Abstract
Objective: To establish a predictive method using whole genome genotyping for early intervention in canine hip dysplasia (CHD) risk management, for the prevention of the progression of secondary osteoarthritis (OA), and for selective breeding. Design: Two sets of dogs (six breeds) were genotyped with dense SNPs covering the entire canine genome. The first set contained 359 dogs upon which a predictive formula for genomic breeding value (GBV) was derived by using their estimated breeding value (EBV) of the Norberg angle (a measure of CHD) and their genotypes. To investigate how well the formula would work for an individual dog with genotype only (without using EBV), a cross validation was performed by masking the EBV of one dog at a time. The genomic data and the EBV of the remaining dogs were used to predict the GBV for the single dog that was left out. The second set of dogs included 38 new Labrador retriever dogs, which had no pedigree relationship to the dogs in the first set. Results: The cross validation showed a strong correlation (R> 0.7) between the EBV and the GBV. The independent validation showed a moderate correlation (R= 0.5) between GBV for the Norberg angle and the observed Norberg angle (no EBV was available for the new 38 dogs). Sensitivity, specificity, positive and negative predictive values of the genomic data were all above 70%. Conclusions: Prediction of CHD from genomic data is feasible, and can be applied for risk management of CHD and early selection for genetic improvement to reduce the prevalence of CHD in breeding programs. The prediction can be implemented before maturity, at which age current radiographic screening programs are traditionally applied, and as soon as DNA is available.
| Language | English (US) |
|---|---|
| Pages | 420-429 |
| Number of pages | 10 |
| Journal | Osteoarthritis and Cartilage |
| Volume | 19 |
| Issue number | 4 |
| DOIs | |
| State | Published - Apr 1 2011 |
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Keywords
- Breeding value
- Canine hip dysplasia
- GWAS
- Genomic prediction
- QTL
Cite this
Canine hip dysplasia is predictable by genotyping. / Guo, G.; Zhou, Z.; Wang, Y.; Zhao, K.; Zhu, L.; Lust, G.; Hunter, L.; Friedenberg, S.; Li, J.; Zhang, Y.; Harris, S.; Jones, P.; Sandler, J.; Krotscheck, U.; Todhunter, R.; Zhang, Z.
In: Osteoarthritis and Cartilage, Vol. 19, No. 4, 01.04.2011, p. 420-429.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Canine hip dysplasia is predictable by genotyping
AU - Guo, G.
AU - Zhou, Z.
AU - Wang, Y.
AU - Zhao, K.
AU - Zhu, L.
AU - Lust, G.
AU - Hunter, L.
AU - Friedenberg, S.
AU - Li, J.
AU - Zhang, Y.
AU - Harris, S.
AU - Jones, P.
AU - Sandler, J.
AU - Krotscheck, U.
AU - Todhunter, R.
AU - Zhang, Z.
PY - 2011/4/1
Y1 - 2011/4/1
N2 - Objective: To establish a predictive method using whole genome genotyping for early intervention in canine hip dysplasia (CHD) risk management, for the prevention of the progression of secondary osteoarthritis (OA), and for selective breeding. Design: Two sets of dogs (six breeds) were genotyped with dense SNPs covering the entire canine genome. The first set contained 359 dogs upon which a predictive formula for genomic breeding value (GBV) was derived by using their estimated breeding value (EBV) of the Norberg angle (a measure of CHD) and their genotypes. To investigate how well the formula would work for an individual dog with genotype only (without using EBV), a cross validation was performed by masking the EBV of one dog at a time. The genomic data and the EBV of the remaining dogs were used to predict the GBV for the single dog that was left out. The second set of dogs included 38 new Labrador retriever dogs, which had no pedigree relationship to the dogs in the first set. Results: The cross validation showed a strong correlation (R> 0.7) between the EBV and the GBV. The independent validation showed a moderate correlation (R= 0.5) between GBV for the Norberg angle and the observed Norberg angle (no EBV was available for the new 38 dogs). Sensitivity, specificity, positive and negative predictive values of the genomic data were all above 70%. Conclusions: Prediction of CHD from genomic data is feasible, and can be applied for risk management of CHD and early selection for genetic improvement to reduce the prevalence of CHD in breeding programs. The prediction can be implemented before maturity, at which age current radiographic screening programs are traditionally applied, and as soon as DNA is available.
AB - Objective: To establish a predictive method using whole genome genotyping for early intervention in canine hip dysplasia (CHD) risk management, for the prevention of the progression of secondary osteoarthritis (OA), and for selective breeding. Design: Two sets of dogs (six breeds) were genotyped with dense SNPs covering the entire canine genome. The first set contained 359 dogs upon which a predictive formula for genomic breeding value (GBV) was derived by using their estimated breeding value (EBV) of the Norberg angle (a measure of CHD) and their genotypes. To investigate how well the formula would work for an individual dog with genotype only (without using EBV), a cross validation was performed by masking the EBV of one dog at a time. The genomic data and the EBV of the remaining dogs were used to predict the GBV for the single dog that was left out. The second set of dogs included 38 new Labrador retriever dogs, which had no pedigree relationship to the dogs in the first set. Results: The cross validation showed a strong correlation (R> 0.7) between the EBV and the GBV. The independent validation showed a moderate correlation (R= 0.5) between GBV for the Norberg angle and the observed Norberg angle (no EBV was available for the new 38 dogs). Sensitivity, specificity, positive and negative predictive values of the genomic data were all above 70%. Conclusions: Prediction of CHD from genomic data is feasible, and can be applied for risk management of CHD and early selection for genetic improvement to reduce the prevalence of CHD in breeding programs. The prediction can be implemented before maturity, at which age current radiographic screening programs are traditionally applied, and as soon as DNA is available.
KW - Breeding value
KW - Canine hip dysplasia
KW - GWAS
KW - Genomic prediction
KW - QTL
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UR - http://www.scopus.com/inward/citedby.url?scp=79952819264&partnerID=8YFLogxK
U2 - 10.1016/j.joca.2010.12.011
DO - 10.1016/j.joca.2010.12.011
M3 - Article
VL - 19
SP - 420
EP - 429
JO - Osteoarthritis and Cartilage
T2 - Osteoarthritis and Cartilage
JF - Osteoarthritis and Cartilage
SN - 1063-4584
IS - 4
ER -