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PI_HAT

Definition
AI-generated

PI_HAT is a PLINK summary statistic for pairwise relatedness that approximates the proportion of the genome shared identical by descent.

Topics
Population genetics
Related
Cryptic Relatedness Identity by Descent (IBD) Kinship Coefficient

Why it matters in GWAS

PI_HAT is widely used in QC to flag duplicate samples and close relatives before association testing or before constructing an unrelated subset for PCA.

Example usage

"Pairs with PI_HAT above 0.1875 were treated as likely second-degree relatives or closer."

Cryptic Relatedness Identity by Descent (IBD) Kinship Coefficient Relatedness 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

  • Purcell S, et al. (2007). PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet.
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