Skip to content

PRS Clumping and Thresholding

Definition
AI-generated

Clumping and thresholding (C+T) is a polygenic score construction strategy: variants are first clumped to reduce linkage disequilibrium redundancy (one “index” SNP per LD block), then SNPs are included according to a series of P-value thresholds from the base GWAS, often selecting the threshold that maximizes prediction in a validation set.

Topics
Post-GWAS
Synonyms
C+T (polygenic score)
Related
GWAS Summary Statistics LD Clumping Linkage Disequilibrium (LD)

Why it matters in GWAS

C+T is simple, interpretable, and widely implemented (e.g. PRSice-2, PLINK-based workflows); understanding it clarifies why LD reference choice and multiple testing over thresholds require careful reporting.

Example usage

"The methods explicitly include PRS Clumping and Thresholding to support interpretation of the main findings."

GWAS Summary Statistics LD Clumping Linkage Disequilibrium (LD) Polygenic Risk Score (PRS) PRS Base Cohort PRS Target Cohort PRSice-2
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

  • Choi SW, Mak TSH, O'Reilly PF. (2020). Tutorial: a guide to performing polygenic risk score analyses. Nat Protoc. https://doi.org/10.1038/s41596-020-0353-1
  • Purcell SM, et al. (2009). Common polygenic variation contributes to risk of schizophrenia and bipolar disorder. Nature.
← PRS Base Cohort PRS Target Cohort →

Last updated (UTC · Git history)