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The candidate gene approach to conducting genetic association studies focuses on genetic variation within pre-specified genes of interest. This is in contrast to genome-wide association studies (GWAS), which scan the entire genome for common genetic variation. Candidate genes are generally selected for study based on a priori knowledge of the gene’s biological functional impact on the trait or disease in question. The rationale behind focusing on allelic variation in specific, biologically relevant regions of the genome is that certain mutations will directly impact the function of the gene in question, and lead to the phenotype or disease state being investigated. This approach generally uses the case-control study design to try to answer the question, “Is one allele of a candidate gene more frequently seen in subjects with the disease than in subjects without the disease?”

Selecting a Candidate Gene
Suitable candidate genes are generally selected based on known biological, physiological, or functional relevance to the disease in question. This approach is limited by its reliance on existing knowledge about known or theoretical biology of disease. However, more recently developed molecular tools are allowing insight into disease mechanisms and pinpointing potential regions of interest in the genome. Genome-wide association studies and quantitative trait locus (QTL) mapping examine common variation across the entire genome, and as such can detect a new region of interest that is in or near a potential candidate gene. Microarray data allow researchers to examine differential gene expression between cases and controls, and can help pinpoint new potential genes of interest In addition, the availability of genetic information through online databases enables researchers to mine existing data and web-based resources for new candidate gene targets.