The world's largest malaria data sets
Parasites and mosquitoes are continually adapting in response to the genetic pressure exerted by disease control methods such as antimalarial drugs, insecticides and other public health interventions. To tackle this disease we need to understand which genetic variations and molecular process could be the target for control interventions in malaria transmitting species.
The MalariaGEN's community is building genomic data resources to answer questions on how natural genetic variation in human, Plasmodium and Anopheles populations affects the biology and epidemiology of malaria. Genomic surveillance is shedding light on the key molecular processes of malaria and informing decision on malaria control.
Partnerships that generate genetic data
MalariaGEN provides a plaform for large-scale collaborative studies and has over 100 partners, in more than twenty countries, each with independent scientific objectives. By accessing MalariaGEN's large-scale high-throughput sequencing facilities, via Wellcome Sanger Institute, and it's frameworks for genetic sequencing and data sharing, partners can use the wider project data to lead research studies relevant to their region.
Genomic surveillance projects
By whole-genome sequencing (WGS) and analysis of entire parasite, mosquito and human genomes MalariaGEN has build a high resloution genetic data resource that is a reference point for genetic variations in parasites and humans. This vital for identifying and characterising mutations that drive drug or insecticide resistance and for tracking emerging resistant populations.
Amplicon sequencing is key tool within MalariaGEN's sequencing platform as it is simple and fast and enables partners to analyse genetic variation specific genomic regions associated with drug resistance. Using the simple PCR amplication methods to create sequences of DNA (amplicons), partners can pool different samples by adding a barcode so they can be used for variant detection.
Curating large-scale data
MalariaGEN's multidisiplinary team, which includes bioinformaticians, data scientist, statisticians and geneticisits, turn raw genomic sequences into high-value, analysis-ready data resources. Each project has developed a data curation processes that filters and annotes genetic features to ensure that the data is robust and high quality and can offer definitive answers to important scientific and operational questions . Curation work varys between projects and is dependent on a range of factors including the state of the closest reference genome, or the availability of established protocols for variant calling. The curation process provides annotations on sequence alignments, variant calls and haplotypes as well as inclusion of population-level data such as allele frequencies and maps of the distribution and spread of insecticide resistance mutations.