Candidate gene association analysis.

Candidate gene association study is the most common method for associating human genetic variations with the phenotypes they produce, due to the relative simplicity of acquiring patient samples and genotype data. The study design begins with identifying appropriate DNA samples and an appropriate phenotype for analysis. The candidate genes and polymorphisms must then be chosen. After genotyping the candidate genes in the DNA samples, the results are checked to ensure appropriate quality and association analysis is performed. The raw results are interpreted and placed into context and follow-up analysis is carried out to validate and refine the findings. A wide range of software packages are available for both the association analysis and other steps in the study. This chapter describes the use of PLINK as the analysis tool in an example, as that suite has emerged as the most popular option for genetic association testing.