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Open Access Research article

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

Tyren M Dodgen1, Warren E Hochfeld1, Heidi Fickl2, Sahle M Asfaha2, Chrisna Durandt2, Paul Rheeder3, Britt I Drögemöller4, Galen E B Wright4, Louise Warnich4, Christiaan DJ Labuschagne5, Antoinette van Schalkwyk5, Andrea Gaedigk6 and Michael S Pepper27*

Author Affiliations

1 Department of Pharmacology, University of Pretoria, Pretoria, South Africa

2 Department of Immunology, University of Pretoria, Pretoria, South Africa

3 Division of Clinical Epidemiology, School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa

4 Department of Genetics, Stellenbosch University, Stellenbosch, South Africa

5 Inqaba Biotechnical Industries, Pretoria, South Africa

6 Section of Developmental Pharmacology and Experimental Therapeutics, Children’s Mercy Hospital & Clinics, Kansas City, Missouri, USA

7 Department of Genetic Medicine and Development, University Medical Centre, University of Geneva, Geneva, Switzerland

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BMC Medical Genetics 2013, 14:20  doi:10.1186/1471-2350-14-20

Published: 29 January 2013

Abstract

Background

Adverse drug reactions and lack of therapeutic efficacy associated with currently prescribed pharmacotherapeutics may be attributed, in part, to inter-individual variability in drug metabolism. Studies on the pharmacogenetics of Cytochrome P450 (CYP) enzymes offer insight into this variability. The objective of this study was to compare the AmpliChip CYP450 Test® (AmpliChip) to alternative genotyping platforms for phenotype prediction of CYP2C19 and CYP2D6 in a representative cohort of the South African population.

Methods

AmpliChip was used to screen for thirty-three CYP2D6 and three CYP2C19 alleles in two different cohorts. As a comparison cohort 2 was then genotyped using a CYP2D6 specific long range PCR with sequencing (CYP2D6 XL-PCR + Sequencing) platform and a PCR-RFLP platform for seven CYP2C19 alleles.

Results

Even though there was a low success rate for the AmpliChip, allele frequencies for both CYP2D6 and CYP2C19 were very similar between the two different cohorts. The CYP2D6 XL-PCR + Sequencing platform detected CYP2D6*5 more reliably and could correctly distinguish between CYP2D6*2 and *41 in the Black African individuals. Alleles not covered by the AmpliChip were identified and four novel CYP2D6 alleles were also detected. CYP2C19 PCR-RFLP identified CYP2C19*9,*15, *17 and *27 in the Black African individuals, with *2, *17 and *27 being relatively frequent in the cohort. Eliminating mismatches and identifying additional alleles will contribute to improving phenotype prediction for both enzymes. Phenotype prediction differed between platforms for both genes.

Conclusion

Comprehensive genotyping of CYP2D6 and CYP2C19 with the platforms used in this study, would be more appropriate than AmpliChip for phenotypic prediction in the South African population. Pharmacogenetically important novel alleles may remain undiscovered when using assays that are designed according to Caucasian specific variation, unless alternate strategies are utilised.