Issues in Association Analysis: Error Control in Case-Control Association Studies for Disease Gene Discovery

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Abstract
Several sources of errors are discussed. While genotyping errors have little effect on power in case-control association studies, they tend to strongly increase false positive results in TDT type tests unless occurrence of errors is allowed for in the analysis (e.g., TDTae test). Disregarding non-genetic risk factors is shown to lead to a form of hidden heterogeneity, which can strongly reduce power. Stratification of data into more homogeneous subgroups is advocated as a simple solution to allowing for non-genetic risk factors such as socio-economic status and food preferences.