UNASSIGNED: We explored the potential of pooled sequencing to swiftly and economically identify selective sweeps due to emerging @entity507 (ART) resistance in a South-East Asian @entity311 parasite population. ART resistance is defined by slow parasite clearance from the blood of ART-treated @entity1 and mutations in the @entity68691 gene (chr. 13) have been strongly implicated to play a role. We constructed triplicate pools of 70 slow-clearing (resistant) and 70 fast-clearing (sensitive) infections collected from the Thai-Myanmar border and sequenced these to high (~150-fold) read depth. Allele frequency estimates from pools showed almost perfect correlation (Lin's concordance = 0.98) with allele frequencies at 93 SNPs measured directly from individual infections, giving us confidence in the accuracy of this approach. By mapping genome-wide divergence (FST) between pools of drug resistant and drug sensitive parasites we identified two large (>150kb) regions (on chrs. 13 and 14) and 17 smaller candidate genome regions. To identify individual genes within these genome regions we re-sequenced an additional 38 parasite genomes (16 slow and 22 fast-clearing) and performed rare variant association tests. These confirmed @entity68691 as a major molecular marker for ART resistance (p=6.03*10(-6)). This two-tier approach is powerful because pooled sequencing rapidly narrows down genome regions of interest, while targeted rare variant association testing within these regions can pinpoint the genetic basis of resistance. We show that our approach is robust to recurrent mutation and the generation of soft selective sweeps, which are predicted to be common in pathogen populations with large effective population sizes, and may confound more traditional gene mapping approaches.

Pooled sequencing and rare variant association tests for identifying the determinants of emerging drug resistance in XXXX parasites.

@entity1 :: ('9606', 'Species') :: ['patients'] @entity311 :: ('MESH:D008288', 'Disease') :: ['malaria'] @entity68691 :: ('11275', 'Gene') :: ['kelch'] @entity507 :: ('MESH:C031327', 'Chemical') :: ['artemisinin']
@entity311 :: (MESH:D008288,Disease) :: ['malaria']
