Extensive whole genome sequencing comparisons in dogs elucidates a putative novel candidate gene for retinal degeneration.

Presenter Rebekkah Hitti
Authors Rebekkah J. Hitti (1,2), James A. Oliver (1), Ellen C. Schofield (1), Anina Bauer (3), Tosso Leeb (3), David Sargan (2), Cathryn S. Mellersh (1)
Affiliations 1. Kennel Club Genetics Centre, Animal Health Trust, Lanwades Park, Newmarket, Suffolk, CB8 7UU, United Kingdom. 2. Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom. 3.Institute of Genetics, University of Bern, 3001 Bern, Switzerland.
Presentation Type Talk


Retinitis pigmentosas (RP) are genetically heterogeneous, progressive diseases characterised by retinal degeneration and causing loss of vision before middle age, and affecting in 1 in 2000 humans. The canine equivalent, progressive retinal atrophy (PRA) is untreatable and affects multiple dog breeds, significantly impacting dog welfare.

A novel form of PRA was diagnosed in a family of Giant Schnauzer dogs, where three out of seven littermates presented with clinical signs of PRA around four years of age. The sire and dam were clinically unaffected and therefore considered likely to be obligate carriers of an autosomal recessive mutation causing PRA in this family. We sought to identify the causal mutation of PRA in this Giant Schnauzer family with the ultimate aim of developing a DNA test, a tool which breeders could utilise to prevent this form of PRA becoming widespread in the breed.

Whole genome sequencing (WGS) of two PRA affected full-siblings and their unaffected parents was performed. Variants were filtered based on those segregating appropriately for an autosomal recessive disorder and those with a predicted pathogenic effect on the coding sequence and protein. Successive filtering against a total of 568 genomes (including genomes from the Dog Biomedical Variant Database Consortium and the Animal Health Trust Give a Dog a Genome bank) reduced an initial set of > 20 million variants down to a single candidate variant in a novel gene not previously associated with retinal degeneration in any species.

The candidate variant was genotyped in a total of 1,444 dogs of 175 breeds, 10 cross breed dogs and 3 wolves, with our three PRA-affected Giant Schnauzers being the only homozygotes identified to date. Nine Giant Schnauzer heterozygotes were identified in addition to heterozygotes in three additional breeds of German origin, including the German Giant (Gross) and Medium (Mittel) Spitz and Miniature Longhaired Dachshund (MLHD). The genotyping of German Spitz varieties, including 110 Giant Spitz, 21 Medium Spitz, 24 Miniature (Klein) Spitz, 17 Pomeranian (Zwerg) Spitz, and an additional 27 Giant Schnauzers was carried out by collaborators at the University of Bern. We screened a total of 163 MLHD for the candidate variant. Seven German Giant Spitz, one German Medium Spitz and six MLHD heterozygotes were identified, suggesting this may be an ancestral, but rare, mutation.

This study highlights the power of using WGS to identify novel genes associated with disease using a very small number of cases. This novel candidate gene, harbouring a variant that is predicted to be the causal mutation of PRA in the Giant Schnauzer, could provide insights into gene discoveries in human retinal degenerations. Further functional study options are being explored to confirm the candidate gene’s role in retinal function and maintenance.