Pooled deep sequencing of Plasmodium falciparum isolates: an efficient and scalable tool to quantify prevailing malaria drug-resistance genotypes.
Published
Journal Article
Molecular surveillance for drug-resistant malaria parasites requires reliable, timely, and scalable methods. These data may be efficiently produced by genotyping parasite populations using second-generation sequencing (SGS). We designed and validated a SGS protocol to quantify mutant allele frequencies in the Plasmodium falciparum genes dhfr and dhps in mixed isolates. We applied this new protocol to field isolates from children and compared it to standard genotyping using Sanger sequencing. The SGS protocol accurately quantified dhfr and dhps allele frequencies in a mixture of parasite strains. Using SGS of DNA that was extracted and then pooled from individual isolates, we estimated mutant allele frequencies that were closely correlated to those estimated by Sanger sequencing (correlations, >0.98). The SGS protocol obviated most molecular steps in conventional methods and is cost saving for parasite populations >50. This SGS genotyping method efficiently and reproducibly estimates parasite allele frequencies within populations of P. falciparum for molecular epidemiologic studies.
Full Text
Duke Authors
Cited Authors
- Taylor, SM; Parobek, CM; Aragam, N; Ngasala, BE; Mårtensson, A; Meshnick, SR; Juliano, JJ
Published Date
- December 15, 2013
Published In
Volume / Issue
- 208 / 12
Start / End Page
- 1998 - 2006
PubMed ID
- 23908494
Pubmed Central ID
- 23908494
Electronic International Standard Serial Number (EISSN)
- 1537-6613
Digital Object Identifier (DOI)
- 10.1093/infdis/jit392
Language
- eng
Conference Location
- United States