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Table 1 Summary of terms

From: Estimation of malaria haplotype and genotype frequencies: a statistical approach to overcome the challenge associated with multiclonal infections

Genetic study In a genetic study, Plasmodium falciparum DNA is extracted from infected human blood and genotyped to test for the presence of parasites that bear genetic markers of resistance (for a recent example see [13]).
Genetic markers of resistance Markers of resistance are alleles in the parasite’s genome that have been associated with anti-malarial resistance either clinically or in the laboratory. The markers considered here are located at single nucleotide polymorphisms (SNPs) found within genes that encode anti-malarial drug targets. In the case of Pfdhfr and Pfdhps, markers of resistance are non-synonymous mutations, while sensitive markers are wild type alleles [1416].
Sulphadoxine-pyrimethamine Sulphadoxine-pyrimethamine (SP) is an anti-malarial drug comprising sulphadoxine and pyrimethamine. Both components act on the folate biosynthesis pathway: sulphadoxine inhibits dihydropteroate synthase, whereas pyrimethamine inhibits dihydrofolate reductase (reviewed in [17]). SP was widely used in the latter half of the 20th Century, and resistance to the drug is now extensive, particularly in Southeast Asia, and Eastern and Southern Africa (see [18] for a comprehensive review of antifolate resistance). Nonetheless, SP is still recommended for intermittent preventative treatment of malaria during infancy and pregnancy in many parts of sub-Saharan Africa, seasonal malaria chemoprevention (SMC) in combination with amodiaquine and as a partner drug of artemisinin derivatives in South Asia and the Horn of Africa [19, 20].
Haplotypes, genotypes and linkage phase Linkage phase describes the alignment of consecutive genetic markers on a chromosome. The resulting aligned set of multiple markers is called a haplotype. When markers are located in different genes and/or chromosomes, genotype defines the combination of haplotypes within a single parasite. Plasmodium falciparum is haploid throughout the human stage of its life cycle [21], so if a sample from a single patient is monoclonal, each of these genetic motifs can be clearly defined. However, it is often the case that a patient’s blood sample contains more than one clone. If these parasites differ with respect to two or more of the markers being examined, the molecular assay will show more than one marker at two or more positions (see Table 2). Then, it is not possible to define unambiguously the linkage phase, haplotype or genotype in a particular parasite.