LDSC
I applied Linkage Disequilibrium Score Regression1 to the CRP GWAS of Said et al.2 to estimate heritability and look for signs of population stratification or confounding.
The results are in the table below:
| Parameter | Value |
|---|---|
| h2_liab | 0.1683 |
| h2_liab_se | 0.03026 |
| Lambda_gc | 1.72 |
| Mean_chi2 | 2.813 |
| Intercept | 1.065 |
| Intercept_se | 0.01747 |
| Ratio | 0.0357 |
| Ratio_se | 0.009638 |
A heritability of 0.1683 is low-to-moderate, while a LDSC intercept 1.065 suggested a well-structured GWAS without obvious confounding or stratification. The high mean chi-squared (2.813) indicates a highly polygenic trait.
-
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/. ↩
-
Anurag Verma, Jennifer E Huffman, Alex Rodriguez, Mitchell Conery, Molei Liu, Yuk-Lam Ho, Youngdae Kim, David A Heise, Lindsay Guare, Vidul Ayakulangara Panickan, and others. Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program. Science, 385(6706):eadj1182, 2024. URL: https://www.science.org/doi/10.1126/science.adj1182. ↩