Table 2

Reclassification of SNP allele calls by use of polar transformation compared to conventional methods

Genotype

Dhfr Locus 59

Chr1SNP

Chr7SNP

Chr8SNP

Chr9SNP

Chr13SNP

Status

XYa

Polarb

XYa

Polarb

XYa

Polarb

XYa

Polarb

XYa

Polarb

XYa

Polarb


Not Infected

127

137

77

104

92

92

70

28

66

95

92

93

Inf. w/Allele 1

25c

63

19

28

48

60

141

147

4

127

47

108

Inf. w/Allele 2

25d

37

46

166

102

152

42

27

44

71

77

83

Mixed Infection

87

17

215

24

115

28

41

34

243

36

141

41

Uncertaine

-

10

-

35

-

25

-

58

-

28

-

32


Total Samplesf

264

357

357

294

357

357

Reclassifiedg

86

226

96

76

237

126


aCounts determined based on the conventional threshold of 3× standard deviations above the mean - see Figure 4A.

bCounts determined after applying polar transformation method - see Figure 4C.

cFor Dhfr locus 59, allele 1 is associated with drug sensitivity.

dFor Dhfr locus 59, allele 2 is associated with drug resistance.

eNo samples are considered uncertain by conventional (XY) methods, as confidence intervals are not considered.

fThe total number of samples genotyped at each locus.

gThe number of samples whose allele calls differed between the XY and polar transformation methods.

DaRe et al. BMC Genetics 2010 11:57   doi:10.1186/1471-2156-11-57

Open Data