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.

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.

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.

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.

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.

Secreted frizzled-related protein 2 (SFRP2) is highly expressed in canine mammary gland tumors but not in normal mammary glands.

Canine mammary gland tumor (MGT) is the commonest tumor in female dogs and a good animal model of human breast cancer. A group of newly identified genes encoding secreted frizzled-related proteins (SFRP) have been implicated in apoptosis regulation and tumorigenesis. Canine mammary tissues from 50 spontaneous MGTs and 10 normal mammary glands (MGs) were obtained from surgically excised specimens and analyzed for expression of SFRP2, beta-catenin, and cyclin D1. By RT-PCR and in situ hybridization, SFRP2 gene was found abundantly expressed in neoplastic mammary tissues but not in normal mammary tissues, suggesting that SFRP2 may contribute as a tumor marker in canine MGTs. By immunohistochemical staining, the immunoreactivity of the SFRP2 protein was detected in more diverse areas than SFRP2 mRNA expression, including nuclei or/and cytoplasm and extracellular matrix of the tumor. In tumor masses, beta-catenin lost its tight association with the membrane and diffused into the nucleus. The expression of beta-catenin (79.4% positive) and cyclin D1 (71.4% positive) was also increased in MGTs. In the course of tumor progression, SFRP2 mRNA ( p < 0.05) and beta-catenin protein ( p < 0.01) steadily increased but not in cyclin D1. The level of SFRP2 was linearly correlated with its downstream target beta-catenin ( p < 0.05), but not correlated with cyclin D1 ( p < 0.5). As revealed in this study, the exclusive overexpression of SFRP2 in canine MGTs suggests that SFRP2 is a potential candidate gene for further investigation of mammary tumorigenesis and complex etiology of the canine model of mammary neoplasms.

Karyotype of canine soft tissue sarcomas: a multi-colour, multi-species approach to canine chromosome painting.

Many canine tumour types represent useful models for tumours also found in humans. Studies of chromosomal abnormalities in canine tumours have been impeded by the complexity of the canine karyotype (2n = 78), which has made accurate identification of rearranged chromosomes difficult and laborious. To overcome this difficulty we have developed a seven-colour paint system for canine chromosomes, with six sets of chromosome paints covering all chromosomes except Y. Several pairs of canine autosomes co-locate in the flow karyotype. To distinguish these autosomes from each other, paint sets were supplemented with chromosomes of red fox and Japanese raccoon dog. Paints were used in fluorescence in-situ hybridization to analyse karyotypes in fourteen canine soft tissue sarcomas. Rearranged karyotypes were observed in seven tumours, but there was evidence for loss of rearrangement during tissue culture. Five tumours had rearrangements involving four chromosomes or fewer; one, a chondrosarcoma, had lost seven chromosomes whilst the last, a spindle cell sarcoma, had rearrangements involving eighteen chromosome pairs. The paint sets described here facilitate the complete cytogenetic analysis of balanced translocations and other inter-chromosomal rearrangements in canine tumours. We believe that this is the first canine tumour series to be subjected to this level of analysis.