This paper identifies issues associated with field disease data and their implications on the interpretation of estimated genetic parameters and experimental designs. The main focus is on concepts relating to the impacts of diagnostic test properties and exposure to infection, and how exposure to infection is intricately related to within-herd epidemic dynamics. The following are raised challenges: (i) to more fully understand and describe the dynamic impacts of disease epidemics on genetic interpretations; (ii) to develop statistical methods to jointly estimate epidemiological and genetic parameters from complex epidemiological data; (iii) to develop and explore optimal experimental designs for case-control studies, exploiting field disease data. Solving these problems would add insight to both disease genetic and epidemiological studies, as well as enabling us to better select animals for increased disease resistance.
Keywords: animal; epidemiology; field data; genome wide association analysis; heritability.