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Table 3 CYP2C19 allele and predicted phenotype frequency in a demographically representative South African (SA) cohort (n=100) compared to other cohorts sampled in SA

From: Introduction of the AmpliChip CYP450 Test to a South African cohort: a platform comparative prospective cohort study

 

Cohort 1 AmpliChip

Comparison

Cohort 2 AmpliChip

Comparison

PCR-RFLP

Dandara et al. 2001

Dandara et al. 2011 [32]

Drögemöller et al. 2010

Ikediobi et al. 2011 [33]

Matimba et al. 2009

Allele

Activity

Black African

White Caucasian

Coloured

Indian

Fischer's Exact

Black African

White Caucasian

Coloured

Indian

Fischer's Exact

Black African

White Caucasian

Coloured

Indian

SA Venda

SA Bt20 (mixed Black)

SA Xhosa

SA Coloured

SA Xhosa

SA Coloured

SA Venda

Allele Frequency (%)

*1+

Normal

85.7

75.0

75.0

60.0

1.000

82.1

95.0

65.0

65.0

0.000

32.1

70.0

40.0

40.0

78.0

23.0

17.0

41.0

63.0

71.0

77.0

*2

Absent

116

25.0

25.0

40.0

0.784

17.9

5.0

35.0

35.0

1.000

17.9

5.0

35.0

35.0

22.0

61.0

21.0

17.0

22.0

20.0

17.0

*3

Absent

2.7

0.0

0.0

0.0

0.084

0.0

0.0

0.0

0.0

1.000

0.0

0.0

0.0

0.0

0.0

16.0

0.0

7.0

-

-

0.0

*9

Decreased

-

-

-

-

-

-

-

-

-

0.058

3.6

0.0

0.0

0.0

-

-

9.0

4.0

-

-

6.0

*15

Unknown

-

-

-

-

-

-

-

-

-

0.002

5.7

0.0

10.0

0.0

-

-

9.0

8.0

-

-

0.0

*17

Increaased

-

-

-

-

-

-

-

-

-

0.000

16.4

25.0

0.0

5.0

-

-

10.0

14.0

15.0

9.0

-

*27

Decreased

-

-

-

-

-

 

-

--

-

0.000

24.3

0.0

15.0

20.0

-

-

33.0

8.0

-

-

-

*28

Unknown

-

-

-

-

-

-

-

-

-

1.000

0.0

0.0

0.0

0.0

-

-

1.0

1.0

-

-

0.0

Alleles identified (n)

112.0

12.0

20.0

20.0

 

140.0

20.0

20.0

20.0

 

140.0

20.0

20.0

20.0

152.0

1964-1970

200.0

150.0

218.0

134.0

18.0

Predicted Phenotype Frequency (%)

PM

 

3.5

16.7

10.0

30.0

 

7.1

0.0

10.0

10.0

 

5.7

0.0

20.0

50.0

5.3

1.5

3.0

8.0

-

-

-

IM

 

0.0

0.0

0.0

0.0

 

0.0

0.0

0.0

0.0

 

21.4

10.0

50.0

40.0

32.9

13.0

49.0

40.0

-

-

-

EM

 

94.7

83.3

90.0

70.0

 

92.9

100.0

90.0

90.0

 

45.7

90.0

30.0

0.0

61.6

85.5

39.0

35.0

-

-

-

UM

 

0.0

0.0

0.0

0.0

 

0.0

0.0

0.0

0.0

 

27.1

0.0

0.0

10.0

0.0

0.0

9.0

17.0

-

-

-

Failure

 

1.8

0.0

0.0

0.0

 

0.0

0.0

0.0

0.0

 

0.0

0.0

0.0

0.0

0.0

1.1-0.8

0.0

0.0

0.0

0.0

0.0

Cohort (n)

57

6

10

10

 

70

10

10

10

 

70

10

10

10

76

982-985

100

75

109

67

9

  1. Allele frequencies for each allele were compared between cohorts and platforms. Allele frequencies for different ethnicities were summed for comparison. Genetic material for cohort 2 was genotyped using PCR-RFLP to evaluate AmpliChip CYP450 Test® (AmpliChip) genotype calls. CYP2C19*1+ : wild type and any unidentified alleles; —:alleles not identified by assay or predicted phenotype not reported.