title: A comparison of methods to detect and quantify the markers of antimalarial drug resistance.
abstract: We compare, contrast, and evaluate methods to quantify genetic markers of antimalarial drug resistance. Frequency estimates should be reported along with crude prevalence. There are four main potential methods to estimate frequencies in blood samples: simple counting of single nucleotide polymorphisms (SNPs) and haplotypes in samples with multiplicity of infection (MOI) = 1; SNP counting in samples with MOI < or = 2; SNP and haplotypes counting in samples with unambiguous genotypes; statistical inference using SNP and MOI data from all samples. Large differences between the methods became apparent when analyzing field data with high MOI. Simple counting dramatically reduced sample size and estimate precision, and we show that analysis of unambiguous samples is biased, leaving maximum likelihood or similar statistical inference as the only practical option. It is essential to account for genotyping missing minor clones; ignoring this phenomenon resulted in a 2-fold underestimation of SNPs and haplotypes present at low frequencies.
authors.affiliation: Molecular and Biochemical Parasitology, Liverpool School of Tropical Medicine, Liverpool, UK. hastings@liverpool.ac.uk
authors.forename: Ian M
authors.initials: IM
authors.lastname: Hastings
authors.forename: Christian
authors.initials: C
authors.lastname: Nsanzabana
authors.forename: Tom A
authors.initials: TA
authors.lastname: Smith
mesh_terms: D000818:Animals; D000962:Antimalarials / Q000494:pharmacology*; D004351:Drug Resistance / Q000235:genetics*; D005819:Genetic Markers; D006801:Humans; D008288:Malaria / Q000097:blood / Q000188:drug therapy*; D009154:Mutation; D020641:Polymorphism, Single Nucleotide
chemical_list: D000962:Antimalarials; D005819:Genetic Markers
references.citation: Malar J. 2007 Sep 06;6:121
references.pmid: 17822535
references.citation: Am J Trop Med Hyg. 2003 Sep;69(3):236-7
references.pmid: 14628936
references.citation: Am J Trop Med Hyg. 2008 Aug;79(2):178-84
references.pmid: 18689621
references.citation: Trends Parasitol. 2006 Feb;22(2):71-7
references.pmid: 16406706
references.citation: Malar J. 2008 Jul 15;7:130
references.pmid: 18627599
references.citation: Malar J. 2009 May 04;8:89
references.pmid: 19413906
references.citation: Stat Med. 1998 Apr 30;17(8):857-72
references.pmid: 9595616
references.citation: Am J Trop Med Hyg. 2003 Sep;69(3):238-43
references.pmid: 14628937
references.citation: Trans R Soc Trop Med Hyg. 2001 Mar-Apr;95(2):225-32
references.pmid: 11355566
references.citation: Lancet. 1994 Oct 29;344(8931):1175-81
references.pmid: 7934537
references.citation: J Infect Dis. 2010 Feb 1;201(3):435-43
references.pmid: 20047502
references.citation: Malar J. 2008 May 06;7:78
references.pmid: 18460212
references.citation: Trends Parasitol. 2001 Dec;17(12):582-8
references.pmid: 11756042
references.citation: Proc Biol Sci. 1995 Dec 22;262(1365):249-57
references.pmid: 8587883
references.citation: Malar J. 2004 Oct 18;3:35
references.pmid: 15491495
references.citation: Am J Trop Med Hyg. 2008 Jun;78(6):892-4
references.pmid: 18541765
references.citation: Malar J. 2009 Mar 16;8:47
references.pmid: 19291288
references.citation: Parasitol Today. 1994 Dec;10(12):489-93
references.pmid: 15275519
references.citation: Trans R Soc Trop Med Hyg. 1993 Jan-Feb;87(1):75-8
references.pmid: 8465404
references.citation: Am J Trop Med Hyg. 2007 Dec;77(6 Suppl):160-9
references.pmid: 18165489
references.citation: Mol Biol Evol. 2005 Dec;22(12):2362-74
references.pmid: 16093566
references.citation: J Infect Dis. 2005 Mar 15;191(6):1014-7
references.pmid: 15717281