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Jankelunas L, Murthy VD, Chen AV, Minor KM, Friedenberg SG, Cullen JN, Guo LT, Mickelson JR, Shelton GD. Novel COL6A3 frameshift variant in American Staffordshire Terrier dogs with Ullrich-like congenital muscular dystrophy. J Vet Intern Med 2023; 37:2504-2509. [PMID: 37706358 PMCID: PMC10658572 DOI: 10.1111/jvim.16862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/24/2023] [Indexed: 09/15/2023] Open
Abstract
Two (male and female) 10-month-old American Staffordshire Terrier littermates presented for progressive weakness, joint contracture, and distal limb joint hyperlaxity beginning around 6 months of age. Neurological examination, serum creatine kinase activity, infectious disease titers, cerebrospinal fluid analysis, and electrodiagnostic testing were performed. Muscle biopsies were collected for histopathology and immunofluorescence staining for localization of dystrophy associated proteins. Whole-genome sequencing (WGS) was performed on 1 affected dog. Variants were compared to a database of 671 unaffected dogs of multiple breeds. Histopathology confirmed a dystrophic phenotype and immunofluorescence staining of muscle cryosections revealed an absence of staining for collagen-6. WGS identified a homozygous 1 bp deletion in the COL6A3 gene, unique to the first affected dog. Sanger sequencing confirmed the homozygous presence of the frameshift variant in both affected dogs. This report describes the clinical features and most likely genetic basis of an Ullrich-like recessively inherited form of congenital muscular dystrophy in American Staffordshire Terriers.
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Affiliation(s)
- Leanne Jankelunas
- Department of Veterinary Clinical Sciences, College of Veterinary MedicineWashington State UniversityPullmanWashingtonUSA
| | - Vishal D. Murthy
- Department of Veterinary Clinical Sciences, College of Veterinary MedicineWashington State UniversityPullmanWashingtonUSA
| | - Annie V. Chen
- Department of Veterinary Clinical Sciences, College of Veterinary MedicineWashington State UniversityPullmanWashingtonUSA
| | - Katie M. Minor
- Department of Veterinary Clinical Sciences, College of Veterinary MedicineUniversity of MinnesotaSaint PaulMinnesotaUSA
| | - Steven G. Friedenberg
- Department of Veterinary Clinical Sciences, College of Veterinary MedicineUniversity of MinnesotaSaint PaulMinnesotaUSA
| | - Jonah N. Cullen
- Department of Veterinary Clinical Sciences, College of Veterinary MedicineUniversity of MinnesotaSaint PaulMinnesotaUSA
| | - Ling T. Guo
- Department of Pathology, School of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - James R. Mickelson
- Department of Veterinary and Biomedical Sciences, College of Veterinary MedicineUniversity of MinnesotaSaint PaulMinnesotaUSA
| | - G. Diane Shelton
- Department of Pathology, School of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
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Cullen JN, Friedenberg SG. Whole Animal Genome Sequencing: user-friendly, rapid, containerized pipelines for processing, variant discovery, and annotation of short-read whole genome sequencing data. G3 (BETHESDA, MD.) 2023; 13:jkad117. [PMID: 37243692 PMCID: PMC10411559 DOI: 10.1093/g3journal/jkad117] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 02/24/2023] [Accepted: 05/20/2023] [Indexed: 05/29/2023]
Abstract
Advancements in massively parallel short-read sequencing technologies and the associated decreasing costs have led to large and diverse variant discovery efforts across species. However, processing high-throughput short-read sequencing data can be challenging with potential pitfalls and bioinformatics bottlenecks in generating reproducible results. Although a number of pipelines exist that address these challenges, these are often geared toward human or traditional model organism species and can be difficult to configure across institutions. Whole Animal Genome Sequencing (WAGS) is an open-source set of user-friendly, containerized pipelines designed to simplify the process of identifying germline short (SNP and indel) and structural variants (SVs) geared toward the veterinary community but adaptable to any species with a suitable reference genome. We present a description of the pipelines [adapted from the best practices of the Genome Analysis Toolkit (GATK)], along with benchmarking data from both the preprocessing and joint genotyping steps, consistent with a typical user workflow.
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Affiliation(s)
- Jonah N Cullen
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, 1352 Boyd Ave, Saint Paul, MN 55108, USA
| | - Steven G Friedenberg
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, 1352 Boyd Ave, Saint Paul, MN 55108, USA
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Shelton GD, Minor KM, Friedenberg SG, Cullen JN, Guo LT, Mickelson JR. Current Classification of Canine Muscular Dystrophies and Identification of New Variants. Genes (Basel) 2023; 14:1557. [PMID: 37628610 PMCID: PMC10454810 DOI: 10.3390/genes14081557] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/21/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023] Open
Abstract
The spectrum of canine muscular dystrophies has rapidly grown with the recent identification of several more affected breeds and associated mutations. Defects include those in genes and protein products associated with the sarcolemma (dystrophin deficient X-linked muscular dystrophy and sarcoglycan-deficient limb-girdle muscular dystrophy) and with the extracellular matrix (collagen 6, laminin α2, and α-dystroglycan-deficient congenital muscular dystrophies). With the increasing application of whole genome sequencing and whole exome sequencing, the clinical and pathological spectra associated with specific neuromuscular genetic defects are constantly evolving. In this report, we provide a brief overview of the current status of gene defects reported in canine muscular dystrophies. We also report the causative mutations for novel forms of X-linked muscular dystrophy in Brittany spaniels and in a French bulldog.
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Affiliation(s)
- G. Diane Shelton
- Department of Pathology, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA;
| | - Katie M. Minor
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN 55108, USA; (K.M.M.); (J.R.M.)
| | - Steven G. Friedenberg
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN 55108, USA; (S.G.F.); (J.N.C.)
| | - Jonah N. Cullen
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN 55108, USA; (S.G.F.); (J.N.C.)
| | - Ling T. Guo
- Department of Pathology, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA;
| | - James R. Mickelson
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN 55108, USA; (K.M.M.); (J.R.M.)
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Dog-human translational genomics: state of the art and genomic resources. J Appl Genet 2022; 63:703-716. [PMID: 36074326 DOI: 10.1007/s13353-022-00721-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 08/26/2022] [Accepted: 08/30/2022] [Indexed: 10/14/2022]
Abstract
Innovative models for medical research are strongly required nowadays. Convincing evidence supports dog as the most suitable spontaneous model for several human genetic diseases. Decades of studies on dog genome allowed the identification of hundreds of mutations causing genetic disorders, many of which are proposed as counterparts responsible for human diseases. Traditionally, the murine model is the most extensively used in human translational research. However, this species shows large physiological differences from humans, and it is kept under a controlled artificial environment. Conversely, canine genetic disorders often show pathophysiological and clinical features highly resembling the human counterpart. In addition, dogs share the same environment with humans; therefore, they are naturally exposed to many risk factors. Thus, different branches of translational medicine aim to study spontaneously occurring diseases in dogs to provide a more reliable model for human disorders. This review offers a comprehensive overview of the knowledge and resources available today for all the researchers involved in the field of dog-human translational medicine. Some of the main successful examples from dog-human translational genomics are reported, such as the canine association studies which helped to identify the causal mutation in the human counterpart. We also illustrated the ongoing projects aiming to create public canine big datasets. Finally, specific online databases are discussed along with several information resources that can speed up clinical translational research.
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Shelton GD, Minor KM, Thomovsky S, Guo LT, Friedenberg SG, Cullen JN, Mickelson JR. Congenital muscular dystrophy in a dog with a LAMA2 gene deletion. J Vet Intern Med 2021; 36:279-284. [PMID: 34854126 PMCID: PMC8783360 DOI: 10.1111/jvim.16330] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 12/01/2022] Open
Abstract
A 2-year-old female spayed dog was presented with a chronic history of short-strided gait and inability to completely open the jaw. Clinical signs were present since the dog was adopted from a humane society at a few months of age. Serum creatine kinase activity was abnormally high. Neurological examination, electromyography, muscle biopsies with immunofluorescent staining, and whole genome sequencing (WGS) were performed. A dystrophic phenotype was identified histologically in muscle biopsies, deficiency of laminin α2 protein was confirmed by immunofluorescent staining, and a deletion in the LAMA2 gene was identified by analysis of the WGS data. Congenital muscular dystrophy associated with a disease variant in LAMA2 was identified.
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Affiliation(s)
- G Diane Shelton
- Department of Pathology, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Katie M Minor
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Stephanie Thomovsky
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, Indiana, USA
| | - Ling T Guo
- Department of Pathology, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Steven G Friedenberg
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Jonah N Cullen
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - James R Mickelson
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
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Christen M, Indzhova V, Guo LT, Jagannathan V, Leeb T, Shelton GD, Brocal J. LAMA2 Nonsense Variant in an Italian Greyhound with Congenital Muscular Dystrophy. Genes (Basel) 2021; 12:1823. [PMID: 34828429 PMCID: PMC8618982 DOI: 10.3390/genes12111823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/12/2021] [Accepted: 11/18/2021] [Indexed: 11/30/2022] Open
Abstract
A 4-month-old, male Italian Greyhound with clinical signs of a neuromuscular disease was investigated. The affected dog presented with an abnormal short-strided gait, generalized muscle atrophy, and poor growth since 2-months of age. Serum biochemistry revealed a marked elevation in creatine kinase activity. Electrodiagnostic testing supported a myopathy. Histopathology of muscle biopsies confirmed a dystrophic phenotype with excessive variability in myofiber size, degenerating fibers, and endomysial fibrosis. A heritable form of congenital muscular dystrophy (CMD) was suspected, and a genetic analysis initiated. We sequenced the genome of the affected dog and compared the data to that of 795 control genomes. This search revealed a private homozygous nonsense variant in LAMA2, XM_022419950.1:c.3285G>A, predicted to truncate 65% of the open reading frame of the wild type laminin α2 protein, XP_022275658.1:p.(Trp1095*). Immunofluorescent staining performed on muscle cryosections from the affected dog confirmed the complete absence of laminin α2 in skeletal muscle. LAMA2 loss of function variants were shown to cause severe laminin α2-related CMD in humans, mouse models, and in one previously described dog. Our data together with current knowledge on other species suggest the LAMA2 nonsense variant as cause for the CMD phenotype in the investigated dog.
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Affiliation(s)
- Matthias Christen
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (M.C.); (V.J.)
| | - Victoria Indzhova
- Neurology-Neurosurgery Service, Willows Veterinary Centre and Referral Service, Solihull B90 4NH, West Midlands, UK;
| | - Ling T. Guo
- Department of Pathology, School of Medicine, University of California San Diego, La Jolla, CA 92093-0709, USA; (L.T.G.); (G.D.S.)
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (M.C.); (V.J.)
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (M.C.); (V.J.)
| | - G. Diane Shelton
- Department of Pathology, School of Medicine, University of California San Diego, La Jolla, CA 92093-0709, USA; (L.T.G.); (G.D.S.)
| | - Josep Brocal
- Department of Neurology and Neurosurgery, Anderson Moores Veterinary Specialists, Winchester SO21 2LL, Hampshire, UK;
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