A de novo in-frame duplication in the COL1A2 gene in a Lagotto Romagnolo dog with osteogenesis imperfecta

Naturally occurring genetic diseases caused by de novo variants in domestic animals

With the advent of next-generation sequencing, an increasing number of cases of de novo variants in domestic animals have been reported in scientific literature primarily associated with clinically severe phenotypes. The emergence of new variants at each generation is a crucial aspect in understanding the pathology of early-onset diseases in animals and can provide valuable insights into similar diseases in humans. With the aim of collecting deleterious de novo variants in domestic animals, we searched the scientific literature and compiled reports on 42 de novo variants in 31 genes in domestic animals. No clear disease-associated phenotype has been established in humans for three of these genes (NUMB, ANKRD28 and KCNG1). For the remaining 28 genes, a strong similarity between animal and human phenotypes was recognized from available information in OMIM and OMIA, revealing the importance of comparative studies and supporting the use of domestic animals as natural models for human diseases, in line with the One Health approach.

PKD1 Nonsense Variant in a Lagotto Romagnolo Family with Polycystic Kidney Disease

A female Lagotto Romagnolo dog with polycystic kidney disease (PKD) and her progeny, including PKD-affected offspring, were studied. All affected dogs appeared clinically inconspicuous, while sonography revealed the presence of renal cysts. The PKD-affected index female was used for breeding and produced two litters with six affected offspring of both sexes and seven unaffected offspring. The pedigrees suggested an autosomal dominant mode of inheritance of the trait. A trio whole genome sequencing analysis of the index female and her unaffected parents identified a de novo heterozygous nonsense variant in the coding region of the PKD1 gene. This variant, NM_001006650.1:c.7195G>T, is predicted to truncate 44% of the open reading frame of the wild-type PKD1 protein, NP_001006651.1:p.(Glu2399*). The finding of a de novo variant in an excellent functional candidate gene strongly suggests that the PKD1 nonsense variant caused the observed phenotype in the affected dogs. Perfect co-segregation of the mutant allele with the PKD phenotype in two litters supports the hypothesized causality. To the best of our knowledge, this is the second description of a PKD1-related canine form of autosomal dominant PKD that may serve as an animal model for similar hepatorenal fibrocystic disorders in humans.

A multicenter retrospective evaluation of the prevalence of known and presumed hereditary eye diseases in Lagotto Romagnolo dog breed within a referral population in Italy (2012-2020)

OBJECTIVE

To describe the ophthalmological findings of Lagotto Romagnolo dog breed and to report the prevalence of Known and Presumed Hereditary Eye Diseases (KP-HED).

ANIMALS STUDIED

Two hundred sixteen dogs were examined and included in this retrospective study.

PROCEDURES

Medical records of Lagotto Romagnolo dogs between 2012 and 2020 were included. Data about the ocular status were collected through ocular screening examinations (OSE) or clinical ophthalmic examinations (COE). The prevalence of each KP-HED was expressed as a function of the total number of the KP-HED in this referral population.

RESULTS

A total of 85 dogs (39.35%) were ophthalmologically healthy, ocular diseases presumably not hereditary were found in 43 dogs (19.91%), and 88 dogs (40.74%) were affected by one KP-HED. The most common KP-HEDs diagnosed were cataract (28/88; 31.82%), corneal endothelial dystrophy (17/88; 19.32%), retinal dysplasia (9/88; 10.23%), lens instability (7/88; 7.95%), progressive retinal atrophy (6/88, 6.82%), and keratoconjunctivitis sicca (6/88, 6.82%). Most of dogs with a KP-HED (77.27%, 68/88) were identified within COE group.

CONCLUSIONS

To the authors' knowledge, this is the first report of the prevalence of ocular disease in the Lagotto Romagnolo dog breed within a referral population in Italy. This study suggests a relatively high prevalence of KP-HED, with a characteristic late-onset presentation in some diseases. Many of these KP-HED's, lead to ocular pain and irreversible blindness, for this reason, the authors highlight the importance of aiming for an early diagnosis. Breeder's efforts and breeding programs should be directed at limiting such disorders.

Severe osteogenesis imperfecta caused by CREB3L1 mutation in a cat

We examined the clinical features and pathology, and identified the causative mutation, of osteogenesis imperfecta in a 2-mo-old kitten with growth retardation and abnormal gait. Blood and radiographic examinations were performed on presentation. Radiographs revealed decreased opacity of numerous bones. Fractures were observed in some long bones, including femur and tibia. Histologic examination of the tibia showed decreased osteoid and osteoblasts at the primary spongiosa extending from the growth plate. The periosteum was thickened, and cortical bone and osteoblasts were decreased. Consequently, osteogenesis imperfecta was diagnosed. Genomic DNA and total RNA were extracted from the skin and used for PCR. Whole-genome sequencing identified a 2-bp deletion (c.370_371delTG; p.C124fs), which resulted in a homozygous frameshift mutation on exon 3 of CREB3L1. This mutation introduced a premature stop codon, suggesting production of the truncated protein without a functional domain as a transcription factor for expression of COL1A1 mRNA. This error may have affected collagen fibril formation, leading to the development of osteogenesis imperfecta.

MIA3 Splice Defect in Cane Corso Dogs with Dental-Skeletal-Retinal Anomaly (DSRA)

We investigated a hereditary syndrome in Cane Corso dogs. Affected dogs developed dental-skeletal-retinal anomaly (DSRA), clinically characterized by brittle, discolored, translucent teeth, disproportionate growth and progressive retinal degeneration resulting in vision loss. Combined linkage and homozygosity mapping delineated a 5.8 Mb critical interval. The comparison of whole genome sequence data of an affected dog to 789 control genomes revealed a private homozygous splice region variant in the critical interval. It affected the MIA3 gene encoding the MIA SH3 domain ER export factor 3, which has an essential role in the export of collagen and other secreted proteins. The identified variant, XM_005640835.3:c.3822+3_3822+4del, leads to skipping of two exons from the wild type transcript, XM_005640835.3:r.3712_3822del. Genotypes at the variant were consistent with monogenic autosomal recessive mode of inheritance in a complete family and showed perfect genotype-phenotype association in 18 affected and 22 unaffected Cane Corso dogs. MIA3 variants had previously been shown to cause related phenotypes in humans and mice. Our data in dogs together with the existing functional knowledge of MIA3 variants in other mammalian species suggest the MIA3 splice defect and a near complete loss of gene function as causative molecular pathomechanism for the DSRA phenotype in the investigated dogs.

Osteogenesis Imperfecta in Two Finnish Lapphund Puppies

Two 8-week-old Finnish Lapphund dogs presented with pain on manipulation, abnormal long bone conformation, retrognathism, and stunted growth compared to their litter mates. Multiple long bone fractures were evident on radiographs. Clinical pathology showed an atypically normal serum alkaline phosphatase activity for dogs this age. Due to poor quality of life, the dogs were humanely euthanized and subjected to a complete necropsy. On necropsy, all bones were soft and easily broken. Histologic examination revealed that the secondary spongiosa was diminished with abnormal bony trabeculae embedded in abundant loose vascular stroma. No Haversian canals were observed and the cortices contained abundant woven bone separated by fibrovascular tissue consistent with the diagnosis of osteogenesis imperfecta (OI). Inbreeding of the sire and female offspring led to a suspicion of recessive inheritance and the particular genetic collagen disorder remains to be identified in this breed.

A De Novo Mutation in COL1A1 in a Holstein Calf with Osteogenesis Imperfecta Type II

Osteogenesis imperfecta (OI) type II is a genetic connective tissue disorder characterized by bone fragility, severe skeletal deformities and shortened limbs. OI usually causes perinatal death of affected individuals. OI type II diagnosis in humans is established by the identification of heterozygous mutations in genes coding for collagens. The purpose of this study was to characterize the pathological phenotype of an OI type II-affected neonatal Holstein calf and to identify the causative genetic variant by whole-genome sequencing (WGS). The calf had acute as well as intrauterine fractures, abnormally shaped long bones and localized arthrogryposis. Genetic analysis revealed a private heterozygous missense variant in COL1A1 (c.3917T>A) located in the fibrillar collagen NC1 domain (p.Val1306Glu) that most likely occurred de novo. This confirmed the diagnosis of OI type II and represents the first report of a pathogenic variant in the fibrillar collagen NC domain of COL1A1 associated to OI type II in domestic animals. Furthermore, this study highlights the utility of WGS-based precise diagnostics for understanding congenital disorders in cattle and the need for continued surveillance for rare lethal genetic disorders in cattle.

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

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