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Examination of Thymic Positive and Negative Selection by Flow Cytometry
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Extreme Polygenicity of Complex Traits Is Explained by Negative Selection.

Luke J O'Connor1, Armin P Schoech2, Farhad Hormozdiari2

  • 1Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Program in Bioinformatics and Integrative Genomics, Harvard Graduate School of Arts and Sciences, Boston, MA 02115, USA.

American Journal of Human Genetics
|August 13, 2019
PubMed
Summary
This summary is machine-generated.

Complex traits are highly polygenic due to negative selection, which flattens heritability across many loci. Few genes are critical; common variants associate with thousands of less important regions.

Keywords:
GWASSLD4Mheritabilitynegative selectionpolygenicity

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Area of Science:

  • Genetics
  • Evolutionary Biology
  • Statistical Genetics

Background:

  • Complex traits and common diseases involve thousands of genetic loci.
  • The distribution of heritability across these loci is not fully understood.
  • Negative selection may influence the observed polygenicity.

Purpose of the Study:

  • To investigate the role of negative selection in shaping the polygenicity of complex traits.
  • To quantify the phenomenon of 'flattening' where heritability is spread across many loci.
  • To develop a method for estimating the effective number of independently associated SNPs (Me).

Main Methods:

  • Developed stratified LD fourth moments regression (S-LD4M) to estimate Me.
  • Analyzed data from 33 complex traits with an average sample size of 361,000.
  • Employed evolutionary modeling of new mutations.

Main Results:

  • Heritability is spread approximately 4x more evenly among common SNPs than low-frequency SNPs.
  • Negative selection significantly increases the polygenicity of complex traits.
  • Functionally important regions show even heritability spread, not increased causal effect sizes, due to selective constraint.

Conclusions:

  • Complex traits would be far less polygenic without negative selection.
  • The genes with critical biological effects often differ from those with strong common-variant associations.
  • Selective constraint in important regions prevents large-effect common variants.