AlleleFetch: Pedigree tracking of alleles causing hereditary disorders in dogs

Dog genetic diseases vary greatly between breeds. This project will contribute to managing genetic dog diseases by developing AlleleFetch – a tool for tracing genes causing dog diseases.

For some diseases, breeders can use genetic (DNA) testing to determine their dog's genotype, whether it carries two desired genes, one desired and one undesired gene, or two undesired genes. For some other diseases, breeders can only clinically diagnose their dogs, which gives phenotype information. Phenotyping can be subjective, unclear about dogs' genotypes, and generally done late in life after selection and reproductive choices for the particular dog has already been made. When both genotype and phenotype information are available, they can be combined. However, this is challenging due to gene interactions, genes with unclear effects, numerous genes, apparently contradictory phenotypes, or some dogs with genotype information but others only with phenotype information.

We need a general tool to combine gene and phenotype information. To this end, we will develop AlleleFetch, which will combine gene and phenotype information in a general way using a Bayesian network technique. This technique can work with different sources of information and combine them to help make decisions. We will develop and test AlleleFetch using the following three examples:

• single-gene condition with genotype information with a simple penetrance function,
• single-gene condition with genotype and phenotype information with simple penetrance functions, and
• multi-gene condition with complex genotype-to-phenotype penetrance function.

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