A model for family-based case-control studies of genetic imprinting and epistasis

Xin Li, Yihan Sui, Tian Liu, Jianxin Wang, Yongci Li, Zhenwu Lin, John Hegarty, Walter A. Koltun, Zuoheng Wang, Rongling Wu

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

Genetic imprinting, or called the parent-of-origin effect, has been recognized to play an important role in the formation and pathogenesis of human diseases. Although the epigenetic mechanisms that establish genetic imprinting have been a focus of many genetic studies, our knowledge about the number of imprinting genes and their chromosomal locations and interactions with other genes is still scarce, limiting precise inference of the genetic architecture of complex diseases. In this article, we present a statistical model for testing and estimating the effects of genetic imprinting on complex diseases using a commonly used case-control design with family structure. For each subject sampled from a case and control population, we not only genotype its own single nucleotide polymorphisms (SNPs) but also collect its parents' genotypes. By tracing the transmission pattern of SNP alleles from parental to offspring generation, the model allows the characterization of genetic imprinting effects based on Pearson tests of a 2 × 2 contingency table. The model is expanded to test the interactions between imprinting effects and additive, dominant and epistatic effects in a complex web of genetic interactions. Statistical properties of the model are investigated, and its practical usefulness is validated by a real data analysis. The model will provide a useful tool for genome-wide association studies aimed to elucidate the picture of genetic control over complex human diseases.

Original languageEnglish (US)
Pages (from-to)1069-1079
Number of pages11
JournalBriefings in bioinformatics
Volume15
Issue number6
DOIs
StatePublished - Aug 2 2013

Fingerprint

Genetic Epistasis
Genomic Imprinting
Case-Control Studies
Genes
Statistical Models
Nucleotides
Polymorphism
Single Nucleotide Polymorphism
Genotype
Genome-Wide Association Study
Epigenomics
Alleles
Testing
Population

All Science Journal Classification (ASJC) codes

  • Information Systems
  • Molecular Biology

Cite this

Li, Xin ; Sui, Yihan ; Liu, Tian ; Wang, Jianxin ; Li, Yongci ; Lin, Zhenwu ; Hegarty, John ; Koltun, Walter A. ; Wang, Zuoheng ; Wu, Rongling. / A model for family-based case-control studies of genetic imprinting and epistasis. In: Briefings in bioinformatics. 2013 ; Vol. 15, No. 6. pp. 1069-1079.
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Li, X, Sui, Y, Liu, T, Wang, J, Li, Y, Lin, Z, Hegarty, J, Koltun, WA, Wang, Z & Wu, R 2013, 'A model for family-based case-control studies of genetic imprinting and epistasis', Briefings in bioinformatics, vol. 15, no. 6, pp. 1069-1079. https://doi.org/10.1093/bib/bbt050

A model for family-based case-control studies of genetic imprinting and epistasis. / Li, Xin; Sui, Yihan; Liu, Tian; Wang, Jianxin; Li, Yongci; Lin, Zhenwu; Hegarty, John; Koltun, Walter A.; Wang, Zuoheng; Wu, Rongling.

In: Briefings in bioinformatics, Vol. 15, No. 6, 02.08.2013, p. 1069-1079.

Research output: Contribution to journalArticle

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AU - Sui, Yihan

AU - Liu, Tian

AU - Wang, Jianxin

AU - Li, Yongci

AU - Lin, Zhenwu

AU - Hegarty, John

AU - Koltun, Walter A.

AU - Wang, Zuoheng

AU - Wu, Rongling

PY - 2013/8/2

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