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Srikanth K, von Pfeil DJF, Stanley BJ, Griffitts C, Huson HJ. Genome Wide Association Study with Imputed Whole Genome Sequence Data Identifies a 431 kb Risk Haplotype on CFA18 for Congenital Laryngeal Paralysis in Alaskan Sled Dogs. Genes (Basel) 2022; 13:genes13101808. [PMID: 36292693 PMCID: PMC9602090 DOI: 10.3390/genes13101808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/03/2022] [Accepted: 10/04/2022] [Indexed: 11/16/2022] Open
Abstract
Congenital laryngeal paralysis (CLP) is an inherited disorder that affects the ability of the dog to exercise and precludes it from functioning as a working sled dog. Though CLP is known to occur in Alaskan sled dogs (ASDs) since 1986, the genetic mutation underlying the disease has not been reported. Using a genome-wide association study (GWAS), we identified a 708 kb region on CFA 18 harboring 226 SNPs to be significantly associated with CLP. The significant SNPs explained 47.06% of the heritability of CLP. We narrowed the region to 431 kb through autozygosity mapping and found 18 of the 20 cases to be homozygous for the risk haplotype. Whole genome sequencing of two cases and a control ASD, and comparison with the genome of 657 dogs from various breeds, confirmed the homozygous status of the risk haplotype to be unique to the CLP cases. Most of the dogs that were homozygous for the risk allele had blue eyes. Gene annotation and a gene-based association study showed that the risk haplotype encompasses genes implicated in developmental and neurodegenerative disorders. Pathway analysis showed enrichment of glycoproteins and glycosaminoglycans biosynthesis, which play a key role in repairing damaged nerves. In conclusion, our results suggest an important role for the identified candidate region in CLP.
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Affiliation(s)
- Krishnamoorthy Srikanth
- Department of Animal Science, College of Agriculture and Life Science, Cornell University, Ithaca, NY 14850, USA
| | | | - Bryden J. Stanley
- Department of Small Animal Clinical Sciences, Michigan State University, East Lansing, MI 48824, USA
| | | | - Heather J. Huson
- Department of Animal Science, College of Agriculture and Life Science, Cornell University, Ithaca, NY 14850, USA
- Correspondence:
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Letko A, Minor KM, Friedenberg SG, Shelton GD, Salvador JP, Mandigers PJJ, Leegwater PAJ, Winkler PA, Petersen-Jones SM, Stanley BJ, Ekenstedt KJ, Johnson GS, Hansen L, Jagannathan V, Mickelson JR, Drögemüller C. A CNTNAP1 Missense Variant Is Associated with Canine Laryngeal Paralysis and Polyneuropathy. Genes (Basel) 2020; 11:E1426. [PMID: 33261176 PMCID: PMC7761076 DOI: 10.3390/genes11121426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/25/2020] [Accepted: 11/26/2020] [Indexed: 02/06/2023] Open
Abstract
Laryngeal paralysis associated with a generalized polyneuropathy (LPPN) most commonly exists in geriatric dogs from a variety of large and giant breeds. The purpose of this study was to discover the underlying genetic and molecular mechanisms in a younger-onset form of this neurodegenerative disease seen in two closely related giant dog breeds, the Leonberger and Saint Bernard. Neuropathology of an affected dog from each breed showed variable nerve fiber loss and scattered inappropriately thin myelinated fibers. Using across-breed genome-wide association, haplotype analysis, and whole-genome sequencing, we identified a missense variant in the CNTNAP1 gene (c.2810G>A; p.Gly937Glu) in which homozygotes in both studied breeds are affected. CNTNAP1 encodes a contactin-associated protein important for organization of myelinated axons. The herein described likely pathogenic CNTNAP1 variant occurs in unrelated breeds at variable frequencies. Individual homozygous mutant LPPN-affected Labrador retrievers that were on average four years younger than dogs affected by geriatric onset laryngeal paralysis polyneuropathy could be explained by this variant. Pathologic changes in a Labrador retriever nerve biopsy from a homozygous mutant dog were similar to those of the Leonberger and Saint Bernard. The impact of this variant on health in English bulldogs and Irish terriers, two breeds with higher CNTNAP1 variant allele frequencies, remains unclear. Pathogenic variants in CNTNAP1 have previously been reported in human patients with lethal congenital contracture syndrome and hypomyelinating neuropathy, including vocal cord palsy and severe respiratory distress. This is the first report of contactin-associated LPPN in dogs characterized by a deleterious variant that most likely predates modern breed establishment.
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Affiliation(s)
- Anna Letko
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland; (V.J.); (C.D.)
| | - 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;
| | - G. Diane Shelton
- Department of Pathology, School of Medicine, University of California San Diego, La Jolla, CA 92093-0709, USA; (G.D.S.); (J.P.S.)
| | - Jill Pesayco Salvador
- Department of Pathology, School of Medicine, University of California San Diego, La Jolla, CA 92093-0709, USA; (G.D.S.); (J.P.S.)
| | - Paul J. J. Mandigers
- Department of Clinical Sciences, Utrecht University, 3584 CM Utrecht, The Netherlands; (P.J.J.M.); (P.A.J.L.)
| | - Peter A. J. Leegwater
- Department of Clinical Sciences, Utrecht University, 3584 CM Utrecht, The Netherlands; (P.J.J.M.); (P.A.J.L.)
| | - Paige A. Winkler
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA; (P.A.W.); (S.M.P.-J.); (B.J.S.)
| | - Simon M. Petersen-Jones
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA; (P.A.W.); (S.M.P.-J.); (B.J.S.)
| | - Bryden J. Stanley
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA; (P.A.W.); (S.M.P.-J.); (B.J.S.)
| | - Kari J. Ekenstedt
- Department of Basic Medical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47907, USA;
| | - Gary S. Johnson
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA; (G.S.J.); (L.H.)
| | - Liz Hansen
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA; (G.S.J.); (L.H.)
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland; (V.J.); (C.D.)
| | - 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.)
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland; (V.J.); (C.D.)
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Gurtner C, Hug P, Kleiter M, Köhler K, Dietschi E, Jagannathan V, Leeb T. YARS2 Missense Variant in Belgian Shepherd Dogs with Cardiomyopathy and Juvenile Mortality. Genes (Basel) 2020; 11:genes11030313. [PMID: 32183361 PMCID: PMC7140874 DOI: 10.3390/genes11030313] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/09/2020] [Accepted: 03/10/2020] [Indexed: 01/03/2023] Open
Abstract
Dog puppy loss by the age of six to eight weeks after normal development is relatively uncommon. Necropsy findings in two spontaneously deceased Belgian Shepherd puppies indicated an abnormal accumulation of material in several organs. A third deceased puppy exhibited mild signs of an inflammation in the central nervous system and an enteritis. The puppies were closely related, raising the suspicion of a genetic cause. Pedigree analysis suggested a monogenic autosomal recessive inheritance. Combined linkage and homozygosity mapping assigned the most likely position of a potential genetic defect to 13 genome segments totaling 82 Mb. The genome of an affected puppy was sequenced and compared to 645 control genomes. Three private protein changing variants were found in the linked and homozygous regions. Targeted genotyping in 96 Belgian Shepherd dogs excluded two of these variants. The remaining variant, YARS2:1054G>A or p.Glu352Lys, was perfectly associated with the phenotype in a cohort of 474 Belgian Shepherd dogs. YARS2 encodes the mitochondrial tyrosyl-tRNA synthetase 2 and the predicted amino acid change replaces a negatively charged and evolutionary conserved glutamate at the surface of the tRNA binding domain of YARS2 with a positively charged lysine. Human patients with loss-of-function variants in YARS2 suffer from myopathy, lactic acidosis, and sideroblastic anemia 2, a disease with clinical similarities to the phenotype of the studied dogs. The carrier frequency was 27.2% in the tested Belgian Shepherd dogs. Our data suggest YARS2:1054G>A as the candidate causative variant for the observed juvenile mortality.
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Affiliation(s)
- Corinne Gurtner
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland;
| | - Petra Hug
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (P.H.); (E.D.); (V.J.)
| | - Miriam Kleiter
- Department/Hospital for Companion Animals and Horses, University Clinic for Small Animals, Internal Medicine Small Animals, University of Veterinary Medicine, 1210 Vienna, Austria;
| | - Kernt Köhler
- Institute of Veterinary Pathology, Justus-Liebig-University Giessen, 35392 Giessen, Germany;
| | - Elisabeth Dietschi
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (P.H.); (E.D.); (V.J.)
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (P.H.); (E.D.); (V.J.)
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (P.H.); (E.D.); (V.J.)
- Correspondence: ; Tel.: +41-31-631-23-26
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