Use of high-density tiling microarrays to identify mutations globally and elucidate mechanisms of drug resistance in Plasmodium falciparum

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Use of high-density tiling microarrays to identify mutations globally and elucidate mechanisms of drug resistance in Plasmodium falciparum

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Title: Use of high-density tiling microarrays to identify mutations globally and elucidate mechanisms of drug resistance in Plasmodium falciparum
Author: Dharia, Neekesh V; Cassera, María Belén; Westenberger, Scott J; Bopp, Selina ER; Eastman, Rich T; Plouffe, David; Batalov, Serge; Zhou, Yingyao; Fidock, David A; Winzeler, Elizabeth A; Sidhu, Amar Bir; Park, Daniel John; Volkman, Sarah K.; Wirth, Dyann Fergus

Note: Order does not necessarily reflect citation order of authors.

Citation: Dharia, Neekesh V., Amar Bir Singh Sidhu, María Belén Cassera, Scott J. Westenberger, Selina E. R. Bopp, Rich T. Eastman, David Plouffe, et al. 2009. Use of high-density tiling microarrays to identify mutations globally and elucidate mechanisms of drug resistance in Plasmodium falciparum. Genome Biology 10(2): R21.
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Abstract: Background: The identification of genetic changes that confer drug resistance or other phenotypic changes in
pathogens can help optimize treatment strategies, support the development of new therapeutic agents, and
provide information about the likely function of genes. Elucidating mechanisms of phenotypic drug resistance can
also assist in identifying the mode of action of uncharacterized but potent antimalarial compounds identified in
high-throughput chemical screening campaigns against Plasmodium falciparum.
Results: Here we show that tiling microarrays can detect de novo a large proportion of the genetic changes that
differentiate one genome from another. We show that we detect most single nucleotide polymorphisms or small
insertion deletion events and all known copy number variations that distinguish three laboratory isolates using
readily accessible methods. We used the approach to discover mutations that occur during the selection process
after transfection. We also elucidated a mechanism by which parasites acquire resistance to the antimalarial
fosmidomycin, which targets the parasite isoprenoid synthesis pathway. Our microarray-based approach allowed
us to attribute in vitro derived fosmidomycin resistance to a copy number variation event in the pfdxr gene, which
enables the parasite to overcome fosmidomycin-mediated inhibition of isoprenoid biosynthesis.
Conclusions: We show that newly emerged single nucleotide polymorphisms can readily be detected and that
malaria parasites can rapidly acquire gene amplifications in response to in vitro drug pressure. The ability to define
comprehensively genetic variability in P. falciparum with a single overnight hybridization creates new opportunities
to study parasite evolution and improve the treatment and control of malaria.
Published Version: doi:10.1186/gb-2009-10-2-r21
Other Sources: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2688282/pdf/
Terms of Use: This article is made available under the terms and conditions applicable to Other Posted Material, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of-use#LAA
Citable link to this page: http://nrs.harvard.edu/urn-3:HUL.InstRepos:11213316
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