schistosome Populations.Genome biology and evolution · 2025Article
- HapCNV: A Comprehensive Framework for CNV Detection in Low-input DNA Sequencing Data.bioRxiv : the preprint server for biology · 2025Article
- Pf8: an open dataset ofWellcome open research · 2025Article
- Rapid profiling of Plasmodium parasites from genome sequences to assist malaria control.Genome medicine · 2023Article
- Whole Genome Sequencing Contributions and Challenges in Disease Reduction Focused on Malaria.Biology · 2022Review
- Using deep learning to identify recent positive selection in malaria parasite sequence data.Malaria journal · 2021Article
- Single-cell sequencing of the small and AT-skewed genome of malaria parasites.Genome medicine · 2021Article
- Drug resistance profile and clonality of Plasmodium falciparum parasites in Cape Verde: the 2017 malaria outbreak.Malaria journal · 2021Article
- The Future of Livestock Management: A Review of Real-Time Portable Sequencing Applied to Livestock.Genes · 2020Review
- Article
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
The evolution of genetic mechanisms for host immune evasion and anti-malarial resistance has enabled the Plasmodium falciparum malaria parasite to inflict high morbidity and mortality on human populations. Most studies of P. falciparum genetic diversity have focused on single-nucleotide polymorphisms (SNPs), assisting the identification of drug resistance-associated loci such as the chloroquine related crt and sulfadoxine-pyrimethamine related dhfr. Whilst larger structural variants are known to impact adaptation, for example, mdr1 duplications with anti-malarial resistance, no large-scale, genome-wide study on clinical isolates has been undertaken using whole genome sequencing data. By applying a structural variant detection pipeline across whole genome sequence data from 2,855 clinical isolates in 21 malaria-endemic countries, we identified >70,000 specific deletions and >600 duplications. Most structural variants are rare (48.5% of deletions and 94.7% of duplications are found in single isolates) with 2.4% of deletions and 0.2% of duplications found in >5% of global isolates. A subset of variants was present at high frequency in drug-resistance related genes including mdr1, the gch1 promoter region, and a putative novel duplication of crt. Regional-specific variants were identified, and a companion visualisation tool has been developed to assist web-based investigation of these polymorphisms by the wider scientific community.
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