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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.