Bayesian Mapping of Genomewide Interacting Quantitative Trait Loci for Ordinal Traits

Nengjun Yi; Banerjee, Samprit; Pomp, Daniel; Yandeilt, Brian S.
July 2007
Genetics;Jul2007, Vol. 176 Issue 3, p1855
Academic Journal
Development of statistical methods and software for mapping interacting QTL has been the focus of much recent research. We previously developed a Bayesian model selection framework, based on the composite model space approach, for mapping multiple epistatic QTL affecting continuous traits. In this study we extend the composite model space approach to complex ordinal traits in experimental crosses. We jointly model main and epistatic effects of QTL and environmental factors on the basis of the ordinal probit model (also called threshold model) that assumes a latent continuous trait underlies the generation of the ordinal phenotypes through a set of unknown thresholds. A data augmentation approach is developed to jointly generate the latent data and the thresholds. The proposed ordinal probit model, combined with the composite model space framework for continuous traits, offers a convenient way for genomewide interacting QTL analysis of ordinal traits. We illustrate the proposed method by detecting new QTL and epistatic effects for an ordinal trait, dead fetuses, in a F2 intercross of mice. Utility and flexibility of the method are also demonstrated using a simulated data set. Our method has been implemented in the freely available package R/qtlbim, which greatly facilitates the general usage of the Bayesian methodology for genomewide interacting QTL analysis for continuous, binary, and ordinal trails in experimental crosses.


Related Articles

  • Bayesian Inference of Recent Migration Rates Using Multilocus Genotypes. Wilson, Gregory A.; Rannala, Bruce // Genetics;Mar2003, Vol. 163 Issue 3, p1177 

    A new Bayesian method that uses individual multilocus genotypes to estimate rates of recent immigration (over the last several generations) among populations is presented. The method also estimates the posterior probability distributions of individual immigrant ancestries, population allele...

  • phenosim - A software to simulate phenotypes for testing in genome-wide association studies.  // BMC Bioinformatics;2011 Supplement 6, Vol. 12 Issue Suppl 6, p265 

    The article offers information on the study related to the development of a software phenosim, a software to add a phenotype to genotypes generated in time-efficient coalescent simulations. It states that Both qualitative and quantitative phenotypes can be generated and it is possible to...

  • Multitrait analysis of quantitative trait loci using Bayesian composite space approach. Ming Fang; Dan Jiang; Li Jun Pu; Hui Jiang Gao; Peng Ji; Hong Yi Wang; Run Qing Yang // BMC Genetics;2008, Vol. 9, Special section p1 

    Background: Multitrait analysis of quantitative trait loci can capture the maximum information of experiment. The maximum-likelihood approach and the least-square approach have been developed to jointly analyze multiple traits, but it is difficult for them to include multiple QTL simultaneously...

  • Another Look at Bayesian Analysis of AMMI Models for Genotype-Environment Data. Josse, Julie; Eeuwijk, Fred; Piepho, Hans-Peter; Denis, Jean-Baptiste // Journal of Agricultural, Biological & Environmental Statistics (;Jun2014, Vol. 19 Issue 2, p240 

    Linear-bilinear models are frequently used to analyze two-way data such as genotype-by-environment data. A well-known example of this class of models is the additive main effects and multiplicative interaction effects model (AMMI). We propose a new Bayesian treatment of such models offering a...

  • Mapping quantitative trait loci using the MCMC procedure in SAS. Xu, S; Hu, Z // Heredity;Feb2011, Vol. 106 Issue 2, p357 

    The MCMC procedure in SAS (called PROC MCMC) is particularly designed for Bayesian analysis using the Markov chain Monte Carlo (MCMC) algorithm. The program is sufficiently general to handle very complicated statistical models and arbitrary prior distributions. This study introduces the SAS/MCMC...

  • A Flexible Bayesian Model for Studying Gene--Environment Interaction. Kai Yu; Wacholder, Sholom; Wheeler, William; Zhaoming Wang; Caporaso, Neil; Landi, Maria Teresa; Liang, Faming // PLoS Genetics;Jan2012, Vol. 8 Issue 1, Special section p1 

    An important follow-up step after genetic markers are found to be associated with a disease outcome is a more detailed analysis investigating how the implicated gene or chromosomal region and an established environment risk factor interact to influence the disease risk. The standard approach to...

  • Gene-Environment Interactions: How Many False Positives? Matullo, Giuseppe; Berwick, Marianne; Vineis, Paolo // JNCI: Journal of the National Cancer Institute;4/20/2005, Vol. 97 Issue 8, p550 

    Comments on the study on the association between base excision repair gene polymorphisms and lung cancer risk. Application of Bayesian statistics and clinical epidemiology in investigating the association; Analysis of the approaches in assessing the validity of the increasing number of...

  • Empirical Bayesian LASSO-logistic regression for multiple binary trait locus mapping. Huang, Anhui; Xu, Shizhong; Cai, Xiaodong // BMC Genetics;2013, Vol. 14 Issue 1, p1 

    Background: 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 geneenvironment interactions. Although a number of QTL mapping methods...

  • Bayesian QTL mapping for recombinant inbred lines derived from a four-way cross. Hayashi, Takeshi; Ohyama, Akio; Iwata, Hiroyoshi // Euphytica;Feb2012, Vol. 183 Issue 3, p277 

    Recombinant inbred lines (RILs) are created by a cross between inbred lines followed by repeated selfing or sib-mating, which include many different types of new inbred lines with many recombination events on the genome. The phenotype of each RIL can be assessed based on multiple individuals...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics