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Anderson H, Davison S, Lytle KM, Honkanen L, Freyer J, Mathlin J, Kyöstilä K, Inman L, Louviere A, Chodroff Foran R, Forman OP, Lohi H, Donner J. Genetic epidemiology of blood type, disease and trait variants, and genome-wide genetic diversity in over 11,000 domestic cats. PLoS Genet 2022; 18:e1009804. [PMID: 35709088 PMCID: PMC9202916 DOI: 10.1371/journal.pgen.1009804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 05/06/2022] [Indexed: 11/30/2022] Open
Abstract
In the largest DNA-based study of domestic cats to date, 11,036 individuals (10,419 pedigreed cats and 617 non-pedigreed cats) were genotyped via commercial panel testing elucidating the distribution and frequency of known disease, blood type, and physical trait associated genetic variants across cat breeds. This study provides allele frequencies for many disease-associated variants for the first time and provides updates on previously reported information with evidence suggesting that DNA testing has been effectively used to reduce disease associated variants within certain pedigreed cat populations over time. We identified 13 disease-associated variants in 47 breeds or breed types in which the variant had not previously been documented, highlighting the relevance of comprehensive genetic screening across breeds. Three disease-associated variants were discovered in non-pedigreed cats only. To investigate the causality of nine disease-associated variants in cats of different breed backgrounds our veterinarians conducted owner interviews, reviewed clinical records, and invited cats to have follow-up clinical examinations. Additionally, genetic variants determining blood types A, B and AB, which are relevant clinically and in cat breeding, were genotyped. Appearance-associated genetic variation in all cats is also discussed. Lastly, genome-wide SNP heterozygosity levels were calculated to obtain a comparable measure of the genetic diversity in different cat breeds. This study represents the first comprehensive exploration of informative Mendelian variants in felines by screening over 10,000 pedigreed cats. The results qualitatively contribute to the understanding of feline variant heritage and genetic diversity and demonstrate the clinical utility and importance of such information in supporting breeding programs and the research community. The work also highlights the crucial commitment of pedigreed cat breeders and registries in supporting the establishment of large genomic databases, that when combined with phenotype information can advance scientific understanding and provide insights that can be applied to improve the health and welfare of cats. Domestic cats are one of the world’s most popular companion animals, of which pedigreed cats represent small unique subpopulations. Genetic research on pedigreed cats has facilitated discoveries of heritable conditions resulting in the availability of DNA testing for studying and managing inherited disorders and traits in specific cat breeds. We have explored an extensive study cohort of 11,036 domestic cat samples representing pedigreed cats of 90 breeds and breed types. This work provided insight into the heritage of feline disease and trait alleles. We gained knowledge on the most common and relevant genetic markers for inherited disorders and physical traits, and the genetic determinants of the clinically relevant AB blood group system. We also used a measure of genetic diversity to compare inbreeding levels within and between breeds. This information can help support sustainable breeding goals within the cat fancy. Direct-to-consumer genetic tests help to raise awareness of various inherited single gene conditions in cats and provide information that owners can share with their veterinarians. In due course, ventures of this type will enable the genetics of common complex feline disease to be deciphered, paving the way for precision healthcare with the potential to ultimately improve welfare for all cats.
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Affiliation(s)
- Heidi Anderson
- Wisdom Panel Research Team, Wisdom Panel, Kinship, Portland, Oregon, United States of America
- * E-mail:
| | - Stephen Davison
- Wisdom Panel Research Team, Wisdom Panel, Kinship, Portland, Oregon, United States of America
| | - Katherine M. Lytle
- Wisdom Panel Research Team, Wisdom Panel, Kinship, Portland, Oregon, United States of America
| | - Leena Honkanen
- Wisdom Panel Research Team, Wisdom Panel, Kinship, Portland, Oregon, United States of America
| | - Jamie Freyer
- Wisdom Panel Research Team, Wisdom Panel, Kinship, Portland, Oregon, United States of America
| | - Julia Mathlin
- Wisdom Panel Research Team, Wisdom Panel, Kinship, Portland, Oregon, United States of America
| | - 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
| | - Laura Inman
- Wisdom Panel Research Team, Wisdom Panel, Kinship, Portland, Oregon, United States of America
| | - Annette Louviere
- Wisdom Panel Research Team, Wisdom Panel, Kinship, Portland, Oregon, United States of America
| | - Rebecca Chodroff Foran
- Wisdom Panel Research Team, Wisdom Panel, Kinship, Portland, Oregon, United States of America
| | - Oliver P. Forman
- Wisdom Panel Research Team, Wisdom Panel, Kinship, Portland, Oregon, United States of America
| | - 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
| | - Jonas Donner
- Wisdom Panel Research Team, Wisdom Panel, Kinship, Portland, Oregon, United States of America
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Letko A, Dijkman R, Strugnell B, Häfliger IM, Paris JM, Henderson K, Geraghty T, Orr H, Scholes S, Drögemüller C. Deleterious AGXT Missense Variant Associated with Type 1 Primary Hyperoxaluria (PH1) in Zwartbles Sheep. Genes (Basel) 2020; 11:E1147. [PMID: 33003365 PMCID: PMC7600965 DOI: 10.3390/genes11101147] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 09/15/2020] [Accepted: 09/26/2020] [Indexed: 11/23/2022] Open
Abstract
Severe oxalate nephropathy has been previously reported in sheep and is mostly associated with excessive oxalate in the diet. However, a rare native Dutch breed (Zwartbles) seems to be predisposed to an inherited juvenile form of primary hyperoxaluria and no causative genetic variant has been described so far. This study aims to characterize the phenotype and genetic etiology of the inherited metabolic disease observed in several purebred Zwartbles sheep. Affected animals present with a wide range of clinical signs including condition loss, inappetence, malaise, and, occasionally, respiratory signs, as well as an apparent sudden unexpected death. Histopathology revealed widespread oxalate crystal deposition in kidneys of the cases. Whole-genome sequencing of two affected sheep identified a missense variant in the ovine AGXT gene (c.584G>A; p.Cys195Tyr). Variants in AGXT are known to cause type I primary hyperoxaluria in dogs and humans. Herein, we present evidence that the observed clinicopathological phenotype can be described as a form of ovine type I primary hyperoxaluria. This disorder is explained by a breed-specific recessively inherited pathogenic AGXT variant. Genetic testing enables selection against this fatal disorder in Zwartbles sheep as well as more precise diagnosis in animals with similar clinical phenotype. Our results have been incorporated in the Online Mendelian Inheritance in Animals (OMIA) database (OMIA 001672-9940).
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Affiliation(s)
- Anna Letko
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland; (A.L.); (I.M.H.); (J.M.P.)
| | | | - Ben Strugnell
- Farm Post Mortems Ltd., Hamsterley, Bishop Auckland, County Durham DL13 3QF, UK;
| | - Irene M. Häfliger
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland; (A.L.); (I.M.H.); (J.M.P.)
| | - Julia M. Paris
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland; (A.L.); (I.M.H.); (J.M.P.)
| | - Katrina Henderson
- SRUC Consulting Veterinary Services, Pentlands Science Park, Bush Estate Loan, Penicuik, Midlothian EH26 0PZ, UK; (K.H.); (T.G.); (H.O.); (S.S.)
| | - Tim Geraghty
- SRUC Consulting Veterinary Services, Pentlands Science Park, Bush Estate Loan, Penicuik, Midlothian EH26 0PZ, UK; (K.H.); (T.G.); (H.O.); (S.S.)
| | - Hannah Orr
- SRUC Consulting Veterinary Services, Pentlands Science Park, Bush Estate Loan, Penicuik, Midlothian EH26 0PZ, UK; (K.H.); (T.G.); (H.O.); (S.S.)
| | - Sandra Scholes
- SRUC Consulting Veterinary Services, Pentlands Science Park, Bush Estate Loan, Penicuik, Midlothian EH26 0PZ, UK; (K.H.); (T.G.); (H.O.); (S.S.)
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland; (A.L.); (I.M.H.); (J.M.P.)
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Mitchell EP, Church ME, Nemser SM, Yakes BJ, Evans ER, Reimschuessel R, Lemberger K, Thompson PN, Terio KA. Pathology and Epidemiology of Oxalate Nephrosis in Cheetahs. Vet Pathol 2017; 54:977-985. [PMID: 28891390 DOI: 10.1177/0300985817728556] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
To investigate cases of acute oxalate nephrosis without evidence of ethylene glycol exposure, archived data and tissues from cheetahs ( Acinonyx jubatus) from North America ( n = 297), southern Africa ( n = 257), and France ( n = 40) were evaluated. Renal and gastrointestinal tract lesions were characterized in a subset of animals with ( n = 100) and without ( n = 165) oxalate crystals at death. Crystals were confirmed as calcium oxalate by Raman spectroscopy in 45 of 47 cheetahs tested. Crystals were present in cheetahs from 3.7 months to 15.9 years old. Cheetahs younger than 1.5 years were less likely to have oxalates than older cheetahs ( P = .034), but young cheetahs with oxalates had more oxalate crystals than older cheetahs ( P < .001). Cheetahs with oxalate crystals were more likely to have renal amyloidosis, interstitial nephritis, or colitis and less likely to have glomerular loop thickening or gastritis than those without oxalates. Crystal number was positively associated with renal tubular necrosis ( P ≤ .001), regeneration ( P = .015), and casts ( P ≤ .001) but inversely associated with glomerulosclerosis, renal amyloidosis, and interstitial nephritis. Crystal number was unrelated to the presence or absence of colitis and was lower in southern African than American and European animals ( P = .01). This study found no evidence that coexisting chronic renal disease (amyloidosis, interstitial nephritis, or glomerulosclerosis), veno-occlusive disease, gastritis, or enterocolitis contributed significantly to oxalate nephrosis. Oxalate-related renal disease should be considered as a potential cause of acute renal failure, especially in young captive cheetahs. The role of location, diet, stress, and genetic predisposition in the pathogenesis of oxalate nephrosis in cheetahs warrants further study.
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Affiliation(s)
- Emily P Mitchell
- 1 Department of Research and Scientific Services, National Zoological Gardens of South Africa, Pretoria, South Africa.,2 Department of Paraclinical Sciences, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
| | - Molly E Church
- 3 Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Sarah M Nemser
- 4 Veterinary Laboratory Investigation and Response Network, Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, MD, USA
| | - Betsy Jean Yakes
- 5 Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, USA
| | - Eric R Evans
- 4 Veterinary Laboratory Investigation and Response Network, Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, MD, USA
| | - Renate Reimschuessel
- 4 Veterinary Laboratory Investigation and Response Network, Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, MD, USA
| | | | - Peter N Thompson
- 7 Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
| | - Karen A Terio
- 8 Zoological Pathology Program, University of Illinois, Brookfield, IL, USA
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Abstract
PRACTICAL RELEVANCE The health of the cat is a complex interaction between its environment (nurture) and its genetics (nature). Over 70 genetic mutations (variants) have been defined in the cat, many involving diseases, structural abnormalities and clinically relevant health concerns. As more of the cat's genome is deciphered, less commonly will the term 'idiopathic' be used regarding the diagnosis of diseases and unique health conditions. State-of-the-art health care will include DNA profiling of the individual cat, and perhaps its tumor, to establish the best treatment approaches. Genetic testing and eventually whole genome sequencing should become routine diagnostics for feline health care. GLOBAL IMPORTANCE Cat breeds have disseminated around the world. Thus, practitioners should be aware of the breeds common to their region and the mutations found in those regional populations. Specific random-bred populations can also have defined genetic characteristics and mutations. AUDIENCE This review of 'the good, the bad and the ugly' DNA variants provides the current state of knowledge for genetic testing and genetic health management for cats. It is aimed at feline and general practitioners wanting to update and review the basics of genetics, what tests are available for cats and sources for genetic testing. The tables are intended to be used as references in the clinic. Practitioners with a high proportion of cat breeder clientele will especially benefit from the review. EVIDENCE BASE The data presented is extracted from peer-reviewed publications pertaining to mutation identification, and relevant articles concerning the heritable trait and/or disease. The author also draws upon personal experience and expertise in feline genetics.
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Affiliation(s)
- Leslie A Lyons
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri - Columbia, Columbia, MO 65201, USA
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Lyons LA. Genetic testing in domestic cats. Mol Cell Probes 2012; 26:224-30. [PMID: 22546621 PMCID: PMC3541004 DOI: 10.1016/j.mcp.2012.04.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Revised: 04/12/2012] [Accepted: 04/13/2012] [Indexed: 12/29/2022]
Abstract
Varieties of genetic tests are currently available for the domestic cat that support veterinary health care, breed management, species identification, and forensic investigations. Approximately thirty-five genes contain over fifty mutations that cause feline health problems or alterations in the cat's appearance. Specific genes, such as sweet and drug receptors, have been knocked-out of Felidae during evolution and can be used along with mtDNA markers for species identification. Both STR and SNP panels differentiate cat race, breed, and individual identity, as well as gender-specific markers to determine sex of an individual. Cat genetic tests are common offerings for commercial laboratories, allowing both the veterinary clinician and the private owner to obtain DNA test results. This article will review the genetic tests for the domestic cat, and their various applications in different fields of science. Highlighted are genetic tests specific to the individual cat, which are a part of the cat's genome.
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Affiliation(s)
- Leslie A Lyons
- Department of Population Health & Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, CA 95616, USA.
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Vidgren G, Vainio-Siukola K, Honkasalo S, Dillard K, Anttila M, Vauhkonen H. Primary hyperoxaluria in Coton de Tulear. Anim Genet 2011; 43:356-61. [DOI: 10.1111/j.1365-2052.2011.02260.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Strugnell BW, Gaudie CM, Wessels M, Schock A, Davies I. Severe oxalate nephropathy in Zwartbles sheep. Vet Rec 2011; 169:81. [PMID: 21765146 DOI: 10.1136/vr.d4471] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Abstract
DNA testing for domestic cat diseases and appearance traits is a rapidly growing asset for veterinary medicine. Approximately 33 genes contain 50 mutations that cause feline health problems or alterations in the cat's appearance. A variety of commercial laboratories can now perform cat genetic diagnostics, allowing both the veterinary clinician and the private owner to obtain DNA test results. DNA is easily obtained from a cat via a buccal swab with a standard cotton bud or cytological brush, allowing DNA samples to be easily sent to any laboratory in the world. The DNA test results identify carriers of the traits, predict the incidence of traits from breeding programs, and influence medical prognoses and treatments. An overall goal of identifying these genetic mutations is the correction of the defect via gene therapies and designer drug therapies. Thus, genetic testing is an effective preventative medicine and a potential ultimate cure. However, genetic diagnostic tests may still be novel for many veterinary practitioners and their application in the clinical setting needs to have the same scrutiny as any other diagnostic procedure. This article will review the genetic tests for the domestic cat, potential sources of error for genetic testing, and the pros and cons of DNA results in veterinary medicine. Highlighted are genetic tests specific to the individual cat, which are a part of the cat's internal genome.
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Affiliation(s)
- Leslie A Lyons
- Department of Population Health & Reproduction, University of California, Davis, CA, USA.
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