A missense variant in the NSDHL gene in a Chihuahua with a congenital cornification disorder resembling inflammatory linear verrucous epidermal nevi

Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture

BACKGROUND

The international Dog10K project aims to sequence and analyze several thousand canine genomes. Incorporating 20 × data from 1987 individuals, including 1611 dogs (321 breeds), 309 village dogs, 63 wolves, and four coyotes, we identify genomic variation across the canid family, setting the stage for detailed studies of domestication, behavior, morphology, disease susceptibility, and genome architecture and function.

RESULTS

We report the analysis of > 48 M single-nucleotide, indel, and structural variants spanning the autosomes, X chromosome, and mitochondria. We discover more than 75% of variation for 239 sampled breeds. Allele sharing analysis indicates that 94.9% of breeds form monophyletic clusters and 25 major clades. German Shepherd Dogs and related breeds show the highest allele sharing with independent breeds from multiple clades. On average, each breed dog differs from the UU_Cfam_GSD_1.0 reference at 26,960 deletions and 14,034 insertions greater than 50 bp, with wolves having 14% more variants. Discovered variants include retrogene insertions from 926 parent genes. To aid functional prioritization, single-nucleotide variants were annotated with SnpEff and Zoonomia phyloP constraint scores. Constrained positions were negatively correlated with allele frequency. Finally, the utility of the Dog10K data as an imputation reference panel is assessed, generating high-confidence calls across varied genotyping platform densities including for breeds not included in the Dog10K collection.

CONCLUSIONS

We have developed a dense dataset of 1987 sequenced canids that reveals patterns of allele sharing, identifies likely functional variants, informs breed structure, and enables accurate imputation. Dog10K data are publicly available.

Identification of Genetic Risk Factors for Monogenic and Complex Canine Diseases

Advances in DNA sequencing and other technologies have greatly facilitated the identification of genetic risk factors for inherited diseases in dogs. We review recent technological developments based on selected examples from canine disease genetics. The identification of disease-causing variants in dogs with monogenic diseases may become a widely employed diagnostic approach in clinical veterinary medicine in the not-too-distant future. Diseases with complex modes of inheritance continue to pose challenges to researchers but have also become much more tangible than in the past. In addition to strategies for identifying genetic risk factors, we provide some thoughts on the interpretation of sequence variants that are largely inspired by developments in human clinical genetics.

Genetics of inherited skin disorders in dogs

Canine genodermatoses represent a broad spectrum of diseases with diverse phenotypes. Modern genetic technology including whole genome sequencing has expedited the identification of novel genes and greatly simplified the establishment of genetic diagnoses in such heterogeneous disorders. The precise genetic diagnosis of a heritable skin disorder is essential for the appropriate counselling of owners regarding the course of the disease, prognosis and implications for breeding. Understanding the underlying pathophysiology is a prerequisite to developing specific, targeted or individualized therapeutic approaches. This review aims to create a comprehensive overview of canine genodermatoses and their respective genetic aetiology known to date. Raising awareness of genodermatoses in dogs is important and this review may help clinicians to apply modern genetics in daily clinical practice, so that a precise diagnoses can be established in suspected genodermatoses.

Ichthyosis and hereditary cornification disorders in dogs

The stratum corneum (SC), the outermost layer of the epidermis, serves a crucial role in maintaining body hydration and protection from environmental insults. When the stratum corneum is injured or when the genetic blueprints are flawed, the body is at risk of dehydration, secondary infections and allergen sensitization. Advancements in veterinary dermatology have revealed a wide gamut of disease from relatively benign to lethal that specifically arise from flawed structural proteins, enzymes or lipids needed to create the corneocytes and lipid bilayers of the SC. Some conditions closely mimic their human counterparts while others are unique to the dog. This review will focus on forms of ichthyosis in the dog.

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.

NSDHL Frameshift Deletion in a Mixed Breed Dog with Progressive Epidermal Nevi

Loss-of-function variants in the NSDHL gene have been associated with epidermal nevi in humans with congenital hemidysplasia, ichthyosiform nevi, and limb defects (CHILD) syndrome and in companion animals. The NSDHL gene codes for the NAD(P)-dependent steroid dehydrogenase-like protein, which is involved in cholesterol biosynthesis. In this study, a female Chihuahua cross with a clinical and histological phenotype consistent with progressive epidermal nevi is presented. All exons of the NSDHL candidate gene were amplified by PCR and analyzed by Sanger sequencing. A heterozygous frameshift variant, c.718_722delGAACA, was identified in the affected dog. In lesional skin, the vast majority of NSDHL transcripts lacked the five deleted bases. The variant is predicted to produce a premature stop codon truncating 34% of the encoded protein, p.Glu240Profs*17. The mutant allele was absent from 22 additionally genotyped Chihuahuas, as well as from 647 control dogs of diverse breeds and eight wolves. The available experimental data together with current knowledge about NSDHL variants and their functional impact in humans, dogs, and other species prompted us to classify this variant as pathogenic according to the ACMG guidelines that were previously established for human sequence variants. Therefore, we propose the c.718_722delGAACA variant as causative variant for the observed skin lesions in this dog.

Transcriptome Profiling and Differential Gene Expression in Canine Microdissected Anagen and Telogen Hair Follicles and Interfollicular Epidermis

The transcriptome profile and differential gene expression in telogen and late anagen microdissected hair follicles and the interfollicular epidermis of healthy dogs was investigated by using RNAseq. The genes with the highest expression levels in each group were identified and genes known from studies in other species to be associated with structure and function of hair follicles and epidermis were evaluated. Transcriptome profiling revealed that late anagen follicles expressed mainly keratins and telogen follicles expressed GSN and KRT15. The interfollicular epidermis expressed predominately genes encoding for proteins associated with differentiation. All sample groups express genes encoding for proteins involved in cellular growth and signal transduction. The expression pattern of skin-associated genes in dogs is similar to humans. Differences in expression compared to mice and humans include BMP2 expression mainly in telogen and high KRT17 expression in the interfollicular epidermis of dogs. Our data provide the basis for the investigation of the structure and function of canine skin or skin disease and support the use of dogs as a model for human cutaneous disease by assigning gene expression to specific tissue states.