Discovery of phenotypic networks from genotypic association studies with application to obesity

Christine W. Duarte, Yann C Klimentidis, Jacqueline J. Harris, Michelle Cardel, José R. Fernández

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Genome-wide Association Studies (GWAS) have resulted in many discovered risk variants for several obesity-related traits. However, before clinical relevance of these discoveries can be achieved, molecular or physiological mechanisms of these risk variants needs to be discovered. One strategy is to perform data mining of phenotypically-rich data sources such as those present in dbGAP (database of Genotypes and Phenotypes) for hypothesis generation. Here we propose a technique that combines the power of existing Bayesian Network (BN) learning algorithms with the statistical rigour of Structural Equation Modelling (SEM) to produce an overall phenotypic network discovery system with optimal properties. We illustrate our method using the analysis of a candidate SNP data set from the AMERICO sample, a multi-ethnic cross-sectional cohort of roughly 300 children with detailed obesity-related phenotypes. We demonstrate our approach by showing genetic mechanisms for three obesity-related SNPs.

Original languageEnglish (US)
Pages (from-to)129-143
Number of pages15
JournalInternational Journal of Data Mining and Bioinformatics
Volume12
Issue number2
DOIs
StatePublished - 2015

Fingerprint

Obesity
Single Nucleotide Polymorphism
Bayesian networks
Learning algorithms
Data mining
Phenotype
Data Mining
Genes
Information Storage and Retrieval
Genome-Wide Association Study
candidacy
Genotype
Learning
Databases
learning
Datasets
Power (Psychology)

Keywords

  • Bayesian networks
  • Genetic networks
  • GWAS
  • Obesity
  • Structural equation modelling

ASJC Scopus subject areas

  • Library and Information Sciences
  • Information Systems
  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Discovery of phenotypic networks from genotypic association studies with application to obesity. / Duarte, Christine W.; Klimentidis, Yann C; Harris, Jacqueline J.; Cardel, Michelle; Fernández, José R.

In: International Journal of Data Mining and Bioinformatics, Vol. 12, No. 2, 2015, p. 129-143.

Research output: Contribution to journalArticle

Duarte, Christine W. ; Klimentidis, Yann C ; Harris, Jacqueline J. ; Cardel, Michelle ; Fernández, José R. / Discovery of phenotypic networks from genotypic association studies with application to obesity. In: International Journal of Data Mining and Bioinformatics. 2015 ; Vol. 12, No. 2. pp. 129-143.
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