ArticleGenome medicine2017
New var reconstruction algorithm exposes high var sequence diversity in a single geographic location in Mali.
Article in Genome medicine, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 21 citations in OpenAlex.
- Population genomics of virulence genes of Plasmodium falciparum in clinical isolates from Uganda.Scientific reports · 2017Trial
- Diamonds in the rif: Alignment-free comparative genomics analysis reveals strain-transcendent Plasmodium falciparum antigens amidst extensive genetic diversity.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2025Article
- 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
- Article
- A novel computational pipeline foreLife · 2024Article
- Sensitive, Highly Multiplexed Sequencing of Microhaplotypes From the Plasmodium falciparum Heterozygome.The Journal of infectious diseases · 2022Article
- UnravellingFrontiers in parasitology · 2022Article
- Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential.Genome medicine · 2020Article
- Serologic responses to the PfEMP1 DBL-CIDR head structure may be a better indicator of malaria exposure than those to the DBL-α tag.Malaria journal · 2019Article
- Evolutionary analysis of the most polymorphic gene family inWellcome open research · 2019Article
- Article
- A new method for sequencing the hypervariable Plasmodium falciparum gene var2csa from clinical samples.Malaria journal · 2017Article
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Authors and funding
23 authors at 2 institutions in 2 countries.
Funding
Abstract
backgroundEncoded by the var gene family, highly variable Plasmodium falciparum erythrocyte membrane protein-1 (PfEMP1) proteins mediate tissue-specific cytoadherence of infected erythrocytes, resulting in immune evasion and severe malaria disease. Sequencing and assembling the 40-60 var gene complement for individual infections has been notoriously difficult, impeding molecular epidemiological studies and the assessment of particular var elements as subunit vaccine candidates.
methodsWe developed and validated a novel algorithm, Exon-Targeted Hybrid Assembly (ETHA), to perform targeted assembly of var gene sequences, based on a combination of Pacific Biosciences and Illumina data.
resultsUsing ETHA, we characterized the repertoire of var genes in 12 samples from uncomplicated malaria infections in children from a single Malian village and showed them to be as genetically diverse as vars from isolates from around the globe. The gene var2csa, a member of the var family associated with placental malaria pathogenesis, was present in each genome, as were vars previously associated with severe malaria.
conclusionETHA, a tool to discover novel var sequences from clinical samples, will aid the understanding of malaria pathogenesis and inform the design of malaria vaccines based on PfEMP1. ETHA is available at: https://sourceforge.net/projects/etha/ .
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