1
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Bauer A, Hadji Rasouliha S, Brunner MT, Jagannathan V, Bucher I, Bannoehr J, Varjonen K, Bond R, Bergvall K, Welle MM, Roosje P, Leeb T. Corrigendum: A second KRT71 allele in curly coated dogs. Anim Genet 2021; 52:575. [PMID: 34196995 DOI: 10.1111/age.13098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- A Bauer
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland.,Dermfocus, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - S Hadji Rasouliha
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland.,Dermfocus, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - M T Brunner
- Dermfocus, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland.,Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - V Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland.,Dermfocus, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - I Bucher
- Dermfocus, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland.,Division of Clinical Dermatology, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - J Bannoehr
- Dermfocus, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland.,Division of Clinical Dermatology, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland.,Dermatology Department, Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk, CB8 7UU, UK
| | - K Varjonen
- Department Veterinary Clinical Sciences, Royal Veterinary College, Hatfield, AL9 7TA, UK.,Anicura Albano Animal Hospital, Danderyd, 18236, Sweden
| | - R Bond
- Department Veterinary Clinical Sciences, Royal Veterinary College, Hatfield, AL9 7TA, UK
| | - K Bergvall
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Box 7054, Uppsala, 750 07, Sweden
| | - M M Welle
- Dermfocus, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland.,Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - P Roosje
- Dermfocus, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland.,Division of Clinical Dermatology, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - T Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland.,Dermfocus, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
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2
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Thilagam L, Mohapatra D, Obaidurrahman K, Jagannathan V. Simulations for worth determination of CPSARs in VVER-1000 reactor using EXCEL and TRIHEX-FA code system. ANN NUCL ENERGY 2021. [DOI: 10.1016/j.anucene.2020.107921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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3
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Dettwiler M, Leuthard F, Bauer A, Jagannathan V, Lourenço AM, Pereira H, Leeb T, Welle MM. A nonsense variant in the KRT14 gene in a domestic shorthair cat with epidermolysis bullosa simplex. Anim Genet 2020; 51:829-832. [PMID: 32657488 DOI: 10.1111/age.12979] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2020] [Indexed: 12/27/2022]
Abstract
Epidermolysis bullosa simplex (EBS) is a hereditary blistering disease affecting the skin and mucous membranes. It has been reported in humans, cattle, buffaloes and dogs, but so far not in cats. In humans, EBS is most frequently caused by variants in the KRT5 or KRT14 genes. Here, we report a case of feline epidermolysis bullosa simplex and describe the causative genetic variant. An 11-month-old male domestic shorthair cat presented with a history of sloughed paw pads and ulcerations in the oral cavity and inner aspect of the pinnae, starting a few weeks after birth. Clinical and histopathological findings suggested a congenital blistering disease with a split formation within the basal cell layer of the epidermis and oral mucous epithelium. The genetic investigation revealed a homozygous nonsense variant in the KRT14 gene (c.979C>T, p.Gln327*). Immunohistochemistry showed a complete absence of keratin 14 staining in all epithelia present in the biopsy. To the best of our knowledge, this is the first report of feline EBS, and the first report of a spontaneous pathogenic KRT14 variant in a non-human species. The homozygous genotype in the affected cat suggests an autosomal recessive mode of inheritance.
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Affiliation(s)
- M Dettwiler
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, Bern, 3001, Switzerland.,Dermfocus, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - F Leuthard
- Dermfocus, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland.,Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, Bern, 3001, Switzerland
| | - A Bauer
- Dermfocus, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland.,Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, Bern, 3001, Switzerland
| | - V Jagannathan
- Dermfocus, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland.,Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, Bern, 3001, Switzerland
| | - A M Lourenço
- Dermatology Service, Faculty of Veterinary Medicine, Centre for Interdisciplinary Research in Animal Health, University of Lisbon, Av. Universidade Técnica, Lisboa, 1300-477, Portugal
| | - H Pereira
- Dermatology Service, Faculty of Veterinary Medicine, Centre for Interdisciplinary Research in Animal Health, University of Lisbon, Av. Universidade Técnica, Lisboa, 1300-477, Portugal
| | - T Leeb
- Dermfocus, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland.,Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, Bern, 3001, Switzerland
| | - M M Welle
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, Bern, 3001, Switzerland.,Dermfocus, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
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4
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Gerber N, Brunner M, Jagannathan V, Leeb T, Gerhards N, Welle M, Dettwiler M. Searching for Diagnostic Biomarkers Discriminating Early Canine Cutaneous Epitheliotropic Lymphoma and Immune-Mediated Dermatoses by RNA Sequencing. J Comp Pathol 2020. [DOI: 10.1016/j.jcpa.2019.10.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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5
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Torrecilha RBP, Milanesi M, Wade CM, Gallana M, Falbo AK, Reichler IM, Hug P, Jagannathan V, Trigo BB, Paulan SC, Bruno DB, Garcia SD, Scaramele NF, Lopes FL, Dolf G, Leeb T, Sölkner J, Garcia JF, Pieńkowska-Schelling A, Schelling C, Utsunomiya YT. Association of missense variants in GDF9 with litter size in Entlebucher Mountain dogs. Anim Genet 2019; 51:78-86. [PMID: 31802524 DOI: 10.1111/age.12882] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/06/2019] [Indexed: 12/28/2022]
Abstract
In the past two decades, average litter size (ALS) in Entlebucher Mountain dogs decreased by approximately 0.8 puppies. We conducted a GWAS for ALS using the single-step methodology to take advantage of 1632 pedigree records, 892 phenotypes and 372 genotypes (173 662 markers) for which only 12% of the dogs had both phenotypes and genotypes available. Our analysis revealed associations towards the growth differentiation factor 9 gene (GDF9), which is known to regulate oocyte maturation. The trait heritability was estimated at 43.1%, from which approximately 15% was accountable by the GDF9 locus alone. Therefore, markers flanking GDF9 explained approximately 6.5% of the variance in ALS. Analysis of WGSs revealed two missense substitutions in GDF9, one of which (g.11:21147009G>A) affected a highly conserved nucleotide in vertebrates. The derived allele A was validated in 111 dogs and shown to be associated with decreased ALS (-0.75 ± 0.22 puppies per litter). The variant was further predicted to cause a proline to serine substitution. The affected residue was immediately followed by a six-residue deletion that is fixed in the canine species but absent in non-canids. We further confirmed that the deletion is prevalent in the Canidae family by sequencing three species of wild canids. Since canids uniquely ovulate oocytes at the prophase stage of the first meiotic division, requiring maturation in the oviduct, we conjecture that the amino acid substitution and the six-residue deletion of GDF9 may serve as a model for insights into the dynamics of oocyte maturation in canids.
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Affiliation(s)
- R B P Torrecilha
- Department of Preventive Veterinary Medicine and Animal Reproduction, School of Agriculture and Veterinarian Sciences, São Paulo State University (Unesp), Via de acesso Prof. Paulo Donato Castellane s/n, 14884-900, Jaboticabal, São Paulo, Brazil.,International Atomic Energy Agency Collaborating Centre on Animal Genomics and Bioinformatics, Clóvis Pestana, 793, 16050-680, Araçatuba, São Paulo, Brazil
| | - M Milanesi
- International Atomic Energy Agency Collaborating Centre on Animal Genomics and Bioinformatics, Clóvis Pestana, 793, 16050-680, Araçatuba, São Paulo, Brazil.,Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), Clóvis Pestana, 793, 16050-680, Araçatuba, São Paulo, Brazil
| | | | - M Gallana
- Clinic of Reproductive Medicine, Vetsuisse-Faculty University of Zurich, Eschikon 27, Lindau, 8315, Switzerland
| | - A-K Falbo
- Clinic of Reproductive Medicine, Vetsuisse-Faculty University of Zurich, Eschikon 27, Lindau, 8315, Switzerland
| | - I M Reichler
- Clinic of Reproductive Medicine, Vetsuisse-Faculty University of Zurich, Winterthurerstr. 260, Zürich, 8057, Switzerland
| | - P Hug
- Institute of Genetics, Vetsuisse-Faculty University of Bern, Bremgartenstrasse 109A, Bern, 3012, Switzerland
| | - V Jagannathan
- Institute of Genetics, Vetsuisse-Faculty University of Bern, Bremgartenstrasse 109A, Bern, 3012, Switzerland
| | - B B Trigo
- International Atomic Energy Agency Collaborating Centre on Animal Genomics and Bioinformatics, Clóvis Pestana, 793, 16050-680, Araçatuba, São Paulo, Brazil.,Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), Clóvis Pestana, 793, 16050-680, Araçatuba, São Paulo, Brazil
| | - S C Paulan
- International Atomic Energy Agency Collaborating Centre on Animal Genomics and Bioinformatics, Clóvis Pestana, 793, 16050-680, Araçatuba, São Paulo, Brazil.,Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), Clóvis Pestana, 793, 16050-680, Araçatuba, São Paulo, Brazil
| | - D B Bruno
- Department of Clinics, Surgery and Animal Reproduction, School of Veterinary Medicine, São Paulo State University (Unesp), Clóvis Pestana, 793,, 16050-680, Araçatuba, São Paulo, Brazil
| | - S D Garcia
- Department of Clinics, Surgery and Animal Reproduction, School of Veterinary Medicine, São Paulo State University (Unesp), Clóvis Pestana, 793,, 16050-680, Araçatuba, São Paulo, Brazil
| | - N F Scaramele
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), Clóvis Pestana, 793, 16050-680, Araçatuba, São Paulo, Brazil
| | - F L Lopes
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), Clóvis Pestana, 793, 16050-680, Araçatuba, São Paulo, Brazil
| | - G Dolf
- Institute of Genetics, Vetsuisse-Faculty University of Bern, Bremgartenstrasse 109A, Bern, 3012, Switzerland
| | - T Leeb
- Institute of Genetics, Vetsuisse-Faculty University of Bern, Bremgartenstrasse 109A, Bern, 3012, Switzerland
| | - J Sölkner
- Division of Livestook Sciences, Department of Sustainable Agriculture System, BOKU - University of Natural Resource and Live Sciences, Gregor-Mendel-Straße 33, 1180, Vienna, Austria
| | - J F Garcia
- Department of Preventive Veterinary Medicine and Animal Reproduction, School of Agriculture and Veterinarian Sciences, São Paulo State University (Unesp), Via de acesso Prof. Paulo Donato Castellane s/n, 14884-900, Jaboticabal, São Paulo, Brazil.,International Atomic Energy Agency Collaborating Centre on Animal Genomics and Bioinformatics, Clóvis Pestana, 793, 16050-680, Araçatuba, São Paulo, Brazil.,Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), Clóvis Pestana, 793, 16050-680, Araçatuba, São Paulo, Brazil
| | - A Pieńkowska-Schelling
- Clinic of Reproductive Medicine, Vetsuisse-Faculty University of Zurich, Eschikon 27, Lindau, 8315, Switzerland.,Institute of Genetics, Vetsuisse-Faculty University of Bern, Bremgartenstrasse 109A, Bern, 3012, Switzerland
| | - C Schelling
- Clinic of Reproductive Medicine, Vetsuisse-Faculty University of Zurich, Eschikon 27, Lindau, 8315, Switzerland
| | - Y T Utsunomiya
- International Atomic Energy Agency Collaborating Centre on Animal Genomics and Bioinformatics, Clóvis Pestana, 793, 16050-680, Araçatuba, São Paulo, Brazil.,Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), Clóvis Pestana, 793, 16050-680, Araçatuba, São Paulo, Brazil
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6
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Jagannathan V, Drögemüller C, Leeb T. A comprehensive biomedical variant catalogue based on whole genome sequences of 582 dogs and eight wolves. Anim Genet 2019; 50:695-704. [PMID: 31486122 PMCID: PMC6842318 DOI: 10.1111/age.12834] [Citation(s) in RCA: 132] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2019] [Indexed: 12/16/2022]
Abstract
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.
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Affiliation(s)
- V Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - C Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - T Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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7
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Letko A, Ammann B, Jagannathan V, Henkel J, Leuthard F, Schelling C, Carneiro M, Drögemüller C, Leeb T. A deletion spanning the promoter and first exon of the hair cycle-specific ASIP transcript isoform in black and tan rabbits. Anim Genet 2019; 51:137-140. [PMID: 31729778 DOI: 10.1111/age.12881] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/08/2019] [Accepted: 10/25/2019] [Indexed: 01/01/2023]
Abstract
Black and tan animals have tan-coloured ventral body surfaces separated by sharp boundaries from black-coloured dorsal body surfaces. In the at mouse mutant, a retroviral 6 kb insertion located in the hair cycle-specific promoter of the murine Asip gene encoding agouti signalling protein causes the black and tan phenotype. In rabbits, three ASIP alleles are thought to exist, including an at allele causing a black and tan coat colour that closely resembles the mouse black and tan phenotype. The goal of our study was to identify the functional genetic variant causing the rabbit at allele. We performed a WGS-based comparative analysis of the ASIP gene in one black and tan and three wt agouti-coloured rabbits. The analysis identified 75 at -associated variants including an 11 kb deletion. The deletion is located in the region of the hair cycle-specific ASIP promoter and thus in a region homologous to the site of the retroviral insertion causing the at allele in mice. We observed perfect association of the genotypes at this deletion with the coat colour phenotype in 49 rabbits. The comparative analysis and the previous knowledge about the regulation of ASIP expression suggest that the 11 kb deletion is the most likely causative variant for the black and tan phenotype in rabbits.
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Affiliation(s)
- A Letko
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - B Ammann
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - V Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.,Dermfocus, University of Bern, 3001, Bern, Switzerland
| | - J Henkel
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.,Dermfocus, University of Bern, 3001, Bern, Switzerland
| | - F Leuthard
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.,Dermfocus, University of Bern, 3001, Bern, Switzerland
| | - C Schelling
- Vetsuisse Faculty, Clinic for Reproductive Medicine and Center of Clinical Studies, University of Zurich, 8315, Lindau, Switzerland
| | - M Carneiro
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, 4485-661, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, 4169-007, Portugal
| | - C Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.,Dermfocus, University of Bern, 3001, Bern, Switzerland
| | - T Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.,Dermfocus, University of Bern, 3001, Bern, Switzerland
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8
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Leuthard F, Lehner G, Jagannathan V, Leeb T, Welle M. A missense variant in the NSDHL gene in a Chihuahua with a congenital cornification disorder resembling inflammatory linear verrucous epidermal nevi. Anim Genet 2019; 50:768-771. [PMID: 31571289 DOI: 10.1111/age.12862] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/04/2019] [Indexed: 11/27/2022]
Abstract
Congenital hemidysplasia with ichthyosiform nevus and limb defects syndrome in humans is a genodermatosis characterized by inflammatory linear verrucous epidermal nevi (ILVEN), often showing a striking lateralization pattern. It is caused by variants in the NSDHL gene encoding a 3β-hydroxysteroid dehydrogenase involved in the cholesterol biosynthesis pathway. In the present study, we investigated a female Chihuahua, which showed clinical and histological signs of ILVEN. We performed a candidate gene analysis in the affected animal. This analysis revealed a single missense variant in the NSDHL gene in the affected dog (XM_014111859.2:c.700G>A). The variant is predicted to cause a non-conservative amino acid change from glycine to arginine, XP_013967334.1:p.(Gly234Arg). The mutant allele was absent from WGS data of 594 genetically diverse dogs and eight wolves. Sanger sequencing confirmed that the variant was heterozygous in the affected dog and absent from 22 control Chihuahuas. Based on the knowledge about the functional impact of NSDHL variants in dogs and other species, c.700G>A is probably pathogenic and a convincing candidate causative variant for the observed skin lesions in the affected Chihuahua.
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Affiliation(s)
- F Leuthard
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
| | - G Lehner
- Kleintierpraxis Lehner Dermatologie, 89290, Buch, Germany
| | - V Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
| | - T Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
| | - M Welle
- DermFocus, University of Bern, 3001, Bern, Switzerland.,Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
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9
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Hug P, Jude R, Henkel J, Jagannathan V, Leeb T. A novel
KIT
deletion variant in a German Riding Pony with white‐spotting coat colour phenotype. Anim Genet 2019; 50:761-763. [DOI: 10.1111/age.12840] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2019] [Indexed: 11/28/2022]
Affiliation(s)
- P. Hug
- Institute of Genetics, Vetsuisse Faculty University of Bern Bern 3001 Switzerland
- DermFocus University of Bern Bern 3001 Switzerland
| | - R. Jude
- RJC Weilerswist 53919 Germany
| | - J. Henkel
- Institute of Genetics, Vetsuisse Faculty University of Bern Bern 3001 Switzerland
- DermFocus University of Bern Bern 3001 Switzerland
| | - V. Jagannathan
- Institute of Genetics, Vetsuisse Faculty University of Bern Bern 3001 Switzerland
- DermFocus University of Bern Bern 3001 Switzerland
| | - T. Leeb
- Institute of Genetics, Vetsuisse Faculty University of Bern Bern 3001 Switzerland
- DermFocus University of Bern Bern 3001 Switzerland
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10
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Bauer A, de Lucia M, Leuthard F, Jagannathan V, Leeb T. Compound heterozygosity for TNXB genetic variants in a mixed-breed dog with Ehlers-Danlos syndrome. Anim Genet 2019; 50:546-549. [PMID: 31365140 DOI: 10.1111/age.12830] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2019] [Indexed: 11/30/2022]
Abstract
The Ehlers-Danlos syndromes (EDSs) are a heterogeneous group of inherited connective tissue disorders characterized by skin hyperextensibility, joint hypermobility and tissue fragility. Inherited disorders similar to human EDS have been reported in different mammalian species. In the present study, we investigated a female mixed-breed dog with clinical signs of EDS. Whole-genome sequencing of the affected dog revealed two missense variants in the TNXB gene, encoding the extracellular matrix protein tenascin XB. In humans, TNXB genetic variants cause classical-like EDS or the milder hypermobile EDS. The affected dog was heterozygous at both identified variants. Each variant allele was transmitted from one of the case's parents, consistent with compound heterozygosity. Although one of the variant alleles, XM_003431680.3:c.2012G>A, p.(Ser671Asn), was private to the family of the affected dog and absent from whole-genome sequencing data of 599 control dogs, the second variant allele, XM_003431680.3:c.2900G>A, p.(Gly967Asp), is present at a low frequency in the Chihuahua and Poodle population. Given that TNXB is a functional candidate gene for EDS, we suggest that compound heterozygosity for the identified TNXB variants may have caused the EDS-like phenotype in the affected dog. Chihuahuas and Poodles should be monitored for EDS cases, which might confirm the hypothesized pathogenic effect of the segregating TNXB variant.
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Affiliation(s)
- A Bauer
- Vetsuisse Faculty, Institute of Genetics, University of Bern, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
| | - M de Lucia
- San Marco Veterinary Clinic and Laboratory, Via Dell'Industria 3, 35030, Veggiano, Italy
| | - F Leuthard
- Vetsuisse Faculty, Institute of Genetics, University of Bern, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
| | - V Jagannathan
- Vetsuisse Faculty, Institute of Genetics, University of Bern, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
| | - T Leeb
- Vetsuisse Faculty, Institute of Genetics, University of Bern, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
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11
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Vimercati S, Elli S, Jagannathan V, Pandey AV, Peduto N, Leeb T, Mevissen M. In silico and in vitro analysis of genetic variants of the equine CYP3A94, CYP3A95 and CYP3A97 isoenzymes. Toxicol In Vitro 2019; 60:116-124. [PMID: 31108125 DOI: 10.1016/j.tiv.2019.05.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/08/2019] [Accepted: 05/14/2019] [Indexed: 11/28/2022]
Abstract
Cytochrome P450 enzymes (CYPs) of the equine CYP3A subfamily are predominantly involved in drug metabolism. In this study, genetic variants of the equine CYP3A94, CYP3A95, and CYP3A97 were identified and characterized using in silico modeling and in vitro enzyme kinetics. The genomes of 81 horses were sequenced to obtain the genetic variants. Structural CYP modifications of the most frequent variants were analyzed in silico using the 3D-structures predicted by homology modeling. Enzyme kinetic analyses were performed using testosterone as substrate. Twenty genetic variants were found including five missense variants (CYP3A94:p.Asp217Asn, CYP3A95:p.Asp214His, CYP3A95:p.Ser392Thr, CYP3A97:p.Ile119Thr, CYP3A97:p.Met500Val) with a higher percentage of minor allele frequency (MAF) (range 0.2-0.4). A splice-site variant (c.798 + 1G > A) in CYP3A94, likely to generate a truncated protein, was found in 50% of the horses. CYP3A94:p.Asp217Asn and CYP3A95:p.Asp214His were localized on the CYP F-α-helix, an important region for the substrate interactions in the human CYP3A4. Testosterone 2β-hydroxylation was diminished in CYP3A94217Asn and CYP3A95392Thr. Ketoconazole inhibited 2β-hydroxylation differently in the five variants with the most pronounced inhibition obtained for CYP3A95392Thr. In vitro and in silico analyses of genetic variants allow unraveling structural features in equine CYPs that correlate with changes in the CYP activity.
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Affiliation(s)
- S Vimercati
- Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University of Bern, Länggassstrasse 124, 3012 Bern, Switzerland.
| | - S Elli
- Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni, Via G. Colombo 81, 20133 Milano, Italy.
| | - V Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3012 Bern, Switzerland.
| | - A V Pandey
- Department of Pediatrics, Division of Pediatric Endocrinology and Diabetology, University Children's Hospital, Bern, Switzerland.
| | - N Peduto
- Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University of Bern, Länggassstrasse 124, 3012 Bern, Switzerland.
| | - T Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3012 Bern, Switzerland.
| | - M Mevissen
- Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University of Bern, Länggassstrasse 124, 3012 Bern, Switzerland.
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12
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Henkel J, Lafayette C, Brooks SA, Martin K, Patterson-Rosa L, Cook D, Jagannathan V, Leeb T. Whole-genome sequencing reveals a large deletion in the MITF gene in horses with white spotted coat colour and increased risk of deafness. Anim Genet 2019; 50:172-174. [PMID: 30644113 DOI: 10.1111/age.12762] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2018] [Indexed: 01/18/2023]
Abstract
White spotting phenotypes in horses are highly valued in some breeds. They are quite variable and may range from the common white markings up to completely white horses. EDNRB, KIT, MITF, PAX3 and TRPM1 represent known candidate genes for white spotting phenotypes in horses. For the present study, we investigated an American Paint Horse family segregating a phenotype involving white spotting and blue eyes. Six of eight horses with the white-spotting phenotype were deaf. We obtained whole-genome sequence data from an affected horse and specifically searched for structural variants in the known candidate genes. This analysis revealed a heterozygous ~63-kb deletion spanning exons 6-9 of the MITF gene (chr16:21 503 211-21 566 617). We confirmed the breakpoints of the deletion by PCR and Sanger sequencing. PCR-based genotyping revealed that all eight available affected horses from the family carried the deletion. The finding of an MITF variant fits well with the syndromic phenotype involving both depigmentation and an increased risk for deafness and corresponds to human Waardenburg syndrome type 2A. Our findings will enable more precise genetic testing for depigmentation phenotypes in horses.
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Affiliation(s)
- J Henkel
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
| | | | - S A Brooks
- Department of Animal Sciences, University of Florida, Gainesville, FL, 32611-0910, USA
| | - K Martin
- Etalon Inc., Menlo Park, CA, 94025, USA
| | - L Patterson-Rosa
- Department of Animal Sciences, University of Florida, Gainesville, FL, 32611-0910, USA
| | - D Cook
- Etalon Inc., Menlo Park, CA, 94025, USA
| | - V Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
| | - T Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
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13
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Jagannathan V, Gerber V, Rieder S, Tetens J, Thaller G, Drögemüller C, Leeb T. Comprehensive characterization of horse genome variation by whole-genome sequencing of 88 horses. Anim Genet 2018; 50:74-77. [PMID: 30525216 DOI: 10.1111/age.12753] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2018] [Indexed: 11/29/2022]
Abstract
Whole-genome sequencing studies are vital to gain a thorough understanding of genomic variation. Here, we summarize the results of a whole-genome sequencing study comprising 88 horses and ponies from diverse breeds at 19.1× average coverage. The paired-end reads were mapped to the current EquCab3.0 horse reference genome assembly, and we identified approximately 23.5 million single nucleotide variants and 2.3 million short indel variants. Our dataset included at least 7 million variants that were not previously reported. On average, each individual horse genome carried ∼5.7 million single nucleotides and 0.8 million small indel variants with respect to the reference genome assembly. The variants were functionally annotated. We provide two examples for potentially deleterious recessive alleles that were identified in a heterozygous state in individual genome sequences. Appropriate management of such deleterious recessive alleles in horse breeding programs should help to improve fertility and reduce the prevalence of heritable diseases. This comprehensive dataset has been made publicly available, will represent a valuable resource for future horse genetic studies and supports the goal of accelerating the rates of genetic gain in domestic horse.
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Affiliation(s)
- V Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - V Gerber
- Department of Clinical Veterinary Medicine, Swiss Institute of Equine Medicine, Vetsuisse Faculty, University of Bern, and Agroscope, Länggassstrasse 124, 3012, Bern, Switzerland
| | - S Rieder
- Swiss National Stud Farm, Agroscope, 1580, Avenches, Switzerland
| | - J Tetens
- Department of Animal Sciences, Functional Breeding Group, Georg-August University Göttingen, Burckhardtweg 2, 37077, Göttingen, Germany
| | - G Thaller
- Institute of Animal Breeding and Husbandry, Christian-Albrechts University Kiel, Hermann-Rodewald-Strasse 6, 24098, Kiel, Germany
| | - C Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - T Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
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14
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Hofstetter S, Seefried F, Häfliger IM, Jagannathan V, Leeb T, Drögemüller C. A non-coding regulatory variant in the 5'-region of the MITF gene is associated with white-spotted coat in Brown Swiss cattle. Anim Genet 2018; 50:27-32. [PMID: 30506810 DOI: 10.1111/age.12751] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2018] [Indexed: 01/29/2023]
Abstract
Recently, the Swiss breeding association reported an increasing number of white-spotted cattle in the Brown Swiss breed, which is normally solid brown coloured. A total of 60 Brown Swiss cattle with variably sized white abdominal spots, facial markings and depigmented claws were collected for this study. A genome-wide association study using 40k SNP genotypes of 20 cases and 1619 controls enabled us to identify an associated genome region on chromosome 22 containing the MITF gene, encoding the melanogenesis associated transcription factor. Variants at the MITF locus have been reported before to be associated with white or white-spotted phenotypes in other species such as horses, dogs and mice. Whole-genome sequencing of a single white-spotted cow and subsequent genotyping of 172 Brown Swiss cattle revealed two significantly associated completely linked single nucleotide variants (rs722765315 and rs719139527). Both variants are located in the 5'-regulatory region of the bovine MITF gene, and comparative sequence analysis showed that the variant rs722765315, located 139 kb upstream of the transcription start site of the bovine melanocyte-specific MITF transcript, is situated in a multi-species conserved sequence element which is supposed to be regulatory important. Therefore, we hypothesize that rs722765315 represents the most likely causative variant for the white-spotting phenotype observed in Brown Swiss cattle. Presence of the mutant allele in a heterozygous or homozygous state supports a dominant mode of inheritance with incomplete penetrance and results in a variable extent of coat colour depigmentation.
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Affiliation(s)
- S Hofstetter
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | | | - I M Häfliger
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - V Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - T Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - C Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
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15
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Bauer A, Hadji Rasouliha S, Brunner MT, Jagannathan V, Bucher I, Bannoehr J, Varjonen K, Bond R, Bergvall K, Welle MM, Roosje P, Leeb T. A second KRT71 allele in curly coated dogs. Anim Genet 2018; 50:97-100. [PMID: 30444027 DOI: 10.1111/age.12743] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2018] [Indexed: 01/20/2023]
Abstract
Major characteristics of coat variation in dogs can be explained by variants in only a few genes. Until now, only one missense variant in the KRT71 gene, p.Arg151Trp, has been reported to cause curly hair in dogs. However, this variant does not explain the curly coat in all breeds as the mutant 151 Trp allele, for example, is absent in Curly Coated Retrievers. We sequenced the genome of a Curly Coated Retriever at 22× coverage and searched for variants in the KRT71 gene. Only one protein-changing variant was present in a homozygous state in the Curly Coated Retriever and absent or present in a heterozygous state in 221 control dogs from different dog breeds. This variant, NM_001197029.1:c.1266_1273delinsACA, was an indel variant in exon 7 that caused a frameshift and an altered and probably extended C-terminus of the KRT71 protein NP_001183958.1:p.(Ser422ArgfsTer?). Using Sanger sequencing, we found that the variant was fixed in a cohort of 125 Curly Coated Retrievers and segregating in five of 14 additionally tested breeds with a curly or wavy coat. KRT71 variants cause curly hair in humans, mice, rats, cats and dogs. Specific KRT71 variants were further shown to cause alopecia. Based on this knowledge from other species and the predicted molecular consequence of the newly identified canine KRT71 variant, it is a compelling candidate causing a second curly hair allele in dogs. It might cause a slightly different coat phenotype than the previously published p.Arg151Trp variant and could potentially be associated with follicular dysplasia in dogs.
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Affiliation(s)
- A Bauer
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland.,Dermfocus, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - S Hadji Rasouliha
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland.,Dermfocus, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - M T Brunner
- Dermfocus, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland.,Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - V Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland.,Dermfocus, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - I Bucher
- Dermfocus, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland.,Division of Clinical Dermatology, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - J Bannoehr
- Dermfocus, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland.,Division of Clinical Dermatology, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland.,Dermatology Department, Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk, CB8 7UU, UK
| | - K Varjonen
- Department Clinical Sciences and Services, Royal Veterinary College, Hatfield, AL9 7TA, UK.,Anicura Albano Animal Hospital, Danderyd, 18236, Sweden
| | - R Bond
- Department Clinical Sciences and Services, Royal Veterinary College, Hatfield, AL9 7TA, UK
| | - K Bergvall
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Box 7054, Uppsala, 750 07, Sweden
| | - M M Welle
- Dermfocus, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland.,Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - P Roosje
- Dermfocus, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland.,Division of Clinical Dermatology, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - T Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland.,Dermfocus, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
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16
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Gallana M, Utsunomiya YT, Dolf G, Pintor Torrecilha RB, Falbo AK, Jagannathan V, Leeb T, Reichler I, Sölkner J, Schelling C. Genome-wide association study and heritability estimate for ectopic ureters in Entlebucher mountain dogs. Anim Genet 2018; 49:645-650. [PMID: 30276844 DOI: 10.1111/age.12728] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2018] [Indexed: 11/28/2022]
Abstract
An ectopic ureter is a congenital anomaly which may lead to urinary incontinence and without a surgical intervention even to end-stage kidney disease. A genetic component contributes to the development of this anomaly in Entlebucher mountain dogs (EMD); however, its nature remains unclear. Using the Illumina CanineHD bead chip, a case-control genome-wide association study was performed to identify SNPs associated with the trait. Six loci on canine chromosomes 3, 17, 27 and 30 were identified with 16 significantly associated SNPs. There was no single outstanding SNP associated with the phenotype, and the association signals were not close to known genes involved in human congenital anomalies of the kidney or lower urinary tract. Additional research will be necessary to elucidate the potential role of the associated genes in the development of ectopic ureters in the EMD breed.
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Affiliation(s)
- M Gallana
- Clinic for Reproductive Medicine, Vetsuisse-Faculty, University of Zurich, Winterthurerstrasse 260, 8057, Zurich, Switzerland
| | - Y T Utsunomiya
- Department of Preventive Veterinary Medicine and Animal Reproduction, School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), 14884-900, Jaboticabal, São Paulo, Brazil
| | - G Dolf
- Vetsuisse-Faculty, Institute of Genetics, University of Bern, Bremgartenstrasse 109a, 3012, Bern, Switzerland
| | - R B Pintor Torrecilha
- Department of Preventive Veterinary Medicine and Animal Reproduction, School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), 14884-900, Jaboticabal, São Paulo, Brazil
| | - A-K Falbo
- Clinic for Reproductive Medicine, Vetsuisse-Faculty, University of Zurich, Winterthurerstrasse 260, 8057, Zurich, Switzerland
| | - V Jagannathan
- Vetsuisse-Faculty, Institute of Genetics, University of Bern, Bremgartenstrasse 109a, 3012, Bern, Switzerland
| | - T Leeb
- Vetsuisse-Faculty, Institute of Genetics, University of Bern, Bremgartenstrasse 109a, 3012, Bern, Switzerland
| | - I Reichler
- Clinic for Reproductive Medicine, Vetsuisse-Faculty, University of Zurich, Winterthurerstrasse 260, 8057, Zurich, Switzerland
| | - J Sölkner
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences, Gregor Mendel Straße 33, 1180, Vienna, Austria
| | - C Schelling
- Vetsuisse-Faculty, Clinic for Reproductive Medicine and Center of Clinical Studies, University of Zurich, Eschikon 27, EHB F 22.1, 8315, Lindau, Switzerland
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17
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Spycher M, Bauer A, Jagannathan V, Frizzi M, De Lucia M, Leeb T. A frameshift variant in the COL5A1 gene in a cat with Ehlers-Danlos syndrome. Anim Genet 2018; 49:641-644. [PMID: 30246406 DOI: 10.1111/age.12727] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/21/2018] [Indexed: 11/27/2022]
Abstract
Ehlers-Danlos syndrome (EDS) is a group of heritable connective tissue disorders caused by defective collagen synthesis or incorrect assembly of the collagen triple helical structure. EDS is characterised by joint hypermobility, skin hyperextensibility, abnormal scarring, poor wound healing and tissue friability. Human EDS may be caused by variants in several different genes including COL5A1, which encodes the collagen type V alpha 1 chain. For the present study we investigated a 1.5-year-old, spayed female, domestic shorthair cat with EDS. The affected cat showed multiple recurrent skin tears, hyperextensibility of the skin and joint abnormalities. We obtained whole genome sequencing data from the affected cat and searched for variants in candidate genes known to cause EDS. We detected a heterozygous single base-pair deletion in exon 43 of the COL5A1 gene, namely c.3420delG. The deletion was predicted to result in a frameshift and premature stop codon: p.(Leu1141SerfsTer134). Sanger sequencing confirmed that the variant was present in the affected cat and absent from 103 unaffected cats from different breeds. The variant was also absent from a Burmese cat with EDS. Based on knowledge about the functional impact of COL5A1 variants in other species, COL5A1:c.3420delG represents a compelling candidate causative variant for the observed EDS in the affected cat.
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Affiliation(s)
- M Spycher
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
| | - A Bauer
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
| | - V Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
| | - M Frizzi
- San Marco Veterinary Clinic, Via Sorio 114/C, 35141, Padova, Italy
| | - M De Lucia
- San Marco Veterinary Clinic, Via Sorio 114/C, 35141, Padova, Italy.,San Marco Veterinary Laboratory, Via Sorio 114/C, 35141, Padova, Italy
| | - T Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
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18
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Dürig N, Letko A, Lepori V, Hadji Rasouliha S, Loechel R, Kehl A, Hytönen MK, Lohi H, Mauri N, Dietrich J, Wiedmer M, Drögemüller M, Jagannathan V, Schmutz SM, Leeb T. Two MC1R loss-of-function alleles in cream-coloured Australian Cattle Dogs and white Huskies. Anim Genet 2018; 49:284-290. [PMID: 29932470 DOI: 10.1111/age.12660] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/19/2018] [Indexed: 11/27/2022]
Abstract
Loss-of-function variants in the MC1R gene cause recessive red or yellow coat-colour phenotypes in many species. The canine MC1R:c.916C>T (p.Arg306Ter) variant is widespread and found in a homozygous state in many uniformly yellow- or red-coloured dogs. We investigated cream-coloured Australian Cattle Dogs whose coat colour could not be explained by this variant. A genome-wide association study with 10 cream and 123 red Australian Cattle Dogs confirmed that the cream locus indeed maps to MC1R. Whole-genome sequencing of cream dogs revealed a single nucleotide variant within the MITF binding site of the canine MC1R promoter. We propose to designate the mutant alleles at MC1R:c.916C>T as e1 and at the new promoter variant as e2 . Both alleles segregate in the Australian Cattle Dog breed. When we considered both alleles in combination, we observed perfect association between the MC1R genotypes and the cream coat colour phenotype in a cohort of 10 cases and 324 control dogs. Analysis of the MC1R transcript levels in an e1 /e2 compound heterozygous dog confirmed that the transcript levels of the e2 allele were markedly reduced with respect to the e1 allele. We further report another MC1R loss-of-function allele in Alaskan and Siberian Huskies caused by a 2-bp deletion in the coding sequence, MC1R:c.816_817delCT. We propose to term this allele e3 . Huskies that carry two copies of MC1R loss-of-function alleles have a white coat colour.
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Affiliation(s)
- N Dürig
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
| | - A Letko
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
| | - V Lepori
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
| | - S Hadji Rasouliha
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
| | | | - A Kehl
- Laboklin, 97688, Bad Kissingen, Germany
| | - M K Hytönen
- Department of Veterinary Biosciences, University of Helsinki, 00014, Helsinki, Finland.,Research Programs Unit, Molecular Neurology, University of Helsinki, 00014, Helsinki, Finland.,Folkhälsan Institute of Genetics, University of Helsinki, 00290, Helsinki, Finland
| | - H Lohi
- Department of Veterinary Biosciences, University of Helsinki, 00014, Helsinki, Finland.,Research Programs Unit, Molecular Neurology, University of Helsinki, 00014, Helsinki, Finland.,Folkhälsan Institute of Genetics, University of Helsinki, 00290, Helsinki, Finland
| | - N Mauri
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
| | - J Dietrich
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
| | - M Wiedmer
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
| | - M Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
| | - V Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
| | - S M Schmutz
- Department of Animal and Poultry Science, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - T Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
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19
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Minor KM, Letko A, Becker D, Drögemüller M, Mandigers PJJ, Bellekom SR, Leegwater PAJ, Stassen QEM, Putschbach K, Fischer A, Flegel T, Matiasek K, Ekenstedt KJ, Furrow E, Patterson EE, Platt SR, Kelly PA, Cassidy JP, Shelton GD, Lucot K, Bannasch DL, Martineau H, Muir CF, Priestnall SL, Henke D, Oevermann A, Jagannathan V, Mickelson JR, Drögemüller C. Canine NAPEPLD-associated models of human myelin disorders. Sci Rep 2018; 8:5818. [PMID: 29643404 PMCID: PMC5895582 DOI: 10.1038/s41598-018-23938-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 03/20/2018] [Indexed: 01/05/2023] Open
Abstract
Canine leukoencephalomyelopathy (LEMP) is a juvenile-onset neurodegenerative disorder of the CNS white matter currently described in Rottweiler and Leonberger dogs. Genome-wide association study (GWAS) allowed us to map LEMP in a Leonberger cohort to dog chromosome 18. Subsequent whole genome re-sequencing of a Leonberger case enabled the identification of a single private homozygous non-synonymous missense variant located in the highly conserved metallo-beta-lactamase domain of the N-acyl phosphatidylethanolamine phospholipase D (NAPEPLD) gene, encoding an enzyme of the endocannabinoid system. We then sequenced this gene in LEMP-affected Rottweilers and identified a different frameshift variant, which is predicted to replace the C-terminal metallo-beta-lactamase domain of the wild type protein. Haplotype analysis of SNP array genotypes revealed that the frameshift variant was present in diverse haplotypes in Rottweilers, and also in Great Danes, indicating an old origin of this second NAPEPLD variant. The identification of different NAPEPLD variants in dog breeds affected by leukoencephalopathies with heterogeneous pathological features, implicates the NAPEPLD enzyme as important in myelin homeostasis, and suggests a novel candidate gene for myelination disorders in people.
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Affiliation(s)
- K M Minor
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN, 55108, USA
| | - A Letko
- Institute of Genetics, University of Bern, Bern, 3001, Switzerland
| | - D Becker
- Institute of Genetics, University of Bern, Bern, 3001, Switzerland
| | - M Drögemüller
- Institute of Genetics, University of Bern, Bern, 3001, Switzerland
| | - P J J Mandigers
- Department of Clinical Sciences of Companion Animals, Utrecht University, Utrecht, 3508, CM, The Netherlands
| | - S R Bellekom
- Department of Clinical Sciences of Companion Animals, Utrecht University, Utrecht, 3508, CM, The Netherlands
| | - P A J Leegwater
- Department of Clinical Sciences of Companion Animals, Utrecht University, Utrecht, 3508, CM, The Netherlands
| | - Q E M Stassen
- Department of Clinical Sciences of Companion Animals, Utrecht University, Utrecht, 3508, CM, The Netherlands
| | - K Putschbach
- Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-University, Munich, 80539, Germany
| | - A Fischer
- Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-University, Munich, 80539, Germany
| | - T Flegel
- Department of Small Animal Medicine, University of Leipzig, Leipzig, 04103, Germany
| | - K Matiasek
- Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-University, Munich, 80539, Germany
| | - K J Ekenstedt
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - E Furrow
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN, 55108, USA
| | - E E Patterson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN, 55108, USA
| | - S R Platt
- Small Animal Medicine and Surgery, University of Georgia, Athens, GA, 30602, USA
| | - P A Kelly
- Veterinary Sciences Centre, University College Dublin, Dublin, D04 V1W8, Ireland
| | - J P Cassidy
- Veterinary Sciences Centre, University College Dublin, Dublin, D04 V1W8, Ireland
| | - G D Shelton
- Department of Pathology, University of California, La Jolla, CA, 92093, USA
| | - K Lucot
- Department of Population Health and Reproduction, University of California-Davis, Davis, CA, 95616, USA
| | - D L Bannasch
- Department of Population Health and Reproduction, University of California-Davis, Davis, CA, 95616, USA
| | - H Martineau
- Pathobiology and Population Sciences, The Royal Veterinary College, North Mymms, AL9 7TA, UK
| | - C F Muir
- Pathobiology and Population Sciences, The Royal Veterinary College, North Mymms, AL9 7TA, UK
| | - S L Priestnall
- Pathobiology and Population Sciences, The Royal Veterinary College, North Mymms, AL9 7TA, UK
| | - D Henke
- Division of Clinical Neurology, University of Bern, Bern, 3001, Switzerland
| | - A Oevermann
- Division of Neurological Sciences, University of Bern, Bern, 3001, Switzerland
| | - V Jagannathan
- Institute of Genetics, University of Bern, Bern, 3001, Switzerland
| | - J R Mickelson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN, 55108, USA
| | - C Drögemüller
- Institute of Genetics, University of Bern, Bern, 3001, Switzerland.
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20
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Bauer A, Nimmo J, Newman R, Brunner M, Welle MM, Jagannathan V, Leeb T. A splice site variant in the SUV39H2 gene in Greyhounds with nasal parakeratosis. Anim Genet 2018; 49:137-140. [PMID: 29423952 DOI: 10.1111/age.12643] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/19/2017] [Indexed: 11/27/2022]
Abstract
Hereditary nasal parakeratosis (HNPK), described in the Labrador Retriever breed, is a monogenic autosomal recessive disorder that causes crusts and fissures on the nasal planum of otherwise healthy dogs. Our group previously showed that this genodermatosis may be caused by a missense variant located in the SUV39H2 gene encoding a histone 3 lysine 9 methyltransferase, a chromatin modifying enzyme with a potential role in keratinocyte differentiation. In the present study, we investigated a litter of Greyhounds in which six out of eight puppies were affected with parakeratotic lesions restricted to the nasal planum. Clinically and histologically, the lesions were comparable to HNPK in Labrador Retrievers. Whole genome sequencing of one affected Greyhound revealed a 4-bp deletion at the 5'-end of intron 4 of the SUV39H2 gene that was absent in 188 control dog and three wolf genomes. The variant was predicted to disrupt the 5'-splice site with subsequent loss of SUV39H2 function. The six affected puppies were homozygous for the variant, whereas the two non-affected littermates were heterozygous. Genotyping of a larger cohort of Greyhounds revealed that the variant is segregating in the breed and that this breed might benefit from genetic testing to avoid carrier × carrier matings.
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Affiliation(s)
- A Bauer
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
| | - J Nimmo
- ASAP Laboratory, Mulgrave, Vic., 3170, Australia
| | - R Newman
- Mobile Vet Services and Supplies, Warwick, Qld, 4370, Australia
| | - M Brunner
- DermFocus, University of Bern, 3001, Bern, Switzerland.,Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - M M Welle
- DermFocus, University of Bern, 3001, Bern, Switzerland.,Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - V Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
| | - T Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
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21
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Abstract
Coat colour dilution may be the result of altered melanosome transport in melanocytes. Loss-of-function variants in the melanophilin gene (MLPH) cause a recessively inherited form of coat colour dilution in many mammalian and avian species including the dog. MLPH corresponds to the D locus in many domestic animals, and recessive alleles at this locus are frequently denoted with d. In this study, we investigated dilute coloured Chow Chows whose coat colour could not be explained by their genotype at the previously known MLPH:c.-22G>A variant. Whole genome sequencing of such a dilute Chow Chow revealed another variant in the MLPH gene: MLPH:c.705G>C. We propose to designate the corresponding mutant alleles at these two variants d1 and d2 . We performed an association study in a cohort of 15 dilute and 28 non-dilute Chow Chows. The dilute dogs were all either compound heterozygous d1 /d2 or homozygous d2 /d2 , whereas the non-dilute dogs carried at least one wildtype allele D. The d2 allele did not occur in 417 dogs from diverse other breeds. However, when we genotyped a Sloughi family, in which a dilute coloured puppy had been born out of non-dilute parents, we again observed perfect co-segregation of the newly discovered d2 allele with coat colour dilution. Finally, we identified a blue Thai Ridgeback with the d1 /d2 genotype. Thus, our data identify the MLPH:c.705G>C as a variant explaining a second canine dilution allele. Although relatively rare overall, this d2 allele is segregating in at least three dog breeds, Chow Chows, Sloughis and Thai Ridgebacks.
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Affiliation(s)
- A Bauer
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
| | - A Kehl
- Laboklin, 97688, Bad Kissingen, Germany
| | - V Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
| | - T Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
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22
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Felkel S, Vogl C, Rigler D, Jagannathan V, Leeb T, Fries R, Neuditschko M, Rieder S, Velie B, Lindgren G, Rubin CJ, Schlötterer C, Rattei T, Brem G, Wallner B. Asian horses deepen the MSY phylogeny. Anim Genet 2018; 49:90-93. [PMID: 29333704 DOI: 10.1111/age.12635] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2017] [Indexed: 01/09/2023]
Abstract
Humans have shaped the population history of the horse ever since domestication about 5500 years ago. Comparative analyses of the Y chromosome can illuminate the paternal origin of modern horse breeds. This may also reveal different breeding strategies that led to the formation of extant breeds. Recently, a horse Y-chromosomal phylogeny of modern horses based on 1.46 Mb of the male-specific Y (MSY) was generated. We extended this dataset with 52 samples from five European, two American and seven Asian breeds. As in the previous study, almost all modern European horses fall into a crown group, connected via a few autochthonous Northern European lineages to the outgroup, the Przewalski's Horse. In total, we now distinguish 42 MSY haplotypes determined by 158 variants within domestic horses. Asian horses show much higher diversity than previously found in European breeds. The Asian breeds also introduce a deep split to the phylogeny, preliminarily dated to 5527 ± 872 years. We conclude that the deep splitting Asian Y haplotypes are remnants of a far more diverse ancient horse population, whose haplotypes were lost in other lineages.
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Affiliation(s)
- S Felkel
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria.,Vienna Graduate School of Population Genetics, Vienna, Austria
| | - C Vogl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | - D Rigler
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | - V Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - T Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - R Fries
- Lehrstuhl für Tierzucht, Technische Universität München, Freising, Germany
| | - M Neuditschko
- Agroscope, Swiss National Stud Farm, Avenches, Switzerland
| | - S Rieder
- Agroscope, Swiss National Stud Farm, Avenches, Switzerland
| | - B Velie
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - G Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - C-J Rubin
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - C Schlötterer
- Institut für Populationsgenetik, University of Veterinary Medicine Vienna, Vienna, Austria
| | - T Rattei
- Department of Microbiology and Ecosystem Science, Division of Computational Systems Biology, University of Vienna, Vienna, Austria
| | - G Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | - B Wallner
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
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23
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Högler S, Mauri N, Kleiter M, Leschnik M, Oevermann A, Henke D, Dietschi E, Wiedmer M, Dietrich J, Steffen F, Schuller S, Gurtner C, Stokar-Regenscheit N, O'Toole D, Bilzer T, Herden C, Jagannathan V, Leeb T. Genetic Variants in Kcnj10 and Atp1b2 in Malinois Puppies with Spongy Degeneration and Cerebellar Ataxia. J Comp Pathol 2018. [DOI: 10.1016/j.jcpa.2017.10.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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24
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Caduff M, Bauer A, Jagannathan V, Leeb T. A single base deletion in the SLC45A2 gene in a Bullmastiff with oculocutaneous albinism. Anim Genet 2017; 48:619-621. [PMID: 28737247 DOI: 10.1111/age.12582] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2017] [Indexed: 11/29/2022]
Abstract
Oculocutaneous albinism type 4 (OCA4) in humans and similar phenotypes in many animal species are caused by variants in the SLC45A2 gene, encoding a putative sugar transporter. In dog, two independent SLC45A2 variants are known that cause oculocutaneous albinism in Doberman Pinschers and several small dog breeds respectively. For the present study, we investigated a Bullmastiff with oculocutaneous albinism. The affected dog was highly inbred and resulted from the mating of a sire to its own grandmother. We obtained whole genome sequence data from the affected dog and searched specifically for variants in candidate genes known to cause albinism. We detected a single base deletion in exon 6 of the SLC45A2 gene (NM_001037947.1:c.1287delC) that has not been reported thus far. This deletion is predicted to result in an early premature stop codon. It was confirmed by Sanger sequencing and perfectly co-segregated with the phenotype in the available family members. We genotyped 174 unrelated dogs from diverse breeds, all of which were homozygous wildtype. We therefore suggest that SLC45A2:c.1287delC causes the observed oculocutaneous albinism in the affected Bullmastiff.
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Affiliation(s)
- M Caduff
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
| | - A Bauer
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
| | - V Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
| | - T Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
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25
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Khan SA, Kannan U, Jagannathan V. Development of whole core pin-by-pin transport theory model in hexagonal geometry. ANN NUCL ENERGY 2017. [DOI: 10.1016/j.anucene.2017.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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26
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Jagannathan V, Jain RP, Kumar V, Gupta HC, Krishnani PD. A Diffusion Iterative Model for Simulation of Reactivity Devices in Pressurized Heavy Water Reactors. NUCL SCI ENG 2017. [DOI: 10.13182/nse90-a23722] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- V. Jagannathan
- Bhabha Atomic Research Center, Reactor Analysis and Systems Division Central Complex, 5th Floor, Bombay 400 085, India
| | - R. P. Jain
- Bhabha Atomic Research Center, Theoretical Physics Division Central Complex, 5th Floor, Bombay 400 085, India
| | - Vinod Kumar
- Bhabha Atomic Research Center, Theoretical Physics Division Central Complex, 5th Floor, Bombay 400 085, India
| | - H. C. Gupta
- Bhabha Atomic Research Center, Theoretical Physics Division Central Complex, 5th Floor, Bombay 400 085, India
| | - P. D. Krishnani
- Bhabha Atomic Research Center, Reactor Analysis and Systems Division Central Complex, 5th Floor, Bombay 400 085, India
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27
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Dürig N, Jude R, Holl H, Brooks SA, Lafayette C, Jagannathan V, Leeb T. Whole genome sequencing reveals a novel deletion variant in the KIT
gene in horses with white spotted coat colour phenotypes. Anim Genet 2017; 48:483-485. [DOI: 10.1111/age.12556] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/13/2017] [Indexed: 01/24/2023]
Affiliation(s)
- N. Dürig
- Vetsuisse Faculty; Institute of Genetics; University of Bern; 3001 Bern Switzerland
- DermFocus; University of Bern; 3001 Bern Switzerland
| | - R. Jude
- Vetsuisse Faculty; Institute of Genetics; University of Bern; 3001 Bern Switzerland
- DermFocus; University of Bern; 3001 Bern Switzerland
- RJC; 53919 Weilerswist Germany
| | - H. Holl
- Department of Animal Sciences; University of Florida; Gainesville FL 32611-0910 USA
- Etalon Inc.; Menlo Park CA 94025 USA
| | - S. A. Brooks
- Department of Animal Sciences; University of Florida; Gainesville FL 32611-0910 USA
| | | | - V. Jagannathan
- Vetsuisse Faculty; Institute of Genetics; University of Bern; 3001 Bern Switzerland
- DermFocus; University of Bern; 3001 Bern Switzerland
| | - T. Leeb
- Vetsuisse Faculty; Institute of Genetics; University of Bern; 3001 Bern Switzerland
- DermFocus; University of Bern; 3001 Bern Switzerland
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28
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Jagannathan V, Pal U, Karthikeyan R, Ganesan S, Jain RP, Kamat SU. ATBR—A Thorium Breeder Reactor Concept for Early Induction of Thorium in an Enriched Uranium Reactor. NUCL TECHNOL 2017. [DOI: 10.13182/nt01-a3156] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
| | - Usha Pal
- Bhabha Atomic Research Centre Mumbai 400 085, India
| | | | - S. Ganesan
- Bhabha Atomic Research Centre Mumbai 400 085, India
| | - R. P. Jain
- Bhabha Atomic Research Centre Mumbai 400 085, India
| | - S. U. Kamat
- Bhabha Atomic Research Centre Mumbai 400 085, India
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29
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Hirz M, Drögemüller M, Schänzer A, Jagannathan V, Dietschi E, Goebel HH, Hecht W, Laubner S, Schmidt MJ, Steffen F, Hilbe M, Köhler K, Drögemüller C, Herden C. Neuronal ceroid lipofuscinosis (NCL) is caused by the entire deletion of CLN8 in the Alpenländische Dachsbracke dog. Mol Genet Metab 2017; 120:269-277. [PMID: 28024876 DOI: 10.1016/j.ymgme.2016.12.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 12/14/2016] [Accepted: 12/15/2016] [Indexed: 11/20/2022]
Abstract
Neuronal ceroid lipofuscinoses (NCLs) are inherited lysosomal storage diseases that have been described in a variety of dog breeds, where they are caused by different mutations in different genes. However, the causative gene defect in the breed Alpenländische Dachsbracke remained unknown so far. Here we present two confirmed cases of NCL in Alpenländische Dachsbracke dogs from different litters of the same sire with a different dam harboring the same underlying novel mutation in the CLN8 gene. Case 1, a 2-year-old male Alpenländische Dachsbracke was presented with neurological signs including disorientation, character changes including anxiety states and aggressiveness, sudden blindness and reduction of food intake. Magnetic resonance imaging (MRI) scans showed cerebral atrophy with dilation of all cerebral ventricles, thinning of the intermediate mass of the thalamus and widening of the cerebral sulci. Postmortem examination of the central nervous system (CNS) showed neuronal loss in the cerebral cortex, cerebellum and spinal cord with massive intracellular deposits of ceroid pigment. Additional ceroid-lipofuscin deposits were observed in the enteric nervous system and in macrophages within spleen, lymph nodes and lung. Ultrastructural analyses confirmed NCL with the presence of osmiophilic membrane bounded lamellar-like structures. Case 2, a 1,5-year old female Alpenländische Dachsbracke was presented with progressive generalized forebrain disease including mental changes such as fearful reactions to various kinds of external stimuli and disorientation. The dog also displayed seizures, absence of menace reactions and negative cotton-ball test with normal pupillary light reactions. The clinical and post mortem examination yielded similar results in the brain as in Case 1. Whole genome sequencing of Case 1 and PCR results of both cases revealed a homozygous deletion encompassing the entire CLN8 gene as the most likely causative mutation for the NCL form observed in both cases. The deletion follows recessive inheritance since the dam and a healthy male littermate of Case 1 were tested as heterozygous carriers. This is the first detailed description of CLN8 gene associated NCL in Alpenländische Dachsbracke dogs and thus provides a novel canine CLN8 model for this lysosomal storage disease. The presence of ceroid lipofuscin in extracerebral tissues may help to confirm the diagnosis of NCL in vivo, especially in new dog breeds where the underlying mutation is not known.
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Affiliation(s)
- M Hirz
- Institute of Veterinary Pathology, Justus-Liebig-University Giessen, Germany.
| | - M Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Switzerland
| | - A Schänzer
- Institute of Neuropathology, Justus-Liebig-University Giessen, Germany
| | - V Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Switzerland
| | - E Dietschi
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Switzerland
| | - H H Goebel
- Institute of Neuropathology Charité, University Berlin, Germany
| | - W Hecht
- Institute of Veterinary Pathology, Justus-Liebig-University Giessen, Germany
| | - S Laubner
- Clinic for Small Animals - Surgery, Justus-Liebig-University Giessen, Germany
| | - M J Schmidt
- Clinic for Small Animals - Surgery, Justus-Liebig-University Giessen, Germany
| | - F Steffen
- Clinic for Small Animals - Neurology, Vetsuisse Faculty, University of Zurich, Switzerland
| | - M Hilbe
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Switzerland
| | - K Köhler
- Institute of Veterinary Pathology, Justus-Liebig-University Giessen, Germany
| | - C Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Switzerland
| | - C Herden
- Institute of Veterinary Pathology, Justus-Liebig-University Giessen, Germany
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30
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Khan SA, Jagannathan V, Kannan U, Mathur A. Study of VVER-1000 OECD LEU and MOX Computational Benchmark with VISWAM Code System. Nuclear Energy and Technology 2016. [DOI: 10.1016/j.nucet.2016.11.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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31
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Murgiano L, Waluk D, Towers R, Wiedemar N, Dietrich J, Jagannathan V, Drögemüller M, Druet T, Galichet A, Penedo MC, Müller E, Roosje P, Welle M, Leeb T. P6015 An intronic MBTPS2 variant results in a splicing defect in horses with brindle coat texture. J Anim Sci 2016. [DOI: 10.2527/jas2016.94supplement4155a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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32
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Murgiano L, Jagannathan V, Piffer C, Drögemüller C, Gentile A. P6028 A frameshift mutation in MOCOS is associated with familial renal syndrome in Tyrolean Gray cattle. J Anim Sci 2016. [DOI: 10.2527/jas2016.94supplement4162a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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33
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Brinkmann J, Jagannathan V, Drögemüller C, Rieder S, Leeb T, Thaller G, Tetens J. Genetic variability of the equine casein genes. J Dairy Sci 2016; 99:5486-5497. [DOI: 10.3168/jds.2015-10652] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 03/09/2016] [Indexed: 12/23/2022]
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34
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Khan SA, Mathur A, Jagannathan V. Incorporation of interface current method based on 2D CP approach in VISWAM code system for hexagonal geometry. ANN NUCL ENERGY 2016. [DOI: 10.1016/j.anucene.2016.01.041] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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35
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Brinkmann J, Jagannathan V, Drögemüller C, Rieder S, Leeb T, Thaller G, Tetens J. DNA-based analysis of protein variants reveals different genetic variability of the paralogous equine ß-lactoglobulin genes LGB1 and LGB2. Livest Sci 2016. [DOI: 10.1016/j.livsci.2016.03.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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36
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Menzi F, Besuchet-Schmutz N, Fragnière M, Hofstetter S, Jagannathan V, Mock T, Raemy A, Studer E, Mehinagic K, Regenscheit N, Meylan M, Schmitz-Hsu F, Drögemüller C. A transposable element insertion in APOB causes cholesterol deficiency in Holstein cattle. Anim Genet 2016; 47:253-7. [PMID: 26763170 PMCID: PMC4849205 DOI: 10.1111/age.12410] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2015] [Indexed: 11/29/2022]
Abstract
Cholesterol deficiency, a new autosomal recessive inherited genetic defect in Holstein cattle, has been recently reported to have an influence on the rearing success of calves. The affected animals show unresponsive diarrhea accompanied by hypocholesterolemia and usually die within the first weeks or months of life. Here, we show that whole genome sequencing combined with the knowledge about the pedigree and inbreeding status of a livestock population facilitates the identification of the causative mutation. We resequenced the entire genomes of an affected calf and a healthy partially inbred male carrying one copy of the critical 2.24‐Mb chromosome 11 segment in its ancestral state and one copy of the same segment with the cholesterol deficiency mutation. We detected a single structural variant, homozygous in the affected case and heterozygous in the non‐affected carrier male. The genetic makeup of this key animal provides extremely strong support for the causality of this mutation. The mutation represents a 1.3kb insertion of a transposable LTR element (ERV2‐1) in the coding sequence of the APOB gene, which leads to truncated transcripts and aberrant splicing. This finding was further supported by RNA sequencing of the liver transcriptome of an affected calf. The encoded apolipoprotein B is an essential apolipoprotein on chylomicrons and low‐density lipoproteins, and therefore, the mutation represents a loss of function mutation similar to autosomal recessive inherited familial hypobetalipoproteinemia‐1 (FHBL1) in humans. Our findings provide a direct gene test to improve selection against this deleterious mutation in Holstein cattle.
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Affiliation(s)
- F Menzi
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a CH-3001, Bern, Switzerland
| | - N Besuchet-Schmutz
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a CH-3001, Bern, Switzerland
| | - M Fragnière
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a CH-3001, Bern, Switzerland
| | - S Hofstetter
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a CH-3001, Bern, Switzerland
| | - V Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a CH-3001, Bern, Switzerland
| | - T Mock
- Clinic for Ruminants, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a CH-3001, Bern, Switzerland
| | - A Raemy
- Clinic for Ruminants, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a CH-3001, Bern, Switzerland
| | - E Studer
- Clinic for Ruminants, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a CH-3001, Bern, Switzerland
| | - K Mehinagic
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122 CH-3001, Bern, Switzerland
| | - N Regenscheit
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122 CH-3001, Bern, Switzerland
| | - M Meylan
- Clinic for Ruminants, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a CH-3001, Bern, Switzerland
| | - F Schmitz-Hsu
- Swissgenetics, Meielenfeldweg 12 CH-3052, Zollikofen, Switzerland
| | - C Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a CH-3001, Bern, Switzerland
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37
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Wiedemar N, Riedi AK, Jagannathan V, Drögemüller C, Meylan M. Genetic Abnormalities in a Calf with Congenital Increased Muscular Tonus. J Vet Intern Med 2015; 29:1418-21. [PMID: 26289121 PMCID: PMC4858041 DOI: 10.1111/jvim.13599] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Revised: 05/06/2015] [Accepted: 07/21/2015] [Indexed: 12/12/2022] Open
Affiliation(s)
- N Wiedemar
- Institute of Genetics, Vetsuisse Faculty, University of Berne, Berne, Switzerland
| | - A-K Riedi
- Clinic for Ruminants, Vetsuisse Faculty, University of Berne, Berne, Switzerland
| | - V Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Berne, Berne, Switzerland
| | - C Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Berne, Berne, Switzerland
| | - M Meylan
- Clinic for Ruminants, Vetsuisse Faculty, University of Berne, Berne, Switzerland
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Abstract
Interleukin-26 (IL26) is a member of the IL10 cytokine family. The IL26 gene is located between two other well-known cytokines genes of this family encoding interferon-gamma (IFNG) and IL22 in an evolutionary conserved gene cluster. In contrast to humans and most other mammals, mice lack a functional Il26 gene. We analyzed the genome sequences of other vertebrates for the presence or absence of functional IL26 orthologs and found that the IL26 gene has also become inactivated in several equid species. We detected a one-base pair frameshift deletion in exon 2 of the IL26 gene in the domestic horse (Equus caballus), Przewalski horse (Equus przewalskii) and donkey (Equus asinus). The remnant IL26 gene in the horse is still transcribed and gives rise to at least five alternative transcripts. None of these transcripts share a conserved open reading frame with the human IL26 gene. A comparative analysis across diverse vertebrates revealed that the IL26 gene has also independently been inactivated in a few other mammals, including the African elephant and the European hedgehog. The IL26 gene thus appears to be highly variable, and the conserved open reading frame has been lost several times during mammalian evolution.
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Affiliation(s)
- M Shakhsi-Niaei
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland; Genetics Group, Science Faculty, University of Shahrekord, Rahbar Boulevard, Shahrekord, Iran
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Ramakrishna A, Jagannathan V, Jain R. Analysis of regularly perturbed lattices and reaction rate distributions from TIC experiments for X7 lattices. ANN NUCL ENERGY 2011. [DOI: 10.1016/j.anucene.2011.02.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Obaidurrahman K, Doshi J, Jain R, Jagannathan V. DEVELOPMENT AND VALIDATION OF COUPLED DYNAMICS CODE 'TRIKIN' FOR VVER REACTORS. Nuclear Engineering and Technology 2010. [DOI: 10.5516/net.2010.42.3.259] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Thilagam L, Karthikeyan R, Jagannathan V, Subbaiah K, Lee S. Inter-comparison of JEF-2.2 and JEFF-3.1 evaluated nuclear data through Monte Carlo analysis of VVER-1000 MOX Core Computational Benchmark. ANN NUCL ENERGY 2010. [DOI: 10.1016/j.anucene.2009.11.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Thilagam L, Sunil Sunny C, Jagannathan V, Subbaiah K. A VVER-1000 LEU and MOX assembly computational benchmark analysis using the lattice burnup code EXCEL. ANN NUCL ENERGY 2009. [DOI: 10.1016/j.anucene.2008.12.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Abstract
OBJECTIVE The authors developed a natural language processing (NLP) framework that could be used to extract clinical findings and diagnoses from dictated physician documentation. DESIGN De-identified documentation was made available by i2b2 Bio-informatics research group as a part of their NLP challenge focusing on obesity and its co-morbidities. The authors describe their approach, which used a combination of concept detection, context validation, and the application of a variety of rules to conclude patient diagnoses. RESULTS The framework was successful at correctly identifying diagnoses as judged by NLP challenge organizers when compared with a gold standard of physician annotations. The authors overall kappa values for agreement with the gold standard were 0.92 for explicit textual results and 0.91 for intuited results. The NLP framework compared favorably with those of the other entrants, placing third in textual results and fourth in intuited results in the i2b2 competition. CONCLUSIONS The framework and approach used to detect clinical conditions was reasonably successful at extracting 16 diagnoses related to obesity. The system and methodology merits further development, targeting clinically useful applications.
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Jagannathan V, Mullett CJ, Arbogast JG, Halbritter KA, Yellapragada D, Regulapati S, Bandaru P. Assessment of commercial NLP engines for medication information extraction from dictated clinical notes. Int J Med Inform 2009; 78:284-91. [DOI: 10.1016/j.ijmedinf.2008.08.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2007] [Revised: 08/15/2008] [Accepted: 08/19/2008] [Indexed: 11/29/2022]
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Pal U, Jagannathan V. Radionuclide inventories in the discharged fuels of PHWR-220, BWR-160, VVER-1000 and the conceptual ATBR-600 reactors – A case study. ANN NUCL ENERGY 2008. [DOI: 10.1016/j.anucene.2008.04.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Pal U, Jagannathan V. Physics principles to achieve comparable fission power from fertile and fissile rods of the conceptual ATBR/FTBR reactors. ANN NUCL ENERGY 2008. [DOI: 10.1016/j.anucene.2008.02.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Pal U, Jagannathan V. Physics design of initial and approach to equilibrium cores of a reactor concept for thorium utilization. ANN NUCL ENERGY 2008. [DOI: 10.1016/j.anucene.2007.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Jagannathan V. Experimenting with semantic web services to understand the role of NLP technologies in healthcare. AMIA Annu Symp Proc 2006; 2006:966. [PMID: 17238585 PMCID: PMC1839741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
NLP technologies can play a significant role in healthcare where a predominant segment of the clinical documentation is in text form. In a graduate course focused on understanding semantic web services at West Virginia University, a class project was designed with the purpose of exploring potential use for NLP-based abstraction of clinical documentation. The role of NLP-technology was simulated using human abstractors and various workflows were investigated using public domain workflow and semantic web service technologies. This poster explores the potential use of NLP and the role of workflow and semantic web technologies in developing healthcare IT environments.
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Affiliation(s)
- V Jagannathan
- MedQuist & West Virginia University, 235 High Street, Suite 213, Morgantown, WV 26505, USA.
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Chockalingam A, Gnanavelu G, Venkatesan S, Elangovan S, Jagannathan V, Subramaniam T, Alagesan R, Dorairajan S. Efficacy and optimal dose of sildenafil in primary pulmonary hypertension. Int J Cardiol 2005; 99:91-5. [PMID: 15721505 DOI: 10.1016/j.ijcard.2003.12.023] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2003] [Revised: 11/24/2003] [Accepted: 12/25/2003] [Indexed: 11/23/2022]
Abstract
PURPOSE We aimed to assess the effects of sildenafil and evaluate optimal dosing in primary pulmonary hypertension (PPH). Sildenafil selectively inhibits phosphodiesterase 5 (PDE5), which is abundant in pulmonary and penile tissue. This results in increasing nitric oxide (NO) at tissue level leading to pulmonary vasodilatation. SUBJECTS AND METHODS Our study was a prospective study of sildenafil in 15 consecutive patients with severe symptomatic PPH of NYHA class III-IV. All patients were stabilized for a minimum period of 5 days with antifailure medications. Sildenafil was started at 50 mg twice daily for 4 weeks and increased to 100 mg bid for 4 more weeks in a step-up protocol. Primary end-points were change in Borg dyspnea index, NYHA class and 6-min walk distance, estimated at baseline 1, 2, 4 and 8 weeks. RESULTS NYHA class (baseline 3.8 +/- 0.4 vs. 4 weeks 2.4 +/- 0.5, p = 0.002), Borg dyspnea index (8.1 +/- 1.7 vs. 4.4 +/- 1.9, p = 0.0007), 6-min walk distance (234 +/- 44 vs. 377 +/- 128 m, p = 0.001) and Pulmonary artery pressure (125 +/- 15 vs. 113 +/- 18 mm Hg p = 0.05) are significantly improved with sildenafil 50 mg bid at 4 weeks. Increasing the dose to 100 mg bid did not produce further benefit. Echocardiography parameters of right heart dimensions and functions did not change markedly in the study period. CONCLUSION Sildenafil is well tolerated with no adverse effects in severe pulmonary hypertension. It reduces symptoms, improves effort tolerance and controls refractory heart failure significantly by 2 weeks in 70% of patients at 50 mg twice daily. Three patients (20%) failed to respond with sildenafil.
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Affiliation(s)
- Anand Chockalingam
- Department of Cardiology, Madras Medical College and Research Institute, Chennai 600 003, India.
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Sangareddi V, Chockalingam A, Gnanavelu G, Subramaniam T, Jagannathan V, Elangovan S. Canadian Cardiovascular Society classification of effort angina: an angiographic correlation. Coron Artery Dis 2004; 15:111-4. [PMID: 15024299 DOI: 10.1097/00019501-200403000-00007] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND The Canadian Cardiovascular Society classification (CCSC) remains the standard for grading angina in patients with chronic stable angina. The utility value of this angina grading system in predicting the severity of coronary artery disease is not clear. AIM We studied the relationship between the clinical angina grade and the angiographic severity of underlying coronary artery disease. MATERIALS AND METHODS The participants in the study were 493 patients with stable angina who had undergone coronary angiography from 1998 to 2001. They were grouped according to their anginal grading and the number of vessels diseased. Significant lesions were defined as 50% narrowing for the left main and 70% for the left and right coronaries and their major branches. STATISTICAL ANALYSIS The chi2-test was used for statistical analysis and a P-value <0.05 was taken as significant. RESULTS There was no significant difference between the four angina class patients and the incidence of single-, double- and triple-vessel involvement. Class 1 patients had less left main trunk disease than class 4 patients. Class 3 and 4 patients had significantly fewer normal coronary angiograms. CONCLUSIONS There is generally little correlation between coronary artery disease and the CCSC of effort angina except for left main disease. Presence or absence of angina rather than the CCSC should indicate the need for coronary angiography.
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Affiliation(s)
- Venkatesan Sangareddi
- Department of Cardiology, Madras Medical College and Research Institute, Chennai, India
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