A web resource on DNA tests for canine and feline hereditary diseases

Molecular epidemiological study of germline APC variant associated with hereditary gastrointestinal polyposis in dogs: current frequency in Jack Russell Terriers in Japan and breed distribution

Background

Cases of gastrointestinal (GI) neoplastic polyps in Jack Russell Terriers (JRTs) have increased in Japan since the late 2000s. We recently demonstrated that JRTs with GI polyps heterozygously harbor an identical germline variant in the adenomatous polyposis coli (APC) gene, c.[462_463delinsTT]; therefore, this is an autosomal dominant hereditary disease. We conducted a molecular epidemiological study to explore the current frequency of the APC variant in JRTs in Japan and the breed distribution of this disease.

Results

Peripheral blood samples from 792 JRTs were collected at 93 veterinary hospitals in Japan in 2020. Using an established polymerase chain reaction-restriction fragment length polymorphism assay, the germline APC variant was detected in 15 JRTs, with an overall frequency of 1.89%. The frequency was not significantly different for sex, age, and coat type criteria. Notably, the variant carriers had a current or previous history of GI neoplastic polyps, providing further evidence of the association of the germline APC variant with GI polyposis. Pedigree analysis of carrier dogs revealed that the germline APC variant was no longer confined to a few specific families but was widely spread among JRTs in Japan. Furthermore, some ancestors of the carriers were from Australia or New Zealand, suggesting the possible presence of carriers in countries other than Japan. Next, we retrospectively investigated the germline APC variant status of dogs with GI epithelial tumors using genomic DNA samples extracted from archived pathological specimens (28 purebred dogs of 14 breeds and four mixed-breed dog), as well as those stored in a canine genome bank (38 dogs of 18 breeds and a mixed-breed dogs). In total, 66 purebred dogs of 25 breeds, including another four JRTs, and five mixed-breed dogs were examined. While three variant carriers were found in JRTs, the germline APC variant was not detected in any of the other breeds.

Conclusion

The current frequency of the germline APC variant was approximately 2% in JRTs in Japan and the frequency remained roughly flat during the last 15 years. In addition, hereditary GI polyposis associated with the variant was virtually specific to JRTs.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12917-022-03338-w.

Web resource on available DNA variant tests for hereditary diseases and genetic predispositions in dogs and cats: An Update

Vast progress has been made in the clinical diagnosis and molecular basis of hereditary diseases and genetic predisposition in companion animals. The purpose of this report is to provide an update on the availability of DNA testing for hereditary diseases and genetic predispositions in dogs and cats utilizing the WSAVA-PennGen DNA Testing Database web resource (URL: http://research.vet.upenn.edu/WSAVA-LabSearch ). Information on hereditary diseases, DNA tests, genetic testing laboratories and afflicted breeds added to the web-based WSAVA-PennGen DNA Testing Database was gathered. Following verification through original research and clinical studies, searching various databases on hereditary diseases in dogs and cats, and contacting laboratories offering DNA tests, the data were compared to the resource reported on in 2013. The number of molecularly defined Mendelian inherited diseases and variants in companion animals listed in the WSAVA-PennGen DNA Testing Database in 2020 drastically increased by 112% and 141%, respectively. The number of DNA variant tests offered by each laboratory has also doubled for dogs and cats. While the overall number of laboratories has only slightly increased from 43 to 47, the number of larger corporate laboratories increased, while academic laboratories have declined. In addition, there are now several laboratories that are offering breed-specific or all-breed panel tests rather than single-DNA tests for dogs and cats. This unique regularly updated searchable web-based database allows veterinary clinicians, breeders and pet owners to readily find available DNA tests, laboratories performing these DNA tests worldwide, and canine and feline breeds afflicted and also serves as a valuable resource for comparative geneticists.

PCR-based genotyping assays to detect germline APC variant associated with hereditary gastrointestinal polyposis in Jack Russell terriers

Background

The prevalence of gastrointestinal (GI) neoplastic polyps in Jack Russell terriers (JRTs) has increased in Japan since the late 2000s. Recently, we demonstrated that JRTs with GI polyps harbor identical germline variant in the APC gene (c.[462_463delinsTT]) in the heterozygous state. Thus, this disease is an autosomal dominant hereditary disorder. Although the affected JRTs have distinct features, such as the development of multiple GI polyps and an early age of disease onset, genetic testing is indispensable for a definitive diagnosis. Here, polymerase chain reaction (PCR)-based assays capable of detecting germline APC variant were designed and validated using synthetic wild-type and mutant DNAs and genomic DNAs from carrier and non-carrier dogs.

Result

First, the PCR-restriction fragment length polymorphism (PCR-RFLP) assay was developed by taking advantage of the germline APC variant creating a new restriction site for MseI. In the PCR-RFLP assay, the 156-bp region containing the variant site was amplified by PCR and subsequently digested with MseI, yielding diagnostic 51 and 58 bp fragments from the mutant allele and allowing determination of the APC genotypes. It was possible to determine the genotypes using genomic DNA extracted from the peripheral blood, buccal swab, or formalin-fixed paraffin-embedded tissue. Next, a TaqMan duplex real-time PCR assay was developed, where a 78-bp region flanking the variant was amplified in the presence of wild-type allele- and mutant allele-specific fluorescent probes. Using blood-derived DNA, altogether 40 cycles of PCR amplification determined the APC genotypes of all examined samples by measuring the fluorescence intensities. Importantly, false-positive and false-negative errors were never detected in both assays.

Conclusion

In this study, we developed highly reliable genetic tests for hereditary GI polyposis in JRTs, providing accurate assessment of the presence of the causative germline APC variant. The genotyping assays could contribute to the diagnosis and prevention of hereditary GI polyposis in dogs.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12917-020-02731-7.

Initial survey of PLA2G6 missense variant causing neuroaxonal dystrophy in Papillon dogs in North America and Europe

BACKGROUND

An autosomal recessive, rapidly progressive degenerative neuropathy known as infantile neuroaxonal dystrophy (NAD) was originally reported in Papillion puppies in 1995. In 2015, a causative missense variant in the PLA2G6 gene was identified in three affected puppies. Archived samples from Papillons clinically diagnosed with NAD prior to 2015 as well as samples obtained from 660 Papillons from North America and Europe between 2015 and 2017 were screened for the presence of this PLA2G6 gene variant (XM_022424454.1:c.1579G > A) using a TaqMan assay.

RESULTS

Archived samples from affected puppies diagnosed prior to 2015 and three more recently acquired samples from Papillons clinically affected with NAD were all homozygous for the variant. SIFT analysis predicts that the PLA2G6 missense substitution (XP_022280162.1:p.Ala527Thr) will not be tolerated in the iPLA2β protein. Notably, 17.5% of the 660 tested Papillons were heterozygotes, resulting in a variant allele frequency of 0.092 in this initial survey. Since then, screening for NAD in Papillons by at least 10 other laboratories and data from the Health Committee of Papillon Club of America gathered between 2017 and 2019 reveal a variant allele frequency of 0.047.

CONCLUSIONS

This survey and data from other laboratories documents the widespread presence of the PLA2G6 variant in the Papillon population in North America and Europe. Despite the apparent declining prevalence of the PLA2G6 variant, screening of Papillons intended for breeding is still recommended to avoid inadvertent production of puppies with infantile NAD.

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.

Veterinary informatics: forging the future between veterinary medicine, human medicine, and One Health initiatives-a joint paper by the Association for Veterinary Informatics (AVI) and the CTSA One Health Alliance (COHA)

Objectives

This manuscript reviews the current state of veterinary medical electronic health records and the ability to aggregate and analyze large datasets from multiple organizations and clinics. We also review analytical techniques as well as research efforts into veterinary informatics with a focus on applications relevant to human and animal medicine. Our goal is to provide references and context for these resources so that researchers can identify resources of interest and translational opportunities to advance the field.

Methods and Results

This review covers various methods of veterinary informatics including natural language processing and machine learning techniques in brief and various ongoing and future projects. After detailing techniques and sources of data, we describe some of the challenges and opportunities within veterinary informatics as well as providing reviews of common One Health techniques and specific applications that affect both humans and animals.

Discussion

Current limitations in the field of veterinary informatics include limited sources of training data for developing machine learning and artificial intelligence algorithms, siloed data between academic institutions, corporate institutions, and many small private practices, and inconsistent data formats that make many integration problems difficult. Despite those limitations, there have been significant advancements in the field in the last few years and continued development of a few, key, large data resources that are available for interested clinicians and researchers. These real-world use cases and applications show current and significant future potential as veterinary informatics grows in importance. Veterinary informatics can forge new possibilities within veterinary medicine and between veterinary medicine, human medicine, and One Health initiatives.

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.

Genetic Panel Screening of Nearly 100 Mutations Reveals New Insights into the Breed Distribution of Risk Variants for Canine Hereditary Disorders

Background

The growing number of identified genetic disease risk variants across dog breeds challenges the current state-of-the-art of population screening, veterinary molecular diagnostics, and genetic counseling. Multiplex screening of such variants is now technologically feasible, but its practical potential as a supportive tool for canine breeding, disease diagnostics, pet care, and genetics research is still unexplored.

Results

To demonstrate the utility of comprehensive genetic panel screening, we tested nearly 7000 dogs representing around 230 breeds for 93 disease-associated variants using a custom-designed genotyping microarray (the MyDogDNA® panel test). In addition to known breed disease-associated mutations, we discovered 15 risk variants in a total of 34 breeds in which their presence was previously undocumented. We followed up on seven of these genetic findings to demonstrate their clinical relevance. We report additional breeds harboring variants causing factor VII deficiency, hyperuricosuria, lens luxation, von Willebrand’s disease, multifocal retinopathy, multidrug resistance, and rod-cone dysplasia. Moreover, we provide plausible molecular explanations for chondrodysplasia in the Chinook, cerebellar ataxia in the Norrbottenspitz, and familiar nephropathy in the Welsh Springer Spaniel.

Conclusions

These practical examples illustrate how genetic panel screening represents a comprehensive, efficient and powerful diagnostic and research discovery tool with a range of applications in veterinary care, disease research, and breeding. We conclude that several known disease alleles are more widespread across different breeds than previously recognized. However, careful follow up studies of any unexpected discoveries are essential to establish genotype-phenotype correlations, as is readiness to provide genetic counseling on their implications for the dog and its breed.

Genetics of Adiposity in Large Animal Models for Human Obesity-Studies on Pigs and Dogs

The role of domestic mammals in the development of human biomedical sciences has been widely documented. Among these model species the pig and dog are of special importance. Both are useful for studies on the etiology of human obesity. Genome sequences of both species are known and advanced genetic tools [eg, microarray SNP for genome wide association studies (GWAS), next generation sequencing (NGS), etc.] are commonly used in such studies. In the domestic pig the accumulation of adipose tissue is an important trait, which influences meat quality and fattening efficiency. Numerous quantitative trait loci (QTLs) for pig fatness traits were identified, while gene polymorphisms associated with these traits were also described. The situation is different in dog population. Generally, excessive accumulation of adipose tissue is considered, similar to humans, as a complex disease. However, research on the genetic background of canine obesity is still in its infancy. Between-breed differences in terms of adipose tissue accumulation are well known in both animal species. In this review we show recent advances of studies on adipose tissue accumulation in pigs and dogs, and their potential importance for studies on human obesity.

Germline gene polymorphisms predisposing domestic mammals to carcinogenesis

Cancer is a complex disease caused in part by predisposing germline gene polymorphisms. Knowledge of carcinogenesis in companion mammals (dog and cat) and some livestock species (pig and horse) is quite advanced. The prevalence of certain cancers varies by breed in these species, suggesting the presence of predisposing genetic variants in susceptible breeds. This review summarizes the present understanding of germline gene polymorphisms, including BRCA1, BRCA2, MC1R, KIT, NRAS and RAD51, associated with predisposition to melanoma, mammary cancer, osteosarcoma and histiocytic sarcoma in dogs, cats, pigs and horses. The predisposing variants in these species are discussed in the context of human germline gene polymorphisms associated with the same types of cancer.

Mucopolysaccharidosis type VI in a juvenile miniature schnauzer dog with concurrent hypertriglyceridemia, necrotizing pancreatitis, and diabetic ketoacidosis

A 7-month-old, neutered male miniature schnauzer dog with a history of cryptorchidism and umbilical hernia was referred for diabetic ketoacidosis. Clinical evaluation revealed stunted growth, skeletal abnormalities, hypertriglyceridemia, diabetic ketoacidosis, and acute necrotizing pancreatitis. Further testing was diagnostic for mucopolysaccharidosis type VI causing the stunted growth and skeletal deformities, but no connection between mucopolysaccharidosis type VI, hypertriglyceridemia, and pancreatic diseases was found.

Inherited epilepsy in dogs

Epilepsy is the most common neurologic disease in dogs and many forms are considered to have a genetic basis. In contrast, some seizure disorders are also heritable, but are not technically defined as epilepsy. Investigation of true canine epilepsies has uncovered genetic associations in some cases, however, many remain unexplained. Gene mutations have been described for 2 forms of canine epilepsy: primary epilepsy (PE) and progressive myoclonic epilepsies. To date, 9 genes have been described to underlie progressive myoclonic epilepsies in several dog breeds. Investigations into genetic PE have been less successful, with only 1 causative gene described. Genetic testing as an aid to diagnosis, prognosis, and breeding decisions is available for these 10 forms. Additional studies utilizing genome-wide tools have identified PE loci of interest; however, specific genetic tests are not yet developed. Many studies of dog breeds with PE have failed to identify genes or loci of interest, suggesting that, similar to what is seen in many human genetic epilepsies, inheritance is likely complex, involving several or many genes, and reflective of environmental interactions. An individual dog's response to therapeutic intervention for epilepsy may also be genetically complex. Although the field of inherited epilepsy has faced challenges, particularly with PE, newer technologies contribute to further advances.

Dog as a model in studies on human hereditary diseases and their gene therapy

During the last 15 years spectacular progress has been achieved in knowledge on the dog genome organization and the molecular background of hereditary diseases in this species. A majority of canine genetic diseases have their counterparts in humans and thus dogs are considered as a very important large animal model in human biomedicine. Among canine monogenic diseases with known causative gene mutations there are two large groups classified as retinal dystrophies and lysosomal storage diseases. Specific types of these diseases are usually diagnosed in a single or several breeds. A well known disorder, restricted to a single breed, is congenital stationary night blindness described in Briards. This disease is a counterpart of Leber amaurosis in children. On the other hand, one of the most common monogenic human diseases (Duchenne muscular dystrophy), has its canine counterparts in several breeds (e.g., the Golden retriever, Beagle and German short-haired pointer). For some of the canine diseases gene therapy strategy was successfully applied, e.g., for congenital stationary night blindness, rod-cone dystrophy and muccopolysaccharydoses type I, IIIB and VII. Since phenotypic variability between the breeds is exceptionally high, the dog is an interesting model to study the molecular background of congenital malformations (e.g., dwarfism and osteoporosis imperfecta). Also disorders of sexual development (DSD), especially testicular or ovotesticular DSD (78,XX; SRY-negative), which is widely distributed across dozens of breeds, are of particular interest. Studies on the genetic background of canine cancers, a major health problem in this species, are also quite advanced. On the other hand, genetic studies on canine counterparts of major human complex diseases (e.g., obesity, the metabolic syndrome and diabetes mellitus) are still in their infancy.