LDSC
I applied Linkage Disequlibirum Score Regression1 to the Neale Lab's GWAS of self-reported chronic fatigue syndrome (CFS) in the UK Biobank.
Since the phenotype used in this study is based on a single-question self-report, it is less precise than the detailed phenotyping used in DecodeME. This imprecision combined with the relatively small number of cases in this GWAS is expected to produce noisy summary statistics. Nevertheless, it is still interesting and worthwhile to analyze these summary statistics.
The LDSC results are shown below:
| Parameter | Value |
|---|---|
| h2_liab | 0.08019 |
| h2_liab_se | 0.02978 |
| Lambda_gc | 1.027 |
| Mean_chi2 | 1.028 |
| Intercept | 1.006 |
| Intercept_se | 0.006519 |
| Ratio | 0.1942 |
| Ratio_se | 0.2289 |
The liability-scale heritability of 8% is similar to that seen in DecodeME.
The low intercept and moderate attenuation ratio suggest low risk of confounding by stratification.
-
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/. ↩