Unbiased Enrichment Analysis with 53 Functional Categories
The 53 functional categories, derived from 24 main annotations, were obtained as follows: When we report results in Supplementary Tables 4, 5, and 6, we do not report results from the category containing all SNPs, as it has 100% of the heritability with standard error zero. (It might have a coefficient τc that is non-trivial, but in these tables we report proportions of heritability.) According to our simulations (Figure 2), including these 53 categories in our baseline model allows us to obtain unbiased or nearly unbiased estimates of enrichment for a wide range of potential new categories. To estimate the enrichment of a new annotation, we perform analyses using a model with these 53 annoations plus the new annotation. For example, for the cell-type-specific analysis, we add each cell-type-specific annotation to the baseline model one at a time, and asses enrichment using the z-score of the cell-type-specific annotation.
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Finucane H.K., Bulik-Sullivan B., Gusev A., Trynka G., Reshef Y., Loh P.R., Anttila V., Xu H., Zang C., Farh K., Ripke S., Day F.R., Consortium R., Purcell S., Stahl E., Lindstrom S., Perry J.R., Okada Y., Raychaudhuri S., Daly M., Patterson N., Neale B.M, & Price A.L. (2015). Partitioning heritability by functional annotation using genome-wide association summary statistics. Nature genetics, 47(11), 1228-1235.
Publication 2015
Asses Cell type Snps
Corresponding Organization :
Other organizations :
Massachusetts Institute of Technology, Harvard University, Massachusetts General Hospital, Broad Institute, Brigham and Women's Hospital, Mass General Brigham, Wellcome Sanger Institute, Dana-Farber Cancer Institute, MRC Epidemiology Unit, Medical Research Council, University of Cambridge, Icahn School of Medicine at Mount Sinai, Tokyo Medical and Dental University, RIKEN Center for Integrative Medical Sciences, University of Manchester
Adding each cell-type-specific annotation to the baseline model one at a time
dependent variables
Enrichment of a new annotation
control variables
The 53 functional categories, derived from 24 main annotations, were obtained as follows:
positive controls
The category containing all SNPs, as it has 100% of the heritability with standard error zero
negative controls
Not reported in Supplementary Tables 4, 5, and 6, as it might have a coefficient τ_c that is non-trivial
Annotations
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