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Genomic Inflation Factor (λGC)

Definition
AI-generated

The genomic inflation factor λGC is commonly defined as the ratio of the observed median χ² association statistic to the expected median under the null (≈ 0.455 for 1 df), or equivalently the squared ratio of observed to expected median z-scores.

Topics
GWAS
Related
Bias Population Stratification Quantile-quantile plot (QQ plot)

Why it matters in GWAS

λGC is a quick global check after association; LD score regression intercept can separate confounding inflation from true polygenic signal. Interpret with care for very polygenic traits and case-control imbalance.

Example usage

"LDSC intercept was 1.02 with λGC 1.04, so we proceeded with BOLT-LMM results as primary."

Bias Population Stratification Quantile-quantile plot (QQ plot) Quality Control (QC)
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

  • Devlin B, Roeder K. (1999). Genomic control for association studies. Biometrics.
  • Bulik-Sullivan BK, et al. (2015). LD Score regression distinguishes confounding from polygenicity. Nat Genet.
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