A single nucleotide polymorphism tags variation in the arylamine N-acetyltransferase 2 phenotype in populations of European background

Abstract

The arylamine N-acetyltransferase 2 (NAT2) slow acetylation phenotype is an established risk factor for urinary bladder cancer. We reported earlier on this risk association using NAT2 phenotypic categories inferred from NAT2 haplotypes based on seven single nucleotide polymorphisms (SNPs) in a study in Spain. In a subsequent genome-wide scan, we have identified a single common tag SNP (rs1495741) located in the 3' end of NAT2 that is also associated with bladder cancer risk. The aim of this report is to evaluate the agreement between the common tag SNP and the 7-SNP NAT2 inferred phenotype. The agreement between the 7-SNP NAT2 inferred phenotype and the tag SNP, rs1495741, was initially assessed in 2174 individuals from the Spanish Bladder Cancer Study (SBCS), and confirmed in a subset of individuals from the Main and Vermont component the New England Bladder Cancer Study (NEBCS). We also investigated the association of rs1495741 genotypes with NAT2 catalytic activity in cryopreserved hepatocytes from 154 individuals of European background. We observed very strong agreement between rs1495741 and the 7-SNP inferred NAT2 phenotype: sensitivity and specificity for the NAT2 slow phenotype was 99 and 95%, respectively. Our findings were replicated in an independent population from the NEBCS. Estimates for the association between NAT2 slow phenotype and bladder cancer risk in the SBCS and its interaction with cigarette smoking were comparable for the 7-SNP inferred NAT2 phenotype and rs1495741. In addition, rs1495741 genotypes were strongly related to NAT2 activity measured in hepatocytes (P<0.0001). A novel NAT2 tag SNP (rs1495741) predicts with high accuracy the 7-SNP inferred NAT2 phenotype, and thus can be used as a sole marker in pharmacogenetic or epidemiological studies of populations of European background. These findings illustrate the utility of tag SNPs, often used in genome-wide association studies (GWAS), to identify novel phenotypic markers. Further studies are required to determine the functional implications of rs1495741 and the structure and evolution of the haplotype on which it resides.

Figure 1

Scatter plots of SMZ N-acetyltransferase activities in cryopreserved human hepatocytes from individuals of European background. Each dot represents SMZ N-acetyltransferase activity in each of the 154 human hepatocyte samples, stratified by categories of NAT2 acetylator phenotype inferred from 7 NAT2 SNPs (Panel A), and by genotypes of the NAT2 tag SNP (rs1495741) identified in a genome-wide scan (Panel B). Lines illustrate mean activity in each genotype. ANOVA P-value for differences in SMZ NAT2 mean activity by genotype categories is P<0.0001 in both Panel A and B. Panel A: The slope from a linear regression of SMZ NAT2 activity against NAT2 deduced phenotype (coded as 2=Rapid, 1=Intermediate, 0=Slow) is 0.745 P<0.0001. Panel B: The slope from a linear regression of SMZ NAT2 activity against the rs1495741 genotype (coded as 0=AA, 1=AG and 2=GG) is 0.465, P<0.0001.