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Table 2 The analytical challenge presented by multiclonal infections: a hypothetical example of a multiclonal blood sample

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

Hypothetical multiclonal infection SNPs
   Pfdhfr Pfdhps  
   51 59 108 437 540
Unobserved true genotypes Clone 1 N C S A K
Clone 2 N C S A K
Clone 3 I C N A K
Clone 4 N R N A K
Clone 5 I C N G E
Observed data N/I C/R S/N A/G K/E
Example of an incorrect interpretation of the observed data Genotype of clone inferred by discounting wild type markers I R N G E
  Genotype of clone inferred by discounting minority markers N C N A K
  1. Suppose a P. falciparum multiclonal blood sample was genotyped at single nucleotide polymorphisms (SNPs) in codons 51, 59 and 108 in Pfdhfr and codons 437 and 540 in Pfdhps. Markers are summarized by the amino acid residues they encode, which are denoted using the single letter amino acid code. Residues encoded by codons containing mutations are highlighted bold. The observed data are a direct consequence of the unobserved genotypes. Optimal genotyping sensitivity is assumed (all alleles are detected). Mutations were detected for all five codons genotyped; however, the interpretation that the infection contains the quintuple mutant is incorrect, since the linkage phase of the unobserved genotypes and the MOI are not captured in the observed data.