A LINE-1 insertion situated in the promoter of IMPG2 is associated with autosomal recessive progressive retinal atrophy in Lhasa Apso dogs.

BACKGROUND: Canine progressive retinal atrophies are a group of hereditary retinal degenerations in dogs characterised by depletion of photoreceptor cells in the retina, which ultimately leads to blindness. PRA in the Lhasa Apso (LA) dog has not previously been clinically characterised or described in the literature, but owners in the UK are advised to have their dog examined through the British Veterinary Association/ Kennel Club/ International Sheep Dog Society (BVA/KC/ISDS) eye scheme annually, and similar schemes that are in operation in other countries. After the exclusion of 25 previously reported canine retinal mutations in LA PRA-affected dogs, we sought to identify the genetic cause of PRA in this breed. RESULTS: Analysis of whole-exome sequencing data of three PRA-affected LA and three LA without signs of PRA did not identify any exonic or splice site variants, suggesting the causal variant was non-exonic. We subsequently undertook a genome-wide association study (GWAS), which identified a 1.3 Mb disease-associated region on canine chromosome 33, followed by whole-genome sequencing analysis that revealed a long interspersed element-1 (LINE-1) insertion upstream of the IMPG2 gene. IMPG2 has previously been implicated in human retinal disease; however, until now no canine PRAs have been associated with this gene. The identification of this PRA-associated variant has enabled the development of a DNA test for this form of PRA in the breed, here termed PRA4 to distinguish it from other forms of PRA described in other breeds. This test has been used to determine the genotypes of over 900 LA dogs. A large cohort of genotyped dogs was used to estimate the allele frequency as between 0.07-0.1 in the UK LA population. CONCLUSIONS: Through the use of GWAS and subsequent sequencing of a PRA case, we have identified a LINE-1 insertion in the retinal candidate gene IMPG2 that is associated with a form of PRA in the LA dog. Validation of this variant in 447 dogs of 123 breeds determined it was private to LA dogs. We envisage that, over time, the developed DNA test will offer breeders the opportunity to avoid producing dogs affected with this form of PRA.

Health-related welfare prioritisation of canine disorders using electronic health records in primary care practice in the UK.

BACKGROUND: Evidence-based comparison of the disorder-specific welfare burdens of major canine conditions could better inform targeting of stakeholder resources, to maximise improvement of health-related welfare in UK dogs. Population-level disease related welfare impact offers a quantitative, welfare-centred framework for objective disorder prioritisation, but practical applications have been limited to date due to sparse reliable evidence on disorder-specific prevalence, severity and duration across the canine disease spectrum. The VetCompass™ Programme collects de-identified electronic health record data from dogs attending primary-care clinics UK-wide, and is well placed to fill these information gaps. RESULTS: The eight common, breed-related conditions assessed were anal sac disorder, conjunctivitis, dental disease, dermatitis, overweight/obese, lipoma, osteoarthritis and otitis externa. Annual period prevalence estimates (based on confirming 250 cases from total potential cases identified from denominator population of 455, 557 dogs) were highest for dental disorder (9.6%), overweight/obese (5.7%) and anal sac disorder (4.5%). Dental disorder (76% of study year), osteoarthritis (82%), and overweight/obese (70%) had highest annual duration scores. Osteoarthritis (scoring 13/21), otitis externa (11/21) and dermatitis demonstrated (10/21) highest overall severity scores. Dental disorder (2.47/3.00 summative score), osteoarthritis (2.24/3.00) and overweight/obese (1.67/3.00) had highest VetCompass Welfare Impact scores overall. DISCUSSION: Of the eight common, breed-related disorders assessed, dental disorder, osteoarthritis and overweight/obese demonstrated particular welfare impact, based on combinations of high prevalence, duration and severity. Future work could extend this methodology to cover a wider range of disorders. CONCLUSIONS: Dental disorders, osteoarthritis and overweight/obese have emerged as priority areas for health-related welfare improvement in the UK dog population. This study demonstrated applicability of a standardised methodology to assess the relative health-related welfare impact across a range of canine disorders using VetCompass clinical data.

Validation of exercise testing and laryngeal auscultation for grading brachycephalic obstructive airway syndrome in pugs, French bulldogs, and English bulldogs by using whole-body barometric plethysmography.

OBJECTIVE: To determine whether the sensitivity of clinical examination for assessing upper airway disease severity in 3 breeds of brachycephalic dogs can be improved by incorporating an exercise test (ET) or by auscultation of a laryngeal stridor to predict laryngeal collapse. STUDY DESIGN: Prospective clinical study. ANIMALS: Client-owned brachycephalic dogs (n = 44 ET; n = 57 laryngeal stridor assessment). METHODS: In the first part of the study, clinical examinations were performed at rest and after 5-minute walk and 3-minute trot tests, and a grade reflective of brachycephalic obstructive airway syndrome (BOAS) severity was assigned. Whole-body barometric plethysmography was used as a comparative, objective measure of disease severity. In the second part of the study, the degree of laryngeal collapse present in dogs undergoing BOAS surgery was compared to pre-exercise and postexercise laryngeal stridor detected during functional testing. RESULTS: The sensitivity of clinical examination for BOAS diagnosis was 56.7% pre-ET, 70% after a 5-minute walk test, and 93.3% after a 3-minute trot test. The sensitivity of laryngeal stridor as a predictor of laryngeal collapse was improved after exercise (70%) compared with before exercise (60%). Specificity of laryngeal stridor for laryngeal collapse was 100% (pre-exercise and postexercise). CONCLUSION: The sensitivity of clinical examination for BOAS diagnosis was improved by inclusion of an ET, particularly the 3-minute trot test. Audible laryngeal stridor was highly specific but only moderately sensitive for laryngeal collapse. CLINICAL SIGNIFICANCE: Inclusion of a 3-minute trot test and careful auscultation for laryngeal stridor are recommended during BOAS assessment of brachycephalic dogs.

Objective effectiveness of and indications for laser-assisted turbinectomy in brachycephalic obstructive airway syndrome.

OBJECTIVE: To evaluate the effectiveness of laser-assisted turbinectomy (LATE) in treating brachycephalic obstructive airway syndrome (BOAS) and to investigate the potential indications. STUDY DESIGN: Prospective clinical study. SAMPLE POPULATION: Client-owned pugs, French bulldogs, and English bulldogs (n = 57). METHODS: A BOAS index was obtained from whole-body barometric plethysmography before BOAS conventional multilevel surgery (CMS) and 2-6 months post-CMS. Dogs with BOAS index >50% and BOAS functional grades II-III after CMS were considered candidates for LATE. A BOAS index was repeated 2-6 months after LATE. Intranasal lesions and a measurement of soft tissue proportion at the rostral entrance of choanae (STC) were recorded on the basis of computed tomography images. Logistic regressions were used to assess the intranasal predictors for being LATE candidates. RESULTS: Twenty-nine of 57 dogs were candidates for LATE, all of which were pugs or French bulldogs. The median BOAS index of dogs that were operated on (20/29 candidates) decreased from 67% post-CMS to 42% after LATE (P < .001). Soft tissue proportion at the rostral entrance of choanae was the only predictor for candidacy for LATE. Pugs (P = .021; cutoff = 64%) and French bulldogs (P = .008; cutoff = 55%) with higher STC were more likely to be candidates for LATE. After LATE, 12 of 20 dogs had temporary episodes of reverse sneezing, and nasal noise was noted in 8 of 20 dogs when sniffing and excited. CONCLUSION: Laser-assisted turbinectomy was an effective treatment for dogs with intranasal abnormalities and a poor response to CMS. Soft tissue proportion at the rostral entrance of choanae was a predictor of candidacy for LATE in pugs and French bulldogs. CLINICAL SIGNIFICANCE: Computed tomography-based measurement of STC can be used to predict whether LATE is required in addition to CMS in pugs and French bulldogs with BOAS.

Comprehensive annotation and evolutionary insights into the canine (Canis lupus familiaris) antigen receptor loci.

Dogs are an excellent model for human disease. For example, the treatment of canine lymphoma has been predictive of the human response to that treatment. However, an incomplete picture of canine (Canis lupus familiaris) immunoglobulin (IG) and T cell receptor (TR)-or antigen receptor (AR)-gene loci has restricted their utility. This work advances the annotation of the canine AR loci and looks into breed-specific features of the loci. Bioinformatic analysis of unbiased RNA sequence data was used to complete the annotation of the canine AR genes. This annotation was used to query 107 whole genome sequences from 19 breeds and identified over 5500 alleles across the 550 genes of the seven AR loci: the IG heavy, kappa, and lambda loci; and the TR alpha, beta, gamma, and delta loci. Of note was the discovery that half of the IGK variable (V) genes were located downstream of, and inverted with respect to, the rest of the locus. Analysis of the germline sequences of all the AR V genes identified greater conservation between dog and human than mouse with either. This work brings our understanding of the genetic diversity and expression of AR in dogs to the same completeness as that of mice and men, making it the third species to have all AR loci comprehensively and accurately annotated. The large number of germline sequences serves as a reference for future studies, and has allowed statistically powerful conclusions to be drawn on the pressures that have shaped these loci.

Endotracheal tube placement during computed tomography of brachycephalic dogs alters upper airway dimensional measurements.

Computed tomography (CT) is used to document upper airway lesions in dogs with brachycephalic obstructive airway syndrome. The presence of an endotracheal tube during CT scanning is often required for general anesthesia. We hypothesized that the endotracheal tube placement would change the soft tissue dimensions of the upper airway. The aims of this prospective, method comparison study were to evaluate the reliability of the previously reported upper airway CT measurements with endotracheal tube placement, and to propose measurements that are minimally affected by the endotracheal tube. Twenty brachycephalic dogs were included in this study. Each dog underwent head/neck CT with an endotracheal tube, followed by a second scan without the endotracheal tube. Ten measurements of the soft palate, nasopharynx, and trachea were performed. Tracheal dimension was significantly larger with the endotracheal tube compared to without, whereas the soft palate cross-sectional area was significantly smaller with the endotracheal tube than without the endotracheal tube. The influence of the endotracheal tube on the caudal nasopharynx cross-sectional (transverse-sectional) area varied with a mean proportional absolute difference of 35%. Rostral soft palate thickness, tracheal perimeter, and cross-sectional area of the rostral nasopharynx were the measurements least affected by the endotracheal tube (intraclass correlation coefficient = 0.964, 0.967, and 0.951, respectively). Therefore, we proposed that these three measurements may be most useful for future brachycephalic obstructive airway syndrome studies that require CT scanning of intubated animals. However, with endotracheal tube placement, measurements of soft palate length, caudal nasopharyngeal cross-sectional area, and trachea height and width may not be reliable.

Outcomes and prognostic factors of surgical treatments for brachycephalic obstructive airway syndrome in 3 breeds.

OBJECTIVE: To determine prognostic indicators for the surgical treatment of brachycephalic obstructive airway syndrome (BOAS) and to compare the prognosis of 2 multilevel surgical procedures. STUDY DESIGN: Prospective clinical study. SAMPLE POPULATION: Client-owned pugs, French bulldogs, and bulldogs (n = 50). METHODS: Noninvasive whole-body barometric plethysmography (WBBP) was used to assess respiratory function before, 1 month and 6 months after upper airway corrective surgery. Postoperatively, BOAS indices (ie, ascending severity score generated from WBBP data, 0%-100%) that equaled to or exceeded the cut-off values of BOAS in the diagnostic models were considered to have a "poor prognosis." A multivariate logistic regression was used to assess predictors for prognosis. RESULTS: The median BOAS indices decreased after surgery (from 76% to 63%, P < .0001), although dogs with indices in this range would still be considered clinically affected. Age (odds ratios [OR] = 0.96, 95% confidence interval [CI]: 0.93-0.99, P < .05), body condition (OR = 0.06, 95% CI: 0.01-0.39, P < .01), laryngeal collapse (OR = 6.1, 95% CI: 1-37.22, P < .05), and surgical techniques (OR = 7.94, 95% CI: 1.17-54.01, P < .05) were associated with postoperative prognosis. The multivariate model suggests modified multilevel surgery (MMS) may have a better outcome than traditional multilevel surgery (TMS) (P = .034). The positive predictive value of the logistic model was 84% (95% CI: 68-94%) and the area under the receiver operating characteristic (ROC) curve was 89% (95% CI: 78-99%, P <.0001). CONCLUSIONS: Younger age, normal body condition, presence of laryngeal collapse, and treatment with TMS were negative prognostic factors after surgical treatment of BOAS. MMS is recommended, particularly in dogs with a higher probability of poor prognosis.

Canine genome assembly correction facilitates identification of a MAP9 deletion as a potential age of onset modifier for RPGRIP1-associated canine retinal degeneration.

Retinal degeneration (RD) in the Miniature Long Haired Dachshund (MLHD) is a cone-rod dystrophy resulting in eventual blindness in affected individuals. In a previous study, a 44-nucleotide insertion (ins44) in exon 2 of RPGRIP1 was associated with RD. However, results on an extended population of MLHD revealed a variable RD onset age for ins44 homozygous dogs. Further investigations using a genome-wide association study comparing early onset and late onset RD cases identified an age of onset modifying locus for RD, approximately 30 Mb upstream of RPGRIP1 on chr15. In this investigation, target enriched sequencing identified a MAP9 deletion spanning approximately 22 kb associated with early RD onset. Identification of the deletion required correction to the CanFam3.1 genome build as canine MAP9 is part of a historic tandem duplication, resulting in incomplete assembly of this genome region. The deletion breakpoints were identified in MAP9 intron 10 and in a downstream partial MAP9 pseudogene. The fusion of these two genes, which we have called MAP9 EORD (microtubule-associated protein, early onset retinal degeneration), is in frame and is expressed at the RNA level, with the 3' region containing several predicted deleterious variants. We speculate that MAP9 associates with α-tubulin in the basal body of the cilium. RPGRIP1 is also known to locate to the cilium, where it is closely associated with RPGR. RPGRIP1 mutations also cause redistribution of α-tubulin away from the ciliary region in photoreceptors. Hence, a MAP9 partial deficit is a particularly attractive candidate to synergise with a partial RPGRIP1 deficit to cause a more serious disease.

Histological and Histopathological Features of the Third Metacarpal/Tarsal Parasagittal Groove and Proximal Phalanx Sagittal Groove in Thoroughbred Horses with Racing History.

Information regarding the histopathology of the proximal phalanx (P1) sagittal groove in racehorses is limited. Twenty-nine cadaver limbs from nine Thoroughbred racehorses in racing/race-training underwent histological examination. Histological specimens of the third metacarpal/metatarsal (MC3/MT3) parasagittal grooves and P1 sagittal grooves were graded for histopathological findings in hyaline cartilage (HC), calcified cartilage (CC), and subchondral plate and trabecular bone (SCB/TB) regions. Histopathological grades were compared between (1) fissure and non-fissure locations observed in a previous study and (2) dorsal, middle, and palmar/plantar aspects. (1) HC, CC, and SCB/TB grades were more severe in fissure than non-fissure locations in the MC3/MT3 parasagittal groove (p < 0.001). SCB/TB grades were more severe in fissure than non-fissure locations in the P1 sagittal groove (p < 0.001). (2) HC, CC, and SCB/TB grades including SCB collapse were more severe in the palmar/plantar than the middle aspect of the MC3/MT3 parasagittal groove (p < 0.001). SCB/TB grades including SCB collapse were more severe in the dorsal and middle than the palmar/plantar aspect of the P1 sagittal groove (p < 0.001). Histopathology in the SCB/TB region including bone fatigue injury was related to fissure locations, the palmar/plantar MC3/MT3 parasagittal groove, and the dorsal P1 sagittal groove.

Comparison of cone-beam and fan-beam computed tomography and low-field magnetic resonance imaging for detection of proximal phalanx dorsoproximal osteochondral defects.

BACKGROUND: Dorsoproximal osteochondral defects commonly affect the proximal phalanx, but information about diagnosis on computed tomography (CT) and magnetic resonance imaging (MRI) is limited. OBJECTIVES: To assess CT and MRI diagnoses of osteochondral defects, describe the lesions and compare sensitivity and specificity of the modalities using macroscopic pathology as gold standard. STUDY DESIGN: Cross-sectional study. METHODS: Thirty-five equine cadaver limbs underwent standing cone-beam CT (CBCT), fan-beam CT (FBCT), low-field MRI and pathological examination. CT and MR images were examined for proximal phalanx dorsomedial and dorsolateral eminence osteochondral defects. Defect dimensions were measured. Imaging diagnoses and measurements were compared with macroscopic examination. RESULTS: Fifty-six defects were seen over 70 potential locations. On CBCT and FBCT, osteochondral defects appeared as subchondral irregularity/saucer-shaped defects. On MRI, osteochondral defects were a combination of articular cartilage defect on dorsal images and subchondral flattening/irregularity on sagittal images. Subchondral thickening and osseous short tau inversion recovery hyperintensity were found concurrent with osteochondral defects. Compared with pathological examination, the sensitivity and specificity of diagnosis were 86% (95% confidence interval [95% CI] 75%-93%) and 64% (95% CI 38%-85%) for FBCT; 64% (95% CI 51%-76%) and 71% (95% CI 46%-90%) for CBCT; and 52% (95% CI 39%-65%) and 71% (95% CI 46%-90%) for MRI. Sensitivity of all modalities increased with defect size. Macroscopic defect dimensions were strongly correlated with CBCT (r = 0.76, p < 0.001) and moderately correlated with FBCT and MRI (r = 0.65, p < 0.001). Macroscopic measurements were significantly greater than all imaging modality dimensions (p < 0.001), potentially because macroscopy included articular cartilage pathology. MAIN LIMITATIONS: Influence of motion artefact could not be assessed. CONCLUSIONS: Osteochondral defects could be visualised using both CT and MRI with sensitivity increasing with defect size. Diagnostic performance was best using FBCT, followed by CBCT then MRI, but CBCT-measured defect size best correlated with macroscopic examination. MRI provided useful information on fluid signal associated with defects, which could represent active pathology.

Comparison of cone-beam and fan-beam computed tomography and low-field magnetic resonance imaging for detection of palmar/plantar osteochondral disease in Thoroughbred horses.

BACKGROUND: Palmar/plantar osteochondral disease (POD) of the metacarpal/tarsal condyles is a common pathological finding in racehorses. OBJECTIVE: To compare diagnoses, imaging details, and measurements of POD lesions between cone-beam computed tomography CT (CBCT), fan-beam CT (FBCT), and low-field magnetic resonance imaging (MRI) using macroscopic pathology as a gold standard. STUDY DESIGN: Cross-sectional study. METHODS: Thirty-five cadaver limbs from 10 horses underwent CBCT, FBCT, MRI, and macroscopic examination. CT and MR images were examined for presence of POD, imaging details of POD, and measurements of POD dimensions and areas. Imaging diagnoses, details, and measurements were compared with macroscopic examination and between modalities. RESULTS: Forty-eight POD lesions were seen over 70 condyles. Compared with macroscopic examination the sensitivity and specificity of diagnosis were 95.8% (CI95 = 88%-99%) and 63.6% (CI95 = 43%-81%) for FBCT, 85.4% (CI95 = 74%-94%) and 81.8% (CI95 = 63%-94%) for CBCT, and 69.0% (CI95 = 54%-82%) and 71.4% (CI95 = 46%-90%) for MRI. Inter-modality agreement on diagnosis was moderate between CBCT and FBCT (κ = 0.56, p < 0.001). POD was identified on CT as hypoattenuating lesions with surrounding hyperattenuation and on MRI as either T1W, T2*W, T2W, and STIR hyperintense lesions or T1W and T2*W heterogeneous hypointense lesions with surrounding hypointensity. Agreement on imaging details between CBCT and FBCT was substantial for subchondral irregularity (κ = 0.61, p < 0.001). Macroscopic POD width strongly correlated with MRI (r = 0.81, p < 0.001) and CBCT (r = 0.79, p < 0.001) and moderately correlated with FBCT (r = 0.69, p < 0.001). Macroscopic POD width was greater than all imaging modality (p < 0.001). MAIN LIMITATIONS: Effect of motion artefact in live horse imaging could not be assessed. CONCLUSIONS: All imaging modalities were able to detect POD lesions, but underestimated lesion size. The CT systems were more sensitive, but the differing patterns of signal intensity may suggest that MRI can detect changes associated with POD pathological status or severity. The image features observed by CBCT and FBCT were similar.

Three-Dimensional Imaging and Histopathological Features of Third Metacarpal/Tarsal Parasagittal Groove and Proximal Phalanx Sagittal Groove Fissures in Thoroughbred Horses.

Fissure in the third metacarpal/tarsal parasagittal groove and proximal phalanx sagittal groove is a potential prodromal pathology of fracture; therefore, early identification and characterisation of fissures using non-invasive imaging could be of clinical value. Thirty-three equine cadaver limbs underwent standing cone-beam (CB) computed tomography (CT), fan-beam (FB) CT, low-field magnetic resonance imaging (MRI), and macro/histo-pathological examination. Imaging diagnoses of fissures were compared to microscopic examination. Imaging features of fissures were described. Histopathological findings were scored and compared between locations with and without fissures on CT. Microscopic examination identified 114/291 locations with fissures. The diagnostic sensitivity and specificity were 88.5% and 61.3% for CBCT, 84.1% and 72.3% for FBCT, and 43.6% and 85.2% for MRI. Four types of imaging features of fissures were characterised on CT: (1) CBCT/FBCT hypoattenuating linear defects, (2) CBCT/FBCT striated hypoattenuated lines, (3) CBCT/FBCT subchondral irregularity, and (4) CBCT striated hypoattenuating lines and FBCT subchondral irregularity. Fissures on MRI appeared as subchondral bone hypo-/hyperintense defects. Microscopic scores of subchondral bone sclerosis, microcracks, and collapse were significantly higher in locations with CT-identified fissures. All imaging modalities were able to identify fissures. Fissures identified on CT were associated with histopathology of fatigue injuries.

Identification of Heterotopic Mineralization and Adjacent Pathology in the Equine Fetlock Region by Low-Field Magnetic Resonance Imaging, Cone-Beam and Fan-Beam Computed Tomography.

Heterotopic mineralization in equine distal limbs has been considered an incidental finding and little is known about its imaging features. The study aimed to identify heterotopic mineralization and adjacent pathology in the fetlock region with cone-beam (CB) computed tomography (CT), fan-beam (FB) CT, and low-field magnetic resonance imaging (MRI). Images from 12 equine cadaver limbs were examined for heterotopic mineralization and adjacent pathology and verified by macro-examination. Retrospective review of the CBCT/MR images from 2 standing horses was also included. CBCT and FBCT identified twelve mineralization's with homogeneous hyperattenuation: oblique-sesamoidean-ligament (5) without macroscopic abnormality; deep-digital-flexor-tendon (1) and suspensory-branch (6) with macroscopic abnormalities. MRI failed to identify all mineralization's, but detected suspensory branch splitting, and T2 and STIR hyperintensity in 4 suspensory-branches and 3 oblique-sesamoidean-ligaments. Macro-examination found corresponding disruption/splitting and discoloration. All modalities identified 7 ossified fragments showing cortical/trabecular pattern: capsular (1), palmar sagittal ridge (1), proximal phalanx (2) without macroscopic abnormality, and proximal sesamoid bones (3). On MRI, fragments were most identifiable on T1 images. All abaxial avulsions had suspensory-branch splitting on T1 images with T2 and STIR hyperintensity. Macro-examination showed ligament disruption/splitting and discoloration. Suspensory-branch/intersesamoidean ligament mineralization's were identified by CBCT in standing cases; 1 had associated T2 hyperintensity. Both CT systems were generally superior in identifying heterotopic mineralization's than MRI, while MRI provided information on soft tissue pathology related to the lesions, which may be important for management.

Genome-wide association study in RPGRIP1(-/-) dogs identifies a modifier locus that determines the onset of retinal degeneration.

Cone-rod dystrophy (CRD) is a form of inherited retinal degeneration (RD) causing blindness in man as well as in several breeds of dog. Previously, a 44 bp insertion in RPGRIP1 (retinitis pigmentosa GTPase regulator interacting protein-1) was associated with a recessive early-onset CRD (cone-rod dystrophy 1, cord1) in a Miniature longhaired dachshund (MLHD) research colony. Yet in the MLHD pet population, extensive range of the onset age has been observed among RD cases, with some RPGRIP1(-/-) dogs lacking obvious clinical signs. Phenotypic variation has been known in human homologous diseases, including retinitis pigmentosa and Leber congenital amaurosis, indicating possible involvement of modifiers. To explore additional genetic loci associated with the phenotypic variation observed in MLHDs, a genome-wide association study was carried out using Canine SNP20 arrays in 83 RPGRIP1(-/-) MLHDs with variable ages of onset or no clinical abnormality. Using these samples, comparison of 31 early-onset RD cases against 49 controls (15 late-onset RD and 34 normal dogs combined) identified a strong association (P = 5.05 × 10(-13)) at a single locus on canine chromosome 15. At this locus, the majority of early-onset RD cases but few of the controls were homozygous for a 1.49 Mb interval containing ~11 genes. We conclude that homozygosity at both RPGRIP1 and the newly mapped second locus is necessary to develop early-onset RD, whereas RPGRIP1(-/-) alone leads to late-onset RD or no apparent clinical phenotype. This study establishes a unique model of canine RD requiring homozygous mutations at two distinct genetic loci for the manifestation of early-onset RD.

Development and application of a next-generation sequencing protocol and bioinformatics pipeline for the comprehensive analysis of the canine immunoglobulin repertoire.

Profiling the adaptive immune repertoire using next generation sequencing (NGS) has become common in human medicine, showing promise in characterizing clonal expansion of B cell clones through analysis of B cell receptors (BCRs) in patients with lymphoid malignancies. In contrast, most work evaluating BCR repertoires in dogs has employed traditional PCR-based approaches analyzing the IGH locus only. The objectives of this study were to: (1) describe a novel NGS protocol to evaluate canine BCRs; (2) develop a bioinformatics pipeline for processing canine BCR sequencing data; and (3) apply these methods to derive insights into BCR repertoires of healthy dogs and dogs undergoing treatment for B-cell lymphoma. RNA from peripheral blood mononuclear cells of healthy dogs (n = 25) and dogs newly diagnosed with intermediate-to-large B-cell lymphoma (n = 18) with intent to pursue chemotherapy was isolated, converted into cDNA and sequenced by NGS. The BCR repertoires were identified and quantified using a novel analysis pipeline. The IGK repertoires of the healthy dogs were far less diverse compared to IGL which, as with IGH, was highly diverse. Strong biases at key positions within the CDR3 sequence were identified within the healthy dog BCR repertoire. For a subset of the dogs with B-cell lymphoma, clonal expansion of specific IGH sequences pre-treatment and reduction post-treatment was observed. The degree of expansion and reduction correlated with the clinical outcome in this subset. Future studies employing these techniques may improve disease monitoring, provide earlier recognition of disease progression, and ultimately lead to more targeted therapeutics.

ADAMTS17 mutation associated with primary lens luxation is widespread among breeds.

Primary lens luxation (PLL) is a well-recognized, painful and potentially blinding inherited ocular condition in dogs. We screened PLL-affected dogs of 30 different breeds, to identify those which carried a previously described c.1473+1 G>A mutation in ADAMTS17 that is associated with PLL in Miniature Bull terriers, Lancashire Heelers, and Jack Russell terriers. This ADAMTS17 mutation was identified in PLL-affected dogs from 14 additional breeds. PLL-affected dogs from some breeds (most notably the Shar pei and the Brittany spaniel) did not carry the G1473+1A ADAMTS17 mutation, indicating they must suffer from a genetically distinct form of the condition. We also estimated the frequency of this ADAMTS17 mutation in some of the breeds. Our findings indicate the mutation segregates in a large number of different breeds of dog, many of which are terriers or breeds with terrier co-ancestry, but some of which have more diverse origins. Our results also indicate that the mutation is present at high frequency within most of the breeds in which it segregates. In the miniature bull terrier breed estimates of mutation frequency ranged from 0.27 to 0.39, corresponding to 7.3-15.2% PLL-affected dogs in this breed. We also identified an increased risk of PLL associated with heterozygosity at ADAMTS17, suggesting that carriers carry a low risk of developing PLL.

A Missense Variant in the Bardet-Biedl Syndrome 2 Gene (BBS2) Leads to a Novel Syndromic Retinal Degeneration in the Shetland Sheepdog.

Canine progressive retinal atrophy (PRA) describes a group of hereditary diseases characterized by photoreceptor cell death in the retina, leading to visual impairment. Despite the identification of multiple PRA-causing variants, extensive heterogeneity of PRA is observed across and within dog breeds, with many still genetically unsolved. This study sought to elucidate the causal variant for a distinct form of PRA in the Shetland sheepdog, using a whole-genome sequencing approach. Filtering variants from a single PRA-affected Shetland sheepdog genome compared to 176 genomes of other breeds identified a single nucleotide variant in exon 11 of the Bardet-Biedl syndrome-2 gene (BBS2) (c.1222G>C; p.Ala408Pro). Genotyping 1386 canids of 155 dog breeds, 15 cross breeds and 8 wolves indicated the c.1222G>C variant was only segregated within Shetland sheepdogs. Out of 505 Shetland sheepdogs, seven were homozygous for the variant. Clinical history and photographs for three homozygotes indicated the presence of a novel phenotype. In addition to PRA, additional clinical features in homozygous dogs support the discovery of a novel syndromic PRA in the breed. The development and utilization of a diagnostic DNA test aim to prevent the mutation from becoming more prevalent in the breed.

Phenotypic variation and genotype-phenotype discordance in canine cone-rod dystrophy with an RPGRIP1 mutation.

PURPOSE: Previously, a 44 bp insertion in exon 2 of retinitis pigmentosa GTPase interacting protein 1 (RPGRIP1) was identified as the cause of cone-rod dystrophy 1 (cord1), a recessive form of progressive retinal atrophy (PRA) in the Miniature Longhaired Dachshund (MLHD), a dog model for Leber congenital amaurosis. The cord1 locus was mapped using MLHDs from an inbred colony with a homogeneous early onset disease phenotype. In this paper, the MLHD pet population was studied to investigate phenotypic variation and genotype-phenotype correlation. Further, the cord1 locus was fine-mapped using PRA cases from the MLHD pet population to narrow the critical region. Other dog breeds were also screened for the RGPRIP1 insertion. METHODS: This study examined phenotypic variation in an MLHD pet population that included 59 sporadic PRA cases and 18 members of an extended family with shared environment and having six PRA cases. Ophthalmologic evaluations included behavioral abnormalities, responses to menace and light, fundoscopy, and electroretinography (ERG). The RPGRIP1 insertion was screened for in all cases and 200 apparently normal control MLHDs and in 510 dogs from 66 other breed. To fine-map the cord1 locus in the MLHD, 74 PRA cases and 86 controls aged 4 years or more were genotyped for 24 polymorphic markers within the previously mapped cord1 critical region of 14.15 Mb. RESULTS: Among sporadic PRA cases from the MLHD pet population, the age of onset varied from 4 months to 15 years old; MLHDs from the extended family also showed variable onset and rate of progression. Screening for the insertion in RPGRIP1 identified substantial genotype-phenotype discordance: 16% of controls were homozygous for the insertion (RPGRIP1(-/-)), while 20% of PRA cases were not homozygous for it. Four other breeds were identified to carry the insertion including English Springer Spaniels and Beagles with insertion homozygotes. The former breed included both controls and PRA cases, yet in the latter breed, cone ERG was undetectable in two dogs with no clinically apparent visual dysfunction. Notably, the insertion in the Beagles was a longer variant of that seen in the other breeds. Fine-mapping of the cord1 locus narrowed the critical region on CFA15 from 14.15 Mb to 1.74 Mb which still contains the RPGRIP1 gene. CONCLUSIONS: Extensive phenotypic variations of onset age and progression rate were observed in PRA cases of the MLHD pet population. The insertion in RPGRIP1 showed the strongest association with the disease, yet additional as well as alternative factors may account for the substantial genotype-phenotype discordance.

Disruption of chromosome 11 in canine fibrosarcomas highlights an unusual variability of CDKN2B in dogs.

BACKGROUND: In dogs in the western world neoplasia constitutes the most frequently diagnosed cause of death. Although there appear to be similarities between canine and human cancers, rather little is known about the cytogenetic and molecular alterations in canine tumours. Different dog breeds are susceptible to different types of cancer, but the genetic basis of the great majority of these predispositions has yet to be discovered. In some retriever breeds there is a high incidence of soft tissue sarcomas and we have previously reported alterations of chromosomes 11 and 30 in two poorly differentiated fibrosarcomas. Here we extend our observations and present a case report on detail rearrangements on chromosome 11 as well as genetic variations in a tumour suppressor gene in normal dogs. RESULTS: BAC hybridisations on metaphases of two fibrosarcomas showed complex rearrangements on chromosome 11, and loss of parts of this chromosome. Microsatellite markers on a paired tumour and blood DNA pointed to loss of heterozygosity on chromosome 11 in the CDKN2B-CDKN2A tumour suppressor gene cluster region. PCR and sequencing revealed the homozygous loss of coding sequences for these genes, except for exon 1beta of CDKN2A, which codes for the N-terminus of p14ARF. For CDKN2B exon 1, two alleles were observed in DNA from blood; one of them identical to the sequence in the dog reference genome and containing 4 copies of a 12 bp repeat found only in the canine gene amongst all species so far sequenced; the other allele was shorter due to a missing copy of the repeat. Sequencing of this exon in 141 dogs from 18 different breeds revealed a polymorphic region involving a GGC triplet repeat and a GGGGACGGCGGC repeat. Seven alleles were recorded and sixteen of the eighteen breeds showed heterozygosity. CONCLUSION: Complex chromosome rearrangements were observed on chromosome 11 in two Labrador retriever fibrosarcomas. The chromosome alterations were reflected in the loss of sequences corresponding to two tumour suppressor genes involved in cell-cycle progression. Sequencing of CDKN2B across many different breeds revealed a widespread polymorphism within the first exon of the gene, immediately before the ankyrin coding sequences.

Whole Genome Sequencing of Giant Schnauzer Dogs with Progressive Retinal Atrophy Establishes NECAP1 as a Novel Candidate Gene for Retinal Degeneration.

Canine progressive retinal atrophies (PRA) are genetically heterogeneous diseases characterized by retinal degeneration and subsequent blindness. PRAs are untreatable and affect multiple dog breeds, significantly impacting welfare. Three out of seven Giant Schnauzer (GS) littermates presented with PRA around four years of age. We sought to identify the causal variant to improve our understanding of the aetiology of this form of PRA and to enable development of a DNA test. Whole genome sequencing of two PRA-affected full-siblings and both unaffected parents was performed. Variants were filtered based on those segregating appropriately for an autosomal recessive disorder and predicted to be deleterious. Successive filtering against 568 canine genomes identified a single nucleotide variant in the gene encoding NECAP endocytosis associated 1 (NECAP1): c.544G>A (p.Gly182Arg). Five thousand one hundred and thirty canids of 175 breeds, 10 cross-breeds and 3 wolves were genotyped for c.544G>A. Only the three PRA-affected GS were homozygous (allele frequency in GS, excluding proband family = 0.015). In addition, we identified heterozygotes belonging to Spitz and Dachshund varieties, demonstrating c.544G>A segregates in other breeds of German origin. This study, in parallel with the known retinal expression and role of NECAP1 in clathrin mediated endocytosis (CME) in synapses, presents NECAP1 as a novel candidate gene for retinal degeneration in dogs and other species.