Novel genome methodology advances understanding of malaria evolution

In an important step towards integrating parasite genome sequencing into clinical and epidemiological investigations, fifty-six scientists from across the globe have contributed to the development of new methodology for the large-scale analysis of genetic variation in Plasmodium falciparum. This milestone brings new tools for the development of effective genetic markers to track the spread of antimalarial drug resistance. 

Reported in Nature on June 13, the group collected and analysed P falciparum DNA from patients in Burkina Faso, Kenya, Mali, Papua New Guinea, Cambodia and Thailand. 86,158 single nucleotide polymorphisms that passed genotyping quality control provided genome wide estimates of allele frequency distribution, population structure and linkage disequilibrium.  

Analyses show a greater degree of P falciparum population structure in Southeast Asia than in West Africa, consistent with previous evidence that structure tends to be increased in regions of low or patchy malaria transmission. 

An online (http://www.malariagen.net/resource/10) web application is available. Viewing regional patterns of variation in known antimalarial drug resistance genes demonstrates that the pfcrt K76T allele has different haplotypic backgrounds in Southeast Asia and in Papua New Guinea, consistent with previous evidence that chloroquine resistance has evolved independently in multiple locations.

Reference: Manske M, Miotto O, Campino S, Auburn S, Almagro-Garcia J et al. Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing. Nature 2012; doi:10.1038/nature11174. Published online 13 June 2012.

See also:

Study finds way to track malaria parasite evolution

Blood test to track emergence of drug resistance in malaria parasites