Using hapmap tools to predict oncology-related phenotypes: TPMT activity vs hapmap SNPs

Abstract

13035 Background: Thiopurine S-methyltransferase (TPMT) is a cytosolic enzyme responsible for the S-methylation of thiopurines. There are several functional genetic polymorphisms in TPMT activity, which can lead to drug toxicities; however, among individuals with high TPMT activity, a substantial portion of enzymatic variability remains unexplained. B-lymphoblastoid CEPH cell lines have been genotyped at over 2 million single nucleotide polymorphisms (SNPs) as part of the International HapMap project. Therefore, extensive phenotype-genotype association studies can be conducted in these cell lines by systematic determination of cancer-related phenotypes. Methods: We measured the phenotype of TPMT activity in 82 CEPH cell lines. Of these, 53 had expression data available on over 8000 genes from Affymetrix Focus Array technology. We evaluated whether TPMT activity was associated with HapMap SNPs in TPMT (cis SNPs), genome-wide HapMap SNPs (trans SNPs), and level of gene expression using Kruskal-Wallis test and Spearmans rank correlation. Results: We found associations of TPMT activity with four SNPs (p < 0.05) in TPMT (± 100K bp), one of which (rs1142345, p = 0.009) is a known functional SNP responsible for TPMT deficiency. Two other significant SNPs are in linkage disequilibrium with rs1142345. Associations were also found with 1598 trans SNPs across the genome (p < 0.001). TPMT activity was associated with the expression of eight genes (p < 0.0001, FDR <20%). The only overlapping trans gene is PACSIN2, whose expression most significantly correlated with TPMT activity and also contains two significantly predictive trans SNPs. Conclusions: The CEPH cell lines were useful in that a known functional variant, rs1142345, (serving as a positive control) was associated with TPMT activity, and that additional polymorphisms in TPMT and in potentially important trans-acting factors have been identified as possible additional genomic determinants of TPMT activity. Similar experiments with other phenotypes can likewise capitalize on this publicly available resource. With further validation, these studies may lead to discovery of additional candidate polymorphisms that can lead to further optimization of thiopurine therapy in the clinic. No significant financial relationships to disclose.