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Widespread Allelic Heterogeneity in Complex Traits.

Farhad Hormozdiari1, Anthony Zhu2, Gleb Kichaev3

  • 1Department of Computer Science, University of California, Los Angeles, CA 90095, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.

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Allelic heterogeneity, the presence of multiple causal variants at a genetic locus, is common in complex traits. Our new computational method identified thousands of loci with allelic heterogeneity across GWASs and eQTL studies.

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allelic heterogeneitycausal variantscomplex traitseQTLgene expression

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Area of Science:

  • Genetics
  • Bioinformatics
  • Statistical Genetics

Background:

  • Genome-wide association studies (GWASs) have advanced understanding of complex trait genetics.
  • Allelic heterogeneity (AH), involving multiple causal variants per locus, is an underappreciated aspect of complex trait architecture.
  • Existing methods may not fully capture the complexity of genetic loci.

Purpose of the Study:

  • To develop and apply a computational method for inferring the probability of allelic heterogeneity (AH).
  • To quantify the extent of AH across different genetic datasets, including GWASs and expression quantitative trait loci (eQTLs).
  • To investigate the relationship between statistical power and the detection of AH.

Main Methods:

  • Development of a novel computational approach to estimate the probability of AH.
  • Application of the method to three GWAS datasets and four eQTL datasets.
  • Statistical analysis to assess the correlation between sample size and the proportion of loci exhibiting AH.

Main Results:

  • Identification of 4,152 loci with significant evidence of AH.
  • AH was detected in 4%-23% of eQTL loci, 35% of high-density lipoprotein (HDL) GWAS loci, and 23% of schizophrenia GWAS loci.
  • A strong positive correlation (R² = 0.85) was observed between sample size and the proportion of eQTL loci with AH, suggesting under-detection due to limited power.

Conclusions:

  • Allelic heterogeneity is a significant feature of complex traits, present in a substantial proportion of identified genetic loci.
  • The computational method provides a robust way to infer AH probability.
  • Future research in fine mapping and association mapping should account for the prevalence of AH, especially in studies with lower statistical power.