LDSC
I applied Linkage Disequilibrium Score Regression1 to the triglyceride GWAS of Willer et al.2. The aim was to estimate heritability and look for signs of stratification and confounding.
The results are below:
| Parameter | Value |
|---|---|
| h2_liab | 0.1958 |
| h2_liab_se | 0.0378 |
| Lambda_gc | 1.14 |
| Mean_chi2 | 1.356 |
| Intercept | 1.014 |
| Intercept_se | 0.009635 |
| Ratio | 0.03953 |
| Ratio_se | 0.02706 |
The LDSC intercept of 1.014 suggests minimal evidence for population stratification.
The SNP heritability of 0.1958 is low-to-moderate.
-
Brendan K Bulik-Sullivan, Po-Ru Loh, Hilary K Finucane, Stephan Ripke, Jian Yang, Nick Patterson, Mark J Daly, Alkes L Price, and Benjamin M Neale. LD Score regression distinguishes confounding from polygenicity in genome-wide association studies. Nature Genetics, 47(3):291–295, 2015. URL: https://pmc.ncbi.nlm.nih.gov/articles/PMC4495769/. ↩
-
Global Lipids Genetics Consortium. Discovery and refinement of loci associated with lipid levels. Nature Genetics, 45(11):1274–1283, 2013. URL: https://pmc.ncbi.nlm.nih.gov/articles/PMC3838666/. ↩