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Comparison of statistical procedures for estimating polygenic effects using dense genome-wide marker data
- Source :
- BMC Proceedings, BMC Proceedings, Vol 3, Iss Suppl 1, p S12 (2009)
- Publisher :
- Springer Nature
-
Abstract
- In this study we compared different statistical procedures for estimating SNP effects using the simulated data set from the XII QTL-MAS workshop. Five procedures were considered and tested in a reference population, i.e., the first four generations, from which phenotypes and genotypes were available. The procedures can be interpreted as variants of ridge regression, with different ways for defining the shrinkage parameter. Comparisons were made with respect to the correlation between genomic and conventional estimated breeding values. Moderate correlations were obtained from all methods. Two of them were used to predict genomic breeding values in the last three generations. Correlations between these and the true breeding values were also moderate. We concluded that the ridge regression procedures applied in this study did not outperform the simple use of a ratio of variances in a mixed model method, both providing moderate accuracies of predicted genomic breeding values.
- Subjects :
- Mixed model
True breeding organism
lcsh:Medicine
Bioinformatics
Genome
General Biochemistry, Genetics and Molecular Biology
Correlation
Set (abstract data type)
03 medical and health sciences
Statistics
Medicine
Reference population
lcsh:Science
030304 developmental biology
0303 health sciences
business.industry
lcsh:R
0402 animal and dairy science
04 agricultural and veterinary sciences
General Medicine
040201 dairy & animal science
Regression
Proceedings
lcsh:Q
Three generations
business
Subjects
Details
- Language :
- English
- ISSN :
- 17536561
- Volume :
- 3
- Issue :
- Suppl 1
- Database :
- OpenAIRE
- Journal :
- BMC Proceedings
- Accession number :
- edsair.doi.dedup.....55e4d03b2963664c880fd993bef4cb4b
- Full Text :
- https://doi.org/10.1186/1753-6561-3-s1-s12