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Table 4 CYP2D6 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

XL-PCR + Sequencing

Dandara et al. 2001

Gaedigk et al. 2008

Wright et al. 2010

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 Coloureds

SA Xhosa Control

SA Xhosa Schizophrenia

Allele Frequency (%)

*1

Normal

30.7

40.0

38.9

30.0

0.301

20.0

31.0

37.5

60.0

0.715

25.7

30.0

30.0

45.0

50.0

26.8

23.6

24.5

*2

Normal

4.5

20.0

0.0

30.0

1.000

20.

18.8

18.8

30.0

0.107

8.6

15.0

15.0

30.0

17.8

15.2

12.3

15.7

*4

Absent

2.3

10.0

16.7

10.0

0.795

0.0

31.3

12.5

0.0

0.586

0.0

20.0

15.0

0.0

3.3

7.1

1.9

1.0

*5

Absent

5.7

10.0

0.0

0.0

0.523

4.0

0.0

0.0

0.0

0.037

10.7

5.0

5.0

0.0

4.6

17.2

14.2

18.6

*10

Decreased

6.8

0.0

0.0

10.0

1.000

6.0

6.3

6.3

0.0

0.808

5.7

5.0

5.0

0.0

-

2.5

1.9

2.0

*14

Absent

0.0

0.0

0.0

0.0

1.000

0.0

0.0

0.0

0.0

1.000

0.0

0.0

0.0

0.0

-

0.5

0.0

0.0

*16

Absent

-

-

-

-

-

-

-

-

-

1.000

0.0

0.0

0.0

0.0

-

0.5

0.0

0.0

*17

Decreased

13.6

0.0

11.1

0.0

0.045

31.0

0.0

0.0

0.0

0.584

25.7

0.0

10.0

0.0

24.0

12.6

13.2

16.7

*22

Normal

-

-

-

-

-

-

-

-

-

1.000

0.0

0.0

0.0

5.0

-

*25

Unknown

0.0

0.0

0.0

0.0

1.000

1.0

0.0

0.0

0.0

0.416

0.0

0.0

0.0

0.0

-

*29

Decreased

13.6

0.0

0.0

0.0

1.000

6.0

0.0

6.3

0.0

0.598

4.3

0.0

5.0

0.0

-

4.6

13.2

6.9

*30

Unknown

1.1

0.0

0.0

0.0

0.461

0.0

0.0

0.0

0.0

1.000

0.0

0.0

0.0

0.0

-

0.0

0.0

*33

Normal

-

-

-

-

-

-

-

-

-

1.000

0.0

5.0

0.0

0.0

-

*35

Normal

0.0

0.0

0.0

0.0

1.000

0.0

0.0

6.3

0.0

1.000

0.0

5.0

0.0

0.0

-

*36

Reduced

0.0

0.0

0.0

0.0

1.000

0.0

0.0

0.0

0.0

1.000

0.0

0.0

0.0

0.0

-

0.0

0.0

0.0

*40

Absent

1.1

10.0

5.6

0.0

1.000

3.0

0.0

0.0

0.0

1.000

3.6

0.0

0.0

0.0

-

0.0

1.9

2.9

*41

Decreased

20.5

10.0

27.8

20.0

0.883

26.0

12.5

12.5

10.0

0.000

0.7

15.0

5.0

10.

-

0.0

1.9

1.0

*43

Normal

-

-

-

-

-

-

-

-

-

0.272

0.7

0.0

5.0

5.0

-

0.9

1.0

*45B

Normal

-

-

-

-

-

-

-

-

-

0.020

5.7

0.0

0.0

0.0

-

0.0

10.4

1.0

*46

Normal

-

-

-

-

-

-

-

-

-

1.000

0.7

0.0

0.0

0.0

-

0.0

0.0

0.0

*56B

Absent

-

-

-

-

-

-

-

-

-

1.000

0.7

0.0

0.0

0.0

-

0.0

*59

Decreased

-

-

-

-

-

-

-

-

-

1.000

0.0

0.0

0.5

0.0

-

*64

Unknown

-

-

-

-

-

-

-

-

-

1.000

0.0

0.0

0.0

0.0

-

0.0

0.0

0.0

*65

Unknown

-

-

-

-

-

-

-

-

-

1.000

0.0

0.0

0.0

0.0

-

0.0

0.0

0.0

*73

Unknown

-

-

-

-

-

-

-

-

-

1.000

0.0

0.0

0.0

0.0

-

0.0

1.0

*74

Unknown

-

-

-

-

-

-

-

-

-

1.000

0.0

0.0

0.0

0.0

-

0.0

1.0

*84

Normal

-

-

-

-

-

-

-

-

-

1.000

0.7

0.0

0.0

0.0

-

*85

Normal

-

-

-

-

-

-

-

-

-

1.000

0.7

0.0

0.0

0.0

-

*86

Normal

-

-

-

-

-

-

-

-

-

1.000

0.0

0.0

0.0

5.0

-

*1xN

Increased

0.0

0.0

0.0

0.0

1.000

0.0

0.0

0.0

0.0

1.000

0.0

0.0

0.0

0.0

-

0.0

0.0

1.0

*2xN

Increased

0.0

0.0

0.0

0.0

1.000

1.0

0.0

0.0

0.0

1.000

0.7

0.0

0.0

0.0

-

0.0

2.8

2.9

*4xN

Absent

0.0

0.0

0.0

0.0

1.000

0.0

0.0

0.0

0.0

0.147

2.9

0.0

0.0

0.0

-

0.0

1.9

2.9

Hybrid alleles

 

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

0.0

0.0

0.0

Alleles identified (n)

88

10

18

10

 

100

16

16

10

 

140

20

20

20

152

198

106

102

Predicted Phenotype Frequency (%)

PM

 

3.5

83.3

10.0

0.0

 

0.0

10.0

0.0

0.0

 

0.0

10.0

0.0

0.0

2.6

3.0

3.8

7.8

IM

 

28.1

0.0

20.0

0.0

 

42.9

10.0

20.0

0.0

 

42.9

30.0

50.0

0.0

56.6

53.0

47.2

37.3

EM

 

43.9

0.0

60.0

50.0

 

27.1

60.0

60.0

50.0

 

57.1

60.0

50.0

100.0

40.8

39.0

43.4

47.1

UM

 

0.0

0.0

0.0

0.0

 

0.0

0.0

0.0

0.0

 

0.0

0.0

0.0

0.0

0.0

4.0

5.7

7.8

Unknown

 

1.8

0.0

0.0

0.0

 

1.4

0.0

0.0

0.0

 

0.0

0.0

0.0

0.0

0.0

0.0

0.0

0.0

No call

 

7.0

0.0

0.0

0.0

 

5.7

0.0

0.0

0.0

 

0.0

0.0

0.0

0.0

0.0

0.0

0.0

0.0

Failure

 

15.8

16.7

10.0

40.0

 

22.9

20.0

20.0

50.0

 

0.0

0.0

0.0

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

99

53

51

  1. Allele frequencies for each allele were compared between cohorts and platforms for statistical comparison. Allele frequencies for different ethnicities were summed for comparison. Genetic material for cohort 2 was sequenced to evaluate AmpliChip CYP450 Test® (AmpliChip) genotype calls. Lower allele numbers were reported for the AmpliChip due to “No Calls” and failed chips. Individuals could be predicted as poor (PM), intermediate (IM), extensive (EM) and ultrarapid metabolisers using AmpliChip or activity score prediction models. xN: multiple copies of the allele detected; —, alleles not identified by platform.