Identifying the genotype behind the phenotype: a role model found in VKORC1 and its association with warfarin dosing

Abstract

Genotype-phenotype studies in pharmacogenomics promise to identify the genetic factors that contribute substantially to variation in individual drug response. While most genetic association studies have failed to deliver this promise, several recent examples serve as a reminder that these associations do exist and can be identified when investigated using well-designed studies. Here, we describe the path taken to identify the association between common vitamin K epoxide reductase complex subunit 1 genetic variation and warfarin dosing in patients. We also describe the key elements that led the way, such as definition of the phenotype, confirmation of a genetic component, determination of biological plausibility and selection of genetic polymorphisms. We also describe several avenues that are yet to be explored for the specific vitamin K epoxide reductase complex subunit 1 warfarin example that can also be generalized as future directions for many genetic association studies in pharmacogenomics. These future avenues will be best explored using diverse approaches encompassing clinical, statistical and genomic methods currently being developed for genotype-phenotype studies in human populations.

Figure. Linkage disequilibrium and tagSNP selection for common VKORC1 genetic variation in two populations

VKORC1 was re-sequenced in 23 Euorepan-Americans and 24 African-Americans as previously described [38]. Linkage disequilibrium was calculated using r² by the Genome Variation Server (http://gvs.gs.washington.edu/GVS/) for SNPs with a minor allele frequency (MAF) >5% for each population sample separately. TagSNPs were also determined using the Genome Variation Server for common VKORC1 SNPs (MAF>5%) at default settings (r²>0.80). SNPs are labeled using rs numbers and are color coded so that red represent nonsynonymous SNPs, orange represents SNPs in the untranslated region, bolded represents SNPs in unique sequence regions, and unbolded represents SNPs in repeat sequence regions. DNA samples used in re-sequencing are labeled to the left of the figure using dbSNP nomenclature (population ID:individual ID). SNP genotypes (squares) are color coded so that blue represents homozygosity for the major allele, red represents heterozygosity, and yellow represents homozygosity for the minor allele. Gray squares represent missing data. The bar above the SNPs represents a group or “bin” of SNPs that can be represented by a single tagSNP (denoted by an asterisk above the rs number) from the bin. The triangle plot represents the pair-wise linkage disequilibrium statistics (r²), and the results are color coded so that red represents the highest and blue represents lowest linkage disequilibrium statistics, respectively.