Signatures of Plasmodium falciparum population structure
The MalariaGEN team worked with many groups around the world to establish the Plasmodium falciparum population genomics community project, including developing field sample handling methods, sequencing protocols, and data analysis pipelines. These sample sets also underpinned MalariaGEN’s initial global map of Plasmodium genome variation, and provided opportunities to explore unique features of the population genetics of parasite populations of the local region from where they were collected.
In Mali, Abdoulaye Djimde and colleagues worked with Sarah Auburn in the MalariaGEN team to collect parasite samples from two sites: Kolle and Faladje, rural villages approximately 60 and 80km away from Bamako, the capital of Mali. Samples were used to develop field-friendly leukocyte depletion methods, GoldenGate genotyping assay development, and to contribute to our global P. falciparum genome variation data analysis. Djimde and team are keen to investigate signatures of population structure and other unique features of genome variation between the 2 locations from which samples were collected.
Lead partner
Abdoulaye Djimde
adjimde@icermali.org
Malaria Research and Training Centre, Faculty of Science, Techniques and Technologies, University of Bamako, Mali
Publications
Manske M, Miotto O. et al. Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing. Nature.
DOI: 10.1038/nature11174
ePrint version of article
Auburn S. Characterization of within-host Plasmodium falciparum diversity using next-generation sequence data. PLoS One. 2012;7(2):e32891. Epub 2012 Feb 29. PMID 22393456
Auburn S, Campino S. An effective method to purify Plasmodium falciparum DNA directly from clinical blood samples for whole genome high-throughput sequencing. PLoS One. 2011;6(7):e22213. Epub 2011 Jul 18. PMID 21789235
Campino S, Auburn S. Population genetic analysis of Plasmodium falciparum parasites using a customized Illumina GoldenGate genotyping assay. PLoS One. 2011;6(6):e20251. Epub 2011 Jun 6. PMID 21673999
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