Best linear unbiased estimation and prediction under a selection model.
TL;DR: Methods for dealing with most data available to animal breeders, however, do not meet the usual requirements of random sampling and are likely to yield biased estimates and predictions.
Abstract: Mixed linear models are assumed in most animal breeding applications. Convenient methods for computing BLUE of the estimable linear functions of the fixed elements of the model and for computing best linear unbiased predictions of the random elements of the model have been available. Most data available to animal breeders, however, do not meet the usual requirements of random sampling, the problem being that the data arise either from selection experiments or from breeders' herds which are undergoing selection. Consequently, the usual methods are likely to yield biased estimates and predictions. Methods for dealing with such data are presented in this paper.
Citations
More filters
TL;DR: The GCTA software is a versatile tool to estimate and partition complex trait variation with large GWAS data sets and focuses on the function of estimating the variance explained by all the SNPs on the X chromosome and testing the hypotheses of dosage compensation.
Abstract: For most human complex diseases and traits, SNPs identified by genome-wide association studies (GWAS) explain only a small fraction of the heritability. Here we report a user-friendly software tool called genome-wide complex trait analysis (GCTA), which was developed based on a method we recently developed to address the “missing heritability” problem. GCTA estimates the variance explained by all the SNPs on a chromosome or on the whole genome for a complex trait rather than testing the association of any particular SNP to the trait. We introduce GCTA's five main functions: data management, estimation of the genetic relationships from SNPs, mixed linear model analysis of variance explained by the SNPs, estimation of the linkage disequilibrium structure, and GWAS simulation. We focus on the function of estimating the variance explained by all the SNPs on the X chromosome and testing the hypotheses of dosage compensation. The GCTA software is a versatile tool to estimate and partition complex trait variation with large GWAS data sets.
5,867 citations
Cites methods from "Best linear unbiased estimation and..."
...If the predictions are unbiased, then the regression slope of the observed phenotypes on the predicted genetic values is 1.(14) In that case, the genetic value calculated based on the BLUP of SNP effects is an unbiased predictor of the true genetic value in the validation set (gnew), in the sense that Eðgnewjb gnewÞ 1⁄4 b gnew....
[...]
TL;DR: TASSEL (Trait Analysis by aSSociation, Evolution and Linkage) implements general linear model and mixed linear model approaches for controlling population and family structure and allows for linkage disequilibrium statistics to be calculated and visualized graphically.
Abstract: Summary: Association analyses that exploit the natural diversity of a genome to map at very high resolutions are becoming increasingly important. In most studies, however, researchers must contend with the confounding effects of both population and family structure. TASSEL (Trait Analysis by aSSociation, Evolution and Linkage) implements general linear model and mixed linear model approaches for controlling population and family structure. For result interpretation, the program allows for linkage disequilibrium statistics to be calculated and visualized graphically. Database browsing and data importation is facilitated by integrated middleware. Other features include analyzing insertions/deletions, calculating diversity statistics, integration of phenotypic and genotypic data, imputing missing data and calculating principal components. Availability: The TASSEL executable, user manual, example data sets and tutorial document are freely available at http://www. maizegenetics.net/tassel. The source code for TASSEL can be found at http://sourceforge.net/projects/tassel.
5,460 citations
Cites background or methods from "Best linear unbiased estimation and..."
...Plant, animal or human geneticists and breeders interested in performing association analysis will find this software useful....
[...]
...The statistical model can be described in Henderson’s notation (Henderson, 1975) as follows: y ¼ Xbþ Zuþ e where y is the vector of observations; b is an unknown vector containing fixed effects including genetic marker and population structure (Q); u is an unknown vector of random additive genetic…...
[...]
TL;DR: In this paper, the authors proposed a restricted maximum likelihood (reml) approach which takes into account the loss in degrees of freedom resulting from estimating fixed effects, and developed a satisfactory asymptotic theory for estimators of variance components.
Abstract: Recent developments promise to increase greatly the popularity of maximum likelihood (ml) as a technique for estimating variance components. Patterson and Thompson (1971) proposed a restricted maximum likelihood (reml) approach which takes into account the loss in degrees of freedom resulting from estimating fixed effects. Miller (1973) developed a satisfactory asymptotic theory for ml estimators of variance components. There are many iterative algorithms that can be considered for computing the ml or reml estimates. The computations on each iteration of these algorithms are those associated with computing estimates of fixed and random effects for given values of the variance components.
2,440 citations
TL;DR: In animal breeding, Best Linear Unbiased Prediction (BLUP) as mentioned in this paper is a technique for estimating genetic merits, which can be used to derive the Kalman filter, the method of Kriging used for ore reserve estimation, credibility theory used to work out insurance premiums, and Hoadley's quality measurement plan used to estimate a quality index.
Abstract: In animal breeding, Best Linear Unbiased Prediction, or BLUP, is a technique for estimating genetic merits. In general, it is a method of estimating random effects. It can be used to derive the Kalman filter, the method of Kriging used for ore reserve estimation, credibility theory used to work out insurance premiums, and Hoadley's quality measurement plan used to estimate a quality index. It can be used for removing noise from images and for small-area estimation. This paper presents the theory of BLUP, some examples of its applica- tion and its relevance to the foundations of statistics. Understanding of procedures for estimating random effects should help people to understand some complicated and controversial issues about fixed and random effects models and also help to bridge the apparent gulf between the Bayesian and Classical schools of thought.
1,669 citations
TL;DR: The aim of the American Thoracic Society/European Respiratory Society Task Force on EBC was to identify the important methodological issues surrounding EBC collection and assay, to provide recommendations for the measurements and to highlight areas where further research is required.
Abstract: Collection of exhaled breath condensate (EBC) is a noninvasive method for obtaining samples from the lungs. EBC contains large number of mediators including adenosine, ammonia, hydrogen peroxide, isoprostanes, leukotrienes, nitrogen oxides, peptides and cytokines. Concentrations of these mediators are influenced by lung diseases and modulated by therapeutic interventions. Similarly EBC pH also changes in respiratory diseases. The aim of the American Thoracic Society/European Respiratory Society Task Force on EBC was to identify the important methodological issues surrounding EBC collection and assay, to provide recommendations for the measurements and to highlight areas where further research is required. Based on the currently available evidence and the consensus of the expert panel for EBC collection, the following general recommendations were put together for oral sample collection: collect during tidal breathing using a noseclip and a saliva trap; define cooling temperature and collection time (10 min is generally sufficient to obtain 1-2 mL of sample and well tolerated by patients); use inert material for condenser; do not use resistor and do not use filter between the subject and the condenser. These are only general recommendations and certain circumstances may dictate variation from them. Important areas for future research involve: ascertaining mechanisms and site of exhaled breath condensate particle formation; determination of dilution markers; improving reproducibility; employment of EBC in longitudinal studies; and determining the utility of exhaled breath condensate measures for the management of individual patients. These studies are required before recommending this technique for use in clinical practice.
1,202 citations
References
More filters
TL;DR: In this article, a closed dairy herd which has been maintained over a number of years with selection being practiced is considered, where the records available for assessing any genetic improvemient consist of production records of cows in the various years and can be represented by a two-way classification, cow by year.
Abstract: A very common problem which arises in animal or plant breeding research is that of assessinig the gain which has resulted from a selection program carr'ied oIn ovei a number of years. To be specific, let us suppose that we have a closed dairy herd which has been maintained over a number of years with selection being practiced. The records available for assessing any genetic improvemient consist of production records of cows in the various years and can be represented by a twoway classification, cow by year. At first it might be thought that such a two-way classification could be analyzed by the method of fitting constants [Yates, 1934]. Applications of this technique have, however, led to the apparent conclusion that the environment gradually deteriorated over the period of years, as indicated by the fact that the constants fitted for years tend to decrease year by year. Heinderson [1949] pointed out that a least squares procedure in which the cow effects are regarded as fixed leads to biased estimates. Lush and Shrode [19501 gave a simple explanation of the biases arising in the estimation of age correction factors; similar considerations apply to the estimation of year effects. The present paper is the combined
552 citations