BACKGROUND:Limited data exist on intervertebral disk disease (IVDD) prevalence and risk factors in English cocker spaniels. HYPOTHESIS/OBJECTIVES:IVDD risk factors and prevalence vary between breeds and within sub-populations. ANIMALS:Two thousand six hundred fifty-four English cocker spaniels. METHODS:An online survey investigating prevalence and factors associated with IVDD was distributed via the UK Kennel Club to registered English cocker spaniel owners (November 14, 2022 to February 2, 2023). Prevalence estimates with 95% confidence intervals were calculated (Wilson score interval). Descriptive statistics were applied to demographic, exercise, and diet variables. Univariable associations were explored using unadjusted odds ratios with 95% CI (Wald method). RESULTS:Overall IVDD prevalence was 5.73% (95% CI, 4.82-6.62) and was greater in the show [8.99% (95% CI, 7.30-11.03)] than the working [3.44% (95% CI, 2.61-4.49)] dogs. Dogs in the show group were taller relative to their length compared to those in the working group. The lumbar region accounted for 53.02% (n = 79) cases, with an onset time most frequently of less than one day (40.14%, n = 59). Males were at greater odds of IVDD in our study compared to females (OR:14.39, 95% CI, 7.30-28.36), with neutered males or females at greater odds compared to the entire dogs (OR:7.9, 95% CI, 4.25-14.67). CONCLUSIONS AND CLINICAL IMPORTANCE:IVDD is common in English cocker spaniels, with a higher prevalence in the show dogs.

BACKGROUND:Hereditary neurodegenerative diseases occur in dogs, and a molecular diagnosis can be of value for treatment and prevention. HYPOTHESIS/OBJECTIVES:To describe the clinical presentation of a novel encephalopathy in 4 related Labrador Retrievers. To identify a candidate causal variant for the disease using whole genome sequencing (WGS). ANIMALS:Four related Labrador Retrievers presenting between 4 and 9 months of age. METHODS:Case information and clinical workup were recorded for the 4 dogs in this case series. Two cases underwent WGS to identify candidate causal variants that were validated by genotyping Labradors related and unrelated to the cases, and by screening WGS of other breeds/canid species. RESULTS:Clinical signs in cases included paroxysmal anxiety episodes, and focal and generalized epileptic seizures. Interictal clinical and neurological examinations were normal in all cases. Magnetic resonance imaging of the brain documented bilaterally symmetrical, T2-weighted image hyperintense, T1-weighted image isointense, and non-contrast-enhancing lesions within the lentiform nuclei, caudal colliculi, substantia nigra, and cerebellar nuclei. Investigations to exclude underlying nutritional, toxic, and metabolic causes were within normal limits. All cases had 2 copies of a missense variant in the aldehyde dehydrogenase 5 family member A1 (ALDH5A1) gene that segregated as expected in the family group and was absent in 70 unrelated Labradors and 2339 WGS of multiple breeds/canids. CONCLUSIONS AND CLINICAL IMPORTANCE:The prognosis of this novel hereditary encephalopathy in a family of Labradors appears fair with reasonable clinical response to administration of anti-seizure drugs. A missense variant in ALDH5A1 has been identified as a candidate causal variant for the disease in these dogs.

Obesity is a heritable disease, but its genetic basis is incompletely understood. Canine population history facilitates trait mapping. We performed a canine genome-wide association study for body condition score-a measure of obesity-in 241 Labrador retrievers. Using a cross-species approach, we showed that canine obesity genes are also associated with rare and common forms of obesity in humans. The lead canine association was within the gene DENN domain containing 1B (DENND1B). Each copy of the alternate allele was associated with ~7.5% greater body fat. We demonstrate a role for this gene in regulating signaling and trafficking of melanocortin 4 receptor, a critical controller of energy homeostasis. Thus, canine genetics identified obesity genes and mechanisms relevant to both dogs and humans.

Primary hereditary cataract affects many purebred domestic dog breeds and is a major cause of visual impairment in dogs. Cataracts are common in Northern breeds such as the Siberian Husky, Alaskan Malamute and Samoyed, but their aetiology is currently unknown. Only two genetic loci are known to be causally related to primary hereditary cataracts in the dog. To search for genetic loci associated with cataracts in Northern breeds, we used a genome-wide association study approach in three breeds-Siberian Husky, Alaskan Malamute and Samoyed. Cases were defined as dogs with bilateral posterior polar subcapsular cataracts and controls were at least four years of age with no evidence of cataracts or other ocular abnormality. We found a genome-wide statistical association for cataracts in the Siberian Husky on canine chromosome 18 (P-value: 1.1 x 10 - 7), which was independently replicated in a second larger case-control set (P-value 9.8 x 10 - 29). The Samoyed breed also showed evidence for association in the same genomic region (P-value: 2.4 x 10 - 5). We subsequently used targeted resequencing of the associated region (6.5 Mb) in ten Siberian Huskies and whole genome sequencing of a Husky, Malamute, Samoyed and Norwegian Buhund case to conduct fine-mapping and screen for candidate causal variants. These analyses identified a region of linkage disequilibrium in the four breeds containing common variants in the carnitine palmitoyltransferase 1A (CPT1A) gene that are strongly associated with bilateral posterior polar subcapsular cataracts in the Siberian Husky, Samoyed, Icelandic Sheepdog and Norwegian Buhund and we demonstrate that CPT1A is expressed in the dog lens and retina through RNAseq. Our findings represent a novel locus for cataracts in dogs. However, further work is needed to elucidate the pathophysiology underlying the association between CPT1A and cataracts in Northern breeds.

Retinopathy with vitamin E deficiency is a familial disease in the English Cocker Spaniel dog breed. Ophthalmic abnormalities observed in retinopathy with vitamin E deficiency-affected English Cocker Spaniel include lipofuscin granule deposition within the tapetal fundus and subsequent retinal degeneration resulting in visual deficits. Affected dogs may also exhibit neurological signs that include ataxia and hindlimb proprioceptive deficits. In all cases, circulating plasma concentrations of alpha-tocopherol are low. This study sought to investigate the genetic basis of retinopathy with vitamin E deficiency in the English Cocker Spaniel breed. We undertook a genome-wide association study comprising 30 English Cocker Spaniels with normal fundic examinations aged 6 years or older (controls) and 20 diagnosed with retinopathy with vitamin E deficiency (cases) and identified a statistically associated signal on chromosome 29 (Praw = 1.909 x 10-17). Whole genome sequencing of 2 cases identified a 102 bp deletion in exon 1 of the alpha-tocopherol transfer protein gene (TTPA), truncating the protein by 34 amino acids. The c.23_124del variant segregated with retinopathy with vitamin E deficiency in a total of 30 cases and 43 controls. Variants in TTPA are causal for ataxia with vitamin E deficiency in humans which is a phenotypically similar disease to retinopathy with vitamin E deficiency. The identification of the canine variant is extremely significant as the availability of a DNA test will allow for identification of presymptomatic dogs and early therapeutic intervention which may prevent development of retinopathy and improve neurological signs. Breeders can also use the DNA test to efficiently eradicate the disease from this breed.

Progressive retinal atrophies (PRAs) are a genetically heterogeneous group of inherited eye diseases that affect over 100 breeds of dog. The initial clinical sign is visual impairment in scotopic conditions, as a consequence of rod photoreceptor cell degeneration. Photopic vision degeneration then follows, due to progression of the disease to the cone photoreceptors, and ultimately results in complete blindness. Two full-sibling English Shepherds were diagnosed with PRA at approximately 5 years old and tested clear of all published PRA genetic variants. This study sought to identify the novel PRA-associated variant segregating in the breed. We utilised a combined approach of whole genome sequencing of the probands and homozygosity mapping of four cases and 22 controls and identified a short interspersed nuclear element within an alternatively spliced exon in FAM161A. The XP_005626197.1 c.17929_ins210 variant was homozygous in six PRA cases and heterozygous or absent in control dogs, consistent with a recessive mode of inheritance. The insertion is predicted to extend exon 4 by 39 aberrant amino acids followed by an early termination stop codon. PRA is intractable to treatment, so the development of a genetic screening test, based on the associated variant, is significant, because it provides dog breeders/owners with a means of reducing the frequency of the disease variant within this breed as well as minimising the risk of breeding puppies that will develop this blinding disease.

Multiocular defect has been described in different canine breeds, including the Old English Sheepdog. Affected dogs typically present with multiple and various ocular abnormalities. We carried out whole genome sequencing on an Old English Sheepdog that had been diagnosed with hereditary cataracts at the age of five and then referred to a board-certified veterinary ophthalmologist due to owner-reported visual deterioration. An ophthalmic assessment revealed that there was bilateral vitreal degeneration, macrophthalmos, and spherophakia in addition to cataracts. Follow-up consultations revealed cataract progression, retinal detachment, uveitis and secondary glaucoma. Whole genome sequence filtered variants private to the case, shared with another Old English Sheepdog genome and predicted to be deleterious were genotyped in an initial cohort of six Old English Sheepdogs (three affected by multiocular defect and three control dogs without evidence of inherited eye disease). Only one of the twenty-two variants segregated correctly with multiocular defect. The variant is a single nucleotide substitution, located in the collagen-type gene COL11A1, c.1775T>C, that causes an amino acid change, p.Phe1592Ser. Genotyping of an additional 14 Old English Sheepdogs affected by multiocular defect revealed a dominant mode of inheritance with four cases heterozygous for the variant. Further genotyping of hereditary cataract-affected Old English Sheepdogs revealed segregation of the variant in eight out of nine dogs. In humans, variants in the COL11A1 gene are associated with Stickler syndrome type II, also dominantly inherited.

BACKGROUNDBedlington terrier copper toxicosis (CT) is due to a homozygous exon deletion in COMMD1. CT also occurs in Bedlingtons lacking this deletion. An association with two ABCA12 single nuceotide polymorphism (SNP) splice variants was reported. Labrador retriever CT is associated with a missense mutation in ATP7B, and with a protective mutation in ATP7A.METHODSLiver and DNA samples from 24 affected and 10 unaffected Bedlingtons were assessed for copper and genetic variants. Allelic frequencies were compared. The ATP7B mutation frequency was investigated in 144 dogs of other breeds.RESULTSThe ABCA12 SNPs showed no differences between groups. The COMMD1 deletion was less frequent in unaffected than in affected dogs and in affected dogs post-2001 than pre-2001. The ATP7B mutation was more frequent in affected than unaffected Bedlingtons. Thirty-five of 144 dogs of other breeds were homo- or heterozygous for the ATP7B mutation. The ATP7A mutation was absent from Bedlingtons.LIMITATIONSClinical information and qualitative copper measurements were unavailable for most dogs.CONCLUSIONThe COMMD1 deletion remains present in Bedlington terriers but is no longer the primary cause of CT. ABCA12 SNPs were not associated with CT. The ATP7B:c.4358G>A mutation was significantly associated with Bedlington CT and was more common in dogs of this breed than in the 144 dogs of other breeds.

The equine disease strangles, which is characterized by the formation of abscesses in the lymph nodes of the head and neck, is one of the most frequently diagnosed infectious diseases of horses around the world. The causal agent, Streptococcus equi subspecies equi, establishes a persistent infection in approximately 10 % of animals that recover from the acute disease. Such 'carrier' animals appear healthy and are rarely identified during routine veterinary examinations pre-purchase or transit, but can transmit S. equi to naïve animals initiating new episodes of disease. Here, we report the analysis and visualization of phylogenomic and epidemiological data for 670 isolates of S. equi recovered from 19 different countries using a new core-genome multilocus sequence typing (cgMLST) web bioresource. Genetic relationships among all 670 S. equi isolates were determined at high resolution, revealing national and international transmission events that drive this endemic disease in horse populations throughout the world. Our data argue for the recognition of the international importance of strangles by the Office International des Épizooties to highlight the health, welfare and economic cost of this disease. The Pathogenwatch cgMLST web bioresource described herein is available for tailored genomic analysis of populations of S. equi and its close relative S. equi subspecies zooepidemicus that are recovered from horses and other animals, including humans, throughout the world. This article contains data hosted by Microreact.

Genotype imputation using a reference panel that combines high-density array data and publicly available whole genome sequence consortium variant data is potentially a cost-effective method to increase the density of extant lower-density array datasets. In this study, three datasets (two Border Collie; one Italian Spinone) generated using a legacy array (Illumina CanineHD, 173 662 SNPs) were utilised to assess the feasibility and accuracy of this approach and to gather additional evidence for the efficacy of canine genotype imputation. The cosmopolitan reference panels used to impute genotypes comprised dogs of 158 breeds, mixed breed dogs, wolves and Chinese indigenous dogs, as well as breed-specific individuals genotyped using the Axiom Canine HD array. The two Border Collie reference panels comprised 808 individuals including 79 Border Collies and 426 326 or 426 332 SNPs; and the Italian Spinone reference panel comprised 807 individuals including 38 Italian Spinoni and 476 313 SNPs. A high accuracy for imputation was observed, with the lowest accuracy observed for one of the Border Collie datasets (mean R-2 = 0.94) and the highest for the Italian Spinone dataset (mean R-2 = 0.97). This study's findings demonstrate that imputation of a legacy array study set using a reference panel comprising both breed-specific array data and multi-breed variant data derived from whole genomes is effective and accurate. The process of canine genotype imputation, using the valuable growing resource of publicly available canine genome variant datasets alongside breed-specific data, is described in detail to facilitate and encourage use of this technique in canine genetics.

Abstract 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.

A form of hereditary cerebellar ataxia has recently been described in the Norwegian Buhund dog breed. This study aimed to identify the genetic cause of the disease. Whole-genome sequencing of two Norwegian Buhund siblings diagnosed with progressive cerebellar ataxia was carried out, and sequences compared with 405 whole genome sequences of dogs of other breeds to filter benign common variants. Nine variants predicted to be deleterious segregated among the genomes in concordance with an autosomal recessive mode of inheritance, only one of which segregated within the breed when genotyped in additional Norwegian Buhunds. In total this variant was assessed in 802 whole genome sequences, and genotyped in an additional 505 unaffected dogs (including 146 Buhunds), and only four affected Norwegian Buhunds were homozygous for the variant. The variant identified, a T to C single nucleotide polymorphism (SNP) (NC_006585.3:g.88890674T>C), is predicted to cause a tryptophan to arginine substitution in a highly conserved region of the potassium voltage-gated channel interacting protein KCNIP4. This gene has not been implicated previously in hereditary ataxia in any species. Evaluation of KCNIP4 protein expression through western blot and immunohistochemical analysis using cerebellum tissue of affected and control dogs demonstrated that the mutation causes a dramatic reduction of KCNIP4 protein expression. The expression of alternative KCNIP4 transcripts within the canine cerebellum, and regional differences in KCNIP4 protein expression, were characterised through RT-PCR and immunohistochemistry respectively. The voltage-gated potassium channel protein KCND3 has previously been implicated in spinocerebellar ataxia, and our findings suggest that the Kv4 channel complex KCNIP accessory subunits also have an essential role in voltage-gated potassium channel function in the cerebellum and should be investigated as potential candidate genes for cerebellar ataxia in future studies in other species.

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.

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Seven Northern Inuit Dogs (NID) were diagnosed by pedigree analysis with an autosomal recessive inherited oculoskeletal dysplasia (OSD). Short-limbed dwarfism, angular limb deformities and a variable combination of macroglobus, cataracts, lens coloboma, microphakia and vitreopathy were present in all seven dogs, while retinal detachment was diagnosed in five dogs. Autosomal recessive OSD caused by COL9A3 and COL9A2 mutations have previously been identified in the Labrador Retriever (dwarfism with retinal dysplasia 1—drd1) and Samoyed dog (dwarfism with retinal dysplasia 2—drd2) respectively; both of those mutations were excluded in all affected NID. Nine candidate genes were screened in whole genome sequence data; only one variant was identified that was homozygous in two affected NID but absent in controls. This variant was a nonsense single nucleotide polymorphism in COL9A3 predicted to result in a premature termination codon and a truncated protein product. This variant was genotyped in a total of 1,232 dogs. All seven affected NID were homozygous for the variant allele (T/T), while 31/116 OSD-unaffected NID were heterozygous for the variant (C/T) and 85/116 were homozygous for the wildtype allele (C/C); indicating a significant association with OSD (p = 1.41x10-11). A subset of 56 NID unrelated at the parent level were analysed to determine an allele frequency of 0.08, estimating carrier and affected rates to be 15% and 0.6% respectively in NID. All 1,109 non-NID were C/C, suggesting the variant is rare or absent in other breeds. Expression of retinal mRNA was similar between an OSD-affected NID and OSD-unaffected non-NID. In conclusion, a nonsense variant in COL9A3 is strongly associated with OSD in NID, and appears to be widespread in this breed.

About this supplement These abstracts have been published as Canine Genetics and Epidemiology Volume 5 Supplement 2, 2018: Selected canine abstracts from the Companion Animal Genetic Health conference 2018 (CAGH 2018): Canine Genetics and Epidemiology. A meeting report from the conference has been published as Canine Genetics and Epidemiology Volume 5 Supplement 1, 2018 and is available online at https://doi.org/10.1186/ s40575-018-0061-0. Selected feline abstracts from the conference have been published as Irish Veterinary Journal Volume 71 Supplement 1, 2018 and are available online at https://doi.org/10.1186/s13620-018-0126-0.

and clinical homologies, with comparable subtypes 2 for which a BRAF-MBP gene fusion in one case using RNAseq and are currently for recurrence in the samples, as well as for the presence of this translocation in human glioma cases. Using affected cases and controls of the same breeds, to the identification of somatic alterations by transcriptome analyzes (RNAseq) and exome sequencing (WES) and to carry out genetic linkage and/or genetic association studies (GWAS) to identify genomic regions involved in predisposition. We will also search if and how the artificial selection that led to specific morphological characteristics, such as the shape of the dog ’ s skull (brachycephaly), would have also led to glioma predisposition. improvement in these traits, which is particularly important for HEART – heart conditions are believed to affect as many as 20% of Dobermans, and the symptoms of the disease often appear after a dog has already been used for breeding. Further, significant estimates obtained in the presented analyses indicate validity of the data, thus opening a new window of opportunity for genetic analyses of complex traits in numerically small breeds through the recruitment and collation of data by breed enthusiasts. each dog was measured at the withers. We used linear per allele re- gression to assess the association between ADAMTS17 mutations and height as a continuous variable, and linear regression and log- likelihood ratio tests to assess the shape of the association by comparing a general model with a linear per allele model. The mean heights of affected (n=21), carrier (n=84) and clear (n=122) Petit Basset Griffon Vendeen were 33.41 cm, 34.78 cm and 34.93 cm, respect- ively. The mean heights of affected (n=9), carrier (n=30) and clear (n=26) Shar Pei were 43.32 cm, 47.93 cm and 48.38 cm, respectively. Each breed-specific ADAMTS17 mutation showed a strong association with height in both breeds: Petit Basset Griffon Vendeen (P=7.9 x 10-3); Shar Pei (P=6.9 x 10-5). The shape of the associations ap-peared similar between the two breeds. In humans, ADAMTS17 af- fects skeletal development by modulating the extracellular matrix. A similar mechanism may be present in the dog. We speculate that se- lection for short stature might have inadvertently increased ADAMTS17 mutant allele frequencies and thus increased prevalence of primary open angle glaucoma in these breeds. and Epidemiology 2018, 5(Suppl 2): O5 In domestic dogs, the “ flat-faced ” brachycephalic head shape is a risk factor for developing the respiratory defect, Brachycephalic Obstructive Airway Syndrome (BOAS). As the popularity of breeds such as the French bulldog continues to increase in the UK, so too are the expected incidences of BOAS. For this reason, we be- came interested in the Norwich terrier, a non- brachycephalic breed which presents with Upper Airway Syndrome (UAS), a con- dition highly reminiscent of BOAS. Here, we have studied this single breed to identify genetic association(s) with UAS. Pathological assessments and grading from laryngoscopic examinations held at the Vetsuisse Faculty of the University of Bern, were used as phenotypes in conjunction with microarray genotypes to perform GWAS. In total, 233 Norwich terriers were examined. We identi- fied the same QTL on canine chromosome (CFA) 13 to be associated with the abnormal positioning of laryngeal cartilage and everted saccules in the dogs most severely affected by UAS. We phased genotypes at the CFA13 QTL to conduct haplotype map- ping, which led us to define a 413 kb critical interval which en-compasses a single positional candidate gene. The derived haplotype within this interval is overrepresented: it is found to be homozygous in 61 of 81 (74%) severely affected cases. In con- trast, this homozygous haplotype was identified among 7 of 86 (8.1%) mild/unaffected controls. We have resequenced four dogs representing phenotypic extremes to sixteen-fold depth to identify putatively causal variants. We will provide an update to this ongoing project, which is expected to guide Norwich terrier breeding and inspire additional exploration of the CFA13 locus to improve animal welfare. of multiple transcripts with alternative first exons. of multiple transcripts in the cerebellum through RNA sequencing, RT-PCR of samples from two Buhund cases and dogs of other RT-qPCR analysis and in-silico protein modelling have been used to further investigate the mutation ’ s effect on RNA ex- pression and protein stability. Chronic degenerative diseases (CDGs) are a major welfare concern in canine medicine myxomatous mitral valve disease (MMVD) an For an inher- polygenic and the mechanisms that requires examining molecular events in examination in both temporal and spatial terms changes in gene and pro- tein expression. examined the valvular gene expression at different stages of disease (temporal), different loca- tions (spatial) and in different cell culture models of MMVD. identified as the fundamen- tally important pathway in MMVD initiation and development, and progression to eventual end-stage valve pathology. stringent filtering and quality control, we tested 108,263 SNPs on 42 dogs, comprising 15 cases and 27 controls (call rate ≥ 97%; minor allele frequency ≥ 95%; genotype calls ≥ 90%). Analysis revealed a genome-wide significant association on canine chromosome 33 (-log praw = 2.2 x 10-16) which remained significant after correcting for multiple testing (pgenome = 0.9 x 10-5) and population substructure (p=raw1.6 x 10-17). A 1.3 megabase homozygous disease-associated region was defined, harbouring two candidate genes previously asso- ciated with human retinal degeneration. WGS was undertaken on a single PRA affected LA, and manual inter- rogation of the critical region in identified a long interspersed nu-clear element-1 (LINE-1) insertion, situated within the predicted promotor region of a retinal candidate gene. Due to the position of the LINE-1 insertion, it was not detected in the original WES data of the same case. The LINE-1 insertion was genotyped in 447 dogs across 122 breeds, including 63 LA dogs, and is private to the LA. Seventeen LA dogs (all clinically affected with PRA) were homozygous for the LINE-1 insertions, eight were heterozygous and thirty- eight were homozygous for the wildtype allele. As a result of this study a DNA test for this form of PRA, termed PRA4, has been developed at the Animal Health Trust. To date, 457 LA from 15 countries have been tested for PRA4 (354 UK dogs; car- rier frequency 17%; allele frequency 0.9054). This study highlights the power of utilising several genetic approaches to identify a PRA mutation and develop a diagnostic test to help dog breeders make informed breeding choices, minimising the risk of producing PRA- affected LA dogs. A point mutation in a lincRNA upstream of GDNF is associated with a canine insensitivity to pain: a spontaneous model for human sensory neuropathies. Plos Genetics 2016 Biomedical Variant Database Consortium and the Animal Health Trust Give a Dog a Genome bank) reduced an initial set of > 20 million variants down to a single candidate variant in a novel gene not previously associated with ret- inal degeneration in any species. The candidate variant was genotyped in a total of 1,444 dogs of 175 breeds, 10 cross breed dogs and 3 wolves, with our three PRA-affected Giant Schnauzers being the only homozygotes identified to date. Nine Giant Schnauzer heterozygotes were identified in addition to heterozygotes in three additional breeds of German origin, including the German Giant (Gross) and Medium (Mittel) Spitz and Miniature Longhaired Dachs-hund (MLHD). The genotyping of German Spitz varieties, including 110 Giant Spitz, 21 Medium Spitz, 24 Miniature (Klein) Spitz, 17 Pomeranian (Zwerg) Spitz, and an additional 27 Giant Schnauzers was carried out by collaborators at the University of Bern. We screened a total of 163 MLHD for the candidate variant. Seven German Giant Spitz, one German Medium Spitz and six MLHD heterozygotes were identified, suggesting this may be an ancestral, but rare, mutation. This study highlights the power of using WGS to identify novel genes associated with disease using a very small number of cases. This novel candidate gene, harbouring a variant that is predicted to be the causal mutation of PRA in the Giant Schnauzer, could provide in- sights into gene discoveries in human retinal degenerations. Further functional study options are being explored to confirm the candidate gene ’ s role in retinal function and maintenance. identify the genetic causes or predisposition to canine and human homologous genetic conditions. More recently, the idea emerged that dogs can be of help for therapeutic trials, to screen and validate new drugs in homologous human cancer types. To this aim, we created the canine Cani-DNA biobank in 2003 to col-lect blood and tissue samples from dogs affected with genetic dis- eases and healthy dogs. Cani-DNA contains the native samples and extracted nucleic acids as well as clinical and genealogical data, to distribute samples with high quality controlled procedures. This resource is implemented by a French veterinarian network based on vet practic- es, specialized vet centres and histopathology laborator-ies. In 2012, a contract signed between Cani-DNA and the 4 French vet schools and the Antagene Company allowed a national organization and international visibility. Cani-DNA joined the French consortium of domesticated animals, CRB-Anim (funded by French government 2012-2020), aiming to combine genetic and reproduct- ive resources. To date, Cani-DNA, with its primary site at CNRS Rennes and secondary sites at the fourth Vet Schools and Antagene contains almost 20 000 DNA extracted from blood and 3000 nucleic acids (DNA, RNA) extracted from tissue samples (tumoral and con- trols), representing 300 breeds and over 100 genetic diseases. Samples can be sent to implement Can

The advent of whole genome sequencing (WGS) has promised to revolutionise genetic research, and the rapid fall in per-sample costs in recent years has made the revolution an affordable reality for geneticists. The technology is especially useful for the study of simple Mendelian conditions where disease-causing mutations have the potential to be identified from the WGS of a single case. However, when comparing a typical canine genome with the reference sequence (CanFam3.1) or a control genome, at least 2-3 million variants will typically be identified. Many of these variants are likely common polymorphisms which could be excluded by comparing with multiple control genomes. We devised the Give a Dog a Genome (GDG) project to build a resource of canine genetic variants across the genome using WGS; currently projected to contain 90 genomes from 78 breeds, and investigate genetic diseases in at least 69 breeds. We used a crowd-funding approach, with the costs of the project being shared between multiple stakeholders. To date (two years after GDG was launched), 74 samples from 69 breeds have been sequenced comprising 62 dogs affected with a suspected genetic condition (27 conditions in total) and 12 apparently healthy older dogs. The GDG variant bank has been used to validate several disease-associated mutations and DNA tests have been developed to improve the health and wellbeing of dogs. All of the WGS data generated through GDG will be shared with the Dog Biomedical Variant Database Consortium (DBVDC), and specific sequences will be shared with at least 20 scientists from Europe and the USA to contribute to their research.

Gene modules inferred from WGCNA analysis of microarray time-course. Expression fold changes and associated false discovery rates (adjusted p values) are from RNA-seq data at the 4-h timepoint. (GZ 278 kb)