Scientific Publications

Sequence-based association and selection scans identify drug resistance loci in the Plasmodium falciparum malaria parasite.

Publication TypeJournal Article
AuthorsPark, DJ, Lukens AK, Neafsey DE, Schaffner SF, Chang HH, Valim C., Ribacke U., Van Tyne D., Galinsky K., Galligan M., Becker JS, Ndiaye D., Mboup S., Wiegand RC, Hartl DL, Sabeti PC, Wirth DF, and Volkman SK
AbstractThrough rapid genetic adaptation and natural selection, the Plasmodium falciparum parasite-the deadliest of those that cause malaria-is able to develop resistance to antimalarial drugs, thwarting present efforts to control it. Genome-wide association studies (GWAS) provide a critical hypothesis-generating tool for understanding how this occurs. However, in P. falciparum, the limited amount of linkage disequilibrium hinders the power of traditional array-based GWAS. Here, we demonstrate the feasibility and power improvements gained by using whole-genome sequencing for association studies. We analyzed data from 45 Senegalese parasites and identified genetic changes associated with the parasites' in vitro response to 12 different antimalarials. To further increase statistical power, we adapted a common test for natural selection, XP-EHH (cross-population extended haplotype homozygosity), and used it to identify genomic regions associated with resistance to drugs. Using this sequence-based approach and the combination of association and selection-based tests, we detected several loci associated with drug resistance. These loci included the previously known signals at pfcrt, dhfr, and pfmdr1, as well as many genes not previously implicated in drug-resistance roles, including genes in the ubiquitination pathway. Based on the success of the analysis presented in this study, and on the demonstrated shortcomings of array-based approaches, we argue for a complete transition to sequence-based GWAS for small, low linkage-disequilibrium genomes like that of P. falciparum.
Year of Publication2012
JournalProceedings of the National Academy of Sciences of the United States of America
Volume109
Issue32
Pages13052-7
Date Published (YYYY/MM/DD)2012/08/07
ISSN Number0027-8424
DOI10.1073/pnas.1210585109
PubMedhttp://www.ncbi.nlm.nih.gov/pubmed/22826220?dopt=Abstract