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Series GSE33002 Query DataSets for GSE33002
Status Public on May 01, 2012
Title A major genome region underlying artemisinin resistance in malaria
Organism Plasmodium falciparum
Experiment type Genome variation profiling by genome tiling array
Summary Evolving resistance to artemisinin-based compounds in SE Asia threatens to derail attempts to control and eliminate malaria. Resistance has been confirmed in western Cambodia, has recently emerged in western Thailand, but is absent from neighboring Laos. Artemisinin resistance results in reduced parasite clearance rates (CR) from the blood following treatment. We used a two-phase approach to identify the genes underlying this ongoing selective event. Comparison of geographical differentiation and haplotype structure at 6,969 polymorphic SNPs in 91 parasites from western Cambodia, western Thailand and Laos identified 33 strongly selected genome regions. We screened SNPs and microsatellites within these genome regions in 718 parasites from western Thailand, and identified a 35kb region of chr 13 showing strong association (P=10-6 to 10-11) with slow CR. This region contains several compelling candidate loci, such as HSP70, for assessment by transfection. These results illustrate the efficacy of targeted association for identifying the genetic basis of adaptive traits.
Overall design 91 malaria parasite isolates assayed for single nucleotide polymorphisms across 45K loci
Contributor(s) Cheeseman IH, Anderson TJ
Citation(s) 22491853
Submission date Oct 14, 2011
Last update date Feb 18, 2014
Contact name Michael Ferdig
Phone (574)631-9973
Organization name University of Notre Dame
Department Biological Sciences
Lab Ferdig Lab
Street address 280 Galvin Life Science
City Notre Dame
State/province IN
ZIP/Postal code 46556
Country USA
Platforms (1)
GPL13355 NimbleGen Pfalciparum 720K 1.0
Samples (167)
GSM818073 Cambodia CAM1
GSM818074 Cambodia CAM2
GSM818075 Cambodia CAM3
BioProject PRJNA147999

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE33002_RAW.tar 690.2 Mb (http)(custom) TAR (of BASES)
Processed data not applicable for this record

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