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Boeykens F, Bogaerts E, Vossaert L, Peelman L, Van Nieuwerburgh F, Saunders JH, Broeckx BJ. Whole exome sequencing as a screening tool in dogs: A pilot study. Comput Struct Biotechnol J 2025; 27:960-968. [PMID: 40151526 PMCID: PMC11946360 DOI: 10.1016/j.csbj.2025.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2024] [Revised: 02/20/2025] [Accepted: 03/04/2025] [Indexed: 03/29/2025] Open
Abstract
Background Whole-exome sequencing (WES) is used to selectively sequence all exons of protein-coding genes. WES is considered as a cost-effective and direct approach for identifying phenotype-associated variants in protein-coding regions and is as such situated between the traditional Sanger sequencing and whole genome sequencing (WGS). While WES is already widely used as a clinical tool in human and medical genetics, its use in veterinary medicine is currently restricted to research purposes. In this article, we aimed to provide baseline performance characteristics of a WES design to assess its suitability with future applications in veterinary clinical genetics in mind. Methods To assess the potential of WES in a clinical setting for dogs, 49 canine samples underwent capture, sequencing and analysis for the presence of 352 known phenotype-associated variants. The sequencing performance was compared for three types of variants, based on their size and location: single nucleotide variants (SNVs) inside exons, larger indel variants (≤20 bp) inside exons and intronic variants. Results On average, 85 % and 82 % of the exonic SNPs and larger variants were sequenced at a sequencing depth of ≥ 10x in the 49 samples, respectively. In the best performing sample, 94 % of the exonic SNPs were covered at least 10x, whereas in the worst performing sample, still 71 % of the exonic SNPs had an average sequencing depth of more than 10x. Conclusion To our knowledge, this is the first report that describes the performance of a research-intended WES design if it would be used in clinical genetics. This study found that WES demonstrated high efficacy in detecting variants located within target regions, including those that were not initially included in the design. However, the performance varied across different variants. The next steps would be the development of improved designs and settings to ameliorate the results.
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Affiliation(s)
- Fréderique Boeykens
- Laboratory of Animal Genetics, Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Evelien Bogaerts
- Department of Morphology, Imaging, Orthopedics, Rehabilitation and Nutrition, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Liesbeth Vossaert
- Baylor College of Medicine, Department of Molecular and Human Genetics, Houston, TX United States
| | - Luc Peelman
- Laboratory of Animal Genetics, Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Jimmy H. Saunders
- Department of Morphology, Imaging, Orthopedics, Rehabilitation and Nutrition, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Bart J.G. Broeckx
- Laboratory of Animal Genetics, Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
- Centre for Clinical Genetics of Companion Animals, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
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Bugbee A, Rucinsky R, Cazabon S, Kvitko-White H, Lathan P, Nichelason A, Rudolph L. 2023 AAHA Selected Endocrinopathies of Dogs and Cats Guidelines. J Am Anim Hosp Assoc 2023; 59:113-135. [PMID: 37167252 DOI: 10.5326/jaaha-ms-7368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Canine and feline endocrinopathies reflect an endocrine gland disease or dysfunction with resulting hormonal abnormali ties that can variably affect the patient's wellbeing, quality of life, and life expectancy. These guidelines provide consensus recommendations for diagnosis and treatment of four canine and feline endocrinopathies commonly encountered in clini cal practice: canine hypothyroidism, canine hypercortisolism (Cushing's syndrome), canine hypoadrenocorticism (Addi son's disease), and feline hyperthyroidism. To aid the general practitioner in navigating these common diseases, a stepwise diagnosis and treatment algorithm and relevant background information is provided for managing each of these diseases. The guidelines also describe, in lesser detail, the diagnosis and treatment of three relatively less common endo crinopathies of cats: feline hyperaldosteronism, feline hypothyroidism, and feline hyperadrenocorticism. Additionally, the guidelines present tips on effective veterinary team utilization and client communication when discussing endocrine cases.
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Affiliation(s)
- Andrew Bugbee
- Department of Small Animal Medicine and Surgery, University of Georgia, Athens, Georgia (A.B.); Mid Atlantic Cat Hospital, Mid Atlantic Feline Thyroid Center, Queenstown, Maryland (R.R.); Boston Veterinary Clinic, Boston, Massachusetts (S.C.); KW Veterinary Consulting, LLC, Kansas City, Missouri (H.K.-W.); Mississippi State University, Mississippi State, Mississippi (P.L.); School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin (A.N.); Rowan College of South Jersey, Sewell, New Jersey (L.R.)
| | - Renee Rucinsky
- Department of Small Animal Medicine and Surgery, University of Georgia, Athens, Georgia (A.B.); Mid Atlantic Cat Hospital, Mid Atlantic Feline Thyroid Center, Queenstown, Maryland (R.R.); Boston Veterinary Clinic, Boston, Massachusetts (S.C.); KW Veterinary Consulting, LLC, Kansas City, Missouri (H.K.-W.); Mississippi State University, Mississippi State, Mississippi (P.L.); School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin (A.N.); Rowan College of South Jersey, Sewell, New Jersey (L.R.)
| | - Sarah Cazabon
- Department of Small Animal Medicine and Surgery, University of Georgia, Athens, Georgia (A.B.); Mid Atlantic Cat Hospital, Mid Atlantic Feline Thyroid Center, Queenstown, Maryland (R.R.); Boston Veterinary Clinic, Boston, Massachusetts (S.C.); KW Veterinary Consulting, LLC, Kansas City, Missouri (H.K.-W.); Mississippi State University, Mississippi State, Mississippi (P.L.); School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin (A.N.); Rowan College of South Jersey, Sewell, New Jersey (L.R.)
| | - Heather Kvitko-White
- Department of Small Animal Medicine and Surgery, University of Georgia, Athens, Georgia (A.B.); Mid Atlantic Cat Hospital, Mid Atlantic Feline Thyroid Center, Queenstown, Maryland (R.R.); Boston Veterinary Clinic, Boston, Massachusetts (S.C.); KW Veterinary Consulting, LLC, Kansas City, Missouri (H.K.-W.); Mississippi State University, Mississippi State, Mississippi (P.L.); School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin (A.N.); Rowan College of South Jersey, Sewell, New Jersey (L.R.)
| | - Patty Lathan
- Department of Small Animal Medicine and Surgery, University of Georgia, Athens, Georgia (A.B.); Mid Atlantic Cat Hospital, Mid Atlantic Feline Thyroid Center, Queenstown, Maryland (R.R.); Boston Veterinary Clinic, Boston, Massachusetts (S.C.); KW Veterinary Consulting, LLC, Kansas City, Missouri (H.K.-W.); Mississippi State University, Mississippi State, Mississippi (P.L.); School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin (A.N.); Rowan College of South Jersey, Sewell, New Jersey (L.R.)
| | - Amy Nichelason
- Department of Small Animal Medicine and Surgery, University of Georgia, Athens, Georgia (A.B.); Mid Atlantic Cat Hospital, Mid Atlantic Feline Thyroid Center, Queenstown, Maryland (R.R.); Boston Veterinary Clinic, Boston, Massachusetts (S.C.); KW Veterinary Consulting, LLC, Kansas City, Missouri (H.K.-W.); Mississippi State University, Mississippi State, Mississippi (P.L.); School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin (A.N.); Rowan College of South Jersey, Sewell, New Jersey (L.R.)
| | - Liza Rudolph
- Department of Small Animal Medicine and Surgery, University of Georgia, Athens, Georgia (A.B.); Mid Atlantic Cat Hospital, Mid Atlantic Feline Thyroid Center, Queenstown, Maryland (R.R.); Boston Veterinary Clinic, Boston, Massachusetts (S.C.); KW Veterinary Consulting, LLC, Kansas City, Missouri (H.K.-W.); Mississippi State University, Mississippi State, Mississippi (P.L.); School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin (A.N.); Rowan College of South Jersey, Sewell, New Jersey (L.R.)
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PRESUMPTIVE CONGENITAL HYPOTHYROIDISM IN RED PANDAS ( AILURUS FULGENS FULGENS) FROM FOUR SUCCESSIVE LITTERS. J Zoo Wildl Med 2021; 52:795-805. [PMID: 34130428 DOI: 10.1638/2020-0122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/30/2020] [Indexed: 11/21/2022] Open
Abstract
High neonatal mortality among red pandas (Ailurus fulgens) challenges the long-term sustainability of the Species Survival Plan population. Congenital hypothyroidism (CH) is a rare condition in domestic animals, typically due to an inherited genetic defect. Nongoitrous CH was presumptively diagnosed in 75% (n = 6/8) of red panda neonates from four successive litters, with a common sire and two closely related dams. Antemortem diagnosis of CH was made in three cubs (n = 3/6) based on elevated thyroid stimulating hormone and decreased free thyroxine and total thyroxine levels. Affected cubs also had suggestive clinical signs, which included delayed growth with cretinous dwarf appearance, atonic bladder, delayed gastrointestinal motility, hypercholesterolemia, and hypocalcemia. With sodium levothyroxine therapy, two of the three cubs developed into normal adult red pandas in terms of body size, appearance, and behavior. On necropsy cubs (n = 4) were small with varying degrees of cretin dwarf appearance and hypoplastic thyroids with reduced to no colloid in follicles. These cases demonstrate the importance of collecting thyroid tissue, (or proximal trachea/larynx if gross visualization not possible), in neonates for histopathology. Further investigation into the role of thyroid disease in neonatal red panda mortality is warranted.
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Iturriaga MP, Cocio JA, Barrs VR. Cluster of cases of congenital feline goitrous hypothyroidism in a single hospital. J Small Anim Pract 2020; 61:696-703. [PMID: 32974927 DOI: 10.1111/jsap.13231] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/12/2020] [Accepted: 08/19/2020] [Indexed: 12/11/2022]
Abstract
OBJECTIVES To describe the clinicopathological findings and outcomes of cases of feline congenital hypothyroidism diagnosed in a single veterinary hospital in Santiago, Chile. MATERIALS AND METHODS Medical records were searched for cases of congenital hypothyroidism over an 18-month period. Inclusion criteria were a diagnosis of congenital hypothyroidism based on consistent historical and clinical findings, a low or low-normal serum total T4 and elevated serum canine TSH (cTSH). RESULTS Six unrelated cats ranging in age from 4 to 19 months met the inclusion criteria. The most common historical signs were small stature and lethargy. All cats had disproportionate dwarfism, delayed tooth eruption, retained deciduous teeth, bilateral palpable goitres and low rectal temperatures. Other findings were bradycardia, obesity, poor hair coat and focal alopecia on the ventral aspects of the elbows and hocks. In all cases, cTSH was markedly elevated. Sequential changes noted after the initiation of therapy included normal T4 after 6 weeks, improved hair coat and increased physical activity by 8 weeks, normal cTSH by 10 weeks and normal physical appearance and dentition after 4 months. Goitres shrank markedly but remained palpable. Hypothyroidism was well managed clinically in all cases 2 years after diagnosis except for one cat that died of unrelated causes. CLINICAL SIGNIFICANCE This is the first report to describe a cluster of congenital hypothyroidism cases in non-related cats that were presented over a short period of time. Growth defects resolve with treatment, even in cats diagnosed after puberty. Larger, prospective multi-centre studies are warranted to determine the incidence of congenital hypothyroidism in cats.
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Affiliation(s)
- M P Iturriaga
- Escuela de Medicina Veterinaria, Facultad de Medicina Veterinaria y Agronomía, Universidad de Las Américas, Manuel Montt 948, Providencia, Santiago, 7500975, Chile
| | - J A Cocio
- Hospital Clínico Veterinario Universidad de Chile, Francisco Bilbao 2854, Providencia, Santiago, 7510828, Chile
| | - V R Barrs
- Jockey Club College of Veterinary Medicine and Life Sciences, Department of Veterinary Clinical Sciences, City University of Hong Kong, 31 To Yuen St, Kowloon Tong, Hong Kong, SAR China
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