Validation of Pyrosequencing for accurate and high throughput estimation of allele frequencies in malaria parasites

Institute for Immunology and Infection Research, School of Biological Sciences, The University of Edinburgh, Ashworth Laboratories, The Kings Buildings, West Mains Road, Edinburgh EH9 3JT, UK.
Molecular and Biochemical Parasitology (Impact Factor: 1.79). 05/2007; 152(2):213-9. DOI: 10.1016/j.molbiopara.2006.12.008
Source: PubMed
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    • "By using PS analysis (Hunt et al., 2005) targeting this mutation, it is possible to estimate the relative proportion of AS-ATNMF1 parasites present in a mixture with parasites displaying the wild-type form of this genotype (AS-ATN or AS-ATN27P). This method has been used in similar studies and has shown high level of accuracy (Hunt et al., 2005; Cheesman et al., 2007). However, it was crucial to verify whether the accuracy of quantifying parasite proportions using this method was satisfactory for analysing unknown mixtures in this particular case. "
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    ABSTRACT: If drug-resistant malaria mutants are less fit than sensitive forms, they will wane over time when active drug pressure is removed and the overall sensitivity to the drug may be restored. However, most studies addressing this issue have been largely retrospective. Here, we undertook a predictive study, using mutant rodent malaria parasites resistant to the Artemisinin combination treatment (ACT) version of artesunate+mefloquine (ATN+MF) to gain insights about their ability to compete with ATN+MF-sensitive forms in untreated hosts. Previously, Plasmodium chabaudi parasites resistant to ATN+MF were selected in vivo through prolonged passaging in mice under increasing doses of the two drugs, and shown to harbour duplication of the mdr1 gene. Here, the resistant parasite, AS-ATNMF1, was mixed with its progenitor AS-ATN in different proportions and each mixture was injected into mice that were left untreated. Absolute percentage parasitaemias and the proportion of each parasite were then monitored by microscopy and proportional sequencing, respectively, every two days for a period of 14days. AS-ATNMF1 outperformed its progenitor AS-ATN over the whole sampling period regardless of the relative starting proportion of each parasite clone. In order to assess if consecutive sub-inoculations could have been responsible for the apparent fitness gain of the resistant parasite, its growth was compared to that of AS-ATN27P, a parasite which was passaged the same number of times as AS-ATNMF1, but left untreated. Although small fluctuations in the proportion of each parasite were observed through time, the relative abundance of each on the last day of sampling (Day 14) was virtually identical to that of the starting inoculum. We conclude that there is no fitness cost associated with MDR1-associated ATN+MF resistance in vivo. These observations offer the first insights about the within-host dynamics between ACT-resistant and -sensitive parasites in absence of drug pressure.
    Infection, genetics and evolution: journal of molecular epidemiology and evolutionary genetics in infectious diseases 01/2013; 14(1). DOI:10.1016/j.meegid.2012.12.011 · 3.02 Impact Factor
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    • "The PSQ™ HS-96A pyrosequencing system was used to measure the proportion of AJ alleles in all selected backcross populations. A set of ~96 uniformly spaced, quantitative pyrosequencing assays measuring the proportion of the SNPs between the AS and AJ were designed as previously described [33]. The pyrosequencing assays were prepared and performed according to the manufacturer's instructions, each assay being performed in triplicate, on three different template samples. "
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    ABSTRACT: Drug resistance in the malaria parasite Plasmodium falciparum severely compromises the treatment and control of malaria. A knowledge of the critical mutations conferring resistance to particular drugs is important in understanding modes of drug action and mechanisms of resistances. They are required to design better therapies and limit drug resistance.A mutation in the gene (pfcrt) encoding a membrane transporter has been identified as a principal determinant of chloroquine resistance in P. falciparum, but we lack a full account of higher level chloroquine resistance. Furthermore, the determinants of resistance in the other major human malaria parasite, P. vivax, are not known. To address these questions, we investigated the genetic basis of chloroquine resistance in an isogenic lineage of rodent malaria parasite P. chabaudi in which high level resistance to chloroquine has been progressively selected under laboratory conditions. Loci containing the critical genes were mapped by Linkage Group Selection, using a genetic cross between the high-level chloroquine-resistant mutant and a genetically distinct sensitive strain. A novel high-resolution quantitative whole-genome re-sequencing approach was used to reveal three regions of selection on chr11, chr03 and chr02 that appear progressively at increasing drug doses on three chromosomes. Whole-genome sequencing of the chloroquine-resistant parent identified just four point mutations in different genes on these chromosomes. Three mutations are located at the foci of the selection valleys and are therefore predicted to confer different levels of chloroquine resistance. The critical mutation conferring the first level of chloroquine resistance is found in aat1, a putative aminoacid transporter. Quantitative trait loci conferring selectable phenotypes, such as drug resistance, can be mapped directly using progressive genome-wide linkage group selection. Quantitative genome-wide short-read genome resequencing can be used to reveal these signatures of drug selection at high resolution. The identities of three genes (and mutations within them) conferring different levels of chloroquine resistance generate insights regarding the genetic architecture and mechanisms of resistance to chloroquine and other drugs. Importantly, their orthologues may now be evaluated for critical or accessory roles in chloroquine resistance in human malarias P. vivax and P. falciparum.
    BMC Genomics 03/2012; 13(1):106. DOI:10.1186/1471-2164-13-106 · 3.99 Impact Factor
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    • "The uncloned progeny of a genetic backcross (see Methods) between AS-30CQ and AJ (AS-30CQ × AJ) were treated with artemisinin (100 mg kg-1, 3 days). A genome-wide library of ~100 pyrosequencing assays [26] was then used to measure the proportions of AJ and AS alleles (single nucleotide polymorphisms, SNPs) at pre-mapped loci dispersed across the genome (Additional File 1) in both the drug-treated and the untreated populations. A single dominant selection valley was obtained on chr02 (Figure 3A). "
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    ABSTRACT: Classical and quantitative linkage analyses of genetic crosses have traditionally been used to map genes of interest, such as those conferring chloroquine or quinine resistance in malaria parasites. Next-generation sequencing technologies now present the possibility of determining genome-wide genetic variation at single base-pair resolution. Here, we combine in vivo experimental evolution, a rapid genetic strategy and whole genome re-sequencing to identify the precise genetic basis of artemisinin resistance in a lineage of the rodent malaria parasite, Plasmodium chabaudi. Such genetic markers will further the investigation of resistance and its control in natural infections of the human malaria, P. falciparum. A lineage of isogenic in vivo drug-selected mutant P. chabaudi parasites was investigated. By measuring the artemisinin responses of these clones, the appearance of an in vivo artemisinin resistance phenotype within the lineage was defined. The underlying genetic locus was mapped to a region of chromosome 2 by Linkage Group Selection in two different genetic crosses. Whole-genome deep coverage short-read re-sequencing (Illumina Solexa) defined the point mutations, insertions, deletions and copy-number variations arising in the lineage. Eight point mutations arise within the mutant lineage, only one of which appears on chromosome 2. This missense mutation arises contemporaneously with artemisinin resistance and maps to a gene encoding a de-ubiquitinating enzyme. This integrated approach facilitates the rapid identification of mutations conferring selectable phenotypes, without prior knowledge of biological and molecular mechanisms. For malaria, this model can identify candidate genes before resistant parasites are commonly observed in natural human malaria populations.
    BMC Genomics 09/2010; 11(1):499. DOI:10.1186/1471-2164-11-499 · 3.99 Impact Factor
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