Aneuploidy in dizygotic twin sheep detected using genome-wide single nucleotide polymorphism data from two commonly used commercial vendors
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...
| Main Authors: | , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2018-01-01
|
| Series: | Animal |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S1751731118000204 |
| _version_ | 1818865038661779456 |
|---|---|
| author | D.P. Berry A. O’Brien J. O’Donovan N. McHugh E. Wall S. Randles K. McDermott R.E. O’Connor M.A. Patil J. Ho A. Kennedy N. Byrne D.C. Purfield |
| author_facet | D.P. Berry A. O’Brien J. O’Donovan N. McHugh E. Wall S. Randles K. McDermott R.E. O’Connor M.A. Patil J. Ho A. Kennedy N. Byrne D.C. Purfield |
| author_sort | D.P. Berry |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-19T10:41:12Z |
| format | Article |
| id | doaj.art-030116ff6ccf418f94a85067f2674972 |
| institution | Directory Open Access Journal |
| issn | 1751-7311 |
| language | English |
| last_indexed | 2024-12-19T10:41:12Z |
| publishDate | 2018-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Animal |
| spelling | doaj.art-030116ff6ccf418f94a85067f26749722022-12-21T20:25:26ZengElsevierAnimal1751-73112018-01-01121224622469Aneuploidy in dizygotic twin sheep detected using genome-wide single nucleotide polymorphism data from two commonly used commercial vendorsD.P. Berry0A. O’Brien1J. O’Donovan2N. McHugh3E. Wall4S. Randles5K. McDermott6R.E. O’Connor7M.A. Patil8J. Ho9A. Kennedy10N. Byrne11D.C. Purfield12Teagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork P61 C996, IrelandTeagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork P61 C996, IrelandDepartment of Agriculture, Food and the Marine, Regional Veterinary Laboratory, Model Farm Road, Cork T12 XD51, IrelandTeagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork P61 C996, IrelandSheep Ireland, Bandon, Co. Cork P72 X050, IrelandSheep Ireland, Bandon, Co. Cork P72 X050, IrelandSheep Ireland, Bandon, Co. Cork P72 X050, IrelandUniversity of Kent, School of Biosciences, University of Kent, Canterbury, CT2 7AF, UKThermo Fisher Scientific, 3450 Central Expressway, Santa Clara, CA 95051, USAThermo Fisher Scientific, 3450 Central Expressway, Santa Clara, CA 95051, USATeagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork P61 C996, IrelandTeagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork P61 C996, IrelandTeagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork P61 C996, IrelandEarly 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.http://www.sciencedirect.com/science/article/pii/S1751731118000204mutationchromosomeovineturnerkaryotype |
| spellingShingle | D.P. Berry A. O’Brien J. O’Donovan N. McHugh E. Wall S. Randles K. McDermott R.E. O’Connor M.A. Patil J. Ho A. Kennedy N. Byrne D.C. Purfield Aneuploidy in dizygotic twin sheep detected using genome-wide single nucleotide polymorphism data from two commonly used commercial vendors Animal mutation chromosome ovine turner karyotype |
| title | Aneuploidy in dizygotic twin sheep detected using genome-wide single nucleotide polymorphism data from two commonly used commercial vendors |
| title_full | Aneuploidy in dizygotic twin sheep detected using genome-wide single nucleotide polymorphism data from two commonly used commercial vendors |
| title_fullStr | Aneuploidy in dizygotic twin sheep detected using genome-wide single nucleotide polymorphism data from two commonly used commercial vendors |
| title_full_unstemmed | Aneuploidy in dizygotic twin sheep detected using genome-wide single nucleotide polymorphism data from two commonly used commercial vendors |
| title_short | Aneuploidy in dizygotic twin sheep detected using genome-wide single nucleotide polymorphism data from two commonly used commercial vendors |
| title_sort | aneuploidy in dizygotic twin sheep detected using genome wide single nucleotide polymorphism data from two commonly used commercial vendors |
| topic | mutation chromosome ovine turner karyotype |
| url | http://www.sciencedirect.com/science/article/pii/S1751731118000204 |
| work_keys_str_mv | AT dpberry aneuploidyindizygotictwinsheepdetectedusinggenomewidesinglenucleotidepolymorphismdatafromtwocommonlyusedcommercialvendors AT aobrien aneuploidyindizygotictwinsheepdetectedusinggenomewidesinglenucleotidepolymorphismdatafromtwocommonlyusedcommercialvendors AT jodonovan aneuploidyindizygotictwinsheepdetectedusinggenomewidesinglenucleotidepolymorphismdatafromtwocommonlyusedcommercialvendors AT nmchugh aneuploidyindizygotictwinsheepdetectedusinggenomewidesinglenucleotidepolymorphismdatafromtwocommonlyusedcommercialvendors AT ewall aneuploidyindizygotictwinsheepdetectedusinggenomewidesinglenucleotidepolymorphismdatafromtwocommonlyusedcommercialvendors AT srandles aneuploidyindizygotictwinsheepdetectedusinggenomewidesinglenucleotidepolymorphismdatafromtwocommonlyusedcommercialvendors AT kmcdermott aneuploidyindizygotictwinsheepdetectedusinggenomewidesinglenucleotidepolymorphismdatafromtwocommonlyusedcommercialvendors AT reoconnor aneuploidyindizygotictwinsheepdetectedusinggenomewidesinglenucleotidepolymorphismdatafromtwocommonlyusedcommercialvendors AT mapatil aneuploidyindizygotictwinsheepdetectedusinggenomewidesinglenucleotidepolymorphismdatafromtwocommonlyusedcommercialvendors AT jho aneuploidyindizygotictwinsheepdetectedusinggenomewidesinglenucleotidepolymorphismdatafromtwocommonlyusedcommercialvendors AT akennedy aneuploidyindizygotictwinsheepdetectedusinggenomewidesinglenucleotidepolymorphismdatafromtwocommonlyusedcommercialvendors AT nbyrne aneuploidyindizygotictwinsheepdetectedusinggenomewidesinglenucleotidepolymorphismdatafromtwocommonlyusedcommercialvendors AT dcpurfield aneuploidyindizygotictwinsheepdetectedusinggenomewidesinglenucleotidepolymorphismdatafromtwocommonlyusedcommercialvendors |