Reconstructability analysis as a tool for identifying gene-gene interactions in studies of human diseases

Stephen Shervais, Patricia L. Kramer, Shawn Westaway, Nancy J. Cox, Martin Zwick

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

There are a number of common human diseases for which the genetic component may include an epistatic interaction of multiple genes. Detecting these interactions with standard statistical tools is difficult because there may be an interaction effect, but minimal or no main effect. Reconstructability analysis (RA) uses Shannon's information theory to detect relationships between variables in categorical datasets. We applied RA to simulated data for five different models of gene-gene interaction, and find that even with heritability levels as low as 0.008, and with the inclusion of 50 non-associated genes in the dataset, we can identify the interacting gene pairs with an accuracy of ≥80%. We applied RA to a real dataset of type 2 non-insulin-dependent diabetes (NIDDM) cases and controls, and closely approximated the results of more conventional single SNP disease association studies. In addition, we replicated prior evidence for epistatic interactions between SNPs on chromosomes 2 and 15.

Original languageEnglish (US)
Article number18
JournalStatistical Applications in Genetics and Molecular Biology
Volume9
Issue number1
DOIs
StatePublished - 2010

Fingerprint

Genes
Gene
Interaction
Single Nucleotide Polymorphism
Information Theory
Heritability
Chromosomes, Human, Pair 15
Inborn Genetic Diseases
Chromosomes, Human, Pair 2
Interaction Effects
Diabetes
Main Effect
Information theory
Chromosomes
Medical problems
Categorical
Type 2 Diabetes Mellitus
Chromosome
Inclusion
Human

Keywords

  • Bioinformatics
  • Epistasis
  • Gene interaction modeling
  • Genetics
  • Information theory
  • OCCAM
  • Reconstructability analysis

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology
  • Statistics and Probability
  • Computational Mathematics
  • Medicine(all)

Cite this

Reconstructability analysis as a tool for identifying gene-gene interactions in studies of human diseases. / Shervais, Stephen; Kramer, Patricia L.; Westaway, Shawn; Cox, Nancy J.; Zwick, Martin.

In: Statistical Applications in Genetics and Molecular Biology, Vol. 9, No. 1, 18, 2010.

Research output: Contribution to journalArticle

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