Ethnicity-related polymorphisms and haplotypes in human ABCB1 gene

Chava Kimchi-Sarfaty, Andrew H. Marple, Shiri Shinar, Avraham M. Kimchi, David Scavo, M. Isabella Roma, In Wha Kim, Adam Jones, Mili Arora, John Gribar, David Gurwitz, Michael M. Gottesman

Research output: Contribution to journalArticle

71 Citations (Scopus)

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, 11236C→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 [χ2: 0.30; p≤5 1]; 55.8 and 64.4%, respectively for 2677G→T/A/C [χ2: 1.49; p≤1]), but were different for 3435C→T (24.2% for the US population and 69.3% for the Ashkenazi population [χ2: 39.927; p≤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.

Original languageEnglish (US)
Pages (from-to)29-39
Number of pages11
JournalPharmacogenomics
Volume8
Issue number1
DOIs
StatePublished - Jan 2007
Externally publishedYes

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Haplotypes
Single Nucleotide Polymorphism
Adenosine Triphosphate
P-Glycoprotein
Genotype
Population
Genes
MDR Genes
Information Centers
Disease Susceptibility
Xenobiotics
Drug-Related Side Effects and Adverse Reactions
Drug Resistance
Restriction Fragment Length Polymorphisms
Pharmaceutical Preparations
Exons
Pharmacokinetics
Phenotype
Polymerase Chain Reaction
Membranes

Keywords

  • ABCB1
  • Ethnicity
  • Haplotypes
  • P-glycoprotein
  • SNPs

ASJC Scopus subject areas

  • Molecular Medicine
  • Genetics
  • Pharmacology

Cite this

Kimchi-Sarfaty, C., Marple, A. H., Shinar, S., Kimchi, A. M., Scavo, D., Roma, M. I., ... Gottesman, M. M. (2007). Ethnicity-related polymorphisms and haplotypes in human ABCB1 gene. Pharmacogenomics, 8(1), 29-39. https://doi.org/10.2217/14622416.8.1.29

Ethnicity-related polymorphisms and haplotypes in human ABCB1 gene. / Kimchi-Sarfaty, Chava; Marple, Andrew H.; Shinar, Shiri; Kimchi, Avraham M.; Scavo, David; Roma, M. Isabella; Kim, In Wha; Jones, Adam; Arora, Mili; Gribar, John; Gurwitz, David; Gottesman, Michael M.

In: Pharmacogenomics, Vol. 8, No. 1, 01.2007, p. 29-39.

Research output: Contribution to journalArticle

Kimchi-Sarfaty, C, Marple, AH, Shinar, S, Kimchi, AM, Scavo, D, Roma, MI, Kim, IW, Jones, A, Arora, M, Gribar, J, Gurwitz, D & Gottesman, MM 2007, 'Ethnicity-related polymorphisms and haplotypes in human ABCB1 gene', Pharmacogenomics, vol. 8, no. 1, pp. 29-39. https://doi.org/10.2217/14622416.8.1.29
Kimchi-Sarfaty C, Marple AH, Shinar S, Kimchi AM, Scavo D, Roma MI et al. Ethnicity-related polymorphisms and haplotypes in human ABCB1 gene. Pharmacogenomics. 2007 Jan;8(1):29-39. https://doi.org/10.2217/14622416.8.1.29
Kimchi-Sarfaty, Chava ; Marple, Andrew H. ; Shinar, Shiri ; Kimchi, Avraham M. ; Scavo, David ; Roma, M. Isabella ; Kim, In Wha ; Jones, Adam ; Arora, Mili ; Gribar, John ; Gurwitz, David ; Gottesman, Michael M. / Ethnicity-related polymorphisms and haplotypes in human ABCB1 gene. In: Pharmacogenomics. 2007 ; Vol. 8, No. 1. pp. 29-39.
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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, 11236C→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 [χ2: 0.30; p≤5 1]; 55.8 and 64.4{\%}, respectively for 2677G→T/A/C [χ2: 1.49; p≤1]), but were different for 3435C→T (24.2{\%} for the US population and 69.3{\%} for the Ashkenazi population [χ2: 39.927; p≤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.",
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AU - Marple, Andrew H.

AU - Shinar, Shiri

AU - Kimchi, Avraham M.

AU - Scavo, David

AU - Roma, M. Isabella

AU - Kim, In Wha

AU - Jones, Adam

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N2 - 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, 11236C→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 [χ2: 0.30; p≤5 1]; 55.8 and 64.4%, respectively for 2677G→T/A/C [χ2: 1.49; p≤1]), but were different for 3435C→T (24.2% for the US population and 69.3% for the Ashkenazi population [χ2: 39.927; p≤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.

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