scholarly journals Estimation of genetic correlation using linkage disequilibrium score regression and genomic restricted maximum likelihood

2017 ◽  
Author(s):  
Guiyan Ni ◽  
Gerhard Moser ◽  
Naomi R. Wray ◽  
S. Hong Lee ◽  
Keyword(s):  
Linkage Disequilibrium ◽  
Maximum Likelihood ◽  
Genetic Correlation ◽  
Complex Traits ◽  
Real Data ◽  
Restricted Maximum Likelihood ◽  
Data Sets ◽  
Population Parameter ◽  
Meta Data ◽  
Key Population

ABSTRACTGenetic correlation is a key population parameter that describes the shared genetic architecture of complex traits and diseases. It can be estimated by current state-of-art methods, i.e. linkage disequilibrium score regression (LDSC) and genomic restricted maximum likelihood (GREML). The massively reduced computing burden of LDSC compared to GREML makes it an attractive tool, although the accuracy (i.e., magnitude of standard errors) of LDSC estimates has not been thoroughly studied. In simulation, we show that the accuracy of GREML is generally higher than that of LDSC. When there is genetic heterogeneity between the actual sample and reference data from which LD scores are estimated, the accuracy of LDSC decreases further. In real data analyses estimating the genetic correlation between schizophrenia (SCZ) and body mass index, we show that GREML estimates based on ~150,000 individuals give a higher accuracy than LDSC estimates based on ~400,000 individuals (from combined meta-data). A GREML genomic partitioning analysis reveals that the genetic correlation between SCZ and height is significantly negative for regulatory regions, which whole genome or LDSC approach has less power to detect. We conclude that LDSC estimates should be carefully interpreted as there can be uncertainty about homogeneity among combined meta-data sets. We suggest that any interesting findings from massive LDSC analysis for a large number of complex traits should be followed up, where possible, with more detailed analyses with GREML methods, even if sample sizes are lesser.

scholarly journals Estimation of Genetic Correlation via Linkage Disequilibrium Score Regression and Genomic Restricted Maximum Likelihood

2018 ◽  
Vol 102 (6) ◽  
pp. 1185-1194 ◽  
Author(s):  
Guiyan Ni ◽  
Gerhard Moser ◽  
Naomi R. Wray ◽  
S. Hong Lee ◽  
Stephan Ripke ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Maximum Likelihood ◽  
Genetic Correlation ◽  
Restricted Maximum Likelihood

scholarly journals Transforming variables to central normality

2021 ◽  
Author(s):  
Jakob Raymaekers ◽  
Peter J. Rousseeuw
Keyword(s):  
Maximum Likelihood ◽  
Maximum Likelihood Estimator ◽  
Simulation Study ◽  
Real Data ◽  
Data Sets ◽  
Transformation Parameter ◽  
Likelihood Estimator ◽  
Extensive Simulation ◽  
Highly Sensitive

AbstractMany real data sets contain numerical features (variables) whose distribution is far from normal (Gaussian). Instead, their distribution is often skewed. In order to handle such data it is customary to preprocess the variables to make them more normal. The Box–Cox and Yeo–Johnson transformations are well-known tools for this. However, the standard maximum likelihood estimator of their transformation parameter is highly sensitive to outliers, and will often try to move outliers inward at the expense of the normality of the central part of the data. We propose a modification of these transformations as well as an estimator of the transformation parameter that is robust to outliers, so the transformed data can be approximately normal in the center and a few outliers may deviate from it. It compares favorably to existing techniques in an extensive simulation study and on real data.

scholarly journals The Weibull Birnbaum-Saunders Distribution And Its Applications

2020 ◽  
Vol 9 (1) ◽  
pp. 61-81
Author(s):  
Lazhar BENKHELIFA
Keyword(s):  
Maximum Likelihood ◽  
Estimation Method ◽  
Likelihood Estimation ◽  
Real Data ◽  
Reliability Estimation ◽  
Maximum Likelihood Estimates ◽  
Model Parameters ◽  
Data Sets ◽  
Proposed Model ◽  
Modeling Data

A new lifetime model, with four positive parameters, called the Weibull Birnbaum-Saunders distribution is proposed. The proposed model extends the Birnbaum-Saunders distribution and provides great flexibility in modeling data in practice. Some mathematical properties of the new distribution are obtained including expansions for the cumulative and density functions, moments, generating function, mean deviations, order statistics and reliability. Estimation of the model parameters is carried out by the maximum likelihood estimation method. A simulation study is presented to show the performance of the maximum likelihood estimates of the model parameters. The flexibility of the new model is examined by applying it to two real data sets.

scholarly journals A New Right-Skewed Upside Down Bathtub Shaped Heavy-tailed Distribution and its Applications

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Sandeep Kumar Maurya ◽  
Sanjay K Singh ◽  
Umesh Singh
Keyword(s):  
Maximum Likelihood ◽  
Real Data ◽  
Statistical Properties ◽  
New Right ◽  
Data Sets ◽  
Proposed Model ◽  
Heavy Tailed Distribution ◽  
Heavy Tailed

A one parameter right skewed, upside down bathtub type, heavy-tailed distribution is derived. Various statistical properties and maximum likelihood approaches for estimation purpose are studied. Five different real data sets with four different models are considered to illustrate the suitability of the proposed model.

scholarly journals On Modified Burr XII-Inverse Weibull Distribution: Development, Properties, Characterizations and Applications

2020 ◽  
pp. 721-735
Author(s):  
Fiaz Ahmad Bhatti ◽  
G. G. Hamedani ◽  
Haitham M. Yousof ◽  
Azeem Ali ◽  
Munir Ahmad
Keyword(s):  
Maximum Likelihood ◽  
Hazard Rate ◽  
Maximum Likelihood Method ◽  
Real Data ◽  
Lifetime Distribution ◽  
Maximum Likelihood Estimates ◽  
Likelihood Method ◽  
Data Sets ◽  
Quarterly Earnings ◽  
Inverse Weibull Distribution

A flexible lifetime distribution with increasing, decreasing, inverted bathtub and modified bathtub hazard rate called Modified Burr XII-Inverse Weibull (MBXII-IW) is introduced and studied. The density function of MBXII-IW is exponential, left-skewed, right-skewed and symmetrical shaped.  Descriptive measures on the basis of quantiles, moments, order statistics and reliability measures are theoretically established. The MBXII-IW distribution is characterized via different techniques. Parameters of MBXII-IW distribution are estimated using maximum likelihood method. The simulation study is performed to illustrate the performance of the maximum likelihood estimates (MLEs). The potentiality of MBXII-IW distribution is demonstrated by its application to real data sets: serum-reversal times and quarterly earnings.

Animal x testing environment interaction on postweaning liveweight gains of young bulls

1998 ◽  
Vol 49 (4) ◽  
pp. 607 ◽  
Author(s):  
S. J. Schoeman ◽  
G. G. Jordaan
Keyword(s):  
Maximum Likelihood ◽  
Genetic Correlation ◽  
Variance Components ◽  
Restricted Maximum Likelihood ◽  
Animal Breeding ◽  
Environment Interaction ◽  
Maximum Likelihood Analysis ◽  
Breeding Values ◽  
Testing Environment ◽  
Likelihood Analysis

Postweaning liveweight gain records of 1610 young bulls obtained both in feedlot and under pasture were used to estimate (co)variance components using a multivariate restricted maximum likelihood analysis. The pedigree file included 3477 animals. Heritability estimates for liveweights and gain in both environments correspond to most previously reported estimates. The genetic correlation of gain between the 2 environments was -0·12, suggesting a large genotype testing environment interaction and re-ranking of animal breeding values across environments. Results of this analysis suggest the need for environment-specific breeding values for postweaning gain.

scholarly journals A New Flexible Three-Parameter Model: Properties, Clayton Copula, and Modeling Real Data

Symmetry ◽  
2020 ◽  
Vol 12 (3) ◽  
pp. 440 ◽  
Author(s):  
Abdulhakim A. Al-babtain ◽  
I. Elbatal ◽  
Haitham M. Yousof
Keyword(s):  
Maximum Likelihood ◽  
Maximum Likelihood Method ◽  
Real Data ◽  
Likelihood Method ◽  
Model Parameters ◽  
Simple Type ◽  
Data Sets ◽  
New Model ◽  
Clayton Copula ◽  
Mathematical Properties

In this article, we introduced a new extension of the binomial-exponential 2 distribution. We discussed some of its structural mathematical properties. A simple type Copula-based construction is also presented to construct the bivariate- and multivariate-type distributions. We estimated the model parameters via the maximum likelihood method. Finally, we illustrated the importance of the new model by the study of two real data applications to show the flexibility and potentiality of the new model in modeling skewed and symmetric data sets.

scholarly journals Generalized Truncation Positive Normal Distribution

Symmetry ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 1361
Author(s):  
Héctor J. Gómez ◽  
Diego I. Gallardo ◽  
Osvaldo Venegas
Keyword(s):  
Maximum Likelihood ◽  
Normal Distribution ◽  
Fisher Information ◽  
Fisher Information Matrix ◽  
Information Matrix ◽  
Maximum Likelihood Estimators ◽  
Real Data ◽  
Data Sets ◽  
New Model ◽  
Positive Support

In this article we study the properties, inference, and statistical applications to a parametric generalization of the truncation positive normal distribution, introducing a new parameter so as to increase the flexibility of the new model. For certain combinations of parameters, the model includes both symmetric and asymmetric shapes. We study the model’s basic properties, maximum likelihood estimators and Fisher information matrix. Finally, we apply it to two real data sets to show the model’s good performance compared to other models with positive support: the first, related to the height of the drum of the roller and the second, related to daily cholesterol consumption.

GENETIC PARAMETERS FOR CALVING EASE IN AYRSHIRES

1990 ◽  
Vol 70 (1) ◽  
pp. 67-71 ◽  
Author(s):  
R. I. CUE
Keyword(s):  
Maximum Likelihood ◽  
Key Words ◽  
Genetic Correlation ◽  
Direct Effect ◽  
Fixed Effects ◽  
Genetic Parameters ◽  
Random Effect ◽  
Restricted Maximum Likelihood ◽  
Calving Ease ◽  
Likelihood Model

Estimates of genetic parameters of calving ease were obtained in Ayrshires. A restricted maximum likelihood model was used with the fixed effects of herd, month-season of calving, sex of calf and dam weight, and the random effect of sire (of calf). The heritability of the direct effect in heifers and in adult cows was approximately 2%, with a genetic correlation between the direct effect in heifers and in adult cows of close to 70%. Key words: Variance, heritability, calving ease, Ayrshire

scholarly journals Comparison of methods for estimating genetic correlation between complex traits using GWAS summary statistics

2020 ◽  
Author(s):  
Yiliang Zhang ◽  
Youshu Cheng ◽  
Wei Jiang ◽  
Yixuan Ye ◽  
Qiongshi Lu ◽  
...  
Keyword(s):  
Genetic Correlation ◽  
Complex Traits ◽  
Association Studies ◽  
Genetic Correlations ◽  
Real Data ◽  
Estimation Methods ◽  
Easy Access ◽  
Genome Wide Association Studies ◽  
Summary Statistics ◽  
Correlation Estimation

AbstractGenetic correlation is the correlation of additive genetic effects on two phenotypes. It is an informative metric to quantify the overall genetic similarity between complex traits, which provides insights into their polygenic genetic architecture. Several methods have been proposed to estimate genetic correlations based on data collected from genome-wide association studies (GWAS). Due to the easy access of GWAS summary statistics and computational efficiency, methods only requiring GWAS summary statistics as input have become more popular than methods utilizing individual-level genotype data. Here, we present a benchmark study for different summary-statistics-based genetic correlation estimation methods through simulation and real data applications. We focus on two major technical challenges in estimating genetic correlation: marker dependency caused by linkage disequilibrium (LD) and sample overlap between different studies. To assess the performance of different methods in the presence of these two challenges, we first conducted comprehensive simulations with diverse LD patterns and sample overlaps. Then we applied these methods to real GWAS summary statistics for a wide spectrum of complex traits. Based on these experiments, we conclude that methods relying on accurate LD estimation are less robust in real data applications compared to other methods due to the imprecision of LD obtained from reference panels. Our findings offer a guidance on how to appropriately choose the method for genetic correlation estimation in post-GWAS analysis in interpretation.

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