Segregation analysis generally requires knowledge of the allele frequencies in the founder population. These founder allele frequencies (FAF) are used to generate genotype probabilities for individuals in the population when no data are available, or are combined with small amounts of data. Different FAF can be used to examine the sensitivity of the probabilities to the choice of FAF. Alternatively, as shown by Henshall and Tier (2002), the impact of the FAF on the genotype probabilities can be separated from that of the data in a segregation analysis. FAF also have an important role in computing likelihoods. The use of FAF, with algorithms based on peeling (Elston and Stewart, 1971), has the potential to generate misleading confidence in the genotype probabilities that result from segregation analyses.

B. Tier, J. M Henshall

Proceedings of the World Congress on Genetics Applied to Livestock Production, Volume 2002. Session 16, , 16.17, 2002
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