1
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Bannasch DL, Oertle DT, Vo J, Batcher KL, Stern JA, Kaplan JL, Li RHL, Madden IE, Christen M, Leeb T, Joshi N. Naturally occurring canine laminopathy leading to a dilated and fibrosing cardiomyopathy in the Nova Scotia Duck Tolling Retriever. Sci Rep 2023; 13:19077. [PMID: 37925523 PMCID: PMC10625583 DOI: 10.1038/s41598-023-46601-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 11/02/2023] [Indexed: 11/06/2023] Open
Abstract
Dilated cardiomyopathy (DCM) is characterized by decreased systolic function and dilation of one or both ventricles, often leading to heart failure or sudden death. Two 10-month-old sibling Nova Scotia Duck Tolling Retrievers (NSDTR) died acutely with evidence of dilated cardiomyopathy with myocardial fibrosis. Association analysis using two cases and 35 controls identified three candidate regions homozygous in the two cases. Whole genome sequencing identified a frameshift deletion in the LMNA gene (NC_049228.1:g.41688530del, NP_001274080:p.(Asp576ThrfsTer124)). Three retrospectively identified NSDTRs with sudden death before 2 years of age and severe myocardial fibrosis were also homozygous for the deletion. One 5 year old with sudden death and myocardial fibrosis was heterozygous for the deletion. This variant was not identified in 722 dogs of other breeds, nor was it identified to be homozygous in 784 NSDTR. LMNA codes for lamin A/C proteins, which are type V intermediate filaments that provide structural support to the nuclear membrane. In humans, LMNA variants can cause DCM with sudden death as well as diseases of striated muscles, lipodystrophy, neuropathies, and accelerated aging disorders. This frameshift deletion is predicted to affect processing of prelamin A into lamin A. Pedigree analysis in the NSDTR and functional evaluation of heterozygotes is consistent with a predominantly recessive mode of inheritance and possibly low penetrance in heterozygotes in contrast to people, where most pathogenic LMNA variants are dominantly inherited.
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Affiliation(s)
- Danika L Bannasch
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA, USA.
| | - Danielle T Oertle
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Julia Vo
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Kevin L Batcher
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Joshua A Stern
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Joanna L Kaplan
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Ronald H L Li
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Indiana E Madden
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Matthias Christen
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Nikhil Joshi
- Bioinformatics Core, UC Davis Genome Center, University of California, Davis, CA, USA
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2
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Hytönen MK, Viitanen S, Hundi S, Donner J, Lohi H, Kaukonen M. A frameshift deletion in F8 associated with hemophilia A in Labrador Retriever dogs. Anim Genet 2023; 54:606-612. [PMID: 37438956 DOI: 10.1111/age.13345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/27/2023] [Accepted: 06/27/2023] [Indexed: 07/14/2023]
Abstract
Hemophilia A is the most common inherited coagulation factor disorder in dogs. It manifests as excessive bleeding resulting from pathogenic variants in the X-chromosomal F8 gene encoding coagulation factor VIII (FVIII) protein. In this study, we performed careful clinical phenotyping to confirm hemophilia A in two distinct Labrador Retriever (LR) pedigrees. Whole-genome sequencing on an affected dog from litter 1 identified a case-specific frameshift deletion variant in F8 predicted to cause a premature stop codon (c.2923_2924del, p.(E975Kfs*8)). This variant was hemizygous in all the affected males from litter 1 (n = 3), while all the unaffected LRs in the pedigree were heterozygous or wild-type (n = 22). Additionally, screened samples from 199 LRs were all found to be wild-type. As a result of this study, a gene test can now be developed to screen dogs before breeding to prevent further cases. However, it is important to note that the affected LR with decreased FVIII activity from litter 2 was wild-type for the identified deletion variant, and no segregating F8 variants were detected when this dog's DNA sample was whole-genome sequenced. Thus, the cause of decreased FVIII activity in this dog remains to be unraveled in future studies.
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Affiliation(s)
- Marjo K Hytönen
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
| | - Sanna Viitanen
- Department of Equine and Small Animal Medicine, University of Helsinki, Helsinki, Finland
| | - Sruthi Hundi
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
| | - Jonas Donner
- Wisdom Panel Research Team, Wisdom Panel, Kinship, Helsinki, Finland
| | - Hannes Lohi
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
| | - Maria Kaukonen
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
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3
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Heinonen T, Flegel T, Müller H, Kehl A, Hundi S, Matiasek K, Fischer A, Donner J, Forman OP, Lohi H, Hytönen MK. A loss-of-function variant in canine GLRA1 associates with a neurological disorder resembling human hyperekplexia. Hum Genet 2023; 142:1221-1230. [PMID: 37222814 PMCID: PMC10449970 DOI: 10.1007/s00439-023-02571-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 05/08/2023] [Indexed: 05/25/2023]
Abstract
Hereditary hyperekplexia is a rare neuronal disorder characterized by an exaggerated startle response to sudden tactile or acoustic stimuli. In this study, we present a Miniature Australian Shepherd family showing clinical signs, which have genetic and phenotypic similarities with human hereditary hyperekplexia: episodes of muscle stiffness that could occasionally be triggered by acoustic stimuli. Whole genome sequence data analysis of two affected dogs revealed a 36-bp deletion spanning the exon-intron boundary in the glycine receptor alpha 1 (GLRA1) gene. Further validation in pedigree samples and an additional cohort of 127 Miniature Australian Shepherds, 45 Miniature American Shepherds and 74 Australian Shepherds demonstrated complete segregation of the variant with the disease, according to an autosomal recessive inheritance pattern. The protein encoded by GLRA1 is a subunit of the glycine receptor, which mediates postsynaptic inhibition in the brain stem and spinal cord. The canine GLRA1 deletion is located in the signal peptide and is predicted to cause exon skipping and subsequent premature stop codon resulting in a significant defect in glycine signaling. Variants in GLRA1 are known to cause hereditary hyperekplexia in humans; however, this is the first study to associate a variant in canine GLRA1 with the disorder, establishing a spontaneous large animal disease model for the human condition.
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Affiliation(s)
- Tiina Heinonen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Thomas Flegel
- Department of Small Animals, Leipzig University, Leipzig, Germany
| | - Hanna Müller
- Tieraerztliches Fachzentrum Muehlhausen Dr. Ortmann & Dr. Stief, Muehlhausen/Thueringen, Germany
| | | | - Sruthi Hundi
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Kaspar Matiasek
- Section of Clinical and Comparative Neuropathology, Institute of Veterinary Pathology, Centre for Clinical Veterinary Medicine, LMU Munich, Munich, Germany
| | - Andrea Fischer
- Clinic of Small Animal Medicine, Centre for Clinical Veterinary Medicine, LMU Munich, Munich, Germany
| | - Jonas Donner
- Wisdom Panel Research Team, Wisdom Panel, Kinship, Helsinki, Finland
| | - Oliver P Forman
- Wisdom Panel Research Team, Wisdom Panel, Kinship, Leicestershire, UK
| | - Hannes Lohi
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.
- Folkhälsan Research Center, Helsinki, Finland.
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland.
| | - Marjo K Hytönen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.
- Folkhälsan Research Center, Helsinki, Finland.
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland.
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4
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Hytönen MK, Niskanen JE, Arumilli M, Brookhart-Knox CA, Donner J, Lohi H. Missense variant in LOXHD1 is associated with canine nonsyndromic hearing loss. Hum Genet 2021; 140:1611-1618. [PMID: 33983508 PMCID: PMC8521602 DOI: 10.1007/s00439-021-02286-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 04/20/2021] [Indexed: 11/19/2022]
Abstract
Hearing loss is a common sensory deficit in both humans and dogs. In canines, the genetic basis is largely unknown, as genetic variants have only been identified for a syndromic form of hearing impairment. We observed a congenital or early-onset sensorineural hearing loss in a Rottweiler litter. Assuming an autosomal recessive inheritance, we used a combined approach of homozygosity mapping and genome sequencing to dissect the genetic background of the disorder. We identified a fully segregating missense variant in LOXHD1, a gene that is known to be essential for cochlear hair cell function and associated with nonsyndromic hearing loss in humans and mice. The canine LOXHD1 variant was specific to the Rottweiler breed in our study cohorts of pure-bred dogs. However, it also was present in some mixed-breed dogs, of which the majority showed Rottweiler ancestry. Low allele frequencies in these populations, 2.6% and 0.04%, indicate a rare variant. To summarize, our study describes the first genetic variant for canine nonsyndromic hearing loss, which is clinically and genetically similar to human LOXHD1-related hearing disorder, and therefore, provides a new large animal model for hearing loss. Equally important, the affected breed will benefit from a genetic test to eradicate this LOXHD1-related hearing disorder from the population.
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Affiliation(s)
- Marjo K Hytönen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Folkhälsan Research Center, Helsinki, Finland.,Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Julia E Niskanen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Folkhälsan Research Center, Helsinki, Finland.,Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Meharji Arumilli
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Folkhälsan Research Center, Helsinki, Finland.,Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | | | | | - Hannes Lohi
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland. .,Folkhälsan Research Center, Helsinki, Finland. .,Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland.
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5
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Hytönen MK, Sarviaho R, Jackson CB, Syrjä P, Jokinen T, Matiasek K, Rosati M, Dallabona C, Baruffini E, Quintero I, Arumilli M, Monteuuis G, Donner J, Anttila M, Suomalainen A, Bindoff LA, Lohi H. In-frame deletion in canine PITRM1 is associated with a severe early-onset epilepsy, mitochondrial dysfunction and neurodegeneration. Hum Genet 2021; 140:1593-1609. [PMID: 33835239 PMCID: PMC8519929 DOI: 10.1007/s00439-021-02279-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/27/2021] [Indexed: 11/30/2022]
Abstract
We investigated the clinical, genetic, and pathological characteristics of a previously unknown severe juvenile brain disorder in several litters of Parson Russel Terriers. The disease started with epileptic seizures at 6–12 weeks of age and progressed rapidly to status epilepticus and death or euthanasia. Histopathological changes at autopsy were restricted to the brain. There was severe acute neuronal degeneration and necrosis diffusely affecting the grey matter throughout the brain with extensive intraneuronal mitochondrial crowding and accumulation of amyloid-β (Aβ). Combined homozygosity mapping and genome sequencing revealed an in-frame 6-bp deletion in the nuclear-encoded pitrilysin metallopeptidase 1 (PITRM1) encoding for a mitochondrial protease involved in mitochondrial targeting sequence processing and degradation. The 6-bp deletion results in the loss of two amino acid residues in the N-terminal part of PITRM1, potentially affecting protein folding and function. Assessment of the mitochondrial function in the affected brain tissue showed a significant deficiency in respiratory chain function. The functional consequences of the mutation were modeled in yeast and showed impaired growth in permissive conditions and an impaired respiration capacity. Loss-of-function variants in human PITRM1 result in a childhood-onset progressive amyloidotic neurological syndrome characterized by spinocerebellar ataxia with behavioral, psychiatric and cognitive abnormalities. Homozygous Pitrm1-knockout mice are embryonic lethal, while heterozygotes show a progressive, neurodegenerative phenotype characterized by impairment in motor coordination and Aβ deposits. Our study describes a novel early-onset PITRM1-related neurodegenerative canine brain disorder with mitochondrial dysfunction, Aβ accumulation, and lethal epilepsy. The findings highlight the essential role of PITRM1 in neuronal survival and strengthen the connection between mitochondrial dysfunction and neurodegeneration.
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Affiliation(s)
- Marjo K Hytönen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Folkhälsan Research Center, Helsinki, Finland.,Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Riika Sarviaho
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Folkhälsan Research Center, Helsinki, Finland.,Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Christopher B Jackson
- Department of Biochemistry and Developmental Biology, University of Helsinki, Helsinki, Finland
| | - Pernilla Syrjä
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Tarja Jokinen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Department of Equine and Small Animal Medicine, University of Helsinki, Helsinki, Finland
| | - Kaspar Matiasek
- Faculty of Veterinary Medicine, Centre for Clinical Veterinary Medicine, LMU-Munich, Veterinärstrasse 13, 80539, Munich, Germany
| | - Marco Rosati
- Faculty of Veterinary Medicine, Centre for Clinical Veterinary Medicine, LMU-Munich, Veterinärstrasse 13, 80539, Munich, Germany
| | - Cristina Dallabona
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Enrico Baruffini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Ileana Quintero
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Folkhälsan Research Center, Helsinki, Finland.,Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Meharji Arumilli
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Folkhälsan Research Center, Helsinki, Finland.,Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Geoffray Monteuuis
- Department of Biochemistry and Developmental Biology, University of Helsinki, Helsinki, Finland
| | - Jonas Donner
- Wisdom Health (Genoscoper Laboratories), Helsinki, Finland
| | | | - Anu Suomalainen
- Research Programs Unit, Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
| | - Laurence A Bindoff
- Department of Clinical Medicine (K1), University of Bergen, Bergen, Norway.,Department of Neurology, Neuro-SysMed, Haukeland University Hospital, Bergen, Norway
| | - Hannes Lohi
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland. .,Folkhälsan Research Center, Helsinki, Finland. .,Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland.
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6
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Kaukonen M, Pettinen IT, Wickström K, Arumilli M, Donner J, Juhola IJ, Holopainen S, Turunen JA, Yoshihara M, Kere J, Lohi H. A missense variant in IFT122 associated with a canine model of retinitis pigmentosa. Hum Genet 2021; 140:1569-1579. [PMID: 33606121 PMCID: PMC8519925 DOI: 10.1007/s00439-021-02266-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/10/2021] [Indexed: 11/28/2022]
Abstract
Retinitis pigmentosa (RP) is a blinding eye disease affecting nearly two million people worldwide. Dogs are affected with a similar illness termed progressive retinal atrophy (PRA). Lapponian herders (LHs) are affected with several types of inherited retinal dystrophies, and variants in PRCD and BEST1 genes have been associated with generalized PRA and canine multifocal retinopathy 3 (cmr3), respectively. However, all retinal dystrophy cases in LHs are not explained by these variants, indicating additional genetic causes of disease in the breed. We collected DNA samples from 10 PRA affected LHs, with known PRCD and BEST1 variants excluded, and 34 unaffected LHs. A genome-wide association study identified a locus on CFA20 (praw = 2.4 × 10-7, pBonf = 0.035), and subsequent whole-genome sequencing of an affected LH revealed a missense variant, c.3176G>A, in the intraflagellar transport 122 (IFT122) gene. The variant was also found in Finnish Lapphunds, in which its clinical relevancy needs to be studied further. The variant interrupts a highly conserved residue, p.(R1059H), in IFT122 and likely impairs its function. Variants in IFT122 have not been associated with retinal degeneration in mammals, but the loss of ift122 in zebrafish larvae impaired opsin transport and resulted in progressive photoreceptor degeneration. Our study establishes a new spontaneous dog model to study the role of IFT122 in RP biology, while the affected breed will benefit from a genetic test for a recessive condition.
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Affiliation(s)
- Maria Kaukonen
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland.,Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Folkhälsan Research Center, Helsinki, Finland
| | - Inka-Tuulevi Pettinen
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland.,Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Folkhälsan Research Center, Helsinki, Finland
| | | | - Meharji Arumilli
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland.,Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Folkhälsan Research Center, Helsinki, Finland
| | - Jonas Donner
- Genoscoper Laboratories Ltd (Wisdom Health), Helsinki, Finland
| | - Ida-Julia Juhola
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland.,Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Folkhälsan Research Center, Helsinki, Finland
| | - Saila Holopainen
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland.,Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Folkhälsan Research Center, Helsinki, Finland.,Department of Equine and Small Animal Medicine, University of Helsinki, Helsinki, Finland
| | - Joni A Turunen
- Folkhälsan Research Center, Helsinki, Finland.,Department of Ophthalmology, University of Helsinki, Helsinki University Hospital, Helsinki, Finland
| | - Masahito Yoshihara
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Juha Kere
- Folkhälsan Research Center, Helsinki, Finland.,Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,Stem Cells and Metabolism Research Program STEMM, University of Helsinki, 00014, Helsinki, Finland
| | - Hannes Lohi
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland. .,Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland. .,Folkhälsan Research Center, Helsinki, Finland.
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7
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Kyöstilä K, Niskanen JE, Arumilli M, Donner J, Hytönen MK, Lohi H. Intronic variant in POU1F1 associated with canine pituitary dwarfism. Hum Genet 2021; 140:1553-1562. [PMID: 33550451 PMCID: PMC8519942 DOI: 10.1007/s00439-021-02259-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 01/25/2021] [Indexed: 01/20/2023]
Abstract
The anterior pituitary gland secretes several endocrine hormones, essential for growth, reproduction and other basic physiological functions. Abnormal development or function of the pituitary gland leads to isolated or combined pituitary hormone deficiency (CPHD). At least 30 genes have been associated with human CPHD, including many transcription factors, such as POU1F1. CPHD occurs spontaneously also in mice and dogs. Two affected breeds have been reported in dogs: German Shepherds with a splice defect in the LHX3 gene and Karelian Bear Dogs (KBD) with an unknown genetic cause. We obtained samples from five KBDs presenting dwarfism and abnormal coats. A combined analysis of genome-wide association and next-generation sequencing mapped the disease to a region in chromosome 31 and identified a homozygous intronic variant in the fourth exon of the POU1F1 gene in the affected dogs. The identified variant, c.605-3C>A, resided in the splice region and was predicted to affect splicing. The variant's screening in three new prospective cases, related breeds, and ~ 8000 dogs from 207 breeds indicated complete segregation in KBDs with a carrier frequency of 8%, and high breed-specificity as carriers were found at a low frequency only in Lapponian Herders, a related breed. Our study establishes a novel canine model for CPHD with a candidate POU1F1 defect.
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Affiliation(s)
- Kaisa Kyöstilä
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland.,Folkhälsan Research Center, Helsinki, Finland
| | - Julia E Niskanen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland.,Folkhälsan Research Center, Helsinki, Finland
| | - Meharji Arumilli
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland.,Folkhälsan Research Center, Helsinki, Finland
| | - Jonas Donner
- Genoscoper Laboratories Ltd (Wisdom Health), Helsinki, Finland
| | - Marjo K Hytönen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland.,Folkhälsan Research Center, Helsinki, Finland
| | - Hannes Lohi
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland. .,Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland. .,Folkhälsan Research Center, Helsinki, Finland.
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8
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Wilkey AP, Brown AV, Cannon SB, Cannon EKS. GCViT: a method for interactive, genome-wide visualization of resequencing and SNP array data. BMC Genomics 2020; 21:822. [PMID: 33228531 PMCID: PMC7686774 DOI: 10.1186/s12864-020-07217-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 11/09/2020] [Indexed: 01/07/2023] Open
Abstract
Background Large genotyping datasets have become commonplace due to efficient, cheap methods for SNP identification. Typical genotyping datasets may have thousands to millions of data points per accession, across tens to thousands of accessions. There is a need for tools to help rapidly explore such datasets, to assess characteristics such as overall differences between accessions and regional anomalies across the genome. Results We present GCViT (Genotype Comparison Visualization Tool), for visualizing and exploring large genotyping datasets. GCViT can be used to identify introgressions, conserved or divergent genomic regions, pedigrees, and other features for more detailed exploration. The program can be used online or as a local instance for whole genome visualization of resequencing or SNP array data. The program performs comparisons of variants among user-selected accessions to identify allele differences and similarities between accessions and a user-selected reference, providing visualizations through histogram, heatmap, or haplotype views. The resulting analyses and images can be exported in various formats. Conclusions GCViT provides methods for interactively visualizing SNP data on a whole genome scale, and can produce publication-ready figures. It can be used in online or local installations. GCViT enables users to confirm or identify genomics regions of interest associated with particular traits. GCViT is freely available at https://github.com/LegumeFederation/gcvit. The 1.0 version described here is available at 10.5281/zenodo.4008713.
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Affiliation(s)
- Andrew P Wilkey
- ORISE Fellow, USDA-ARS Corn Insects and Crop Genetics Research Unit, Ames, IA, 50011, USA
| | - Anne V Brown
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Ames, IA, 50011, USA
| | - Steven B Cannon
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Ames, IA, 50011, USA
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9
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Sarviaho R, Hakosalo O, Tiira K, Sulkama S, Niskanen JE, Hytönen MK, Sillanpää MJ, Lohi H. A novel genomic region on chromosome 11 associated with fearfulness in dogs. Transl Psychiatry 2020; 10:169. [PMID: 32467585 PMCID: PMC7256038 DOI: 10.1038/s41398-020-0849-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 05/05/2020] [Accepted: 05/14/2020] [Indexed: 02/07/2023] Open
Abstract
The complex phenotypic and genetic nature of anxieties hampers progress in unravelling their molecular etiologies. Dogs present extensive natural variation in fear and anxiety behaviour and could advance the understanding of the molecular background of behaviour due to their unique breeding history and genetic architecture. As dogs live as part of human families under constant care and monitoring, information from their behaviour and experiences are easily available. Here we have studied the genetic background of fearfulness in the Great Dane breed. Dogs were scored and categorised into cases and controls based on the results of the validated owner-completed behavioural survey. A genome-wide association study in a cohort of 124 dogs with and without socialisation as a covariate revealed a genome-wide significant locus on chromosome 11. Whole exome sequencing and whole genome sequencing revealed extensive regions of opposite homozygosity in the same locus on chromosome 11 between the cases and controls with interesting neuronal candidate genes such as MAPK9/JNK2, a known hippocampal regulator of anxiety. Further characterisation of the identified locus will pave the way for molecular understanding of fear in dogs and may provide a natural animal model for human anxieties.
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Affiliation(s)
- R. Sarviaho
- grid.7737.40000 0004 0410 2071Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland ,grid.7737.40000 0004 0410 2071Department of Medical and Clinical Genetics, University of Helsinki, 00014 Helsinki, Finland ,grid.428673.c0000 0004 0409 6302Folkhälsan Research Center, 00290 Helsinki, Finland
| | - O. Hakosalo
- grid.7737.40000 0004 0410 2071Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland ,grid.7737.40000 0004 0410 2071Department of Medical and Clinical Genetics, University of Helsinki, 00014 Helsinki, Finland ,grid.428673.c0000 0004 0409 6302Folkhälsan Research Center, 00290 Helsinki, Finland
| | - K. Tiira
- grid.7737.40000 0004 0410 2071Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland ,grid.7737.40000 0004 0410 2071Department of Medical and Clinical Genetics, University of Helsinki, 00014 Helsinki, Finland ,grid.428673.c0000 0004 0409 6302Folkhälsan Research Center, 00290 Helsinki, Finland ,grid.7737.40000 0004 0410 2071Equine and Small Animal Medicine, University of Helsinki, Helsinki, Finland
| | - S. Sulkama
- grid.7737.40000 0004 0410 2071Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland ,grid.7737.40000 0004 0410 2071Department of Medical and Clinical Genetics, University of Helsinki, 00014 Helsinki, Finland ,grid.428673.c0000 0004 0409 6302Folkhälsan Research Center, 00290 Helsinki, Finland
| | - J. E. Niskanen
- grid.7737.40000 0004 0410 2071Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland ,grid.7737.40000 0004 0410 2071Department of Medical and Clinical Genetics, University of Helsinki, 00014 Helsinki, Finland ,grid.428673.c0000 0004 0409 6302Folkhälsan Research Center, 00290 Helsinki, Finland
| | - M. K. Hytönen
- grid.7737.40000 0004 0410 2071Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland ,grid.7737.40000 0004 0410 2071Department of Medical and Clinical Genetics, University of Helsinki, 00014 Helsinki, Finland ,grid.428673.c0000 0004 0409 6302Folkhälsan Research Center, 00290 Helsinki, Finland
| | - M. J. Sillanpää
- grid.10858.340000 0001 0941 4873Department of Mathematical Sciences, Biocenter Oulu and Infotech Oulu, University of Oulu, Oulu, Finland
| | - H. Lohi
- grid.7737.40000 0004 0410 2071Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland ,grid.7737.40000 0004 0410 2071Department of Medical and Clinical Genetics, University of Helsinki, 00014 Helsinki, Finland ,grid.428673.c0000 0004 0409 6302Folkhälsan Research Center, 00290 Helsinki, Finland
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