A bayesian approach to the transmission/disequilibrium test for binary traits

Varghese George, Purushottam W. Laud

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

The transmission/disequilibrium test (TDT) for binary traits is a powerful method for detecting linkage between a marker locus and a trait locus in the presence of allelic association. The TDT uses information on the parent-to-offspring transmission status of the associated allele at the marker locus to assess linkage or association in the presence of the other, using one affected offspring from each set of parents. For testing for linkage in the presence of association, more than one offspring per family can be used. However, without incorporating the correlation structure among offspring, it is not possible to correctly assess the association in the presence of linkage. In this presentation, we propose a Bayesian TDT method as a complementary alternative to the classical approach. In the hypothesis testing setup, given two competing hypotheses, the Bayes factor can be used to weigh the evidence in favor of one of them, thus allowing us to decide between the two hypotheses using established criteria. We compare the proposed Bayesian TDT with a competing frequentist-testing method with respect to power and type I error validity. If we know the mode of inheritance of the disease, then the joint and marginal posterior distributions for the recombination fraction (θ) and disequilibrium coefficient (δ) can be obtained via standard MCMC methods, which lead naturally to Bayesian credible intervals for both parameters.

Original languageEnglish (US)
Pages (from-to)41-51
Number of pages11
JournalGenetic Epidemiology
Volume22
Issue number1
DOIs
StatePublished - Jan 10 2002

Fingerprint

Bayes Theorem
Joint Diseases
Genetic Recombination
Alleles

Keywords

  • Association
  • Bayes factor
  • Credible interval
  • Likelihood
  • Linkage
  • Markov chain Monte Carlo method

ASJC Scopus subject areas

  • Epidemiology
  • Genetics(clinical)

Cite this

A bayesian approach to the transmission/disequilibrium test for binary traits. / George, Varghese; Laud, Purushottam W.

In: Genetic Epidemiology, Vol. 22, No. 1, 10.01.2002, p. 41-51.

Research output: Contribution to journalArticle

@article{2ad8c60db5234cfdba450df7c56cd618,
title = "A bayesian approach to the transmission/disequilibrium test for binary traits",
abstract = "The transmission/disequilibrium test (TDT) for binary traits is a powerful method for detecting linkage between a marker locus and a trait locus in the presence of allelic association. The TDT uses information on the parent-to-offspring transmission status of the associated allele at the marker locus to assess linkage or association in the presence of the other, using one affected offspring from each set of parents. For testing for linkage in the presence of association, more than one offspring per family can be used. However, without incorporating the correlation structure among offspring, it is not possible to correctly assess the association in the presence of linkage. In this presentation, we propose a Bayesian TDT method as a complementary alternative to the classical approach. In the hypothesis testing setup, given two competing hypotheses, the Bayes factor can be used to weigh the evidence in favor of one of them, thus allowing us to decide between the two hypotheses using established criteria. We compare the proposed Bayesian TDT with a competing frequentist-testing method with respect to power and type I error validity. If we know the mode of inheritance of the disease, then the joint and marginal posterior distributions for the recombination fraction (θ) and disequilibrium coefficient (δ) can be obtained via standard MCMC methods, which lead naturally to Bayesian credible intervals for both parameters.",
keywords = "Association, Bayes factor, Credible interval, Likelihood, Linkage, Markov chain Monte Carlo method",
author = "Varghese George and Laud, {Purushottam W.}",
year = "2002",
month = "1",
day = "10",
doi = "10.1002/gepi.1042",
language = "English (US)",
volume = "22",
pages = "41--51",
journal = "Genetic Epidemiology",
issn = "0741-0395",
publisher = "Wiley-Liss Inc.",
number = "1",

}

TY - JOUR

T1 - A bayesian approach to the transmission/disequilibrium test for binary traits

AU - George, Varghese

AU - Laud, Purushottam W.

PY - 2002/1/10

Y1 - 2002/1/10

N2 - The transmission/disequilibrium test (TDT) for binary traits is a powerful method for detecting linkage between a marker locus and a trait locus in the presence of allelic association. The TDT uses information on the parent-to-offspring transmission status of the associated allele at the marker locus to assess linkage or association in the presence of the other, using one affected offspring from each set of parents. For testing for linkage in the presence of association, more than one offspring per family can be used. However, without incorporating the correlation structure among offspring, it is not possible to correctly assess the association in the presence of linkage. In this presentation, we propose a Bayesian TDT method as a complementary alternative to the classical approach. In the hypothesis testing setup, given two competing hypotheses, the Bayes factor can be used to weigh the evidence in favor of one of them, thus allowing us to decide between the two hypotheses using established criteria. We compare the proposed Bayesian TDT with a competing frequentist-testing method with respect to power and type I error validity. If we know the mode of inheritance of the disease, then the joint and marginal posterior distributions for the recombination fraction (θ) and disequilibrium coefficient (δ) can be obtained via standard MCMC methods, which lead naturally to Bayesian credible intervals for both parameters.

AB - The transmission/disequilibrium test (TDT) for binary traits is a powerful method for detecting linkage between a marker locus and a trait locus in the presence of allelic association. The TDT uses information on the parent-to-offspring transmission status of the associated allele at the marker locus to assess linkage or association in the presence of the other, using one affected offspring from each set of parents. For testing for linkage in the presence of association, more than one offspring per family can be used. However, without incorporating the correlation structure among offspring, it is not possible to correctly assess the association in the presence of linkage. In this presentation, we propose a Bayesian TDT method as a complementary alternative to the classical approach. In the hypothesis testing setup, given two competing hypotheses, the Bayes factor can be used to weigh the evidence in favor of one of them, thus allowing us to decide between the two hypotheses using established criteria. We compare the proposed Bayesian TDT with a competing frequentist-testing method with respect to power and type I error validity. If we know the mode of inheritance of the disease, then the joint and marginal posterior distributions for the recombination fraction (θ) and disequilibrium coefficient (δ) can be obtained via standard MCMC methods, which lead naturally to Bayesian credible intervals for both parameters.

KW - Association

KW - Bayes factor

KW - Credible interval

KW - Likelihood

KW - Linkage

KW - Markov chain Monte Carlo method

UR - http://www.scopus.com/inward/record.url?scp=0036137021&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0036137021&partnerID=8YFLogxK

U2 - 10.1002/gepi.1042

DO - 10.1002/gepi.1042

M3 - Article

C2 - 11754472

AN - SCOPUS:0036137021

VL - 22

SP - 41

EP - 51

JO - Genetic Epidemiology

JF - Genetic Epidemiology

SN - 0741-0395

IS - 1

ER -