MalariaGEN

MalariaGEN provides integrated parasite genome sequencing and genotype data to support genomic epidemiology and surveillance of Plasmodium falciparum.

Key Features:

• Extensive Genome Variation Data: Curated genotype calls from approximately 7,000 Plasmodium falciparum samples including high-quality calls on ~3 million single nucleotide polymorphisms (SNPs) and short insertions/deletions (indels) produced through a standardized analysis pipeline.
• Drug Resistance Analysis: Analysis of copy number variants associated with antimalarial drug resistance and identification of structural variants that can cause rapid diagnostic test failure.
• Geographic and Genetic Insights: Detection of significant geographic differentiation in genes expressed during the mosquito stage of the parasite life cycle.
• Open Genomic Resource: Maintenance and expansion of an open dataset to support studies of evolutionary processes and the development of molecular surveillance tools for malaria control and elimination.

Scientific Applications:

• Epidemiological Studies: Integration of genomic data with epidemiological investigations to track and predict malaria transmission patterns.
• Drug Resistance Surveillance: Monitoring the spread and genetic basis of drug-resistant Plasmodium falciparum strains to inform treatment protocols and surveillance.
• Evolutionary Biology: Investigation of evolutionary interactions among human hosts, malaria parasites, and mosquito vectors to elucidate adaptive mechanisms.

Methodology:

Employs standardized analysis pipelines to produce high-quality genotype calls for ~3 million SNPs and short indels from sequencing data generated on HiSeq machines at the Wellcome Trust Sanger Institute.