CYP1A2 polymorphism (C > A at position −163) in Ovambos, Koreans and Mongolians

High predictive value of CYP2B6 SNPs for steady-state plasma efavirenz levels in South African HIV/AIDS patients

INTRODUCTION

Efavirenz is primarily metabolized by CYP2B6, with a minor contribution from CYP1A2, CYP2A6, CYP3A4 and CYP3A5. Genetic variability in these genes contributes towards differences in plasma efavirenz concentration, which ultimately leads to either development of adverse drug events or emergence of virus resistance. However, the clinical utility or validity of introducing genotype-assisted dosing is not known. The aim of this study was therefore to evaluate the effects of 14 single-nucleotide polymorphisms (SNPs) in five drug-metabolizing enzyme genes on steady-state plasma efavirenz levels in South African HIV/AIDS patients as well as their clinical validity.

METHODS

HIV/AIDS patients were recruited from Themba Lethu Clinic, at Helen Joseph Hospital, Johannesburg. Blood samples for plasma drug levels and DNA extraction were obtained from each participant. PCR/RFLP and SNaPshot genotyping were used for SNPs in CYP1A2, CYP2A6, CYP2B6, CYP3A4 and CYP3A5 among 464 Bantu-speaking South Africans. Plasma efavirenz concentrations were measured using LC/MS/MS. Genotypes and plasma efavirenz levels were used to calculate predictive values. Multivariate analysis was used to select the minimal set of SNPs with significant clinical validity.

RESULTS

Qualitative and quantitative differences in allele frequencies were observed when comparing South Africans with African, Caucasian and Asian populations. CYP2B6 516T and 785G (*6) and CYP2B6 983C (*18) alleles were significantly associated with high plasma efavirenz levels. CYP2B6 A-G-A-C-C and A-T-G-T-C haplotypes (with respect to CYP2B6 136A>G; CYP2B6 516G>T; CYP2B6 785A>G; CYP2B6 983T>C; and CYP2B6 1459C>T) were associated with higher levels of efavirenz, whereas G-G-A-T-C and A-G-A-T-C haplotypes showed significantly lower levels of efavirenz. The CYP2B6*1/*6 genotype was significantly associated with an increased risk of loss to follow-up. The sensitivity, specificity and positive predictive values for the CYP2B6*6/*6 genotype in predicting efavirenz levels above 4 µg/ml were 46, 97 and 88%, respectively. However, these values improved to 49, 100 and 100%, respectively, when either the CYP1A2 -163A (*1F) allele or the NR1I3 8784C/C genotype was present.

CONCLUSION

Screening for CYP2B6 516G>T SNP has a high specificity and positive predictive value for efavirenz levels above 4 µg/ml and could be used in deciding on efavirenz dosage among individuals homozygous for this variant, which could lead to better precision medication.

Considering CYP1A2 phenotype and genotype for optimizing the dose of olanzapine in the management of schizophrenia

INTRODUCTION

Schizophrenia, a mental disorder, is a debilitating condition which typically strikes young people in their early 20's. Antipsychotic medications are widely prescribed for the treatment of schizophrenia however a balancing act is necessary to provide the correct dose to each patient. It is suggested that a large number of patients discontinue antipsychotic pharmacotherapy because the treatments provided do not always reduce the positive symptoms of the disease, while many have adverse effects on the patients. This implies that neither the incorrect drug nor the optimal dosage for that patient is achieved.

AREAS COVERED

The current review investigates variability in response to olanzapine with a specific focus on the common intrinsic and extrinsic factors that influence both olanzapine and CYP1A2 activity. Furthermore, the authors discuss the utilization of phenotyping and genotyping of CYP1A2 and their potential utility in clinical practice for olanzapine dosing regimens. The authors also consider the potential of pharmacometrics compared to pharmacogenomics as a tool to personalize medicine.

EXPERT OPINION

Careful consideration must be given to the impact of a genetic variant on the disposition of a drug prior to implementing genetic 'tests' to determine response. CYP1A2 phenotypic assessment can yield important information regarding the disposition of olanzapine; however, it relies on the accuracy of the metric and the minimal impact of other metabolic pathways. The application of pharmacometrics provides an effective method to establish covariates that significantly influence olanzapine disposition which can incorporate phenotype and/or genotype.

Cytochrome P450 1A1, glutathione S-transferases M1 and T1 polymorphisms in Ovambos and Mongolians

Cytochrome P450 (CYP) 1A1, glutathione S-transferase (GST) M1, and GSTT1 gene polymorphisms have been shown to be associated with several diseases. In this study, CYP1A1 MspI, GSTM1 and GSTT1 gene polymorphisms were investigated in 134 Ovambo and 207 Mongolians, and the results were compared with those from previous studies. Using polymerase chain reaction/restriction fragment length polymorphism (PCR-RFLP) the frequency of CYP1A1 MspI mutation was determined. The multiplex PCR was used to determine the GSTM1 and GSTT1 polymorphism. The frequencies of wild-type, heterozygous variant and homozygous variant of the CYP1A1 MspI genotypes were 72.4%, 25.4% and 2.2%, and 22.7%, 55.6% and 21.7% in the Ovambos and Mongolians, respectively. The frequencies of GSTM1 (null) and GSTT1 (null) genotypes were 11.2% and 35.8%, and 46.4% and 25.6% in the Ovambos and Mongolians, respectively. The CYP1A1 MspI and GSTT1 (null) genotype distribution of the Ovambos was similar to that of African-Americans and some Caucasians. In contrast, the GSTM1 (null) genotype distribution was different from that of all other populations. Among Mongolians, the CYP1A1 MspI polymorphism showed the highest mutation frequencies, GSTM1 (null) was similar to that of East Asians, and GSTT1 (null) was different from that of almost all the Asians examined.

Sec1-FUT2-Sec1 hybrid allele generated by interlocus gene conversion

BACKGROUND

Many single-nucleotide polymorphisms have been identified in the coding region of the FUT2 locus, which encodes secretor type alpha(1,2)fucosyltransferase. In addition, three recombination alleles have been reported. Of these recombination alleles, a fusion gene generated by an unequal crossing over between Sec1, a pseudogene that locates 23 kb upstream to and has high sequence homology with FUT2 and FUT2, was identified as a Japanese-specific nonsecretor allele (se(fus)).

STUDY DESIGN AND METHODS

During the screening of the se(fus) in Mongolians (n = 118), a hybrid allele of Sec1-FUT2-Sec1 was found.

RESULTS

The DNA sequence suggested that the Sec1-FUT2-Sec1 allele contains a 275-bp sequence (between positions 259 and 533) that is identical to the FUT2 sequence including a 54-bp FUT2-specific region (between positions 417 and 470) and that might have been generated by an interlocus gene conversion.

CONCLUSION

Because the recombination region of se(fus) and the upstream recombination region of Sec1-FUT2-Sec1 are almost identical, this sequence stretch is likely to be the breakpoint for different kinds of recombinations that occur in this family of genes.