A LINE-1 insertion situated in the promoter of IMPG2 is associated with autosomal recessive progressive retinal atrophy in Lhasa Apso dogs

• Published in: BMC genetics 2020-09, Vol.21 (1), p.100-17, Article 100
• Main Authors: Hitti-Malin, Rebekkah J, Burmeister, Louise M, Ricketts, Sally L, Lewis, Thomas W, Pettitt, Louise, Boursnell, Mike, Schofield, Ellen C, Sargan, David, Mellersh, Cathryn S
• Format: Article
• Language: English
• Subjects: Age; Analysis; Animals; Atrophy; Atrophy - genetics; Atrophy - veterinary; Blindness; Breeding; Breeding of animals; Canine; Canine retinal degeneration; Deoxyribonucleic acid; Disease; DNA; Dog; Dog Diseases - genetics; Dogs; Dogs - genetics; Gene Frequency; Genes; Genetic Association Studies - veterinary; Genetic testing; Genome-wide association studies; Genomes; Genomics; Genotype; Genotypes; High-Throughput Nucleotide Sequencing - veterinary; Inherited; Insertion; Long Interspersed Nucleotide Elements; Medical personnel; Mutagenesis, Insertional; Mutation; Photoreceptors; Population genetics; PRA; Progressive retinal atrophy; Promoter Regions, Genetic; Proteoglycans - genetics; Retina; Retina - pathology; Retinal degeneration; Retinal Degeneration - genetics; Retinal Degeneration - veterinary; Thermal cycling; Whole Exome Sequencing - veterinary; Whole genome sequencing
• ISSN: 1471-2156; 1471-2156
• DOI: 10.1186/s12863-020-00911-w

Canine progressive retinal atrophies are a group of hereditary retinal degenerations in dogs characterised by depletion of photoreceptor cells in the retina, which ultimately leads to blindness. PRA in the Lhasa Apso (LA) dog has not previously been clinically characterised or described in the literature, but owners in the UK are advised to have their dog examined through the British Veterinary Association/ Kennel Club/ International Sheep Dog Society (BVA/KC/ISDS) eye scheme annually, and similar schemes that are in operation in other countries. After the exclusion of 25 previously reported canine retinal mutations in LA PRA-affected dogs, we sought to identify the genetic cause of PRA in this breed. Analysis of whole-exome sequencing data of three PRA-affected LA and three LA without signs of PRA did not identify any exonic or splice site variants, suggesting the causal variant was non-exonic. We subsequently undertook a genome-wide association study (GWAS), which identified a 1.3 Mb disease-associated region on canine chromosome 33, followed by whole-genome sequencing analysis that revealed a long interspersed element-1 (LINE-1) insertion upstream of the IMPG2 gene. IMPG2 has previously been implicated in human retinal disease; however, until now no canine PRAs have been associated with this gene. The identification of this PRA-associated variant has enabled the development of a DNA test for this form of PRA in the breed, here termed PRA4 to distinguish it from other forms of PRA described in other breeds. This test has been used to determine the genotypes of over 900 LA dogs. A large cohort of genotyped dogs was used to estimate the allele frequency as between 0.07-0.1 in the UK LA population. Through the use of GWAS and subsequent sequencing of a PRA case, we have identified a LINE-1 insertion in the retinal candidate gene IMPG2 that is associated with a form of PRA in the LA dog. Validation of this variant in 447 dogs of 123 breeds determined it was private to LA dogs. We envisage that, over time, the developed DNA test will offer breeders the opportunity to avoid producing dogs affected with this form of PRA.