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Joining genetic data with phenotype data creates an opportunity to put genetic information into context with observable characteristics. Both genetic and environmental sources can influence phenotypic variation in a given population. An important part of drawing conclusions about the genetic contribution is specifying the phenotype and preparing the data in a suitable manner. That process involves various challenges since phenotypes often vary over time and are susceptible to external influences. In addition, measurement errors can add noise and/or bias to the data.

I will discuss the process of specifying categorical and quantitative phenotypes and preparing the phenotype data for genetic studies. Topics include inverse normal transformation of quantitative phenotypes, adjusting (or not) for individual characteristics, clinical diagnoses vs research definitions, circumstantial datasets vs generated datasets and genotype-to-phenotype studies.