Empirical Bayesian LASSO-logistic regression for multiple binary trait locus mapping.

01:20 EST 29th January 2015 | BioPortfolio

Summary of "Empirical Bayesian LASSO-logistic regression for multiple binary trait locus mapping."


Complex binary traits are influenced by many factors including the main effects of many quantitative trait loci (QTLs), the epistatic effects involving more than one QTLs, environmental effects and the effects of gene-environment interactions. Although a number of QTL mapping methods for binary traits have been developed, there still lacks an efficient and powerful method that can handle both main and epistatic effects of a relatively large number of possible QTLs.
In this paper, we use a Bayesian logistic regression model as the QTL model for binary traits that includes both main and epistatic effects. Our logistic regression model employs hierarchical priors for regression coefficients similar to the ones used in the Bayesian LASSO linear model for multiple QTL mapping for continuous traits. We develop efficient empirical Bayesian algorithms to infer the logistic regression model. Our simulation study shows that our algorithms can easily handle a QTL model with a large number of main and epistatic effects on a personal computer, and outperform five other methods examined including the LASSO, HyperLasso, BhGLM, RVM and the single-QTL mapping method based on logistic regression in terms of power of detection and false positive rate. The utility of our algorithms is also demonstrated through analysis of a real data set. A software package implementing the empirical Bayesian algorithms in this paper is freely available upon request.
The EBLASSO logistic regression method can handle a large number of effects possibly including the main and epistatic QTL effects, environmental effects and the effects of gene-environment interactions. It will be a very useful tool for multiple QTLs mapping for complex binary traits.


Journal Details

This article was published in the following journal.

Name: BMC genetics
ISSN: 1471-2156
Pages: 5


PubMed Articles [12241 Associated PubMed Articles listed on BioPortfolio]

Functional Multi-Locus QTL Mapping of Temporal Trends in Scots Pine Wood Traits.

Quantitative trait loci (QTL) mapping of wood properties in conifer species has focused on single time point measurements or on trait means based on heterogeneous wood samples (e.g. increment cores) t...

Understanding logistic regression analysis.

Logistic regression is used to obtain odds ratio in the presence of more than one explanatory variable. The procedure is quite similar to multiple linear regression, with the exception that the respon...

Single and Multiple Ability Estimation in the SEM Framework: A Non-Informative Bayesian Estimation Approach.

Latent variable models with many categorical items and multiple latent constructs result in many dimensions of numerical integration, and the traditional frequentist estimation approach, such as maxim...

Detecting Genetic Interactions in Pathway-Based Genome-Wide Association Studies.

Pathway-based genome-wide association studies (GWAS) can exploit collective effects of causal variants in a pathway to increase power of detection. However, current methods for pathway-based GWAS do n...

The joint graphical lasso for inverse covariance estimation across multiple classes.

We consider the problem of estimating multiple related Gaussian graphical models from a high-dimensional data set with observations belonging to distinct classes. We propose the joint graphical lasso,...

Clinical Trials [1916 Associated Clinical Trials listed on BioPortfolio]

Model-Free Time Curves for Longitudinal Data Analysis

To enhance statistical methods for epidemiological studies by extending the Disturbed Highest Derivative Polynomial (DHDP) to models for binary-logistic and Poisson data and by including r...

Low Molecular Weight Heparin in Recurrent Implantation Failure

Recurrent implantation failure is the failure to achieve a pregnancy after multiple attempts with in vitro fertilization treatment. The reason is usually obscure. Many empirical treatments...

MK0991 Versus Amphotericin B for Empirical Therapy in Febrile, Neutropenic Pediatric Patients

This study is a double-blind, randomized study of MK0991 versus liposomal amphotericin B in the empirical treatment of pediatric patients (ages 2 through 17 years) who have an absolute neu...

Sickle Cell Trait and the Risk of Venous Thromboembolism

The purpose of this trial is to investigate D-Dimer levels, a surrogate marker of venous thromboembolism, in pregnant/postpartum white women as compared to pregnant/postpartum black women,...

REST Study: Left Ventricular Regression European Study

The purpose of this study is to obtain data regarding the left ventricular mass (LVM) regression 6 months after the implant of an SJM Epic™ and SJM Epic™ Supra valve by comparing LVM r...

Medical and Biotech [MESH] Definitions

Procedures for finding the mathematical function which best describes the relationship between a dependent variable and one or more independent variables. In linear regression (see LINEAR MODELS) the relationship is constrained to be a straight line and LEAST-SQUARES ANALYSIS is used to determine the best fit. In logistic regression (see LOGISTIC MODELS) the dependent variable is qualitative rather than continuously variable and LIKELIHOOD FUNCTIONS are used to find the best relationship. In multiple regression, the dependent variable is considered to depend on more than a single independent variable.

Locations, on the GENOME, of GENES or other genetic elements that encode or control the expression of a quantitative trait (QUANTITATIVE TRAIT, HERITABLE).

The record of descent or ancestry, particularly of a particular condition or trait, indicating individual family members, their relationships, and their status with respect to the trait or condition.

A syndrome of multiple abnormalities characterized by the absence or hypoplasia of the PATELLA and congenital nail dystrophy. It is a genetically determined autosomal dominant trait.

Detailed account or statement or formal record of data resulting from empirical inquiry.

Search BioPortfolio:

Relevant Topic

Latest News Clinical Trials Research Drugs Reports Corporate
Bioinformatics is the application of computer software and hardware to the management of biological data to create useful information. Computers are used to gather, store, analyze and integrate biological and genetic information which can then be applied...


Searches Linking to this Article