Ethnicity-related polymorphisms and haplotypes in the human ABCB1 gene

Abstract

Introduction: The human multidrug resistance gene ATP-binding cassette B1 (ABCB1) codes for P-glycoprotein (P-gp), an important membrane-bound efflux transporter known to confer anticancer drug resistance as well as affect the pharmacokinetics of many drugs and xenobiotics. A number of single nucleotide polymorphisms (SNPs) have been identified throughout the ABCB1 gene that may have an effect on P-gp expression levels and function. Haplotype as well as genotype analysis of SNPs is becoming increasingly important in identifying genetic variants underlying susceptibility to human disease. Three SNPs, 1236C-->T, 2677G-->T and 3435C-->T, have been repeatedly shown to predict changes in the function of P-gp. The frequencies with which these polymorphisms exist in a population have also been shown to be ethnically related.

Methods: In this study, 95 individuals representative of the entire ethnic make-up of the USA were compared with 101 individuals from an Ashkenazi-Jewish population. These individuals were analyzed by genomic sequencing and polymerase chain reaction, using restriction fragment length polymorphisms, to calculate their genotype frequencies.

Results: A total of 25 SNPs were located in the exons of the ABCB1 gene. All of the polymorphisms identified were in parts of the ABCB1 gene product predicted to be intracellular, and 16 appear to be novel as compared with those listed by the National Center for Biotechnological Information. Frequencies of the 1236C-->T and 2677G-->T/A/C SNPs were similar for the US and Ashkenazi populations (64.2 and 60.4%, respectively for 1236C-->T [chi2: 0.30; p < or = 1]; 55.8 and 64.4%, respectively for 2677G-->T/A/C [chi2: 1.49; p < or = 1]), but were different for 3435C-->T (24.2% for the US population and 69.3% for the Ashkenazi population [chi2: 39.927; p < or = 0.001]). The 1236T/ 2677T/3435T haplotype occurred in 23.6% (standard error: 0.013) of the Ashkenazi population.

Conclusion: The SNP at location 3435C-->T plays a significant role in the ABCB1 gene. The haplotype and genotype analysis from these data may be used as a basis for studies on the relationship between ABCB1 genotypes and drug efficacy, drug toxicity, disease susceptibility or other phenotypes.

Figures

Figure 1. Hypothetical structure of P-gp and corresponding SNP locations within the ABCB1 exonic region of the American population

This figure illustrates the approximate locations of amino acid changes along the P-gp protein resulting from non-synonymous polymorphisms. A red “X” marks the approximate location of each polymorphism identified in this study. Black dots represent the approximate locations of common amino acid changes previously reported in the P-gp protein. Exons 1–28 are labeled by color and nucleotide length.

Figure 2. Sequencing and electrophoresis results confirm individual genotype status

DNA sequencing was used to ensure that results obtained by PCR-RFLP were accurate. A. SNP 1236C>T occurs in the third base-pair of the codon B. SNP 2677G>T occurs in the first base-pair of the codon, C. SNP 3435C>T occurs in the first base-pair of the codon. Electrophoresis was performed on 4% TBE agarose gels with a 50 bp Low Range Ladder.