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Quantifying missing heritability at known GWAS loci.

Alexander Gusev1, Gaurav Bhatia2, Noah Zaitlen3

  • 1Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America ; Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America ; Medical and Population Genetics Program, Broad Institute, Cambridge, Massachusetts, United States of America.

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|January 4, 2014
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Summary
This summary is machine-generated.

This study reveals that known genetic loci explain significantly more heritability for complex diseases than previously identified by genome-wide association studies (GWAS). This finding improves our understanding of complex trait architecture and fine-mapping strategies.

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Area of Science:

  • Genetics
  • Complex Trait Heritability
  • Genome-Wide Association Studies

Background:

  • Previous research suggested that most missing heritability in complex traits is explained by all genotyped SNPs.
  • However, the heritability contribution from additional causal variants at known GWAS loci remained unclear.

Purpose of the Study:

  • To quantify the heritability explained by all SNPs within known GWAS loci for nine diseases.
  • To investigate if loci from related traits explain additional heritability at known disease loci.

Main Methods:

  • Utilized variance components to estimate heritability explained by all SNPs at known GWAS loci.
  • Analyzed data from WTCCC1 and WTCCC2 cohorts, excluding the MHC region for autoimmune diseases.
  • Adjusted for Linkage Disequilibrium (LD) between SNPs to correct for potential biases.

Main Results:

  • All SNPs at known GWAS loci explained 1.29 times more heritability than GWAS-associated SNPs on average (P=3.3 x 10⁻⁵).
  • Significant increases were observed for Multiple Sclerosis (2.07x) and Crohn's Disease (1.48x).
  • Union of autoimmune disease loci explained substantially more heritability for MS (7.15x) and CD (2.20x).
  • Rheumatoid Arthritis analysis showed 2.37x more heritability from all SNPs at GWAS loci and 5.33x from all autoimmune disease loci.

Conclusions:

  • Known GWAS loci harbor more heritability than identified by associated SNPs alone.
  • Related traits' loci contribute significantly to heritability at known disease loci.
  • Causal variants at GWAS loci may be skewed towards common alleles, contrasting with a genome-wide enrichment of low-frequency alleles.