A genome-wide search for common SNP x SNP interactions on the risk of venous thrombosis

BMC Med Genet. 2013 Mar 20:14:36. doi: 10.1186/1471-2350-14-36.

Abstract

Background: Venous Thrombosis (VT) is a common multifactorial disease with an estimated heritability between 35% and 60%. Known genetic polymorphisms identified so far only explain ~5% of the genetic variance of the disease. This study was aimed to investigate whether pair-wise interactions between common single nucleotide polymorphisms (SNPs) could exist and modulate the risk of VT.

Methods: A genome-wide SNP x SNP interaction analysis on VT risk was conducted in a French case-control study and the most significant findings were tested for replication in a second independent French case-control sample. The results obtained in the two studies totaling 1,953 cases and 2,338 healthy subjects were combined into a meta-analysis.

Results: The smallest observed p-value for interaction was p = 6.00 10(-11) but it did not pass the Bonferroni significance threshold of 1.69 10(-12) correcting for the number of investigated interactions that was 2.96 10(10). Among the 37 suggestive pair-wise interactions with p-value less than 10(-8), one was further shown to involve two SNPs, rs9804128 (IGFS21 locus) and rs4784379 (IRX3 locus) that demonstrated significant interactive effects (p = 4.83 10(-5)) on the variability of plasma Factor VIII levels, a quantitative biomarker of VT risk, in a sample of 1,091 VT patients.

Conclusion: This study, the first genome-wide SNP interaction analysis conducted so far on VT risk, suggests that common SNPs are unlikely exerting strong interactive effects on the risk of disease.

Publication types

  • Meta-Analysis
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Aged
  • Case-Control Studies
  • Epistasis, Genetic
  • Factor VIII / genetics
  • Factor VIII / metabolism
  • Female
  • France
  • Genetic Predisposition to Disease*
  • Genome-Wide Association Study
  • Homeodomain Proteins / genetics
  • Humans
  • Male
  • Middle Aged
  • Odds Ratio
  • Polymorphism, Single Nucleotide*
  • Transcription Factors / genetics
  • Venous Thrombosis / genetics*
  • White People / genetics

Substances

  • Homeodomain Proteins
  • IRX3 protein, human
  • Transcription Factors
  • Factor VIII