Genetic prevalence and clinical relevance of canine Mendelian disease variants in over one million dogs

Frequency of RPGRIP1 and MAP9 genetic modifiers of canine progressive retinal atrophy, in 132 breeds of dog

Variants in RPGRIP1 and MAP9, termed RPGRIP1ins44 and MAP9del respectively, are both associated with a form of canine progressive retinal atrophy referred to as RPGRIP1-CRD and have both been demonstrated to modify the development and progression of this disease. In the current study both variants were genotyped in at least 50 dogs of 132 diverse breeds and the data reveal that both segregate in multiple breeds. Individually, each variant is common within largely non-overlapping subsets of breed, and there is a negative correlation between their frequencies within breeds that segregate both variants. The frequency of both variants exceeds 0.05 in a single breed only, the Miniature Longhaired Dachshund. These data indicate that both variants are likely to be ancient and predate the development and genetic isolation of modern dog breeds. That both variants are present individually at high frequency in multiple breeds is consistent with the hypothesis that homozygosity of either variant alone is not associated with a clinically relevant phenotype, whereas the negative correlation between the two variants is consistent with the application of selective pressure, from dog breeders, against homozygosity at both loci, probably due to the more severe phenotype associated with homozygosity at both loci.

Large-scale genomic analysis of the domestic dog informs biological discovery

Recent advances in genomics, coupled with a unique population structure and remarkable levels of variation, have propelled the domestic dog to new levels as a system for understanding fundamental principles in mammalian biology. Central to this advance are more than 350 recognized breeds, each a closed population that has undergone selection for unique features. Genetic variation in the domestic dog is particularly well characterized compared with other domestic mammals, with almost 3000 high-coverage genomes publicly available. Importantly, as the number of sequenced genomes increases, new avenues for analysis are becoming available. Herein, we discuss recent discoveries in canine genomics regarding behavior, morphology, and disease susceptibility. We explore the limitations of current data sets for variant interpretation, tradeoffs between sequencing strategies, and the burgeoning role of long-read genomes for capturing structural variants. In addition, we consider how large-scale collections of whole-genome sequence data drive rare variant discovery and assess the geographic distribution of canine diversity, which identifies Asia as a major source of missing variation. Finally, we review recent comparative genomic analyses that will facilitate annotation of the noncoding genome in dogs.

Co-analysis of methylation platforms for signatures of biological aging in the domestic dog reveals previously unexplored confounding factors

Chronological age reveals the number of years an individual has lived since birth. By contrast, biological age varies between individuals of the same chronological age at a rate reflective of physiological decline. Differing rates of physiological decline are related to longevity and result from genetics, environment, behavior, and disease. The creation of methylation biological age predictors is a long-standing challenge in aging research due to the lack of individual pre-mortem longevity data. The consistent differences in longevity between domestic dog breeds enable the construction of biological age estimators which can, in turn, be contrasted with methylation measurements to elucidate mechanisms of biological aging. We draw on three flagship methylation studies using distinct measurement platforms and tissues to assess the feasibility of creating biological age methylation clocks in the dog. We expand epigenetic clock building strategies to accommodate phylogenetic relationships between individuals, thus controlling for the use of breed standard metrics. We observe that biological age methylation clocks are affected by population stratification and require heavy parameterization to achieve effective predictions. Finally, we observe that methylation-related markers reflecting biological age signals are rare and do not colocalize between datasets.

Clinical findings, treatment and outcome of trapped neutrophil syndrome in Border Collies: 12 cases (2011-2022)

OBJECTIVES

This study aimed to evaluate clinical signs, diagnostic findings, treatment administered and short- (survival to 28 days) and long-term prognosis (survival >6 months) in dogs diagnosed with trapped neutrophil syndrome.

MATERIALS AND METHODS

Medical records of 12 dogs (10 Border Collies and two Border Collie Crossbreeds) homozygous for VPS13B gene mutation causing trapped neutrophil syndrome from seven veterinary institutions between January 2011 and June 2022 were evaluated retrospectively.

RESULTS

The most common clinical signs at the time of diagnosis were pyrexia, abnormal gait and gastrointestinal signs. Concurrent metaphyseal osteopathy and immune-mediated polyarthritis were common. Seven dogs had a segmented neutrophil count below, four dogs within and one dog above the analyser reference interval at presentation. Two dogs had a septic source identified and both were additionally identified to be homozygous mutant positive on DNA testing by polymerase chain reaction (PCR) for canine cyclic neutropenia. All dogs received at least one antimicrobial agent and 10 dogs received treatment with prednisone or prednisolone (median starting dose 1 mg/kg/day; range 0.5 to 2.5 mg/kg/day). Nine dogs were alive at 28 days and six dogs were alive at 6 months post-diagnosis.

CLINICAL SIGNIFICANCE

Trapped neutrophil syndrome should be suspected in young Border Collies with pyrexia, lameness and gastrointestinal signs. Neutropenia may not always be present and long-term survival is possible. A septic focus was not commonly identified in our population; however, our results suggest that if identified, testing for concurrent canine cyclic neutropenia should be considered.

Evaluation of taurine and carnitine concentrations in whole blood, plasma, skeletal muscle and cardiac muscle in dogs

Little is known about how plasma and whole blood taurine and plasma carnitine correlate to concentrations in skeletal and cardiac muscle and the effects of diet in dogs. The purpose of this study was to evaluate the correlation among plasma, skeletal and cardiac muscle carnitine and taurine and whole blood taurine and determine the effect of diet. The study protocol was approved by the Pet Food Solutions Institutional Animal Care and Use Committee. Thirty-three mixed-breed hounds and 32 beagles were evaluated at Day 0 then removed from their baseline diet and randomized to a test diet: high animal protein, grain-inclusive (HA-GI), low animal protein, grain-free (LA-GF), low animal protein, grain-inclusive (LA-GI), or high animal protein, grain-free (HA-GF). Blood was drawn every 30 days and endomyocardial (mixed breeds only) and skeletal muscle biopsies were collected at Days 0 and 180. The correlations between plasma and whole blood taurine, or plasma carnitine and skeletal and cardiac muscle concentrations were weak (p < 0.01-0.05). Mixed-breed hounds had increased (p = 0.029) whole blood taurine compared to beagles. Plasma taurine was lower with diet HA-GF, (p = 0.009) however, all diets had increased taurine from Day 0 and were, on average within the laboratory reference range. Dogs fed the HA-GI diet had increased cardiac muscle carnitine esters (p = 0.014). Increased carnitine esters were also appreciated in cardiac muscle in all diets from Day 0 to 180 (p = 0.0001). On Day 180 mixed-breed hounds had increased skeletal total carnitine (p < 0.001) compared to all time points and breeds. This study observed no correlation between plasma, whole blood, skeletal and cardiac muscle taurine concentrations but noted some effects between time, breed and diet.

Prioritization of Appearance over Health and Temperament Is Detrimental to the Welfare of Purebred Dogs and Cats

Fashions in the appearance of purebred dogs and cats are encouraged by celebrity culture, social media, and online impulse buying. The popularity of characteristics perceived as cute, quirky, and anthropomorphic has driven increasingly exaggerated breed features appealing to aesthetics rather than health. 'Hypertypes' of some breeds have emerged that take a breed's distinctive appearance to extremes beyond the intended interpretation of breed standards. This has severe, direct and indirect health and welfare consequences. Extreme conformations are associated with chronic health conditions including brachycephalic obstructive airway disorder, ocular, dental, skin, and musculoskeletal disorders. Puppy and kitten farms and illegal traders that meet the demand for hypertypes are associated with poor husbandry that neglects the physical, behavioral, and mental health of parents and offspring. A multidimensional approach involving collaboration between breeders, geneticists, owners, veterinarians, kennel clubs, cat fanciers' associations, animal charities, the academic and research communities, commercial enterprises, and governments is needed to safeguard breeds and tackle these challenges. There are many ongoing initiatives by national kennel clubs and global partnerships to educate pet owners and support responsible pet ownership and sustainable breeding. The resounding message is that health, temperament, and well-being must be prioritized over appearance.

Consensus guidelines for nomenclature of companion animal inherited retinal disorders

Companion animals, namely dogs, cats, and horses, can be affected with many forms of hereditary retinal disease. The number of such diseases characterized in the last decade has increased substantially, and nomenclature is nonstandardized, heterogenous, and confusing. We provide in this viewpoint article consensus guidelines for naming of companion animal hereditary retinal diseases, either prospectively or retrospectively. These consensus guidelines have been developed with the purpose of standardizing nomenclature. We provide examples for the iterative nomenclature process and a comprehensive File S1 on proposed renaming of previously described diseases.

Allele and genotype frequencies for primary hereditary cataract, multifocal retinopathy 1, and degenerative myelopathy in Pyrenean Mountain dog from Italy

Pyrenean Mountain Dog (PMD) is an ancient dog breed firstly described in XIV century in the Pyrenees Region and nowadays diffused both in Europe and in the US. Hereditary Cataract (HC), defined as the inherited opacity of the lens, involves clinical signs ranging from reduced vision to glaucoma. A molecular basis of HC was firstly described in Staffordshire Bull Terriers and then reported in multiple canine breeds. The HC-associated variation is a single nucleotide deletion in HSF4 gene that introduces a premature stop codon (c.962del, p.Ala321*). Multifocal Retinopathy 1 (MR) is an ocular disorder characterized by multiple areas of retinal degeneration, caused in various dog breeds (including PMD) by a single nucleotide variant (SNV) in BEST1 gene that generates a premature stop codon (c.73G>A, p.Arg25*). Degenerative Myelopathy (DM) is an adult-onset, progressive neurodegenerative disease and it is associated to a SNV in SOD1 gene causing a change in aminoacidic sequence of the protein (c.118G>A, p.Glu40Lys). This causative variant has been described in various dog breeds, including PMD. Aim of this study was to determine the allele frequencies for the abovementioned three genetic diseases in the Italian breeding PMD population. The survey found no dogs carrying the allele (deletion) associated with HC, while three dogs (6 %) were heterozygous (G/A) for the MR-associated variant, and seven dogs (13 %) were heterozygous (G/A) for the DM-associated alteration, indicating that the variant alleles frequency were 0  %, 3 %, and 7 %, respectively. Appropriate mating management is suggested for the prevention of genetic diseases spreading in the PMD population.

Association of the FGF4L2 retrogene with fibrocartilaginous embolic myelopathy in dogs

BACKGROUND

Fibrocartilaginous embolic myelopathy (FCE) is a well-documented condition in dogs although rarely reported in chondrodystrophic breeds. Genetic associations have not been defined.

OBJECTIVES

Define the association of the chondrodystrophy-associated FGF4L2 retrogene with histopathologically confirmed cases of FCE.

ANIMALS

Ninety-eight dogs with a histopathologic diagnosis of FCE.

METHODS

Retrospective multicenter study. Dogs were genotyped for the FGF4L2 and FGF4L1 retrogenes using DNA extracted from formalin-fixed, paraffin-embedded tissue. Associations between breed, FCE and retrogene status were investigated with reference to a hospital population and known breed and general population allele frequencies.

RESULTS

FGF4L2 genotype was defined in 89 FCE cases. Fibrocartilaginous embolic myelopathy was present in 22 dogs from FGF4L2-segregating breeds with allele frequencies of ≥5%; however, all dogs were wild type. Two Labrador retrievers with FCE carried FGF4L2 alleles. Frequency of the FGF4L2 allele was significantly (P < .001) and negatively associated with FCE relative to predicted hospital-population dogs. FCE was overrepresented in Boxer, Great Dane, Yorkshire Terrier, Bernese Mountain Dog, Miniature Schnauzer, Rottweiler, and Shetland Sheepdog breeds.

CONCLUSIONS AND CLINICAL IMPORTANCE

Study data based on genotypically and histopathologically defined cases support the historical observation that FCE is uncommon in chondrodystrophic dog breeds. FGF4 plays an important role in angiogenesis and vascular integrity; anatomical studies comparing chondrodystrophic and non-chondrodystrophic dogs might provide insight into the pathogenesis of FCE.

Genotypic and allelic frequencies of progressive rod-cone degeneration and other main variants associated with progressive retinal atrophy in Italian dogs

Background

Progressive retinal atrophy (PRA) is a group of canine inherited retinal disorders affecting up to 100 breeds. Genetic tests are available. The aim of this study was to retrospectively evaluate the genetic variants associated with PRA among dogs residing in Italy.

Methods

Genetic data of 20 variants associated with different forms of PRA were collected through DNA tests over a 10-year period for several dog breeds in the Italian canine population. Allelic and genotypic frequencies were calculated.

Results

A total of 1467 DNA tests were conducted for 1180 dogs. Progressive rod-cone degeneration (PRCD) was the most tested form of PRA, with 58.15% (n = 853) of the DNA tests. Among the widespread breeds in Italy, Labrador retrievers and toy poodles showed a prevalence of heterozygous carriers higher than 15%. Among the others, 175 DNA tests for golden retrievers (GR) showed a prevalence of heterozygous carriers of 13.04% (n = 12) for GR-PRA1 and 8.43% (n = 7) for GR-PRA2. The zwergschnauzer breed was tested for the type B and/or the type B1 forms of PRA with 25.32% (n = 20) heterozygous carriers and 0%, respectively.

Conclusion

The study offers an overview of the prevalence of PRCD and other PRA forms within some of the most popular breeds in Italy.

An Overview of Canine Inherited Neurological Disorders with Known Causal Variants

Hereditary neurological conditions documented in dogs encompass congenital, neonatal, and late-onset disorders, along with both progressive and non-progressive forms. In order to identify the causal variant of a disease, the main two approaches are genome-wide investigations and candidate gene investigation. Online Mendelian Inheritance in Animals currently lists 418 Mendelian disorders specific to dogs, of which 355 have their likely causal genetic variant identified. This review aims to summarize the current knowledge on the canine nervous system phenes and their genetic causal variant. It has been noted that the majority of these diseases have an autosomal recessive pattern of inheritance. Additionally, the dog breeds that are more prone to develop such diseases are the Golden Retriever, in which six inherited neurological disorders with a known causal variant have been documented, and the Belgian Shepherd, in which five such disorders have been documented. DNA tests can play a vital role in effectively managing and ultimately eradicating inherited diseases.

Global Frequency Analyses of Canine Progressive Rod-Cone Degeneration-Progressive Retinal Atrophy and Collie Eye Anomaly Using Commercial Genetic Testing Data

Hundreds of genetic variants associated with canine traits and disorders have been identified, with commercial tests offered. However, the geographic distributions and changes in allele and genotype frequencies over prolonged, continuous periods of time are lacking. This study utilized a large set of genotypes from dogs tested for the progressive rod-cone degeneration-progressive retinal atrophy (prcd-PRA) G>A missense PRCD variant (n = 86,667) and the collie eye anomaly (CEA)-associated NHEJ1 deletion (n = 33,834) provided by the commercial genetic testing company (Optigen/Wisdom Panel, Mars Petcare Science & Diagnostics). These data were analyzed using the chi-square goodness-of-fit test, time-trend graphical analysis, and regression modeling in order to evaluate how test results changed over time. The results span fifteen years, representing 82 countries and 67 breeds/breed mixes. Both diseases exhibited significant differences in genotype frequencies (p = 2.7 × 10-152 for prcd-PRA and 0.023 for CEA) with opposing graphical trends. Regression modeling showed time progression to significantly affect the odds of a dog being homozygous or heterozygous for either disease, as do variables including breed and breed popularity. This study shows that genetic testing informed breeding decisions to produce fewer affected dogs. However, the presence of dogs homozygous for the disease variant, especially for prcd-PRA, was still observed fourteen years after test availability, potentially due to crosses of unknown carriers. This suggests that genetic testing of dog populations should continue.