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Improved Lasso for genomic selection.
Legarra A, Robert-Granié C, Croiseau P, Guillaume F, Fritz S. Legarra A, et al. Genet Res (Camb). 2011 Feb;93(1):77-87. doi: 10.1017/S0016672310000534. Epub 2010 Dec 14. Genet Res (Camb). 2011. PMID: 21144129
Regular BL uses a common variance parameter for residual and SNP effects (BL1Var). We propose here a BL with different residual and SNP effect variances (BL2Var), equivalent to the original Lasso formulation. ...We also suggest precomputing individual variances of S …
Regular BL uses a common variance parameter for residual and SNP effects (BL1Var). We propose here a BL with different residua …
The effects of selective breeding against scrapie susceptibility on the genetic variability of the Latxa Black-Faced sheep breed.
Alfonso L, Parada A, Legarra A, Ugarte E, Arana A. Alfonso L, et al. Genet Sel Evol. 2006 Sep-Oct;38(5):495-511. doi: 10.1186/1297-9686-38-5-495. Epub 2006 Sep 6. Genet Sel Evol. 2006. PMID: 16954042 Free PMC article.
Breeding sheep populations for scrapie resistance could result in a loss of genetic variability. In this study, the effect on genetic variability of selection for increasing the ARR allele frequency was estimated in the Latxa breed. ...The results based on the genealogical …
Breeding sheep populations for scrapie resistance could result in a loss of genetic variability. In this study, the effect on genetic …
Multi-breed genetic evaluation in a Gelbvieh population.
Legarra A, Bertrand JK, Strabel T, Sapp RL, Sánchez JP, Misztal I. Legarra A, et al. J Anim Breed Genet. 2007 Oct;124(5):286-95. doi: 10.1111/j.1439-0388.2007.00671.x. J Anim Breed Genet. 2007. PMID: 17868081
A multi-breed model was presented for the genetic evaluation of growth traits in beef cattle. In addition to the fixed effects, random direct and maternal genetic effects, and random maternal permanent environmental effects are considered; the model also fits direct and ma
A multi-breed model was presented for the genetic evaluation of growth traits in beef cattle. In addition to the fixed effects, rando
Technical note: Computing strategies in genome-wide selection.
Legarra A, Misztal I. Legarra A, et al. J Dairy Sci. 2008 Jan;91(1):360-6. doi: 10.3168/jds.2007-0403. J Dairy Sci. 2008. PMID: 18096959
This implies dense Henderson's mixed-model equations and considerable computing resources in time and storage, even for a few thousand records. ...Algorithms were tested on a real mouse data set, which included 1,928 records and 10,946 single-nucleotide polymorphism …
This implies dense Henderson's mixed-model equations and considerable computing resources in time and storage, even for a few thousan …
Performance of genomic selection in mice.
Legarra A, Robert-Granié C, Manfredi E, Elsen JM. Legarra A, et al. Genetics. 2008 Sep;180(1):611-8. doi: 10.1534/genetics.108.088575. Epub 2008 Aug 30. Genetics. 2008. PMID: 18757934 Free PMC article.
We analyzed four traits from a heterogeneous mouse population (http://gscan.well.ox.ac.uk/), including 1884 individuals and 10,946 SNP markers. ...In this data set, within-family information was more accurate than across-family information, and populational linkage disequi …
We analyzed four traits from a heterogeneous mouse population (http://gscan.well.ox.ac.uk/), including 1884 individuals and 10,946 SN …
Predicting quantitative traits with regression models for dense molecular markers and pedigree.
de los Campos G, Naya H, Gianola D, Crossa J, Legarra A, Manfredi E, Weigel K, Cotes JM. de los Campos G, et al. Genetics. 2009 May;182(1):375-85. doi: 10.1534/genetics.109.101501. Epub 2009 Mar 16. Genetics. 2009. PMID: 19293140 Free PMC article.
If a large number of markers are included in a regression model, marker-specific shrinkage of regression coefficients may be needed. ...This article adapts the BL to arrive at a regression model where markers, pedigrees, and covariates other than markers are …
If a large number of markers are included in a regression model, marker-specific shrinkage of regression coefficients may be n …
Product versus additive threshold models for analysis of reproduction outcomes in animal genetics.
David I, Bodin L, Gianola D, Legarra A, Manfredi E, Robert-Granié C. David I, et al. J Anim Sci. 2009 Aug;87(8):2510-8. doi: 10.2527/jas.2008-1586. Epub 2009 Apr 24. J Anim Sci. 2009. PMID: 19395507
Taking inspiration from these works, we propose a model (product threshold model) for studying a binary reproduction trait that supposes that the observed phenotype is the product of 2 unobserved phenotypes, 1 for each individual. We developed a Gibbs samplin …
Taking inspiration from these works, we propose a model (product threshold model) for studying a binary reproduction trait tha …
A relationship matrix including full pedigree and genomic information.
Legarra A, Aguilar I, Misztal I. Legarra A, et al. J Dairy Sci. 2009 Sep;92(9):4656-63. doi: 10.3168/jds.2009-2061. J Dairy Sci. 2009. PMID: 19700729
This results in a joint distribution of genotyped and ungenotyped genetic values, with a pedigree-genomic relationship matrix H. ...Matrix H is suitable for iteration on data algorithms that multiply a vector times a matrix, such as preconditioned conj …
This results in a joint distribution of genotyped and ungenotyped genetic values, with a pedigree-genomic relationship matrix …
Linear models for joint association and linkage QTL mapping.
Legarra A, Fernando RL. Legarra A, et al. Genet Sel Evol. 2009 Sep 29;41(1):43. doi: 10.1186/1297-9686-41-43. Genet Sel Evol. 2009. PMID: 19788745 Free PMC article.
Two submodels are presented: a simple and easy to implement Haley-Knott type regression for half-sib families, and a general mixed (variance component) model for general pedigrees. ...CONCLUSION: The linear model theory provides a useful framework for QTL map …
Two submodels are presented: a simple and easy to implement Haley-Knott type regression for half-sib families, and a general m …
Hot topic: a unified approach to utilize phenotypic, full pedigree, and genomic information for genetic evaluation of Holstein final score.
Aguilar I, Misztal I, Johnson DL, Legarra A, Tsuruta S, Lawlor TJ. Aguilar I, et al. J Dairy Sci. 2010 Feb;93(2):743-52. doi: 10.3168/jds.2009-2730. J Dairy Sci. 2010. PMID: 20105546
The first analysis used only a pedigree-based relationship matrix. The second analysis used a relationship matrix based on both pedigree and genomic information (single-step approach). ...The highest coefficient of determination for a single-step approach was …
The first analysis used only a pedigree-based relationship matrix. The second analysis used a relationship matrix based on bot …
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