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LD Pruning

Definition
AI-generated

LD pruning selects a sparse subset of variants that are approximately linkage-disequilibrium–independent, usually by scanning the genome in windows and dropping SNPs that exceed an r² threshold with a retained “anchor” SNP.

Topics
Population genetics
URL
https://www.cog-genomics.org/plink/1.9/ld#indep
Related
Genetic Relationship Matrix (GRM) Linkage Disequilibrium (LD) PLINK

Why it matters in GWAS

Pruned SNP sets are used for principal components, genetic relationship matrices, and relatedness screens so that structure reflects shared ancestry rather than local LD; using correlated SNPs in those steps can distort distances and PCs.

Example usage

"LD Pruning structure informed clumping, fine-mapping, and interpretation of nearby association peaks."

Genetic Relationship Matrix (GRM) Linkage Disequilibrium (LD) PLINK Principal Component Analysis (PCA) Relatedness and Sample Structure
Related-term network

Click any node to open that term page.

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

  • PLINK 1.9 LD pruning: https://www.cog-genomics.org/plink/1.9/ld#indep
  • PLINK 2.0: https://www.cog-genomics.org/plink/2.0/ld#indep
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