Plasmodium falciparum genome-wide scans for positive selection, recombination hot spots and resistance to antimalarial drugs

Nature Genetics

Volumn 42, Issue 3, 2010, Pages 268-271

  Mu, Jianbing ^a   Myers, Rachel A ^b,c   Jiang, Hongying ^a   Liu, Shengfa ^a,d   Ricklefs, Stacy ^e   Waisberg, Michael ^a   Chotivanich, Kesinee ^f   Wilairatana, Polrat ^f   Krudsood, Srivicha ^g   White, Nicholas J ^h   Udomsangpetch, Rachanee ^f   Cui, Liwang ⁱ   Ho, May ^j   Ou, Fengzhen ^k   Li, Haibo ^k   Song, Jianping ^k   Li, Guoqiao ^k   Wang, Xinhua ^l   Seila, Suon ^m   Sokunthea, Sreng ^m   Socheat, Duong ^m   Sturdevant, Daniel E ^e   Porcella, Stephen F ^e   Fairhurst, Rick M ^a   Wellems, Thomas E ^a   Awadalla, Philip ^b   Su, Xin Zhuan ^a   more..

^a NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES   (United States)

^b UNIVERSITÉ DE MONTRÉAL   (Canada)

^c NORTH CAROLINA STATE UNIVERSITY   (United States)

^d XIAMEN UNIVERSITY   (China)

^e NATIONAL INSTITUTES OF HEALTH   (United States)

^f MAHIDOL UNIVERSITY   (Thailand)

^g MAHIDOL UNIVERSITY   (Thailand)

^h MAHIDOL OXFORD TROPICAL MEDICINE RESEARCH UNIT   (Thailand)

ⁱ PENNSYLVANIA STATE UNIVERSITY   (United States)

^j UNIVERSITY OF CALGARY   (Canada)

^k Research Center for Qinghao   (China)

^l GUANGZHOU UNIVERSITY OF CHINESE MEDICINE   (China)

^m National Center for Parasitology Entomology and Malaria Control   (Cambodia)

more..

Author keywords

[No Author keywords available]

Indexed keywords

AMODIAQUINE; ANTIMALARIAL AGENT; CHLOROQUINE; DIHYDROARTEMISININ; FANSIDAR; MEFLOQUINE; PIPERAQUINE; QUININE;

ANTIMALARIAL DRUG RESISTANCE; ARTICLE; GENETIC RECOMBINATION; GENETIC SELECTION; GENETIC TRAIT; IC 50; MOLECULAR PROBE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHARMACOGENETICS; PLASMODIUM FALCIPARUM; POPULATION STRUCTURE; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

ANTIMALARIALS; CHROMOSOME MAPPING; CLUSTER ANALYSIS; COMPARATIVE GENOMIC HYBRIDIZATION; DNA, PROTOZOAN; DRUG RESISTANCE; GENETIC LOCI; GENOME-WIDE ASSOCIATION STUDY; GEOGRAPHY; INHIBITORY CONCENTRATION 50; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLASMODIUM FALCIPARUM; RECOMBINATION, GENETIC; SELECTION, GENETIC;

PLASMODIUM FALCIPARUM;

EID: 77649188974     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.528     Document Type: Article

References (31)

1. Wootton, J.C. et al. Genetic diversity and chloroquine selective sweeps in Plasmodium falciparum. Nature 418, 320-323 (2002).
2. Roper, C. et al. Intercontinental spread of pyrimethamine-resistant malaria. Science 305, 1124 (2004).
3. Mu, J. et al. Genome-wide variation and identifcation of vaccine targets in the Plasmodium falciparum genome. Nat. Genet. 39, 126-130 (2007).
4. Zalis, M.G., Pang, L., Silveira, M.S., Milhous, W.K. & Wirth, D.F. Characterization of Plasmodium falciparum isolated from the Amazon region of Brazil: evidence for quinine resistance. Am. J. Trop. Med. Hyg. 58, 630-637 (1998).
5. Dondorp, A.M. et al. Artemisinin resistance in Plasmodium falciparum malaria. N. Engl. J. Med. 361, 455-467 (2009).
6. Wongsrichanalai, C. & Meshnick, S.R. Declining artesunate-mefoquine effcacy against falciparum malaria on the Cambodia-Thailand border. Emerg. Infect. Dis. 14, 716-719 (2008).
7. Noedl, H. et al. Evidence of artemisinin-resistant malaria in western Cambodia. N. Engl. J. Med. 359, 2619-2620 (2008).
8. Hayton, K. & Su, X.-z. Drug resistance and genetic mapping in Plasmodium falciparum. Curr. Genet. 54, 223-239 (2008).
9. Hardenbol, P. et al. Multiplexed genotyping with sequence-tagged molecular inversion probes. Nat. Biotechnol. 21, 673-678 (2003).
10. Pritchard, J.K., Stephens, M. & Donnelly, P. Inference of population structure using multilocus genotype data. Genetics 155, 945-959 (2000).
11. Price, A.L. et al. Principal components analysis corrects for stratifcation in genome-wide association studies. Nat. Genet. 38, 904-909 (2006).
12. Mu, J. et al. Recombination hotspots and population structure in Plasmodium falciparum. PLoS Biol. 3, e335 (2005).
13. Sabeti, P.C. et al. Detecting recent positive selection in the human genome from haplotype structure. Nature 419, 832-837 (2002).
14. Sabeti, P.C. et al. Genome-wide detection and characterization of positive selection in human populations. Nature 449, 913-918 (2007).
15. Voight, B.F., Kudaravalli, S., Wen, X. & Pritchard, J.K. A map of recent positive selection in the human genome. PLoS Biol. 4, e72 (2006).
16. Pickrell, J.K. et al. Signals of recent positive selection in a worldwide sample of human populations. Genome Res. 19, 826-837 (2009).
17. Escalante, A.A., Lal, A.A. & Ayala, F.J. Genetic polymorphism and natural selection in the malaria parasite Plasmodium falciparum. Genetics 149, 189-202 (1998).
18. Winter, G. et al. SURFIN is a polymorphic antigen expressed on Plasmodium falciparum merozoites and infected erythrocytes. J. Exp. Med. 201, 1853-1863 (2005).
19. Liu, S., Mu, J., Jiang, H. & Su, X.-z. Effects of Plasmodium falciparum mixed infections on in vitro antimalarial drug tests and genotyping. Am. J. Trop. Med. Hyg. 79, 178-184 (2008).
20. Brockman, A. et al. Plasmodium falciparum antimalarial drug susceptibility on the north-western border of Thailand during fve years of extensive use of artesunate-mefoquine. Trans. R. Soc. Trop. Med. Hyg. 94, 537-544 (2000).
21. Basco, L.K. & Le Bras, J. In vitro activity of artemisinin derivatives against African isolates and clones of Plasmodium falciparum. Am. J. Trop. Med. Hyg. 49, 301-307 (1993). (Pubitemid 23289387)
22. Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559-575 (2007).
23. Fidock, D.A. et al. Mutations in the P. falciparum digestive vacuole transmembrane protein PfCRT and evidence for their role in chloroquine resistance. Mol. Cell 6, 861-871 (2000).
24. Ferdig, M.T. et al. Dissecting the loci of low-level quinine resistance in malaria parasites. Mol. Microbiol. 52, 985-997 (2004).
25. Sidhu, A.B., Valderramos, S.G. & Fidock, D.A. Mutations contribute to quinine resistance and enhance mefoquine and artemisinin sensitivity in Plasmodium falciparum. Mol. Microbiol. 57, 913-926 (2005).
26. Cowman, A.F., Galatis, D. & Thompson, J.K. Selection for mefoquine resistance in Plasmodium falciparum is linked to amplifcation of the pfmdr1 gene and cross-resistance to halofantrine and quinine. Proc. Natl. Acad. Sci. USA 91, 1143-1147 (1994).
27. Dharia, N.V. et al. Use of high-density tiling microarrays to identify mutations globally and elucidate mechanisms of drug resistance in Plasmodium falciparum. Genome Biol. 10, R21 (2009).
28. Su, X.-z., Kirkman, L.A., Fujioka, H. & Wellems, T.E. Complex polymorphisms in an approximately 330 kDa protein are linked to chloroquine-resistant P. falciparum in Southeast Asia and Africa. Cell 91, 593-603 (1997).
29. Mu, J. et al. Multiple transporters associated with malaria parasite responses to chloroquine and quinine. Mol. Microbiol. 49, 977-989 (2003).
30. Jiang, H. et al. Genome-wide compensatory changes accompany drug-selected mutations in the Plasmodium falciparum crt gene. PLoS One 3, e2484 (2008).
31. Raj, D.K. et al. Disruption of a Plasmodium falciparum multidrug resistance-associated protein (PFMRP) alters its ftness and transport of antimalarial drugs and glutathione. J. Biol. Chem. 284, 7687-7696 (2008).