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Rudd Garces G, Letko A, Häfliger IM, Müller J, Herden C, Nesseler A, Wagner H, Schmidt MJ, Drögemüller C, Lühken G. MFSD2A frameshift variant in Kerry Hill sheep with microcephaly. Anim Genet 2024; 55:152-157. [PMID: 37921236 DOI: 10.1111/age.13374] [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: 08/21/2023] [Revised: 10/15/2023] [Accepted: 10/17/2023] [Indexed: 11/04/2023]
Abstract
Microcephaly is a rare neurodevelopmental disorder characterized by reduced skull circumference and brain volume that occurs sporadically in farm animals. We investigated an early-onset neurodegenerative disorder observed in seven lambs of purebred Kerry Hill sheep. Clinical signs included inability to stand or severe ataxia, convulsions, and early death. Diagnostic imaging and brain necropsy confirmed microcephaly. The pedigree of the lambs suggested monogenic autosomal recessive inheritance. We sequenced the genome of one affected lamb, and comparison with 115 control genomes revealed a single private protein-changing variant. This frameshift variant, MFSD2A: c.285dupA, p.(Asp96fs*9), represents a 1-bp duplication predicted to truncate 80% of the open reading frame. MFSD2A is a transmembrane protein that is essential for maintaining blood-brain barrier homeostasis and plays a key role in regulating brain lipogenesis. Human MFSD2A pathogenic variants are associated with a neurodevelopmental disorder with progressive microcephaly, spasticity, and brain imaging abnormalities (NEDMISBA, OMIM 616486). Here we present evidence for the occurrence of a recessively inherited form of microcephaly in sheep due to a loss-of-function variant in MFSD2A (OMIA 002371-9940). To the best of our knowledge, this is the first report of a spontaneous MFSD2A variant in domestic animals.
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Affiliation(s)
- Gabriela Rudd Garces
- Institute of Animal Breeding and Genetics, Justus Liebig University Giessen, Giessen, Germany
| | - Anna Letko
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Irene M Häfliger
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Jana Müller
- Institute for Veterinary Pathology, Justus Liebig University Giessen, Giessen, Germany
| | - Christiane Herden
- Institute for Veterinary Pathology, Justus Liebig University Giessen, Giessen, Germany
- Center for Mind, Brain and Behavior, Justus Liebig University Giessen, Giessen, Germany
| | | | - Henrik Wagner
- Veterinary Clinic for Reproduction and Neonatology, Justus Liebig University, Giessen, Germany
| | - Martin J Schmidt
- Clinic for Small Animals, Neurosurgery, Neuroradiology and Clinical Neurology, Justus Liebig University Giessen, Giessen, Germany
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Gesine Lühken
- Institute of Animal Breeding and Genetics, Justus Liebig University Giessen, Giessen, Germany
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Pollott GE, Piercy RJ, Massey C, Salavati M, Cheng Z, Wathes DC. Locating a novel autosomal recessive genetic variant in the cattle glucokinase gene using only WGS data from three cases and six carriers. Front Genet 2022; 13:755693. [PMID: 36105082 PMCID: PMC9465091 DOI: 10.3389/fgene.2022.755693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 07/21/2022] [Indexed: 11/13/2022] Open
Abstract
New Mendelian genetic conditions, which adversely affect livestock, arise all the time. To manage them effectively, some methods need to be devised that are quick and accurate. Until recently, finding the causal genomic site of a new autosomal recessive genetic disease has required a two-stage approach using single-nucleotide polymorphism (SNP) chip genotyping to locate the region containing the new variant. This region is then explored using fine-mapping methods to locate the actual site of the new variant. This study explores bioinformatic methods that can be used to identify the causative variants of recessive genetic disorders with full penetrance with just nine whole genome-sequenced animals to simplify and expedite the process to a one-step procedure. Using whole genome sequencing of only three cases and six carriers, the site of a novel variant causing perinatal mortality in Irish moiled calves was located. Four methods were used to interrogate the variant call format (VCF) data file of these nine animals, they are genotype criteria (GCR), autozygosity-by-difference (ABD), variant prediction scoring, and registered SNP information. From more than nine million variants in the VCF file, only one site was identified by all four methods (Chr4: g.77173487A>T (ARS-UCD1.2 (GCF_002263795.1)). This site was a splice acceptor variant located in the glucokinase gene (GCK). It was verified on an independent sample of animals from the breed using genotyping by polymerase chain reaction at the candidate site and autozygosity-by-difference using SNP-chips. Both methods confirmed the candidate site. Investigation of the GCR method found that sites meeting the GCR were not evenly spread across the genome but concentrated in regions of long runs of homozygosity. Locating GCR sites was best performed using two carriers to every case, and the carriers should be distantly related to the cases, within the breed concerned. Fewer than 20 animals need to be sequenced when using the GCR and ABD methods together. The genomic site of novel autosomal recessive Mendelian genetic diseases can be located using fewer than 20 animals combined with two bioinformatic methods, autozygosity-by-difference, and genotype criteria. In many instances it may also be confirmed with variant prediction scoring. This should speed-up and simplify the management of new genetic diseases to a single-step process.
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Affiliation(s)
- Geoffrey E. Pollott
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, London, United Kingdom
- *Correspondence: Geoffrey E. Pollott,
| | - Richard J. Piercy
- Comparative Neuromuscular Diseases Laboratory, Department of Clinical Sciences and Services, Royal Veterinary College, London, United Kingdom
| | - Claire Massey
- Comparative Neuromuscular Diseases Laboratory, Department of Clinical Sciences and Services, Royal Veterinary College, London, United Kingdom
| | - Mazdak Salavati
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, Hatfield, United Kingdom
- The Roslin Institute, Midlothian, United Kingdom
| | - Zhangrui Cheng
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, Hatfield, United Kingdom
| | - D. Claire Wathes
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, Hatfield, United Kingdom
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Wu X, Mesbah-Uddin M, Guldbrandtsen B, Lund MS, Sahana G. Haplotypes responsible for early embryonic lethality detected in Nordic Holsteins. J Dairy Sci 2019; 102:11116-11123. [PMID: 31548059 DOI: 10.3168/jds.2019-16651] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 08/09/2019] [Indexed: 12/13/2022]
Abstract
Widespread use of a limited number of elite sires in dairy cattle breeding increases the risk of some deleterious allelic variants spreading in the population. Genomic data are being used to detect relatively common (frequency >1%) haplotypes that never occur in the homozygous state in live animals. Such haplotypes likely include recessive lethal or semilethal alleles. The aim of this study was to detect such haplotypes in the Nordic Holstein population and to identify causal genetic factors underlying these haplotypes. Illumina BovineSNP50 BeadChip (Illumina Inc., San Diego, CA) genotypes for 26,312 Nordic Holstein animals were phased to construct haplotypes. Haplotypes that are common in the population but never observed as homozygous were identified. Two such haplotypes overlapped with previously identified recessive lethal mutations in Holsteins-namely, structural maintenance of chromosomes 2 (HH3) and brachyspina. In addition, we identified 9 novel putative recessive lethal-carrying haplotypes, with 26 to 36 homozygous individuals expected among the genotyped animals but only 0 to 3 homozygotes observed. For 2 out of 9 homozygous-deficient haplotypes, insemination records of at-risk mating (carrier bull with daughter of carrier sire) showed reduced insemination success compared with not-at-risk mating (noncarrier bull with daughter of noncarrier sire), supporting early embryonic mortality. To detect the causative variant underlying each homozygous-deficient haplotype, data from the 1000 Bull Genome Project were used. However, no variants or deletions identified in the chromosome regions covered by the haplotypes showed concordance with haplotype carrier status. The carrier status of detected haplotypes could be used to select bulls to reduce the frequency of the latent lethal mutations in the population. If desired, at-risk matings could be avoided.
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Affiliation(s)
- Xiaoping Wu
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, DK-8830 Tjele, Denmark.
| | - Md Mesbah-Uddin
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, DK-8830 Tjele, Denmark; Animal Genetics and Integrative Biology, UMR 1313 GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Bernt Guldbrandtsen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, DK-8830 Tjele, Denmark
| | - Mogens S Lund
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, DK-8830 Tjele, Denmark
| | - Goutam Sahana
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, DK-8830 Tjele, Denmark
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Posbergh CJ, Pollott GE, Southard TL, Divers TJ, Brooks SA. A Nonsynonymous Change in Adhesion G Protein–Coupled Receptor L3 Associated With Risk for Equine Degenerative Myeloencephalopathy in the Caspian Horse. J Equine Vet Sci 2018. [DOI: 10.1016/j.jevs.2018.08.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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