The prevalence of nine genetic disorders in a dog population from Belgium, the Netherlands and Germany

Prevalence of SOD1 allele associated with degenerative myelopathy in canine population in Greece

Canine degenerative myelopathy (CDM) is a late-onset fatal disorder associated with a point mutation of the superoxide dismutase 1 (SOD1) gene (c.118G > A). The purpose of this study was to determine the genotype and allele frequencies of this mutation in 108 dogs, mainly in Belgian Malinois and German Shepherd dogs with (CDM-affected group) and without CDM clinical symptoms (control group) in Greece. Genotyping of the c.118G > A mutation was possible by Sanger sequencing and PCR-RFLP. The observed genotype frequencies for the control group were 89.4% for the homozygous (G/G), 9.6% for the heterozygous (A/G), and 0.96% for the homozygous mutant (A/A) allele. The mutant allele was not common in the Belgian Malinois dogs (allele frequency = 0.029), but quite common in the German Shepherd dogs (allele frequency = 0.138). In the CDM affected group, all 4 dogs were homozygous for the mutant allele. These frequencies were close to those expected, indicating no significant departure from Hardy-Weinberg equilibrium. A strong but not statistically significant association between the mutant allele and CDM was observed. A previously identified deletion upstream of the mutation of interest was found at a high frequency (0.361) in the population.

Molecular Surveillance of Canine Degenerative Myelopathy in Breeding Kennels from Romania

Canine degenerative myelopathy (CDM) is a spontaneous neurodegenerative disease. Genetically, CDM is an autosomal recessive disease with incomplete penetrance, most commonly caused by a genetic mutation in exon 2 of gene SOD1 (c.118G > A). This study aimed to determine the mutant allele frequency associated with CDM in various dog breeds from Romania. Dogs (n = 230) from 26 breeds were included in the study. Genotyping using the PCR-RFLP technique was performed on DNA extracted from oral swabs. The results revealed that 204 dogs were homozygous for the wild-type allele (G/G), 16 were heterozygous (A/G), and 10 were homozygous for the mutant allele (A/A). The mutant allele was identified in Wire Fox Terrier, Romanian Mioritic Shepherd, German Shepherd, Rottweiler, Belgian Shepherd, and Czechoslovakian Wolfdog breeds. The mutant allele frequency (A) within the tested population was 0.0783. The results for Belgian Shepherd, German Shepherd, and Romanian Mioritic Shepherd were in Hardy-Weinberg equilibrium, but a departure was observed for Rottweiler. The current study included a first screening of the Romanian Bucovina Shepherd, Romanian Mioritic Shepherd, and Caucasian Shepherd breeds. Genetic testing for the mutation associated with CDM is important in order to avoid the risk of the emergence of dogs homozygous for the SOD1:c118G > A allele.

Allele and genotype frequencies of the SOD1 gene polymorphism associated with canine degenerative myelopathy in Belgian Malinois dogs in Greece

Background and Aim

Canine degenerative myelopathy (CDM) is an adult-onset fatal disorder associated with a point mutation of the superoxide dismutase 1 (SOD1) gene (SOD1:c.118G>A). This study aimed to determine the allele and genotype frequencies of this mutation in a group of Belgian Malinois dogs in Greece.

Materials and Methods

Samples (n=72) of whole blood were collected from 72 purebred dogs of the Hellenic Armed Forces; these samples were processed for DNA isolation, polymerase chain reaction, and digestion with the restriction endonuclease AcuI. Sample testing was conducted in compliance with ISO17025 accreditation requirements.

Results

The observed relative genotype frequencies were 71% for the homozygous (GG), 25% for the heterozygous (AG), and 4% for the homozygous mutant (AA) alleles. These frequencies were close to those expected, indicating no significant departure from Hardy-Weinberg equilibrium (HWE, p=0.395). The frequency of heterozygous animals indicates that a high risk of developing CDM in forthcoming generations exists in the tested population because mating among carriers would result in 25% AA progeny. The medical record of the group of study animals indicated selection against leishmaniosis, as applied throughout generations by owners and breeders. The potential association of this selection with the HWE status of the study population was discussed.

Conclusion

The SOD1:c.118G>A mutation was common in the tested group of dogs; thus, they are suitable for a follow-up investigation on the development and progression of CDM. A case-control study on animals with evidence of sensitivity to infectious myelopathy could provide new insights into disease pathogenesis.

A Leaky Noisy-OR Bayesian Network Applied to Genetic Counseling in Dogs

Simple Summary

Genetic disorders represent a serious health problem for companion animals and combating such disorders is a real challenge. Bayes networks facilitate the objective assessment of the risk of such disorders. We apply the methodology to answer two typical questions in genetic counselling, i.e., the risk for an animal of showing clinical signs of a genetic disease when the result at the genetic test is known and the risk of testing positive for the mutant allele when the genetic test is not made. Results showed the network is appropriate to answer objectively and transparently both questions under a variety of alternative scenarios. It can be updated automatically and can be represented visually so interactive discussion are easy between the veterinarian and his/her interlocutor.

Abstract

Genetic disorders are very frequent in dogs but evaluating individualized risks of their occurrence can be uncertain. Bayesian networks are tools to characterize and analyze such events. The paper illustrates their benefits and challenges in answering two typical questions in genetic counselling: (1) What is the probability of a test-positive animal showing clinical signs of the disease? (2) What is the risk of testing positive for the mutant allele when one parent presents clinical signs? Current limited knowledge on the hereditary mode of transmission of degenerative myelopathy and on the effects of sex, diet, exercise regimen and age on the occurrence of clinical signs concurrent with the finding of the deleterious mutation was retrieved from the scientific literature. Uncertainty on this information was converted into prior Beta distributions and leaky-noisy OR models were used to construct the conditional probability tables necessary to answer the questions. Results showed the network is appropriate to answer objectively and transparently both questions under a variety of scenarios. Once users of the network have agreed with its structure and the values of the priors, computations are straightforward. The network can be updated automatically and can be represented visually so interactive discussion are easy between the veterinarian and his/her interlocutor.

Canine hip dysplasia screening: Comparison of early evaluation to final grading in 231 dogs with Fédération Cynologique Internationale A and B

OBJECTIVES

This study aimed to verify if a significant difference exists between parameters in the early evaluation of normal and near-normal hip joints, to evaluate the influence of age and breed on the parameters, and to clarify the usefulness of a total score for differentiating between Fédération Cynologique Internationale (FCI) grade A and B hips.

METHODS

A total of 231 dogs were classified according to whether they had FCI A or B hips at adulthood, with measurements obtained at 14-28 weeks of age. The total score was calculated by the summation of the following quantitative parameters: angle of subluxation (AS), angle of reduction (AR), laxity index (LI), and dorsal acetabular rim slope (DARS). Logistic regression analysis was performed to establish the probability of the study population to develop an FCI B hip based on the total score. This was repeated for the highest score in combination with the worst-rated hip and once more for breeds.

RESULTS

No correlation between age and the parameters was found in the cohort, or for FCI A and B. The values of all the parameters were significantly lower in the FCI A group than in the FCI B group (AR: 4.42° ± 6.0° vs 7.62° ± 7.2°; AS: 0.45° ± 1.9° vs 1.55° ± 3.8°; LI: 0.32 ± 0.1 vs 0.36 ± 0.1; DARS: 3.30° ± 1.8° vs 3.77° ± 1.9°; TS: 11.47 ± 8.3 vs 16.65 ± 10.9). Labrador Retrievers and Golden Retrievers showed significant differences between parameters for both FCI grades. The range, where FCI A and B hips can be predicted on the basis of the total score, was different when assessed for the entire cohort, Labrador Retrievers, and Golden Retrievers.

CLINICAL SIGNIFICANCE

Our results show that even in normal and near-normal hips, the parameters significantly differed in the early evaluation. Moreover, cutoff values should be set for different breeds in the prediction of the FCI grade during early evaluation for a better breeding selection regarding canine hip dysplasia, one of the most common orthopedic diseases among large and giant breed dogs.

The dog 2.0: Lessons learned from the past

In recent years, concerns have been raised on the diversity, health and welfare of our (pedigree) dog population. Somewhat justified, the popular sire effect, population bottlenecks, the founder effect and inbreeding have left their marks on the dog as we know it. In order to improve the health and welfare of the canine population in general, individual breeding programs should adhere to the concept of ethical breeding (i.e. "the use of healthy animals true to their species in behaviour and looks, and when applicable, showing a sustainable performance") when population-specific breeding goals are defined. Even though every population has its own problems, the approach to get to possible solution(s) is similar. The starting point will always be the identification of which (un)desirable pheno- and genotypes are segregating and what their prevalence is, followed by an evaluation of the genetic diversity. Based on that information and, when applicable, additional criteria like breed standards, breeding goals can be defined. It is of critical importance that these goals are put forward with a long term vision in mind and with consensus from the stakeholders to ensure collaboration. Upon prioritization of the most important goals, when necessary with the help of specifically developed tools, the final step is choosing the most optimal combination of breeding strategies. This paper aims to provide a stepwise approach to identify and tackle population-specific problems encountered in breeding programs.

Frequency of five disease-causing genetic mutations in a large mixed-breed dog population (2011-2012)

Background

A large and growing number of inherited genetic disease mutations are now known in the dog. Frequencies of these mutations are typically examined within the breed of discovery, possibly in related breeds, but nearly always in purebred dogs. No report to date has examined the frequencies of specific genetic disease mutations in a large population of mixed-breed dogs. Further, veterinarians and dog owners typically dismiss inherited/genetic diseases as possibilities for health problems in mixed-breed dogs, assuming hybrid vigor will guarantee that single-gene disease mutations are not a cause for concern. Therefore, the objective of this study was to screen a large mixed-breed canine population for the presence of mutant alleles associated with five autosomal recessive disorders: hyperuricosuria and hyperuricemia (HUU), cystinuria (CYST), factor VII deficiency (FVIID), myotonia congenita (MYC) and phosphofructokinase deficiency (PKFD). Genetic testing was performed in conjunction with breed determination via the commercially-available Wisdom Panel^TM test.

Results

From a population of nearly 35,000 dogs, homozygous mutant dogs were identified for HUU (n = 57) and FVIID (n = 65). Homozygotes for HUU and FVIID were identified even among dogs with highly mixed breed ancestry. Carriers were identified for all disorders except MYC. HUU and FVIID were of high enough frequency to merit consideration in any mixed-breed dog, while CYST, MYC, and PKFD are vanishingly rare.

Conclusions

The assumption that mixed-breed dogs do not suffer from single-gene genetic disorders is shown here to be false. Within the diseases examined, HUU and FVIID should remain on any practitioner’s rule-out list, when clinically appropriate, for all mixed-breed dogs, and judicious genetic testing should be performed for diagnosis or screening. Future testing of large mixed-breed dog populations that include additional known canine genetic mutations will refine our knowledge of which genetic diseases can strike mixed-breed dogs.

Evidence of a genomic insertion in intron 2 of SOD1 causing allelic drop-out during routine diagnostic testing for canine degenerative myelopathy

Degenerative myelopathy is a severe and progressive neurodegenerative disease and, in the majority of breeds, is associated with the c.118G>A substitution in exon 2 of the canine superoxide dismutase 1 (SOD1) gene. Our laboratories have been engaged in determining the cause of many discordant findings between the parental and the offspring genotypes found by different laboratories. In both cases, the discordant findings refer to actual heterozygous dogs that had been typed as homozygous for the variant allele. To that aim, the genomic context of the causative variant was investigated in two Hovawart dogs. An insertion of 54 nucleotides composed of a poly-T stretch and 15 nucleotides containing the duplication of the exon 2-intron 2 junction was found. The insertion was responsible for the partial mismatch of the reverse primer used for a direct sequencing assay. The mismatch hampered the amplification of the corresponding allele and caused an evident drop-out effect. The insertion is in complete linkage disequilibrium with the c.118G allele. The allele containing the insertion was highly prevalent in Hovawart dogs, accounting for the 26.6% of allele frequency. The insertion was also found in other unrelated breeds such as Rough Collies and Standard Poodles. In conclusion, the study illustrates the importance of correctly designing the primers to avoid inaccurate genotyping of the degenerative myelopathy causative variant in exon 2 of the SOD1 gene.

Long-term outcome of myotonia associated with hyperadrenocorticism in 2 dogs

Two dogs were diagnosed with myotonia associated with hyperadrenocorticism and treated with trilostane. One dog showed temporary improvement, but the other dog showed no improvement. The dogs survived 2383 and 1902 days, respectively. Findings suggest that myotonia persists despite treatment, but this condition is not associated with a poor prognosis for survival.

Improved canine exome designs, featuring ncRNAs and increased coverage of protein coding genes

By limiting sequencing to those sequences transcribed as mRNA, whole exome sequencing is a cost-efficient technique often used in disease-association studies. We developed two target enrichment designs based on the recently released annotation of the canine genome: the exome-plus design and the exome-CDS design. The exome-plus design combines the exons of the CanFam 3.1 Ensembl annotation, more recently discovered protein-coding exons and a variety of non-coding RNA regions (microRNAs, long non-coding RNAs and antisense transcripts), leading to a total size of ≈152 Mb. The exome-CDS was designed as a subset of the exome-plus by omitting all 3’ and 5’ untranslated regions. This reduced the size of the exome-CDS to ≈71 Mb. To test the capturing performance, four exome-plus captures were sequenced on a NextSeq 500 with each capture containing four pre-capture pooled, barcoded samples. At an average sequencing depth of 68.3x, 80% of the regions and well over 90% of the targeted base pairs were completely covered at least 5 times with high reproducibility. Based on the performance of the exome-plus, we estimated the performance of the exome-CDS. Overall, these designs provide flexible solutions for a variety of research questions and are likely to be reliable tools in disease studies.

Development and performance of a targeted whole exome sequencing enrichment kit for the dog (Canis Familiaris Build 3.1)

Whole exome sequencing is a technique that aims to selectively sequence all exons of protein-coding genes. A canine whole exome sequencing enrichment kit was designed based on the latest canine reference genome (build 3.1.72). Its performance was tested by sequencing 2 exome captures, each consisting of 4 pre-capture pooled, barcoded Illumina libraries on an Illumina HiSeq 2500. At an average sequencing depth of 102x, 83 to 86% of the target regions were completely sequenced with a minimum coverage of five and 90% of the reads mapped on the target regions. Additionally, it is shown that the reproducibility within and between captures is high and that pooling four samples per capture is a valid option. Overall, we have demonstrated the strong performance of this WES enrichment kit and are confident it will be a valuable tool in future disease association studies.

Identification and validation of quantitative trait loci (QTL) for canine hip dysplasia (CHD) in German Shepherd Dogs

Canine hip dysplasia (CHD) is the most common hereditary skeletal disorder in dogs. To identify common alleles associated with CHD, we genotyped 96 German Shepherd Dogs affected by mild, moderate and severe CHD and 96 breed, sex, age and birth year matched controls using the Affymetrix canine high density SNP chip. A mixed linear model analysis identified five SNPs associated with CHD scores on dog chromosomes (CFA) 19, 24, 26 and 34. These five SNPs were validated in a by sex, age, birth year and coancestry stratified sample of 843 German Shepherd Dogs including 277 unaffected dogs and 566 CHD-affected dogs. Mean coancestry coefficients among and within cases and controls were <0.1%. Genotype effects of these SNPs explained 20–32% of the phenotypic variance of CHD in German Shepherd Dogs employed for validation. Genome-wide significance in the validation data set could be shown for each one CHD-associated SNP on CFA24, 26 and 34. These SNPs are located within or in close proximity of genes involved in bone formation and related through a joint network. The present study validated positional candidate genes within two previously known quantitative trait loci (QTL) and a novel QTL for CHD in German Shepherd Dogs.