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Hardy-Weinberg Equilibrium (HWE)

Definition
AI-generated

Hardy-Weinberg equilibrium describes expected genotype frequencies (for a bi-allelic site: p^2, 2pq, q^2) under random mating, no selection, no mutation, and infinite population size.

Topics
Core genetics
Related
Controls-Only HWE Genotype Heterozygote

Why it matters in GWAS

Strong HWE violation can indicate genotyping error, batch effects, or population structure; aggressive filtering in cases only can remove disease-associated variants.

Example usage

"We excluded SNPs with controls-only HWE p < 1e-6 in PLINK."

Controls-Only HWE Genotype Heterozygote Heterozygote Deficit Heterozygote Excess Homozygote Inbreeding Coefficient (F) Minor Allele Frequency (MAF) Single Nucleotide Polymorphism (SNP) Zygosity Wahlund Effect
Related-term network

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Node order. The current term is first. Next come every page linked from Related terms, in the same top-to-bottom order as that list. Then new terms appear in two-hop layers: for each of those direct neighbors (in that same order), their related terms are appended if not already listed. A third pass does the same for two-hop nodes. The walk stops when a fixed maximum number of nodes is reached.

References

  • Wigginton JE, Cutler DJ, Abecasis GR. (2005). A note on exact tests of Hardy-Weinberg equilibrium. Am J Hum Genet.
  • GWASTutorial: Genotype Data QC.
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