High-throughput genotyping of single nucleotide polymorphisms in the Plasmodium falciparum dhfr gene by asymmetric PCR and melt-curve analysis.

Journal of Clinical Microbiology
Rochelle E CruzStephanie K Yanow

Abstract

Mutations within the Plasmodium falciparum dihydrofolate reductase gene (Pfdhfr) contribute to resistance to antimalarials such as sulfadoxine-pyrimethamine (SP). Of particular importance are the single nucleotide polymorphisms (SNPs) within codons 51, 59, 108, and 164 in the Pfdhfr gene that are associated with SP treatment failure. Given that traditional genotyping methods are time-consuming and laborious, we developed an assay that provides the rapid, high-throughput analysis of parasite DNA isolated from clinical samples. This assay is based on asymmetric real-time PCR and melt-curve analysis (MCA) performed on the LightCycler platform. Unlabeled probes specific to each SNP are included in the reaction mixture and hybridize differentially to the mutant and wild-type sequences within the amplicon, generating distinct melting curves. Since the probe is present throughout PCR and MCA, the assay proceeds seamlessly with no further addition of reagents. This assay was validated for analytical sensitivity and specificity using plasmids, purified genomic DNA from reference strains, and parasite cultures. For all four SNPs, correct genotypes were identified with 100 copies of the template. The performance of the assay was evaluated...Continue Reading

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Nov 11, 2011·PloS One·Heidie M HornstraTalima Pearson
Jan 31, 2012·Biomedical Papers of the Medical Faculty of the University Palacký, Olomouc, Czechoslovakia·Lenka Ruskova, Vladislav Raclavsky
Oct 28, 2021·Journal of Feline Medicine and Surgery·Andrea V ScorzaMichael R Lappin

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