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Aneuploidy in dizygotic twin sheep detected using genome-wide single nucleotide polymorphism data from two commonly used commercial vendors

Published online by Cambridge University Press:  15 March 2018

D. P. Berry ,
A. O’Brien ,
J. O’Donovan ,
N. McHugh ,
E. Wall ,
S. Randles ,
K. McDermott ,
R. E. O’Connor ,
M. A. Patil  and
J. Ho
...Show all authors
D. P. Berry*
Affiliation:
Teagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork P61 C996, Ireland
A. O’Brien
Affiliation:
Teagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork P61 C996, Ireland
J. O’Donovan
Affiliation:
Department of Agriculture, Food and the Marine, Regional Veterinary Laboratory, Model Farm Road, CorkT12 XD51, Ireland
N. McHugh
Affiliation:
Teagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork P61 C996, Ireland
E. Wall
Affiliation:
Sheep Ireland, Bandon, Co. Cork P72 X050, Ireland
S. Randles
Affiliation:
Sheep Ireland, Bandon, Co. Cork P72 X050, Ireland
K. McDermott
Affiliation:
Sheep Ireland, Bandon, Co. Cork P72 X050, Ireland
R. E. O’Connor
Affiliation:
University of Kent, School of Biosciences, University of Kent, Canterbury, CT2 7AF, UK
M. A. Patil
Affiliation:
Thermo Fisher Scientific, 3450 Central Expressway, Santa Clara, CA 95051, USA
J. Ho
Affiliation:
Thermo Fisher Scientific, 3450 Central Expressway, Santa Clara, CA 95051, USA
A. Kennedy
Affiliation:
Teagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork P61 C996, Ireland
N. Byrne
Affiliation:
Teagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork P61 C996, Ireland
D. C. Purfield
Affiliation:
Teagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork P61 C996, Ireland
*
†E-mail: Donagh.berry@teagasc.ie
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Abstract

Early detection of karyotype abnormalities, including aneuploidy, could aid producers in identifying animals which, for example, would not be suitable candidate parents. Genome-wide genetic marker data in the form of single nucleotide polymorphisms (SNPs) are now being routinely generated on animals. The objective of the present study was to describe the statistics that could be generated from the allele intensity values from such SNP data to diagnose karyotype abnormalities; of particular interest was whether detection of aneuploidy was possible with both commonly used genotyping platforms in agricultural species, namely the Applied BiosystemsTM AxiomTM and the Illumina platform. The hypothesis was tested using a case study of a set of dizygotic X-chromosome monosomy 53,X sheep twins. Genome-wide SNP data were available from the Illumina platform (11 082 autosomal and 191 X-chromosome SNPs) on 1848 male and 8954 female sheep and available from the AxiomTM platform (11 128 autosomal and 68 X-chromosome SNPs) on 383 female sheep. Genotype allele intensity values, either as their original raw values or transformed to logarithm intensity ratio (LRR), were used to accurately diagnose two dizygotic (i.e. fraternal) twin 53,X sheep, both of which received their single X chromosome from their sire. This is the first reported case of 53,X dizygotic twins in any species. Relative to the X-chromosome SNP genotype mean allele intensity values of normal females, the mean allele intensity value of SNP genotypes on the X chromosome of the two females monosomic for the X chromosome was 7.45 to 12.4 standard deviations less, and were easily detectable using either the AxiomTM or Illumina genotype platform; the next lowest mean allele intensity value of a female was 4.71 or 3.3 standard deviations less than the population mean depending on the platform used. Both 53,X females could also be detected based on the genotype LRR although this was more easily detectable when comparing the mean LRR of the X chromosome of each female to the mean LRR of their respective autosomes. On autopsy, the ovaries of the two sheep were small for their age and evidence of prior ovulation was not appreciated. In both sheep, the density of primordial follicles in the ovarian cortex was lower than normally found in ovine ovaries and primary follicle development was not observed. Mammary gland development was very limited. Results substantiate previous studies in other species that aneuploidy can be readily detected using SNP genotype allele intensity values generally already available, and the approach proposed in the present study was agnostic to genotype platform.

Keywords

mutationchromosomeovineturnerkaryotype
Type
Research Article
Information
animal , Volume 12 , Issue 12 , December 2018 , pp. 2462 - 2469
Copyright
© The Animal Consortium 2018 

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References

Baylis, MS, Wayte, DM and Owen, JB 1984. An X0/XX mosaic sheep with associated gonadal dysgenesis. Research in Veterinary Science 36, 125–126.Google Scholar
Berry, DP, Wolfe, A, O’Donovan, J, Byrne, N, Sayers, RG, Dodds, KG, McEwan, JC, O’Connor, RE, McClure, M and Purfield, DC 2017. Characterisation of an X-chromosomal non-mosaic monosomy (59, X0) dairy heifer detected using routinely available single nucleotide polymorphism genotype data. Journal of Animal Science 95, 1042–1049.Google Scholar
Boichard, D, Chung, H, Dassonneville, R, David, X, Eggen, A, Fritz, S, Gietzen, KJ, Hayes, BJ, Lawley, CT, Sonstegard, TS, Van Tassell, CP, VanRaden, PM, Viaud-Martinez, KA, Wiggans, GR and Bovien Low Density Consortium 2012. Design of a bovine low-density SNP array optimized for imputation. PLos One 7, e34130.Google Scholar
Broad, T, Hayes, H and Long, S 1997. Cytogenetics: physical chromosome maps. In The Genetics of Sheep (ed. L Piper and A Ruvinsky), pp. 241–295. CAB International, Wallingford, UK.Google Scholar
Dodds, KG, Auvray, B, Newman, S-A and McEwan, JC 2012. Genomic breed prediction in New Zealand sheep. BMC Genetics 15, 92.Google Scholar
Duchemin, SI, Colombani, C, Legarra, A, Baloche, G, Larroque, H, Astruc, JM, Barillet, F, Robert-Granié, C and Manfredi, E 2012. Genomic selection in the French Lacaune dairy sheep breed. Journal of Dairy Science 95, 2723–2733.Google Scholar
Gilbert, B, Yardin, C, Briault, S, Belin, V, Lienhardt, A, Aubard, Y, Battin, J, Servaud, M, Philippe, HJ and Lacombe, D 2002. Prenatal diagnosis of female monozygotic twins discordant for Turner syndrome: implications for prenatal genetic counselling. Prenatal Diagnostics 22, 697–702.Google Scholar
Gravholt, CH 2005. Epidemiological, endocrine and metabolic features in Turner syndrome. Arquivos Brasileiros de Endocrinologia & Metabologia 49, 145e156.Google Scholar
Hook, EB 1977. Exclusion of chromosomal mosaicism: Tables of 90%, 95% and 99% confidence limits and comments on use. American Journal of Human Genetics 29, 94–97.Google Scholar
International System for Chromosome Nomenclature of Domestic Bovids 2001. Cytogenetics and cell genetics (coordinator ed. D Di Berardino, GP Di Meo GP, DS Gallagher, H Hayes and L Iannuzzi), volume 92, chapter 21, pp. 283–299. Karger Publishers, Basel, Switzerland.Google Scholar
Lin, C-F, Naj, AC and Wang, L-S 2014. Analyzing copy number variation using SNP array data: protocols for calling CNV and association tests. Current Protocols in Human Genetics 18, 79.Google Scholar
Mathur, A, Stekol, L, Schatz, D, MacLaren, NK, Scott, ML and Lippe, B 1991. The parental origin of the single X-chromosome in Turner syndrome: lack of correlation with parental age or clinical phenotype. American Journal of Human Genetics 48, 682–686.Google Scholar
Mohammadpour, AA 2007. Comparative histomorphological study of ovary and ovarian follicles in Iranian Lori-Bakhtiari sheep and native goat. Pakistan Journal of Biological Sciences 10, 673–675.Google Scholar
Nielsen, J 1966. Twins in sibships with Kleinefelter’s syndrome. Journal of Medical Genetics 3, 114–116.Google Scholar
Pescia, G, Ferrier, PE, Wyss-Hutin, D and Klein, D 1975. 45,X Turner’s syndrome in monozygotic twin sisters. Journal of Medical Genetics 12, 390–396.Google Scholar
Raudseep, T and Chowdhary, BP 2016. Chromosome aberrations and fertility disorders in domestic animals. Annual Reviews of Animal Bioscience 4, 15–43.Google Scholar
Rehder, H, Schoner, K, Kluge, B, Louwen, F, Schwinger, E and Neesen, J 2012. Kleinefelter twins presenting with discordant aneuploidies acardia, forked umbilical cord and with different gonadal sex despite monozygosity. Prenatal Diagnosis 32, 173–179.Google Scholar
Romano, JE, Raussdepp, T, Mulon, PY and Villadóniga, GB 2015. Non-mosaic monosomy 59,X in cattle: a case report. Animal Reproduction Science 156, 83–90.Google Scholar
Rongen-Westerlaken, C, Corel, L, van den Broeck, J, Massa, G, Karlberg, J, Albertsson-Wikland, K, Naeraa, RW, Wit, JM and The Dutch and Swedish Study Groups for GH treatment 1997. Reference values for height, height velocity and weight in Turner’s syndrome. Acta Paediatrica 86, 937–942.Google Scholar
Rovet, J and Netley, C 1981. Turner syndrome in a pair of dizygotic twins: a single case study. Behavior Genetics 11, 65–72.Google Scholar
Treff, NR, Su, J, Tao, X, Levy, B and Scott, RT 2011. Accurate single cell 24 chromosome aneuploidy screening using whole genome amplification and single nucleotide polymorphism microarrays. Fertility and Sterility 94, 2017–2021.Google Scholar
Uematsu, A, Yorifuji, T, Muroi, J, Kawai, M, Mamada, M, Kaji, M, Yamanaka, C, Momoi, T and Nakahata, T 2002. Parental origin of normal X chromosomes in Turner syndrome patients with various karyotypes: implications for the mechanism leading to generation of a 45,X karyotype. American Journal of Medical Genetics 111, 134–139.Google Scholar
Visscher, K, Metcalfe, KA and Semple, JL 2015. Breast deformity and reconstruction in Turner syndrome: a collection of case studies. Journal of Plastic, Reconstructive & Aesthetic Surgery Open 4, 16–21.Google Scholar
Xiong, B, Tan, K, Tan, YQ, Gong, F, Zhang, SP, Lu, CF, Luo, KL, Lu, GX and Lin, G. 2014. Using SNP array to identify aneuploidy and segmental imbalance in translocation carriers. Genomics Data. 24, 92–95.Google Scholar
Zartman, DL, Hinesley, LL and Gnatkowski, MW 1981. A 53,X female sheep (Ovis aries). Cytogenetics Cell Genetics 30, 54–58.Google Scholar
Zhang, IL, Couldrey, C and Sherlock, RG 2016. Using genomic information to predict sex in dairy cattle. New Zealand Society of Animal Production 76, 26–30.Google Scholar