An ADAMTS3 missense variant is associated with Norwich Terrier upper airway syndrome

Analysis of canine gene constraint identifies new variants for orofacial clefts and stature

Dog breeding promotes within-group homogeneity through conformation to strict breed standards, while simultaneously driving between-group heterogeneity. There are over 350 recognized dog breeds that provide the foundation for investigating the genetic basis of phenotypic diversity. Typically, breed standard phenotypes such as stature, pelage, and craniofacial structure are analyzed through genetic association studies. However, such analyses are limited to assayed phenotypes only, leaving difficult-to-measure phenotypic subtleties easily overlooked. We investigated coding variation from over 2000 dogs, leading to discoveries of variants related to craniofacial morphology and stature. Breed-enriched variants were prioritized according to gene constraint, which was calculated using a mutation model derived from trinucleotide substitution probabilities. Among the newly found variants is a splice-acceptor variant in PDGFRA associated with bifid nose, a characteristic trait of Çatalburun dogs, implicating the gene's role in midline closure. Two additional LCORL variants, both associated with canine body size are also discovered: a frameshift that causes a premature stop in large breeds (>25 kg) and an intronic substitution found in small breeds (<10 kg), thus highlighting the importance of allelic heterogeneity in selection for breed traits. Most variants prioritized in this analysis are not associated with genomic signatures for breed differentiation, as these regions are enriched for constrained genes intolerant to nonsynonymous variation. This indicates trait selection in dogs is likely a balancing act between preserving essential gene functions and maximizing regulatory variation to drive phenotypic extremes.

Whole exome sequencing as a screening tool in dogs: A pilot study

Background

Whole-exome sequencing (WES) is used to selectively sequence all exons of protein-coding genes. WES is considered as a cost-effective and direct approach for identifying phenotype-associated variants in protein-coding regions and is as such situated between the traditional Sanger sequencing and whole genome sequencing (WGS). While WES is already widely used as a clinical tool in human and medical genetics, its use in veterinary medicine is currently restricted to research purposes. In this article, we aimed to provide baseline performance characteristics of a WES design to assess its suitability with future applications in veterinary clinical genetics in mind.

Methods

To assess the potential of WES in a clinical setting for dogs, 49 canine samples underwent capture, sequencing and analysis for the presence of 352 known phenotype-associated variants. The sequencing performance was compared for three types of variants, based on their size and location: single nucleotide variants (SNVs) inside exons, larger indel variants (≤20 bp) inside exons and intronic variants.

Results

On average, 85 % and 82 % of the exonic SNPs and larger variants were sequenced at a sequencing depth of ≥ 10x in the 49 samples, respectively. In the best performing sample, 94 % of the exonic SNPs were covered at least 10x, whereas in the worst performing sample, still 71 % of the exonic SNPs had an average sequencing depth of more than 10x.

Conclusion

To our knowledge, this is the first report that describes the performance of a research-intended WES design if it would be used in clinical genetics. This study found that WES demonstrated high efficacy in detecting variants located within target regions, including those that were not initially included in the design. However, the performance varied across different variants. The next steps would be the development of improved designs and settings to ameliorate the results.

Anatomical, functional, and blood-born predictors of severity of brachycephalic obstructive airway syndrome severity in French Bulldogs

Brachycephalic breeds suffer from respiratory distress known as brachycephalic obstructive airway syndrome (BOAS) and the multiple comorbidities associated with it. Targeted breeding toward a more BOAS-free phenotype requires accurate and least invasive detection of BOAS severity grades that are accessible and accepted by the breeders and kennel clubs. This study aimed to compare the-outcome of morphometric anatomical examination with functional tests such as exercise tests and plethysmography for the detection of BOAS severity in a group of 84 French Bulldogs. In addition, we investigated the possibility of assessing the severity of BOAS using blood parameters that were found to vary between the brachycephalic and non-brachycephalic dogs in our previous study. We found the results of the trotting test to be most reliable compared to the outcome of respiratory performance assessment using plethysmography. Of all the candidate blood parameters tested, carboxyhemoglobin and oxyhemoglobin levels were the most predictive as on-side but not self-standing indicators of BOAS severity grade. Aggravation of BOAS manifestation was associated with mild stress erythropoiesis and oxidative stress. Based on our findings, we suggest continuing to use the trotting test as the method of choice for the selection of breeding dogs; in questionable cases, a temperature increase of more than 0.4°C indicates at least grade 2. Furthermore, co-oximetry could be used as an additional test to enable assignment to one of the two BOAS grades in dispute. Among the limitations of this study are the focus on one breed and the low number of animals with severe clinical signs of BOAS in the study cohort.

A Splice Site Variant in ADAMTS3 Is the Likely Causal Variant for Pulmonary Hypoplasia with Anasarca in Persian/Persian-Cross Sheep

Pulmonary hypoplasia with anasarca, or hydrops fetalis, is characterized by stillbirth, diffuse oedema, and generalized lymph node hypoplasia. The enlarged fetus frequently causes dystocia. The disease has been reported in cattle and sheep as an inherited condition with a recessive mode of inheritance. This is the first report of the disease in Persian/Persian-cross sheep in Australia. Affected fetuses were reported from three flocks, and a total of eleven affected, eleven obligate carrier, and 188 related Persian/Persian-cross animals were available for analysis, as well as unrelated control animals. SNP genotyping revealed a region of homozygosity in affected animals on ovine chromosome six, which contained the functional candidate gene ADAMTS3. Whole genome sequencing of two affected fetuses and one obligate carrier ewe revealed a single nucleotide deletion, ENSOARG00000013204:g.87124344delC, located 3 bp downstream from a donor splice site region in the ADAMTS3 gene. Sanger sequencing of cDNA containing this variant further revealed that it is likely to introduce an early splice site in exon 14, resulting in a loss of 6 amino acids at the junction of exon 14 and intron 14/15. A genotyping assay was developed, and the ENSOARG00000013204:g.87124344delC segregated with disease in 209 animals, allowing for effective identification of carrier animals.

Evaluation of risk factors for sleep-disordered breathing in dogs

BACKGROUND

Brachycephalic dogs display sleep-disordered breathing (SDB). The risk factors for SDB remain unknown.

OBJECTIVES

To identify risk factors for SDB. We hypothesized that brachycephaly, increasing severity of brachycephalic obstructive airway syndrome (BOAS), excess weight, and aging predispose to SDB.

ANIMALS

Sixty-three privately owned pet dogs were prospectively recruited: 28 brachycephalic and 35 normocephalic (mesaticephalic or dolicocephalic) dogs.

METHODS

Prospective observational cross-sectional study with convenience sampling. Recording with the neckband was done over 1 night at each dog's home. The primary outcome measure was the obstructive respiratory event index (OREI). Body condition score (BCS) was assessed, and BOAS severity was graded for brachycephalic dogs.

RESULTS

Brachycephaly was a significant risk factor for high OREI value (ratio of the geometric means 5.6, 95% confidence interval [CI] 3.2-9.9; P < .001) but aging was not (1.1, 95% CI 1.0-1.2; P = .2). Excess weight, defined as a BCS of over 5/9, (3.5, 95% CI 1.8-6.7; P < .001) was a significant risk factor. In brachycephalic dogs, BOAS-positive class (moderate or severe BOAS signs) was a significant risk factor (2.5, 95% CI 1.1-5.6; P = .03).

CONCLUSIONS AND CLINICAL IMPORTANCE

Brachycephaly decreases welfare in a multitude of ways, including disrupting sleep. Brachycephaly, increasing severity of BOAS and excess weight are risk factors for obstructive SDB.

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.

Results of owner questionnaires describing long-term outcome in Norwich terriers with upper airway syndrome: 2011-2018

Background

Norwich terriers are affected by an upper airway syndrome (NTUAS) but little is known about outcome in affected dogs.

Objective

To determine outcome in dogs with NTUAS using owner questionnaires.

Animals

Thirty‐four client‐owned dogs.

Methods

At initial assessment, owners were questioned about respiratory noises and exercise tolerance. A NTUAS score was prospectively constructed based on the number and severity of obstructive lesions detected endoscopically (range, 0‐25). Owner questionnaires on respiratory noises, exercise tolerance, and quality of life (QOL) were obtained 2.2‐9.3 years (median, 4.2 years) after endoscopy.

Results

Dogs ranged from 0.5 to 10.7 years of age (median, 4.75 years) at initial examination and no correlation was found between age and NTUAS score (median, 13; range, 1‐25). Of 5 possible laryngeal abnormalities, 7 dogs had 1‐2, 10 dogs had 3, and 17 dogs had 4‐5 abnormalities (median, 3.5). Surgery was performed in 15 dogs, which had higher NTUAS scores (18.5 ± 6.3) than dogs that did not have surgery (7.7 ± 4.7, P < .0001). Scores for QOL ranged from 0 to 31 out of 40, with higher scores indicating worse QOL. Owner surveys resulted in QOL scores of ≤3 in 25/31 dogs (81%), with worse scores in dogs that had surgery performed (median 5, vs 0; P = .003). No correlation was noted between NTUAS and QOL scores, but age at follow‐up was weakly associated with worse QOL.

Conclusions and Clinical Importance

Despite variable severity of NTUAS scores, owners reported excellent QOL for most Norwich terriers examined.

A Deletion in GDF7 is Associated with a Heritable Forebrain Commissural Malformation Concurrent with Ventriculomegaly and Interhemispheric Cysts in Cats

An inherited neurologic syndrome in a family of mixed-breed Oriental cats has been characterized as forebrain commissural malformation, concurrent with ventriculomegaly and interhemispheric cysts. However, the genetic basis for this autosomal recessive syndrome in cats is unknown. Forty-three cats were genotyped on the Illumina Infinium Feline 63K iSelect DNA Array and used for analyses. Genome-wide association studies, including a sib-transmission disequilibrium test and a case-control association analysis, and homozygosity mapping, identified a critical region on cat chromosome A3. Short-read whole genome sequencing was completed for a cat trio segregating with the syndrome. A homozygous 7 bp deletion in growth differentiation factor 7 (GDF7) (c.221_227delGCCGCGC [p.Arg74Profs]) was identified in affected cats, by comparison to the 99 Lives Cat variant dataset, validated using Sanger sequencing and genotyped by fragment analyses. This variant was not identified in 192 unaffected cats in the 99 Lives dataset. The variant segregated concordantly in an extended pedigree. In mice, GDF7 mRNA is expressed within the roof plate when commissural axons initiate ventrally-directed growth. This finding emphasized the importance of GDF7 in the neurodevelopmental process in the mammalian brain. A genetic test can be developed for use by cat breeders to eradicate this variant.

Canine Brachycephaly: Anatomy, Pathology, Genetics and Welfare

Brachycephalic dog breeds have experienced a marked rise in popularity in recent years. While numerous people clearly desire this phenotype in their pets, many of these dogs unfortunately experience several concomitant sequelae, including major problems with respiration and thermoregulation, as well as gastrointestinal, ophthalmological, dermatological, reproductive and even dental problems. This mini review focuses on the anatomical and pathological changes associated with brachycephalic skull shape, including brachycephalic obstructive airway syndrome and other co-existent disorders. It then details the known genetic contributors to brachycephaly, and concludes with a brief discourse on the welfare of these animals.

Identification of small and large genomic candidate variants in bovine pulmonary hypoplasia and anasarca syndrome

The pulmonary hypoplasia and anasarca syndrome (PHA) is a congenital lethal disorder, which until now has been reported in cattle and sheep. PHA is characterized by extensive subcutaneous fetal edema combined with hypoplasia or aplasia of the lungs and dysplasia of the lymphatic system. PHA is assumed to be of genetic etiology. This study presents the occurrence of PHA in two different cattle breeds and their genetic causation. Two PHA cases from one sire were observed in Slovenian Cika cattle. Under the assumption of monogenic inheritance, genome-wide homozygosity mapping scaled down the critical regions to 3% of the bovine genome including a 43.6 Mb-sized segment on chromosome 6. Whole-genome sequencing of one case, variant filtering against controls and genotyping of a larger cohort of Cika cattle led to the detection of a likely pathogenic protein-changing variant perfectly associated with the disease: a missense variant on chromosome 6 in ADAMTS3 (NM_001192797.1: c.1222C>T), which affects an evolutionary conserved residue (NP_001179726.1: p.(His408Tyr)). A single PHA case was found in Danish Holstein cattle and was whole-genome sequenced along with its parents. However, as there was no plausible private protein-changing variant, mining for structural variation revealed a likely pathogenic trisomy of the entire chromosome 20. The identified ADAMTS3 associated missense variant and the trisomy 20 are two different genetic causes, which shows a compelling genetic heterogeneity for bovine PHA.

ADAMs and ADAMTSs☆

Proteolysis has emerged as a key post-translational regulator of the function of molecules on the cell surface and in the extracellular milieu. In principle, proteolysis can activate or inactivate a substrate, or can change its functional properties. ADAMs (a disintegrin and metalloprotease) and ADAMTS (a disintegrin-like and metalloprotease domain with thrombospondin type 1 repeats) proteases are related members of a superfamily of metallo-endopeptidases that also includes MMPs and astacins. ADAMs are integral membrane proteins that typically cleave other membrane anchored proteins, whereas ADAMTS proteases lack a membrane anchor, and process both cell-surface and secreted molecules, the latter mostly extracellular matrix (ECM) components. ADAMs are implicated in fertilization, neurogenesis, in regulating the function of ligands for the EGF-receptor, and in the release of proteins such as the pro-inflammatory cytokine TNFα from the plasma membrane. ADAMTS proteases have key roles in embryonic development, including lung development, the molecular maturation of von Willebrand factor and procollagen as well as organization of fibrillin microfibrils in ECM, and are implicated in the pathogenesis of diverse lung and airway disorders. Here, we provide a general overview of the biochemical properties and physiological functions of ADAMs and ADAMTS proteases and describe their relevance to lung and airway disorders.

A comprehensive biomedical variant catalogue based on whole genome sequences of 582 dogs and eight wolves

The domestic dog serves as an excellent model to investigate the genetic basis of disease. More than 400 heritable traits analogous to human diseases have been described in dogs. To further canine medical genetics research, we established the Dog Biomedical Variant Database Consortium (DBVDC) and present a comprehensive list of functionally annotated genome variants that were identified with whole genome sequencing of 582 dogs from 126 breeds and eight wolves. The genomes used in the study have a minimum coverage of 10× and an average coverage of ~24×. In total, we identified 23 133 692 single-nucleotide variants (SNVs) and 10 048 038 short indels, including 93% undescribed variants. On average, each individual dog genome carried ∼4.1 million single-nucleotide and ~1.4 million short-indel variants with respect to the reference genome assembly. About 2% of the variants were located in coding regions of annotated genes and loci. Variant effect classification showed 247 141 SNVs and 99 562 short indels having moderate or high impact on 11 267 protein-coding genes. On average, each genome contained heterozygous loss-of-function variants in 30 potentially embryonic lethal genes and 97 genes associated with developmental disorders. More than 50 inherited disorders and traits have been unravelled using the DBVDC variant catalogue, enabling genetic testing for breeding and diagnostics. This resource of annotated variants and their corresponding genotype frequencies constitutes a highly useful tool for the identification of potential variants causative for rare inherited disorders in dogs.

Facial changes related to brachycephaly in Cavalier King Charles Spaniels with Chiari-like malformation associated pain and secondary syringomyelia

BACKGROUND

Recent studies including an innovative machine learning technique indicated Chiari-like malformation (CM) is influenced by brachycephalic features.

OBJECTIVES

Morphometric analysis of facial anatomy and dysmorphia in CM-associated pain (CM-P) and syringomyelia (SM) in the Cavalier King Charles Spaniel (CKCS).

ANIMALS

Sixty-six client-owned CKCS.

METHODS

Retrospective study of anonymized T2W sagittal magnetic resonance imaging of 3 clinical groups: (1) 11 without central canal dilation (ccd) or SM (CM-N), (2) 15 with CM-P with no SM or <2 mm ccd (CM-P), and (3) 40 with syrinx width ≥4 mm (SM-S). Morphometric analysis assessed rostral skull flattening and position of the hard and soft palate relative to the cranial base in each clinical group and compared CKCS with and without SM-S.

RESULTS

Sixteen of 28 measured variables were associated to SM-S compared to CM-N and CM-P. Of these 6 were common to both groups. Predictive variables determined by discriminant analysis were (1) the ratio of cranial height with cranial length (P < .001 between SM-S and CM-N) and (2) the distance between the cerebrum and the frontal bone (P < .001 between SM-S and CM-P). CM-P had the lowest mean height of the maxillary area.

CONCLUSIONS AND CLINICAL IMPORTANCE

CKCS with CM-P and SM-S have cranial brachycephaly with osseous insufficiency in the skull with rostral flattening and increased proximity of the hard and soft palate to the cranial base. Changes are greatest with CM-P. These findings have relevance for understanding disease pathogenesis and for selection of head conformation for breeding purposes.

A RAPGEF6 variant constitutes a major risk factor for laryngeal paralysis in dogs

Laryngeal paralysis (LP) is the inability to abduct the arytenoid cartilages during inspiration, resulting in a partial to complete airway obstruction and consequent respiratory distress. Different forms of LP with varying age of onset exist in dogs. Hereditary early onset forms were reported in several dog breeds. In most breeds, hereditary LP is associated with other neurologic pathologies. Using a genome-wide association study and haplotype analyses, we mapped a major genetic risk factor for an early onset LP in Miniature Bull Terriers to a ~1.3 Mb interval on chromosome 11. Whole genome sequencing of an affected Miniature Bull Terrier and comparison to 598 control genomes revealed a 36 bp insertion into exon 15 of the RAPGEF6 gene (c.1793_1794ins36). The imperfect genotype-phenotype correlation suggested a complex mode of inheritance with a major genetic risk factor involving a recessive risk allele. Homozygosity for the insertion was associated with a 10- to 17-fold increased risk for LP. The insertion allele was only found in Miniature Bull Terriers and Bull Terriers. It was absent from >1000 control dogs of other dog breeds. The insertion sequence contains a splice acceptor motif leading to aberrant splicing in transcripts originating from the mutant allele (r.1732_1780del). This leads to a frameshift and a premature stop codon, p.(Ile587ProfsTer5), removing 64% of the open reading frame. Our results suggest an important role of RAPGEF6 in laryngeal nerve function and provide new clues to its physiological significance.

Laryngeal paralysis (LP) leads to respiratory distress in affected dogs and can be fatal in severe cases. Many different forms of LP with different etiologies exist. Striking breed predispositions suggest that genetic factors contribute to some forms of LP. During the last years, dog breeders noticed an increased prevalence of an early onset LP in Miniature Bull Terriers. We mapped a major risk locus for this specific form of LP to a ~1.3 Mb interval on dog chromosome 11. Whole genome sequence analysis of an affected dog and comparison to 598 control genomes revealed a single protein-changing genetic variant in the critical interval. This variant, a 36 bp insertion into a coding exon of the RAPGEF6 gene, creates a cryptic splice site and leads to the expression of an aberrantly spliced transcript with a premature stop codon. This suggests that the insertion results in a loss-of-function allele. Dogs that are homozygous for the insertion have a 10- to 17-fold increased risk to develop LP. The genotype-phenotype association is not perfect, suggesting that other genetic and/or environmental factors also contribute to the development of LP. Our results suggest an important role of RAPGEF6 in laryngeal nerve function.