Annotated PGx Gene Information for ABCB1

). Results to date show that cancers exhibiting de novo pharmacoresistance (drug naive), such as leukemias, myeloma, lymphomas, and breast and ovarian cancers, are the most amenable to P-gp modulation with reversal agents as adjunct therapy.

Genetic associations
Disease-causing mutations in fourteen of the ABC superfamily members have been described, as in CFTR (ABCC7) for cystic fibrosis, ABCA4 for macular degeneration, ABCC2 and ABCB11 for biliary dysfunction, and ABCA1, ABCG5, ABCG8, and ABCD1 for fatty acid/lipid disorders [PMID: 12045106]. A large corpus of literature about sequence variations for ABCB1 exists, however there is no clear consensus regarding the contribution of ABCB1 variation to disease risk [PMID: 16969364, 17661727, 18370231]; and despite evidence for inter-individual variability in ABCB1 expression and P-gp function [PMID: 7473127, 14965248, 19285158], the genetic contribution is unclear [PMID: 16969364]. A great number of studies has been carried out to establish the role of ABCB1 genetics in various phenotypes such as P-gp expression, function, drug response, and disease susceptibility with little consensus. Most genotype-phenotype associations are not substantiated by study replication, meaningful sample size, and appropriate multitesting correction. See helpful reviews [PMID: 12505329, 12406646, 14749689, 15212152], including a detailed summary by Leschziner et al. of the discordant literature regarding genetic association of ABCB1 SNPs and haplotypes with P-gp expression, activity, drug response, and disease risk [PMID: 16969364].

Despite much work to ascertain the genetic contribution of ABCB1 on drug disposition and disease susceptibility, the accumulation of studies to date are unclear. Until data is amassed to form a consensus about the role of genetics in P-gp-related phenotypes, the primary clinical focus on P-gp relates to its role in (1) multi-drug resistance, and (2) drug-drug interactions [PMID: 17933685].

ABCB1 variants
As of April 30, 2009 for build 130 of the Single Nucleotide Polymorphism database (dbSNP), there are 1279 SNPs in the ABCB1 gene region, 62 of which are coding (22 synonymous, 41 non-synonymous, and 1 in the start codon). The number and frequency of SNPs observed varies by ethnicity. Excluding SNPs below 5% allele frequency, there are approximately 124 SNPs observed in Caucasians, 134 in African Americans, 153 in Chinese, and 166 in Japanese (see ABCB1 in HapMap at www.hapmap.org). Additional information is available at the University of California, San Francisco Pharmacogenetics of Membrane Transporters Database (see ABCB1 at http://pharmacogenetics.ucsf.edu).

About 2.6 times fewer (n = 4) SNPs occur in the transmembrane domains compared to the intracellular and extracellular regions of the protein. None of the three prime untranslated region (3'UTR) SNPs are reported to alter mRNA stability [PMID: 19285158]. The three most common SNPs in the protein coding region are rs1128503 (1236T>C, Gly412Gly), rs2032582 (2677T>G/A, Ser893Ala/Thr), and rs1045642 (3435T>C, Ile1145Ile) [PMID: 16141795], according to build 130 of (dbSNP). These three SNPs have been the focus of many pharmacokinetic and disease association studies with controversial results [PMID: 16969364] (see Important Variants). Other less frequent variants include -129C>T (5'-UTR), 61A>G (Asn21Asp), and 1199G>A (Ser400Asn), which have been studied in vivo and in vitro. (See coding SNP locations on the secondary structure of P-gp per Fung et al. [PMID: 19285158] as adapted from Ambudkar et al. [PMID: 10331089].)

ABCB1 haplotypes
Closely positioned sequence variants tend not to segregate independently with each generation due to linkage disequilibrium (LD). As a result, multiple variant alleles are inherited together on the same physical chromatid in a particular pattern. That is to say that for linked variant alleles, the occurance of one variant allele informs the valence other alleles with a certain level of predictability. For example, alleles from the three most common coding SNPs at nucleotides 1236, 2677, and 3435, are in high LD [PMID: 16708052] and are observed most frequently as the 893Ala-containing CGC haplotype and 893Ser-containing TTT haplotype in most ethnic groups [PMID: 11503014, 12172212, 12893986, 14976162]. Other observed haplotypes extend beyond the exonic region of ABCB1 [PMID: 16255080]. Leschziner et al. observed LD extending 75 kilobases, linking 3' variant alleles of ABCB1 to coding variant alleles of the adjacent ABC transporter gene, ABCB4 [PMID: 16708052].

Haplotype structure relates to the location of recombination hot spots and ancestry-specific patterns of LD [PMID: 16255080, 18288195]. Tang et al. observed ethnic-specific LD blocks at the ABCB1 locus that are 80, 60, and 40 kilobase in length and distinguish Chinese, Malay, and Indian populations, respectively [PMID: 12172212]. Similarly, comparison of the mutation rate between Beninese Africans (1 variant per 224 basepairs) and American Africans (1 variant per 172 bp) reflects admixture in the U.S. cohort that differentiates the ABCB1 haplotype structure in these populations [PMID: 15692830]. Accordingly, haplotype frequencies differ by ethnic group. For example, the 893Ser-containing TTT haplotype occurs relatively infrequently in African Americans compared to Caucasians [PMID: 11503014, 12893986] and Asians [PMID: 12172212].

A haplotype by definition is not bound by a gene region, but gene-specific haplotypes can acquire allelic designations in the literature. Sequence analysis of ABCB1 in different ethnic groups has been performed [PMID: 11503014, 12172212, 12893986, 14646693, 15692830, 16708052, 17187507] and led to the designation of "star alleles" [PMID: 14646693, 11503014, 12893986], as explained by Robarge et al. [PMID: 17700589] (see Important Haplotypes). Briefly, the designation of ABCB1 star alleles follows rules established by the Cytochrome P450 Allele Nomenclature Committee and others for naming haplotypes observed for cytochrome P450 (CYP450), uridinediphosphate-glucuronosyltransferase (UGT), N-acetyltransferase (NAT), and aldehyde dehydrogenase (ALDH) [PMID: 10862518, 17700589] genes. Star alleles are defined relative to an arbitrarily established reference sequence, denoted *1. ABCB1*1 contains 1236C, 2677G (893Ala), and 3435C. Many star allele designations for ABCB1 are currently not harmonization in the literature. To illustrate, ABCB1*2, as defined by Kim et al., harbors three coding variants, namely 1236T, 2677T (893Ser), and 3435T [PMID: 11503014]; while ABCB1*2, as defined by Kroetz et al., contains 3435T (and is reference for 1236C and 2677G (893Ala)) [PMID: 12893986]. ABCB1*13 per Kroetz et al. (1236T, 2677T (893Ser), 3435T, and 3 intronic SNPs) [PMID: 12893986] is most similar to ABCB1*2 defined by Kim et al. [PMID: 11503014] as they are indistinguishable in terms of the coding region and amino acid sequence.

To investigate the regulatory impact of promoter variants on functional phenotypes, haplotype analysis of the promoter region has also been performed [PMID: 15280437, 16907707, 16608921, 19072639]. Wang et al. observed a haplotype formed from eight low-frequency variants (<5% minor allele frequency) in the promoter region that accounted for 85% of all haplotypes observed in five ethnic groups [PMID: 16608921]. They functionally characterized promoter haplotypes observed in Chinese, Malays, Indians, European Americans, and African Americans using an in vitro reporter assay and found significant ethnic-specific differences in promoter activity, although activity differed by the cell line used in the assay (presumably due to cell-specific regulatory factors). Other work has been done to understand the relationship between regulatory and coding variants for ABCB1 and their potential association with endophenotypes. Takane et al. showed that variation in promoter haplotype activity was independent of variation at the synonymous 3435 SNP, and the methylation status of the proximal promoter did not correlate with ABCB1 mRNA expression [PMID: 15280437] (see Molecular and protein structure, and Compounds that interact with P-gp). Jiang et al. found an association between the promoter methylation status and variation in coding SNPs for ABCB1. They showed that lower promoter methylation was associated with the 3435 TT and 893Ala-containing 2677 genotypes, while the 893Ser-containing TTT (1236, 2677, 3435) haplotype was associated with higher methylation 19072639. More research is needed to elucidate the functional relevance of regulatory variants for ABCB1 and their potential value to predicting P-gp-related phenotypes.