scholarly journals Fine Mapping of Complex Trait Genes Combining Pedigree and Linkage Disequilibrium Information: A Bayesian Unified Framework

Genetics ◽  
2003 ◽  
Vol 163 (4) ◽  
pp. 1497-1510 ◽  
Author(s):  
Miguel Pérez-Enciso
Keyword(s):  
Linkage Disequilibrium ◽  
Fixed Effects ◽  
Simulated Data ◽  
Complex Trait ◽  
Pedigree Information ◽  
Unified Framework ◽  
Linkage Disequilibrium Information ◽  
Sib Families ◽  
Trait Locus ◽  
Better Than

Abstract We present a Bayesian method that combines linkage and linkage disequilibrium (LDL) information for quantitative trait locus (QTL) mapping. This method uses jointly all marker information (haplotypes) and all available pedigree information; i.e., it is not restricted to any specific experimental design and it is not required that phases are known. Infinitesimal genetic effects or environmental noise (“fixed”) effects can equally be fitted. A diallelic QTL is assumed and both additive and dominant effects can be estimated. We have implemented a combined Gibbs/Metropolis-Hastings sampling to obtain the marginal posterior distributions of the parameters of interest. We have also implemented a Bayesian variant of usual disequilibrium measures like D′ and r2 between QTL and markers. We illustrate the method with simulated data in “simple” (two-generation full-sib families) and “complex” (four-generation) pedigrees. We compared the estimates with and without using linkage disequilibrium information. In general, using LDL resulted in estimates of QTL position that were much better than linkage-only estimates when there was complete disequilibrium between the mutant QTL allele and the marker. This advantage, however, decreased when the association was only partial. In all cases, additive and dominant effects were estimated accurately either with or without disequilibrium information.

scholarly journals A comparison between methods for linkage disequilibrium fine mapping of quantitative trait loci

2004 ◽  
Vol 83 (1) ◽  
pp. 41-47 ◽  
Author(s):  
JIHAD M. ABDALLAH ◽  
BRIGITTE MANGIN ◽  
BRUNO GOFFINET ◽  
CHRISTINE CIERCO-AYROLLES ◽  
MIGUEL PÉREZ-ENCISO
Keyword(s):  
Linkage Disequilibrium ◽  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Simulated Data ◽  
Likelihood Method ◽  
Trait Loci ◽  
Single Marker ◽  
Linkage Disequilibrium Information ◽  
Marker Regression ◽  
Trait Locus

We present a maximum likelihood method for mapping quantitative trait loci that uses linkage disequilibrium information from single and multiple markers. We made paired comparisons between analyses using a single marker, two markers and six markers. We also compared the method to single marker regression analysis under several scenarios using simulated data. In general, our method outperformed regression (smaller mean square error and confidence intervals of location estimate) for quantitative trait loci with dominance effects. In addition, the method provides estimates of the frequency and additive and dominance effects of the quantitative trait locus.

scholarly journals Fine Mapping of a Quantitative Trait Locus for Twinning Rate Using Combined Linkage and Linkage Disequilibrium Mapping

Genetics ◽  
2002 ◽  
Vol 161 (1) ◽  
pp. 373-379 ◽  
Author(s):  
Theo H E Meuwissen ◽  
Astrid Karlsen ◽  
Sigbjørn Lien ◽  
Ingrid Olsaker ◽  
Mike E Goddard
Keyword(s):  
Quantitative Trait Locus ◽  
Linkage Disequilibrium ◽  
Quantitative Trait ◽  
Complex Traits ◽  
Middle Part ◽  
Linkage Disequilibrium Mapping ◽  
Chromosome 5 ◽  
Linkage Information ◽  
Linkage Disequilibrium Information ◽  
Trait Locus

Abstract A novel and robust method for the fine-scale mapping of genes affecting complex traits, which combines linkage and linkage-disequilibrium information, is proposed. Linkage information refers to recombinations within the marker-genotyped generations and linkage disequilibrium to historical recombinations before genotyping started. The identity-by-descent (IBD) probabilities at the quantitative trait locus (QTL) between first generation haplotypes were obtained from the similarity of the marker alleles surrounding the QTL, whereas IBD probabilities at the QTL between later generation haplotypes were obtained by using the markers to trace the inheritance of the QTL. The variance explained by the QTL is estimated by residual maximum likelihood using the correlation structure defined by the IBD probabilities. Unlinked background genes were accounted for by fitting a polygenic variance component. The method was used to fine map a QTL for twinning rate in cattle, previously mapped on chromosome 5 by linkage analysis. The data consisted of large half-sib families, but the method could also handle more complex pedigrees. The likelihood of the putative QTL was very small along most of the chromosome, except for a sharp likelihood peak in the ninth marker bracket, which positioned the QTL within a region <1 cM in the middle part of bovine chromosome 5. The method was expected to be robust against multiple genes affecting the trait, multiple mutations at the QTL, and relatively low marker density.

scholarly journals Inferring Linkage Disequilibrium Between a Polymorphic Marker Locus and a Trait Locus in Natural Populations

Genetics ◽  
2000 ◽  
Vol 156 (1) ◽  
pp. 457-467 ◽  
Author(s):  
Z W Luo ◽  
S H Tao ◽  
Z-B Zeng
Keyword(s):  
Linkage Disequilibrium ◽  
Allele Frequency ◽  
Random Mating ◽  
Natural Populations ◽  
Polymorphic Marker ◽  
Marker Locus ◽  
Model Parameters ◽  
Phenotypic Variance ◽  
Wide Range ◽  
Trait Locus

Abstract Three approaches are proposed in this study for detecting or estimating linkage disequilibrium between a polymorphic marker locus and a locus affecting quantitative genetic variation using the sample from random mating populations. It is shown that the disequilibrium over a wide range of circumstances may be detected with a power of 80% by using phenotypic records and marker genotypes of a few hundred individuals. Comparison of ANOVA and regression methods in this article to the transmission disequilibrium test (TDT) shows that, given the genetic variance explained by the trait locus, the power of TDT depends on the trait allele frequency, whereas the power of ANOVA and regression analyses is relatively independent from the allelic frequency. The TDT method is more powerful when the trait allele frequency is low, but much less powerful when it is high. The likelihood analysis provides reliable estimation of the model parameters when the QTL variance is at least 10% of the phenotypic variance and the sample size of a few hundred is used. Potential use of these estimates in mapping the trait locus is also discussed.

A novel GNSS deformation feature extraction method based on ensemble improved LMD threshold denoising

2020 ◽  
Vol 14 (4) ◽  
pp. 445-453
Author(s):  
Qian Fan ◽  
Yiqun Zhu
Keyword(s):  
Feature Extraction ◽  
Spline Interpolation ◽  
Simulated Data ◽  
Mining Area ◽  
Deformation Monitoring ◽  
Denoising Method ◽  
Feature Extraction Method ◽  
Deformation Feature ◽  
Mode Decomposition ◽  
Better Than

AbstractIn order to solve the problem that the moving span of basic local mean decomposition (LMD) method is difficult to choose reasonably, an improved LMD method (ILMD), which uses three cubic spline interpolation to replace the sliding average, is proposed. On this basis, with the help of noise aided calculation, an ensemble improved LMD method (EILMD) is proposed to effectively solve the modal aliasing problem in original LMD. On the basis of using EILMD to effectively decompose the data of GNSS deformation monitoring series, GNSS deformation feature extraction model based on EILMD threshold denoising is given by means of wavelet soft threshold processing mode and threshold setting method in empirical mode decomposition denoising. Through the analysis of simulated data and the actual GNSS monitoring data in the mining area, the results show that denoising effect of the proposed method is better than EILMD, ILMD and LMD direct coercive denoising methods. It is also better than wavelet analysis denoising method, and has good adaptability. This fully demonstrates the feasibility and effectiveness of the proposed method in GNSS feature extraction.

scholarly journals Modeling Linkage Disequilibrium and Identifying Recombination Hotspots Using Single-Nucleotide Polymorphism Data

Genetics ◽  
2003 ◽  
Vol 165 (4) ◽  
pp. 2213-2233 ◽  
Author(s):  
Na Li ◽  
Matthew Stephens
Keyword(s):  
Linkage Disequilibrium ◽  
Recombination Rate ◽  
Population Sample ◽  
Simulated Data ◽  
Region Of Interest ◽  
Population Data ◽  
Recombination Rates ◽  
Single Nucleotide ◽  
Recombination Hotspots ◽  
Genomic Regions

AbstractWe introduce a new statistical model for patterns of linkage disequilibrium (LD) among multiple SNPs in a population sample. The model overcomes limitations of existing approaches to understanding, summarizing, and interpreting LD by (i) relating patterns of LD directly to the underlying recombination process; (ii) considering all loci simultaneously, rather than pairwise; (iii) avoiding the assumption that LD necessarily has a “block-like” structure; and (iv) being computationally tractable for huge genomic regions (up to complete chromosomes). We examine in detail one natural application of the model: estimation of underlying recombination rates from population data. Using simulation, we show that in the case where recombination is assumed constant across the region of interest, recombination rate estimates based on our model are competitive with the very best of current available methods. More importantly, we demonstrate, on real and simulated data, the potential of the model to help identify and quantify fine-scale variation in recombination rate from population data. We also outline how the model could be useful in other contexts, such as in the development of more efficient haplotype-based methods for LD mapping.

Evaluation of genetic markers for litter size in Meishan synthetic and Large White pigs

1996 ◽  
Vol 1996 ◽  
pp. 18-18
Author(s):  
O.I. Southwood ◽  
S. Hoste ◽  
T.H. Short ◽  
A.J. Mileham ◽  
D. Cuthbert-Heavens
Keyword(s):  
Litter Size ◽  
Fixed Effects ◽  
Oestrogen Receptor ◽  
Mixed Model ◽  
Receptor Gene ◽  
Large White ◽  
Service Type ◽  
Sib Families ◽  
Natural Service ◽  
Size Data

A significant relationship between the oestrogen receptor gene (ESR) and litter size has been detected in USA populations of Large White and a synthetic comprising 50% Meishan (Rothschild et al., 1995). Animals carrying two copies of the favourable allele (B) had an extra pig born per litter than those that did not have the allele. This paper reports on results observed in a UK 50% Meishan synthetic and four UK Large White lines.Litter size data from 50% Meishan synthetic (L93) full-sib females where more than one ESR genotype was segregating. Data were analysed using a mixed model with full relationships and including the fixed effects of season of farrowing, parity, ESR genotype (AA, AB or BB) and service type (AI or natural service). Heritiability and permanent environmental effects for litter size were assumed as 0.09 and 0.11, repectively. A total of 27 full-sib families were represented and included 62 sows and 139 litter records. Hypothesis testing used the option in PEST under a mixed model (Groeneveld et al., 1991).

The use of linkage disequilibrium to map quantitative trait loci

2005 ◽  
Vol 45 (8) ◽  
pp. 837 ◽  
Author(s):  
M. E. Goddard ◽  
T. H. E. Meuwissen
Keyword(s):  
Linkage Disequilibrium ◽  
Quantitative Trait Loci ◽  
Statistical Model ◽  
Quantitative Trait ◽  
Linear Models ◽  
Chromosome Segment ◽  
Identical By Descent ◽  
Trait Loci ◽  
Linkage Disequilibrium Information ◽  
Chromosome Segments

This paper reviews the causes of linkage disequilibrium and its use in mapping quantitative trait loci. The many causes of linkage disequilibrium can be understood as due to similarity in the coalescence tree of different loci. Consideration of the way this comes about allows us to divide linkage disequilibrium into 2 types: linkage disequilibrium between any 2 loci, even if they are unlinked, caused by variation in the relatedness of pairs of animals; and linkage disequilibrium due to the inheritance of chromosome segments that are identical by descent from a common ancestor. The extent of linkage disequilibrium due to the latter cause can be logically measured by the chromosome segment homozygosity which is the probability that chromosome segments taken at random from the population are identical by descent. This latter cause of linkage disequilibrium allows us to map quantitative trait loci to chromosome regions. The former cause of linkage disequilibrium can cause artefactual quantitative trait loci at any position in the genome. These artefacts can be avoided by fitting the relatedness of animals in the statistical model used to map quantitative trait loci. In the future it may be convenient to estimate this degree of relatedness between individuals from markers covering the whole genome. The statistical model for mapping quantitative trait loci also requires us to estimate the probability that 2 animals share quantitative trait loci alleles at a particular position because they have inherited a chromosome segment containing the quantitative trait loci identical by descent. Current methods to do this all involve approximations. Methods based on concepts of coalescence and chromosome segment homozygosity are useful, but improvements are needed for practical analysis of large datasets. Once these probabilities are estimated they can be used in flexible linear models that conveniently combine linkage and linkage disequilibrium information.

scholarly journals Tail-Heaviness, Asymmetry, and Profitability Forecasting by Quantile Regression

2020 ◽  
Author(s):  
Hui Tian ◽  
Andrew Yim ◽  
David P. Newton
Keyword(s):  
Quantile Regression ◽  
Forecast Error ◽  
Simulated Data ◽  
Ordinary Least Squares ◽  
Shape Effect ◽  
Forecasting Accuracy ◽  
Forecasting Performance ◽  
Cash Flow Forecasting ◽  
Positive Effect ◽  
Better Than

We show that quantile regression is better than ordinary-least-squares (OLS) regression in forecasting profitability for a range of profitability measures following the conventional setup of the accounting literature, including the mean absolute forecast error (MAFE) evaluation criterion. Moreover, we perform both a simulated-data and an archival-data analysis to examine how the forecasting performance of quantile regression against OLS changes with the shape of the profitability distribution. Considering the MAFE and mean squared forecast error (MSFE) criteria together, we see that the quantile regression is more accurate relative to OLS when the profitability to be forecast has a heavier-tailed distribution. In addition, the asymmetry of the profitability distribution has either a U-shape or an inverted-U-shape effect on the forecasting accuracy of quantile regression. An application of the distributional shape analysis framework to cash flow forecasting demonstrates the usefulness of the framework beyond profitability forecasting, providing additional empirical evidence on the positive effect of tail-heaviness and supporting the notion of an inverted-U-shape effect of asymmetry. This paper was accepted by Shiva Rajgopal, accounting.

scholarly journals Animal Model Versus Polynomial Legendre Test-Day In Dairy Cattle

2020 ◽  
Vol 23 (1) ◽  
pp. 5-12
Author(s):  
Mircea Cătălin Rotar ◽  
Horia Grosu ◽  
Mihail Alexandru Gras ◽  
Rodica Ştefania Pelmuş ◽  
Cristina Lazăr ◽  
...  
Keyword(s):  
Animal Model ◽  
Dairy Cattle ◽  
Fixed Effects ◽  
Rank Correlation ◽  
Pedigree Information ◽  
Lactation Period ◽  
Data Set ◽  
Breeding Values ◽  
Normal Limits ◽  
Model Versus

AbstractThe aim of the study was to compare the classical animal model (based on total milk for 305 days) with the Test-Day model (using monthly records of milk yield from Official Records of Performances). The data set derived from a total 175 animals (cows with records, parents of these animals and the descendants) from two Romanian breeds (Romanian Black Spotted and Montbeliarde), the phenotypic and the pedigree information arisen from National Research Development Institute for Animal Biology and Nutrition (IBNA-Balotesti). The selection criteria to be included in the analysis for each cow was to have at least 3 test-days and the days in milk between 200 and 330 for the Test-Day model and the total amount of the 305- day lactation yield for classical Animal Model respectively. Both models use B.L.U.P methodology and for that reason all the estimates were adjusted for fixed effects and all the breeding values and the solution for fixed effects were estimated simultaneous. For the animal model the fixed effects used was the breed and the year of performing and for the Test-Day model was an extra one, the test day effect. The correlation calculated between test days was very high (over 90%) for consecutive tests, and was getting lower when the days between tests was higher (under 40%). Also, in terms of heritability the values were in normal limits throughout lactation, except at the beginning and end of lactation period where these values were a little bit higher. The comparison of the ranking of breeding values with Spearman rank correlation shows that in 80% of the cases the ranking was similar for both models. As the ranking correlations shows, it is certain that the two models are very similar when they are used for genetic evaluation. But, in conclusion, we can say that for a better lactation curve estimation it is recommending to use test-day model for dairy cattle.

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