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Probabilistic Graphical Models for Genetics, Genomics, and Postgenomics$
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Christine Sinoquet and Raphaël Mourad

Print publication date: 2014

Print ISBN-13: 9780198709022

Published to Oxford Scholarship Online: December 2014

DOI: 10.1093/acprof:oso/9780198709022.001.0001

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Modeling Linkage Disequilibrium and Performing Association Studies through Probabilistic Graphical Models: a Visiting Tour of Recent Advances

Modeling Linkage Disequilibrium and Performing Association Studies through Probabilistic Graphical Models: a Visiting Tour of Recent Advances

Chapter:
(p.217) Chapter 9 Modeling Linkage Disequilibrium and Performing Association Studies through Probabilistic Graphical Models: a Visiting Tour of Recent Advances
Source:
Probabilistic Graphical Models for Genetics, Genomics, and Postgenomics
Author(s):

Christine Sinoquet

Raphaël Mourad

Publisher:
Oxford University Press
DOI:10.1093/acprof:oso/9780198709022.003.0009

This chapter offers an in-depth review of recent developments based on probabilistic graphical models (PGMs) and dedicated to two major concerns: the fundamental task of modeling dependences within genetic data, that is linkage disequilibrium (LD), and the downstream application to genome-wide association studies (GWASs). Throughout the whole chapter, the selected examples illustrate the use of Bayesian networks, as well as that of Markov random fields, including conditional and hidden Markov random fields. First, the chapter surveys PGM-based approaches dedicated to LD modeling. The next section is devoted to PGM-based GWASs and mainly focuses on multilocus approaches, where PGMs allow to fully benefit from LD. This section also provides an illustration for the acknowledgment of confounding factors in GWASs. The next section is dedicated to the detection of epistastic relationships at the genome scale. A recapitulation and a discussion end the chapter. Finally, directions for future works are outlined.

Keywords:   genome-wide association studies, linkage disequilibrium, epistastic relationships

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