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An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations
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Genetic interactions affecting human gene expression identified by variance association mapping.

Andrew Anand Brown1, Alfonso Buil2, Ana Viñuela3

  • 1Human Genetics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.

Elife
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Summary
This summary is machine-generated.

Researchers identified genetic interactions, or epistasis, that explain complex traits. They found gene by environment interactions (GxE) and epistatic interactions using RNA sequencing data, revealing new insights into genetic variation.

Keywords:
epistasisgene expressiongene-environment interactions

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Area of Science:

  • Genetics
  • Genomics
  • Bioinformatics

Background:

  • Complex traits are influenced by genetic factors, but identified genetic loci often explain only a fraction of heritability.
  • Non-additive genetic interactions, known as epistasis, are hypothesized to contribute to this missing heritability.
  • Identifying genetic variants that influence phenotypic variance is a potential strategy to uncover epistasis and gene by environment interactions (GxE).

Purpose of the Study:

  • To identify variance quantitative trait loci (vQTLs) associated with phenotypic variance.
  • To investigate the role of gene by environment interactions (GxE) in vQTL associations.
  • To detect and validate epistatic interactions underlying complex traits.

Main Methods:

  • Analysis of RNA-sequence data from lymphoblastoid cell lines (LCLs) in the TwinsUK cohort.
  • Identification of 508 variance associated single nucleotide polymorphisms (SNPs).
  • Utilizing a twin study design to assess GxE effects and a replication dataset to confirm epistatic interactions.

Main Results:

  • Approximately 70% of the identified vQTL associations were influenced by GxE.
  • 57 epistatic interactions were identified and replicated, explaining an average of 4.3% of phenotypic variance.
  • In 24 instances, epistatic interactions explained more phenotypic variance than their additive genetic contributions.

Conclusions:

  • Variance quantitative trait loci (vQTLs) analysis using molecular phenotypes is a viable approach to uncover genetic interactions.
  • Gene by environment interactions (GxE) play a significant role in genetic variance.
  • Epistasis contributes to the heritability of complex traits and can be detected through vQTL analysis.