In our second set of simulations, we compared stratified LD score regression to REML, a method that also estimates partitioned heritability but requires genotype data, in scenarios with and without model misspecification (Online Methods). We estimated the enrichment of the DHS category, i.e., (Prop. hg2)/(Prop. SNPs), using three methods: (1) REML with two categories (DHS/non-DHS), (2) stratified LD score regression with two categories (DHS/non-DHS), and (3) stratified LD score regression with the full baseline model (53 categories, described above). Since REML with 53 categories did not converge at this sample size and would be computationally intractable at sample sizes in the tens of thousands, we did not include it in our comparison; an advantage of stratified LD score regression is that it is possible to include a large number of categories in the underlying model. We report means and standard errors of the mean over 100 independent simulations.
