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Nair S.,Southwest Foundation for Biomedical Research SFBR | Nkhoma S.,Southwest Foundation for Biomedical Research SFBR | Nosten F.,Shoklo Malaria Research Unit SMRU | Nosten F.,Center for Tropical Medicine and Vaccinology | And 5 more authors.
Molecular and Biochemical Parasitology | Year: 2010

Comparative genomic hybridization studies have revealed elevated copy number (CN) at the reticulocyte-binding protein 1 gene (PfRh1) in fast growing lab-adapted parasites, while genetic manipulation demonstrates a causal link between cell invasion and PfRh1 CN. We therefore examined PfRh1 copy number variation (CNV) in 202 single clone parasite isolates from four countries to quantify the extent of CNV within natural populations. Surprisingly, we found that no natural parasite infections showed elevated CN. In contrast, 4/28 independent laboratory reference strains show elevated CN. One possibility is that amplification of PfRh1 (or neighboring loci) is selected during laboratory culture. In the case of FCR3 group of parasites, clone trees show that PfRh1 amplification arose in laboratory lines following establishment in culture. These data show that CNV at PfRh1 is rare or non-existent in natural populations, but can arise during laboratory propagation. We conclude that PfRh1 CNV is not an important determinant of gene expression, cell invasion or growth rate in natural parasite populations. © 2010 Elsevier B.V.

Anderson T.J.C.,Southwest Foundation for Biomedical Research SFBR | Williams J.T.,Southwest Foundation for Biomedical Research SFBR | Nair S.,Southwest Foundation for Biomedical Research SFBR | Sudimack D.,Southwest Foundation for Biomedical Research SFBR | And 6 more authors.
Proceedings of the Royal Society B: Biological Sciences | Year: 2010

Malaria parasites vary in phenotypic traits of biomedical or biological interest such as growth rate, virulence, sex ratio and drug resistance, and there is considerable interest in identifying the genes that underlie this variation. An important first step is to determine trait heritability (H 2). We evaluate two approaches to measuring H2in natural parasite populations using relatedness inferred from genetic marker data. We collected single-clone Plasmodium falciparum infections from 185 patients from the Thailand-Burma border, monitored parasite clearance following treatment with artemisinin combination therapy (ACT), measured resistance to six antimalarial drugs and genotyped parasites using 335 microsatellites. We found strong relatedness structure. There were 27 groups of two to eight clonally identical (CI) parasites, and 74 per cent of parasites showed significant relatedness to one or more other parasites. Initially, we used matrices of allele sharing and variance components (VC) methods to estimate H2. Inhibitory concentrations (IC2) for six drugs showed significant H 2(0.24 to 0.79, p = 0.06 to 2.85 × 10-9), demonstrating that this study design has adequate power. However, a phenotype of current interest-parasite clearance following ACT-showed no detectable heritability (H2= 0-0.09, ns) in this population. The existence of CI parasites allows the use of a simple ANOVA approach for quantifying H 2, analogous to that used in human twin studies. This gave similar results to the VC method and requires considerably less genotyping information. We conclude (i) that H2can be effectively measured in malaria parasite populations using minimal genotype data, allowing rational design of genome-wide association studies; and (ii) while drug response (IC50) shows significant H2, parasite clearance following ACT was not heritable in the population studied. © 2010 The Royal Society.

Anderson T.J.C.,Southwest Foundation for Biomedical Research SFBR | Nair S.,Southwest Foundation for Biomedical Research SFBR | Nkhorna S.,Southwest Foundation for Biomedical Research SFBR | Williams J.T.,Southwest Foundation for Biomedical Research SFBR | And 10 more authors.
Journal of Infectious Diseases | Year: 2010

In western Cambodia, malaria parasites clear slowly from the blood after treatment with artemisinin derivatives, but it is unclear whether this results from parasite, host, or other factors specific to this population. We measured heritability of clearance rate by evaluating patients infected with identical or nonidentical parasite genotypes, using methods analogous to human twin studies. A substantial proportion (56%-58%) of the variation in clearance rate is explained by parasite genetics. This has 2 important implications: (1) selection with artemisinin derivatives will tend to drive resistance spread and (2) because heritability is high, the genes underlying parasite clearance rate may be identified by genome-wide association. © 2010 by the Infectious Diseases Society of America. All rights reserved.

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