SNP-based heritability and genetic architecture of cranial cruciate ligament rupture in Labrador Retrievers

The association between gonadectomy and timing of gonadectomy, and the risk of canine cranial cruciate ligament disease: A systematic review and meta-analysis

OBJECTIVE

To determine if gonadectomy in dogs is associated with the risk of cranial cruciate ligament disease (CrCLD) and to quantify the magnitude of the association.

STUDY DESIGN

Systematic review and meta-analysis.

SAMPLE POPULATION

Comparative studies with gonadectomized and entire dogs, with CrCLD as an outcome measure.

METHODS

A systematic search of the primary and gray literature was performed. The effect size of the outcome measure was defined as the OR and 95% CI. Subgroup analysis was performed with sex, breed, and age at gonadectomy. A pooled OR (95% CI) was generated from meta-analysis of relevant studies. Certainty in the body of evidence was rated with the Grading of Recommendations Assessment, Development and Evaluation (GRADE) framework.

RESULTS

The literature search yielded 1398 results and 24 relevant studies were included for synthesis. Gonadectomized female (pooled OR = 2.293, 95% CI = 1.768-2.945) and male (pooled OR = 2.117, 95% CI = 1.665-2.691) dogs were both at increased odds of developing CrCLD in comparison with entire female and male dogs, respectively. Subgroup analysis showed that gonadectomy at 1 year or less was consistently associated with an increase in odds of developing CrCLD in both sexes. Overall certainty in the evidence was rated as moderate. All included studies were observational and no controlled trials were available.

CONCLUSION

In data with moderate certainty, gonadectomy is associated with increased odds of developing CrCLD in both sexes, particularly in dogs gonadectomized at 1 year of age or less.

CLINICAL SIGNIFICANCE

This study provides an estimate of the true effect size of gonadectomy on the odds of developing CrCLD, which may be useful for clinical decision making surrounding gonadectomy and the timing of gonadectomy.

Cross-species analysis of genetic architecture and polygenic risk scores for non-contact ACL rupture in dogs and humans

Non-contact anterior cruciate ligament (ACL) rupture is a common serious orthopaedic disease in humans and dogs. Familial risk has been recognized in both species but interactions between genetic effects and environmental risk are not understood. We investigated ACL rupture heritability, genetic architecture, selection pressure, sharing of risk genes and biological pathways, and polygenic risk score (PRS) prediction of disease risk. In both species, ACL rupture has moderate heritability, is likely under negative selection, and has a highly polygenic architecture where thousands of variant effects act together to influence disease risk. In dogs, we found hotspots of regional heritability. We also confirmed sharing of multiple risk genes. Our findings challenge the dogma that non-contact ACL rupture is predominantly due to a single overload injury event. Our results also suggest that accurate PRS prediction of ACL rupture risk is an achievable goal in both species, enabling identification of individuals for personalized medical care.

Heritability and Genome-Wide Association Study of Dog Behavioral Phenotypes in a Commercial Breeding Cohort

Background: Canine behavior plays an important role in the success of the human-dog relationship and the dog's overall welfare, making selection for behavior a vital part of any breeding program. While behaviors are complex traits determined by gene × environment interactions, genetic selection for desirable behavioral phenotypes remains possible. Methods: No genomic association studies of dog behavior to date have been reported on a commercial breeding (CB) cohort; therefore, we utilized dogs from these facilities (n = 615 dogs). Behavioral testing followed previously validated protocols, resulting in three phenotypes/variables [social fear (SF), non-social fear (NSF), and startle response (SR)]. Dogs were genotyped on the 710 K Affymetrix Axiom CanineHD SNP array. Results: Inbreeding coefficients indicated that dogs from CB facilities are statistically less inbred than dogs originating from other breeding sources. Heritability estimates for behavioral phenotypes ranged from 0.042 ± 0.045 to 0.354 ± 0.111. A genome-wide association analysis identified genetic loci associated with SF, NSF, and SR; genes near many of these loci have been previously associated with behavioral phenotypes in other populations of dogs. Finally, genetic risk scores demonstrated differences between dogs that were more or less fearful in response to test stimuli, suggesting that these behaviors could be subjected to genetic improvement. Conclusions: This study confirms several canine genetic behavioral loci identified in previous studies. It also demonstrates that inbreeding coefficients of dogs in CB facilities are typically lower than those in dogs originating from other breeding sources. SF and NSF were more heritable than SR. Risk allele and weighted risk scores suggest that fearful behaviors could be subjected to genetic improvement.

Heritability and genome-wide association study of vaccine-induced immune response in Beagles: A pilot study

Both genetic and non-genetic factors contribute to individual variation in the immune response to vaccination. Understanding how genetic background influences variation in both magnitude and persistence of vaccine-induced immunity is vital for improving vaccine development and identifying possible causes of vaccine failure. Dogs provide a relevant biomedical model for investigating mammalian vaccine genetics; canine breed structure and long linkage disequilibrium simplify genetic studies in this species compared to humans. The objective of this study was to estimate the heritability of the antibody response to vaccination against viral and bacterial pathogens, and to identify genes driving variation of the immune response to vaccination in Beagles. Sixty puppies were immunized following a standard vaccination schedule with an attenuated combination vaccine containing antigens for canine adenovirus type 2, canine distemper virus, canine parainfluenza virus, canine parvovirus, and four strains of Leptospira bacteria. Serum antibody measurements for each viral and bacterial component were measured at multiple time points. Heritability estimations and GWAS were conducted using SNP genotypes at 279,902 markers together with serum antibody titer phenotypes. The heritability estimates were: (1) to Leptospira antigens, ranging from 0.178 to 0.628; and (2) to viral antigens, ranging from 0.199 to 0.588. There was not a significant difference between overall heritability of vaccine-induced immune response to Leptospira antigens compared to viral antigens. Genetic architecture indicates that SNPs of low to high effect contribute to immune response to vaccination. GWAS identified two genetic markers associated with vaccine-induced immune response phenotypes. Collectively, these findings indicate that genetic regulation of the immune response to vaccination is antigen-specific and influenced by multiple genes of small effect.

Identification of genetic variants associated with anterior cruciate ligament rupture and AKC standard coat color in the Labrador Retriever

Canine anterior cruciate ligament (ACL) rupture is a common complex disease. Prevalence of ACL rupture is breed dependent. In an epidemiological study, yellow coat color was associated with increased risk of ACL rupture in the Labrador Retriever. ACL rupture risk variants may be linked to coat color through genetic selection or through linkage with coat color genes. To investigate these associations, Labrador Retrievers were phenotyped as ACL rupture case or controls and for coat color and were single nucleotide polymorphism (SNP) genotyped. After filtering, ~ 697 K SNPs were analyzed using GEMMA and mvBIMBAM for multivariate association. Functional annotation clustering analysis with DAVID was performed on candidate genes. A large 8 Mb region on chromosome 5 that included ACSF3, as well as 32 additional SNPs, met genome-wide significance at P < 6.07E-7 or Log10(BF) = 3.0 for GEMMA and mvBIMBAM, respectively. On chromosome 23, SNPs were located within or near PCCB and MSL2. On chromosome 30, a SNP was located within IGDCC3. SNPs associated with coat color were also located within ADAM9, FAM109B, SULT1C4, RTDR1, BCR, and RGS7. DZIP1L was associated with ACL rupture. Several significant SNPs on chromosomes 2, 3, 7, 24, and 26 were located within uncharacterized regions or long non-coding RNA sequences. This study validates associations with the previous ACL rupture candidate genes ACSF3 and DZIP1L and identifies novel candidate genes. These variants could act as targets for treatment or as factors in disease prediction modeling. The study highlighted the importance of regulatory SNPs in the disease, as several significant SNPs were located within non-coding regions.

Common Orthopedic Traits and Screening for Breeding Programs

Orthopedic diseases are complex traits, meaning genetics and environmental factors affect risk, making identification of genetic associations difficult. In the United States, hip and elbow scores, patellar luxation scores, Legg-Calvé-Perthes disease, and shoulder osteochondrosis affectedness are available in the Orthopedic Foundation for Animals registry. Distraction indices and extended, ventrodorsal hip conformation scores are recorded by PennHIP. Application of estimated breeding values for hip and elbow dysplasia in breeder selection reduces the severity and prevalence of these traits. Genomic prediction and whole-genome sequence technologies and methods should improve knowledge of genetics underlying orthopedic diseases, leading to improved canine orthopedic genetic quality.

Etiopathogenesis of Canine Cruciate Ligament Disease: A Scoping Review

The spontaneous rupture of the cranial cruciate ligament in dogs remains a pathoetiologic puzzle. Despite much progress in research over the past years, the systemic and local mechanisms leading to ligament degeneration and structural failure remain largely obscure. This scoping review focuses on pathogenesis and aims at summarizing and interpreting today's knowledge on causes of canine cruciate ligament rupture, i.e., the multifactorial mechanisms leading to degenerative stifle joint disease with collagen matrix degeneration and structural failures. Thus, the initial view of traumatic ligament rupture, fostered by "wear and tear", has clearly been replaced by a new concept of systemic processes linked to progressive degenerative joint disease and ligament failure; thus, the term "cranial cruciate ligament disease" has been coined and is generally accepted. In addition, cruciate ligament rupture in people shares some similarities with the lesion in dogs; therefore, the review also includes comparative studies. The methods used were based on the PRISMA-ScR model (Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews).

Arthroscopic Treatment of Chronic Cruciate Ligament Rupture in the Dog without Stifle Stabilization: 13 Cases (2001-2020)

Objective

The objective was to study clinical outcomes in dogs with chronic cruciate ligament rupture (CR) treated with palliative arthroscopy as the sole surgical treatment.

Methods

Thirteen client-owned dogs with CR underwent physical examination, stifle radiography, and arthroscopy with resection of damaged meniscal tissue. Records were evaluated, and orthopaedic examination, radiographs, and arthroscopy images were assessed. Long-term clinical outcome was also assessed by use of an owner questionnaire.

Results

Thirteen dogs that underwent arthroscopy at the UW Veterinary Care between 2001 and 2020 were included. Long-term follow-up was available for 7 of 13 dogs. Lameness was static to improved in all dogs in which arthroscopy was performed. Subsequent stifle stabilization was performed after arthroscopy in only 1 of 7 dogs with follow-up data.

Conclusion

Palliative arthroscopy and resection of damaged meniscal tissue in combination with medical management of osteoarthritis can be considered in dogs with chronic CR and cranial tibial subluxation with little passive laxity during examination. Revision surgery with TPLO is uncommon after arthroscopy based on this study.

Across-breed genetic investigation of canine hip dysplasia, elbow dysplasia, and anterior cruciate ligament rupture using whole-genome sequencing

Here, we report the use of genome-wide association study (GWAS) for the analysis of canine whole-genome sequencing (WGS) repository data using breed phenotypes. Single-nucleotide polymorphisms (SNPs) were called from WGS data from 648 dogs that included 119 breeds from the Dog10K Genomes Project. Next, we assigned breed phenotypes for hip dysplasia (Orthopedic Foundation for Animals (OFA) HD, n = 230 dogs from 27 breeds; hospital HD, n = 279 dogs from 38 breeds), elbow dysplasia (ED, n = 230 dogs from 27 breeds), and anterior cruciate ligament rupture (ACL rupture, n = 279 dogs from 38 breeds), the three most important canine spontaneous complex orthopedic diseases. Substantial morbidity is common with these diseases. Previous within- and between-breed GWAS for HD, ED, and ACL rupture using array SNPs have identified disease-associated loci. Individual disease phenotypes are lacking in repository data. There is a critical knowledge gap regarding the optimal approach to undertake categorical GWAS without individual phenotypes. We considered four GWAS approaches: a classical linear mixed model, a haplotype-based model, a binary case-control model, and a weighted least squares model using SNP average allelic frequency. We found that categorical GWAS was able to validate HD candidate loci. Additionally, we discovered novel candidate loci and genes for all three diseases, including FBX025, IL1A, IL1B, COL27A1, SPRED2 (HD), UGDH, FAF1 (ED), TGIF2 (ED & ACL rupture), and IL22, IL26, CSMD1, LDHA, and TNS1 (ACL rupture). Therefore, categorical GWAS of ancestral dog populations may contribute to the understanding of any disease for which breed epidemiological risk data are available, including diseases for which GWAS has not been performed and candidate loci remain elusive.

Surgical treatment of cranial cruciate ligament disease in dogs using Tibial Plateau Leveling Osteotomy or Tibial Tuberosity Advancement-A systematic review with a meta-analytic approach

Tibial Plateau Leveling Osteotomy (TPLO) or Tibial Tuberosity Advancement (TTA) are commonly used surgical techniques for correction of cranial cruciate ligament (CCL) rupture in dogs. This systematic review aims to investigate whether one technique is superior to the other. Seventy-two studies on surgical management of CCL rupture have been identified and evaluated in regard of subjective and objective gait analysis criteria, development of osteoarthritis (OA), thigh circumference measurements, goniometry, joint stability, pain and complication rates. Almost half (47.2 %) of the studies were considered of low quality of evidence, leading to high heterogeneity in quality among studies; this posed a major limitation for an evidence-based systematic review of both surgical techniques. Out of 72 studies, there were only eleven blinded randomized clinical trials, of which five were rated with a low overall risk of bias. However, both techniques were considered to be successful management options. Subjective and objective gait analysis revealed no lameness at long-term evaluation for the majority of the patients. However, it appeared that TTA lead to better OA scores up to 6 months postoperatively, while TPLO had a lower rate of surgical site infections. In summary, no method can be clearly preferred, as most of the study evaluated were subpar. Studies with a high level of evidence are therefore urgently needed for such a common surgical procedure.

Genomic Prediction of Two Complex Orthopedic Traits Across Multiple Pure and Mixed Breed Dogs

Canine hip dysplasia (CHD) and rupture of the cranial cruciate ligament (RCCL) are two complex inherited orthopedic traits of dogs. These two traits may occur concurrently in the same dog. Genomic prediction of these two diseases would benefit veterinary medicine, the dog’s owner, and dog breeders because of their high prevalence, and because both traits result in painful debilitating osteoarthritis in affected joints. In this study, 842 unique dogs from 6 breeds with hip and stifle phenotypes were genotyped on a customized Illumina high density 183 k single nucleotide polymorphism (SNP) array and also analyzed using an imputed dataset of 20,487,155 SNPs. To implement genomic prediction, two different statistical methods were employed: Genomic Best Linear Unbiased Prediction (GBLUP) and a Bayesian method called BayesC. The cross-validation results showed that the two methods gave similar prediction accuracy (r = 0.3–0.4) for CHD (measured as Norberg angle) and RCCL in the multi-breed population. For CHD, the average correlation of the AUC was 0.71 (BayesC) and 0.70 (GBLUP), which is a medium level of prediction accuracy and consistent with Pearson correlation results. For RCCL, the correlation of the AUC was slightly higher. The prediction accuracy of GBLUP from the imputed genotype data was similar to the accuracy from DNA array data. We demonstrated that the genomic prediction of CHD and RCCL with DNA array genotype data is feasible in a multiple breed population if there is a genetic connection, such as breed, between the reference population and the validation population. Albeit these traits have heritability of about one-third, higher accuracy is needed to implement in a natural population and predicting a complex phenotype will require much larger number of dogs within a breed and across breeds. It is possible that with higher accuracy, genomic prediction of these orthopedic traits could be implemented in a clinical setting for early diagnosis and treatment, and the selection of dogs for breeding. These results need continuous improvement in model prediction through ongoing genotyping and data sharing. When genomic prediction indicates that a dog is susceptible to one of these orthopedic traits, it should be accompanied by clinical and radiographic screening at an acceptable age with appropriate follow-up.

The epidemiology of cruciate ligament rupture in an insured Swedish dog population

Cruciate ligament rupture (CLR) is a common orthopedic disorder in dogs. The study objectives were to evaluate incidence rate (IR), cause-specific mortality rate (CSMR) and risk factors for CLR in insured dogs. A single cohort study of dogs insured in Agria Pet Insurance in Sweden (2011–2016) was performed. Age at diagnosis, IR, CSMR and relative risk (RR) for CLR was calculated overall and per breed. The cohort included just over 600,000 dogs. The IR of CLR was 23.8 (95% confidence interval, 23.1–24.6) cases per 10,000 DYAR. The breeds with highest RR of CLR were Boerboel and Dogo Canario, while the breeds with lowest RR were Standard Dachshund and Miniature Pinscher. Dogue de Bordeaux had highest RR of euthanasia due to CLR. The median age at veterinary care claim for CLR was 7.1 (range 0.3–16.0) years and 6.6 (0.3–12) years at life insurance settlement. Large and giant breeds were generally diagnosed and euthanized due to CLR at a younger age compared to smaller breeds. The majority of the breeds with increased RR of CLR diagnosis and CLR-related euthanasia were large or giant. A pattern of increasing size and decreasing age at diagnosis/CLR-related euthanasia was observed.