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Kim C, Loftus JP, Huson HJ. Low alanine aminotransferase activity gene variant in a Siberian Husky with copper-associated hepatopathy. BMC Vet Res 2023; 19:111. [PMID: 37550687 PMCID: PMC10405506 DOI: 10.1186/s12917-023-03681-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 07/28/2023] [Indexed: 08/09/2023] Open
Abstract
BACKGROUND Alanine aminotransferase (ALT) is commonly used as a marker of hepatocellular injury. Increased serum ALT activity due to hepatocyte injury occurs in copper-associated hepatopathy (CuCH) and other necroinflammatory liver conditions. Blood ALT concentrations are frequently used to monitor therapy in cases of CuCH. Low serum ALT activities have been associated with an allele at a CFA13 locus. CASE PRESENTATION A 9-year-old female spayed Siberian Husky was diagnosed with CuCH (hepatic copper dry weight 2680 µg/g [normal, 120-400 µg/g; toxic, > 1500 µg/g]) and a normal ALT (78 U/L; reference range, 10-125 U/L). Mild hepatocellular necrosis was evident histologically. Genetic testing (Embark) revealed that the dog was heterozygous for the low ALT activity gene allele. CONCLUSIONS This case report illustrates the clinical implications for diagnosing and managing necroinflammatory liver disease such as CuCH in dogs with a low ALT activity genotype.
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Affiliation(s)
- Christine Kim
- IronHorse VetCare, 7660 Amador Valley Blvd E, Dublin, CA, 94568, USA
| | - John P Loftus
- Department of Clinical Sciences, Cornell University College of Veterinary Medicine, 930 Campus Rd, Ithaca, NY, 14853, USA.
| | - Heather J Huson
- Department of Animal Sciences, Cornell University College of Agriculture and Life Sciences, 201 Morrison Hall, 507 Tower Road, Ithaca, NY, 14853, USA
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2
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Thorsrud JA, Huson HJ. Description of breed ancestry and genetic health traits in arctic sled dog breeds. Canine Med Genet 2021; 8:8. [PMID: 34544496 PMCID: PMC8454093 DOI: 10.1186/s40575-021-00108-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 09/08/2021] [Indexed: 11/22/2022] Open
Abstract
Background This study describes the presence and frequency of health traits among three populations of dogs traditionally used for sledding and explores their ancestry and breed composition as provided by the commercially available Embark dog DNA test. The three populations include the purebred Siberian Husky and the admixed populations of Alaskan sled dogs and Polar Huskies. While the Siberian Husky represents a well-established breed with extensive historical and health data, the Alaskan sled dog is less studied but has been the subject of nutritional, physiological, and genetic studies related to ancestry and performance. In contrast, the Polar Husky is a relatively obscure and rare group of dogs used for arctic exploration with very little-known information. The three populations were compared using Embark results, providing new insight into the health traits circulating within the populations and the potential ancestral linkage of the health traits between the sledding populations. Embark results are based upon 228,588 single-nucleotide polymorphisms (SNPs) spanning the canine genome, characterized using a custom-designed Illumina beadchip array. Results Specifically, breed composition was summarized for the two admixed populations with most of the dogs being predominantly categorized as Alaskan husky- type dog or “Supermutt”. Mitochondrial and Y chromosome haplogroups and haplotypes were found with Alaskan sled dogs carrying most of the haplogroups and types found in Siberian and Polar Huskies. Genomic principal component analysis reflected population structure corresponding to breed and substructure within the Alaskan sled dogs related to sprint or distance competition. Genetic markers associated with Alanine Aminotransferase activity, Alaskan Husky Encephalopathy, dilated cardiomyopathy, Collie eye anomaly, degenerative myelopathy, ichthyosis, and factor VII deficiency were identified in the populations of sledding breeds. Conclusion These results provide a preliminary description of genetic characteristics found in sledding breeds, improving the understanding and care of working sled dogs. Supplementary Information The online version contains supplementary material available at 10.1186/s40575-021-00108-z.
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Affiliation(s)
- Joseph A Thorsrud
- Department of Animal Sciences, Cornell University College of Agriculture and Life Sciences, 201 Morrison Hall, 507 Tower Road, Ithaca, NY, 14853, USA
| | - Heather J Huson
- Department of Animal Sciences, Cornell University College of Agriculture and Life Sciences, 201 Morrison Hall, 507 Tower Road, Ithaca, NY, 14853, USA.
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3
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Momozawa Y, Merveille AC, Battaille G, Wiberg M, Koch J, Willesen JL, Proschowsky HF, Gouni V, Chetboul V, Tiret L, Fredholm M, Seppälä EH, Lohi H, Georges M, Lequarré AS. Genome wide association study of 40 clinical measurements in eight dog breeds. Sci Rep 2020; 10:6520. [PMID: 32300138 PMCID: PMC7162946 DOI: 10.1038/s41598-020-63457-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/26/2020] [Indexed: 12/29/2022] Open
Abstract
The domestic dog represents an ideal model for identifying susceptibility genes, many of which are shared with humans. In this study, we investigated the genetic contribution to individual differences in 40 clinically important measurements by a genome-wide association study (GWAS) in a multinational cohort of 472 healthy dogs from eight breeds. Meta-analysis using the binary effects model after breed-specific GWAS, identified 13 genome-wide significant associations, three of them showed experimental-wide significant associations. We detected a signal at chromosome 13 for the serum concentration of alanine aminotransferase (ALT) in which we detected four breed-specific signals. A large proportion of the variance of ALT (18.1–47.7%) was explained by this locus. Similarly, a single SNP was also responsible for a large proportion of the variance (6.8–78.4%) for other measurements such as fructosamine, stress during physical exam, glucose, and morphometric measurements. The genetic contribution of single variant was much larger than in humans. These findings illustrate the importance of performing meta-analysis after breed-specific GWAS to reveal the genetic contribution to individual differences in clinically important measurements, which would lead to improvement of veterinary medicine.
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Affiliation(s)
- Yukihide Momozawa
- Unit of Animal Genomics, GIGA Institute, University of Liège, Liège, Belgium. .,Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Kanagawa, 230-0045, Japan.
| | - Anne-Christine Merveille
- Unit of Animal Genomics, GIGA Institute, University of Liège, Liège, Belgium.,Department of Clinical Sciences, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Géraldine Battaille
- Unit of Animal Genomics, GIGA Institute, University of Liège, Liège, Belgium.,Department of Clinical Sciences, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Maria Wiberg
- Department of Equine and Small Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Jørgen Koch
- Faculty of Health and Medical Sciences, University of Copenhagen, 1870, Frederiksberg C, Denmark
| | - Jakob Lundgren Willesen
- Faculty of Health and Medical Sciences, University of Copenhagen, 1870, Frederiksberg C, Denmark
| | | | - Vassiliki Gouni
- U955 - IMRB Inserm and Unité de Cardiologie d'Alfort (UCA), Université Paris-Est, École Nationale Vétérinaire d'Alfort, UPEC, 7 avenue du général de Gaulle, Maisons-Alfort, F-94700, France
| | - Valérie Chetboul
- U955 - IMRB Inserm and Unité de Cardiologie d'Alfort (UCA), Université Paris-Est, École Nationale Vétérinaire d'Alfort, UPEC, 7 avenue du général de Gaulle, Maisons-Alfort, F-94700, France
| | - Laurent Tiret
- U955 - IMRB, Biology of the neuromuscular system, Inserm, National Veterinary School of Alfort (ENVA), Maisons-Alfort, France
| | - Merete Fredholm
- Faculty of Health and Medical Sciences, University of Copenhagen, 1870, Frederiksberg C, Denmark
| | - Eija H Seppälä
- Department of Veterinary Biosciences, Department of Medical and Clinical Genetics, University of Helsinki, Folkhälsan Research Center, Helsinki, Finland
| | - Hannes Lohi
- Department of Veterinary Biosciences, Department of Medical and Clinical Genetics, University of Helsinki, Folkhälsan Research Center, Helsinki, Finland
| | - Michel Georges
- Unit of Animal Genomics, GIGA Institute, University of Liège, Liège, Belgium.,Department of Clinical Sciences, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Anne-Sophie Lequarré
- Unit of Animal Genomics, GIGA Institute, University of Liège, Liège, Belgium. .,Department of Clinical Sciences, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium.
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A Genome-Wide Association Study Identifies Quantitative Trait Loci Affecting Hematological Traits in Camelus bactrianus. Animals (Basel) 2020; 10:ani10010096. [PMID: 31936121 PMCID: PMC7023321 DOI: 10.3390/ani10010096] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/06/2020] [Accepted: 01/06/2020] [Indexed: 12/22/2022] Open
Abstract
Simple Summary Bactrian camels can adapt to harsh natural environments. This unique tolerance of camels is tightly linked to their hematological traits, which are related to their immune, metabolic, and disease status. Therefore, mapping genomic regions that affect blood cell traits can help identify genomic characteristics that can be used as biomarkers of immune, metabolic, and disease states. This knowledge will further our understanding of the camel’s tolerance mechanisms. Abstract Bactrian camels (Camelus bactrianus) are one of the few large livestock species that can survive in the Gobi Desert. Animal immunity and disease resistance are related to hematological traits, which are also associated with tolerance observed in Bactrian camels. However, no genome-wide association studies have examined the genetic mechanism of the immune capability of Bactrian camels. In the present study, we used genotyping-by-sequencing data generated from 366 Bactrian camel accessions to perform a genome-wide association study for 17 hematological traits. Of the 256,616 single-nucleotide polymorphisms (SNPs) obtained, 1,635 trait–SNP associations were among the top quantitative trait locus candidates. Lastly, 664 candidate genes associated with 13 blood traits were identified. The most significant were ZNF772, MTX2, ESRRG, MEI4, IL11, FRMPD4, GABPA, NTF4, CRYBG3, ENPP5, COL16A1, and CD207. The results of our genome-wide association study provide a list of significant SNPs and candidate genes, which offer valuable information for further dissection of the molecular mechanisms that regulate the camel’s hematological traits to ultimately reveal their tolerance mechanisms.
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Imputation of canine genotype array data using 365 whole-genome sequences improves power of genome-wide association studies. PLoS Genet 2019; 15:e1008003. [PMID: 31525180 PMCID: PMC6762211 DOI: 10.1371/journal.pgen.1008003] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 09/26/2019] [Accepted: 08/19/2019] [Indexed: 12/11/2022] Open
Abstract
Genomic resources for the domestic dog have improved with the widespread adoption of a 173k SNP array platform and updated reference genome. SNP arrays of this density are sufficient for detecting genetic associations within breeds but are underpowered for finding associations across multiple breeds or in mixed-breed dogs, where linkage disequilibrium rapidly decays between markers, even though such studies would hold particular promise for mapping complex diseases and traits. Here we introduce an imputation reference panel, consisting of 365 diverse, whole-genome sequenced dogs and wolves, which increases the number of markers that can be queried in genome-wide association studies approximately 130-fold. Using previously genotyped dogs, we show the utility of this reference panel in identifying potentially novel associations, including a locus on CFA20 significantly associated with cranial cruciate ligament disease, and fine-mapping for canine body size and blood phenotypes, even when causal loci are not in strong linkage disequilibrium with any single array marker. This reference panel resource will improve future genome-wide association studies for canine complex diseases and other phenotypes. Complex traits are controlled by more than one gene and as such are difficult to map. For complex trait mapping in the domestic dog, researchers use the current array of 173,000 variants, with only minimal success. Here, we use a method called imputation to increase the number of variants–from 173,000 to 24 million–that can be queried in canine association studies. We use sequence data from the whole genomes of 365 dogs and wolves to accurately predict variants, in a separate cohort of dogs, that are not present on the array. Using dog body size, blood phenotypes, and a common orthopedic disease that involves rupture of the cranial cruciate ligament, we show that the increase in variants results in an increase in mapping power, through the identification of new associations and the narrowing of regions of interest. This imputation panel is particularly important because of its usefulness in improving complex trait mapping in the dog, which has significant implications for discovery of variants in humans with similar diseases.
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Soh PXY, Marin Cely JM, Mortlock SA, Jara CJ, Booth R, Natera S, Roessner U, Crossett B, Cordwell S, Singh Khatkar M, Williamson P. Genome-wide association studies of 74 plasma metabolites of German shepherd dogs reveal two metabolites associated with genes encoding their enzymes. Metabolomics 2019; 15:123. [PMID: 31493001 DOI: 10.1007/s11306-019-1586-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 08/29/2019] [Indexed: 12/12/2022]
Abstract
INTRODUCTION German shepherd dogs (GSDs) are a popular breed affected by numerous disorders. Few studies have explored genetic variations that influence canine blood metabolite levels. OBJECTIVES To investigate genetic variants affecting the natural metabolite variation in GSDs. METHODS A total of 82 healthy GSDs were genotyped on the Illumina CanineHD Beadchip, assaying 173,650 markers. For each dog, 74 metabolites were measured through liquid and gas chromatography mass spectrometry (LC-MS and GC-MS) and were used as phenotypes for genome-wide association analyses (GWAS). Sliding window and homozygosity analyses were conducted to fine-map regions of interest, and to identify haplotypes and gene dosage effects. RESULTS Summary statistics for 74 metabolites in this population of GSDs are reported. Forty-one metabolites had significant associations at a false discovery rate of 0.05. Two associations were located around genes which encode for enzymes for the relevant metabolites: 4-hydroxyproline was significantly associated to D-amino acid oxidase (DAO), and threonine to L-threonine 3-dehydrogenase (LOC477365). Three of the top ten haplotypes associated to 4-hydroxyproline included at least one SNP on DAO. These haplotypes occurred only in dogs with the highest 15 measurements of 4-hydroxyproline, ranging in frequency from 16.67 to 20%. None of the dogs were homozygous for these haplotypes. The top two haplotypes associated to threonine included SNPs on LOC477365 and were also overrepresented in dogs with the highest 15 measurements of threonine. These haplotypes occurred at a frequency of 90%, with 80% of these dogs homozygous for the haplotypes. In dogs with the lowest 15 measurements of threonine, the haplotypes occurred at a frequency of 26.67% and 0% homozygosity. CONCLUSION DAO and LOC477365 were identified as candidate genes affecting the natural plasma concentration of 4-hydroxyproline and threonine, respectively. Further investigations are needed to validate the effects of the variants on these genes.
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Affiliation(s)
- Pamela Xing Yi Soh
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, Australia
| | - Juliana Maria Marin Cely
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, Australia
| | - Sally-Anne Mortlock
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, Australia
| | - Christopher James Jara
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, Australia
| | - Rachel Booth
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, Australia
| | - Siria Natera
- Metabolomics Australia, School of BioSciences, University of Melbourne, Parkville, Australia
| | - Ute Roessner
- Metabolomics Australia, School of BioSciences, University of Melbourne, Parkville, Australia
| | - Ben Crossett
- Sydney Mass Spectrometry, Charles Perkins Centre, University of Sydney, Sydney, Australia
| | - Stuart Cordwell
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, Australia
- Sydney Mass Spectrometry, Charles Perkins Centre, University of Sydney, Sydney, Australia
| | - Mehar Singh Khatkar
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, Australia
| | - Peter Williamson
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, Australia.
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Shaffer LG, Geretschlaeger A, Ramirez CJ, Ballif BC, Carl C. Quality assurance checklist and additional considerations for canine clinical genetic testing laboratories: a follow-up to the published standards and guidelines. Hum Genet 2019; 138:501-508. [PMID: 30982136 PMCID: PMC6536464 DOI: 10.1007/s00439-019-02013-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 04/08/2019] [Indexed: 12/11/2022]
Abstract
There is currently no oversight for canine clinical genetic testing laboratories. We published an initial set of standards and guidelines with the goal of providing a basis for which canine testing laboratories could evaluate their quality assurance programs. To further those standards and guidelines, we have developed a checklist that can be used as a self-evaluation to identify gaps in their programs for continual quality improvement over time. Because there is currently no organization willing to oversee an external proficiency program, the checklist provides the first step toward an internal, self-assessment that can be used periodically to monitor improvements. In addition, we attempt to address concerns from the canine community regarding rare or private mutations, genetic screening using array-based technologies, non-peer reviewed tests that are being offered, and the clinical validity of certain mutations in particular breeds. Through coordination, conversation and hard work, the canine genetic testing community can strive to organize to improve testing and to provide more transparency to consumers and better outcomes for dogs.
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Affiliation(s)
- Lisa G Shaffer
- Paw Print Genetics, Genetic Veterinary Sciences, Inc., 220 E Rowan, Suite 220, Spokane, WA, 99207, USA.
| | | | - Christina J Ramirez
- Paw Print Genetics, Genetic Veterinary Sciences, Inc., 220 E Rowan, Suite 220, Spokane, WA, 99207, USA
| | - Blake C Ballif
- Paw Print Genetics, Genetic Veterinary Sciences, Inc., 220 E Rowan, Suite 220, Spokane, WA, 99207, USA
| | - Casey Carl
- Paw Print Genetics, Genetic Veterinary Sciences, Inc., 220 E Rowan, Suite 220, Spokane, WA, 99207, USA
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Zaldívar-López S, Rowell JL, Fiala EM, Zapata I, Couto CG, Alvarez CE. Comparative genomics of canine hemoglobin genes reveals primacy of beta subunit delta in adult carnivores. BMC Genomics 2017; 18:141. [PMID: 28178945 PMCID: PMC5299747 DOI: 10.1186/s12864-017-3513-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 01/25/2017] [Indexed: 12/11/2022] Open
Abstract
Background The main function of hemoglobin (Hb) is to transport oxygen in the circulation. It is among the most highly studied proteins due to its roles in physiology and disease, and most of our understanding derives from comparative research. There is great diversity in Hb gene evolution in placental mammals, mostly in the repertoire and regulation of the β-globin subunits. Dogs are an ideal model in which to study Hb genes because: 1) they are members of Laurasiatheria, our closest relatives outside of Euarchontoglires (including primates, rodents and rabbits), 2) dog breeds are isolated populations with their own Hb-associated genetics and diseases, and 3) their high level of health care allows for development of biomedical investigation and translation. Results We established that dogs have a complement of five α and five β-globin genes, all of which can be detected as spliced mRNA in adults. Strikingly, HBD, the allegedly-unnecessary adult β-globin protein in humans, is the primary adult β-globin in dogs and other carnivores; moreover, dogs have two active copies of the HBD gene. In contrast, the dominant adult β-globin of humans, HBB, has high sequence divergence and is expressed at markedly lower levels in dogs. We also showed that canine HBD and HBB genes are complex chimeras that resulted from multiple gene conversion events between them. Lastly, we showed that the strongest signal of evolutionary selection in a high-altitude breed, the Bernese Mountain Dog, lies in a haplotype block that spans the β-globin locus. Conclusions We report the first molecular genetic characterization of Hb genes in dogs. We found important distinctions between adult β-globin expression in carnivores compared to other members of Laurasiatheria. Our findings are also likely to raise new questions about the significance of human HBD. The comparative genomics of dog hemoglobin genes sets the stage for diverse research and translation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3513-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sara Zaldívar-López
- Center for Molecular and Human Genetics, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA.,College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA.,Present affiliation: SZL, Departamento. de Genetica, Facultad de Veterinaria, Universidad de Cordoba, Cordoba, Spain
| | - Jennie L Rowell
- Center for Molecular and Human Genetics, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA.,College of Nursing, The Ohio State University, Columbus, OH, USA.,Present affiliation: Center of Excellence in Critical and Complex Care, College of Nursing, The Ohio State University, Columbus, USA
| | - Elise M Fiala
- Center for Molecular and Human Genetics, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Isain Zapata
- Center for Molecular and Human Genetics, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - C Guillermo Couto
- College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA.,Present affiliation: Couto Veterinary Consultants, Hilliard, OH, USA
| | - Carlos E Alvarez
- Center for Molecular and Human Genetics, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA. .,College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA. .,College of Medicine, The Ohio State University, Columbus, OH, USA.
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