Association analysis of genetic variants related to biotransformation, estrogen metabolism, and oxidative stress

Abstract

In a previous study by the NWU eBOSS research group, urinary oestrogen biotransformation metabolite levels and blood oxidative stress markers were measured in African and Caucasian premenopausal South African women. Variation in these metabolites was observed between individuals of the same as well as different ethnic groups. The aim of this hypothesis-generating study was to determine whether these variations correlated with genetic variants in certain biotransformation genes – namely CYP1B1, CYP3A4, CYP1A1/2 and COMT. Genomic DNA was isolated from whole blood using a gDNA isolation with magnetic beads method. Thereafter samples were genotyped at the Centre for Proteomic and Genetic Research (CPGR) in Cape Town using the Global Screening Array (GSA) version 2.0 beadchip and the Illumina iScan. Due to small sample size, only SNPs for which there were at least 10 minor allele carriers (either heterozygous or homozygous for the minor allele), were selected in Haploview. PLINK logistics command highlighted specific SNP and metabolite interactions. Within the program SPSS, general linear models of univariate nature were implemented to determine the significance of these PLINK associations. 29 SNP-metabolite associations were determined to be significant where 15, five, five and four associations were found in Caucasian controls, African controls, Combined controls and Caucasian Combined oral contraceptive (COC) users respectively. Comparing Caucasian controls to African control, differences in metabolite levels and SNP frequencies resulted in no overlapping SNPmetabolite associations except for the Combined controls association being applicable to both population groups. The use of COC results in changes in metabolites levels and highlight new SNPmetabolite associations. Most of these associations have not been published before and may explain the variation in oestrogen metabolite levels and oxidative stress observed between individuals of similar or different ethnic groups.