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. Author manuscript; available in PMC: 2016 May 18.
Published in final edited form as: Nat Genet. 2015 Nov 2;47(12):1385–1392. doi: 10.1038/ng.3431

Figure 4. Inferred heritability of schizophrenia liability due to SNPs of various allele frequencies.

Figure 4

(a) Simulated narrow-sense heritability per MAF bin (hMAF2, dashed blue curves) and estimated SNP-heritability per MAF bin (hg,MAF2, solid red curves) for quantitative phenotypes with genetic architectures in which SNPs of minor allele frequency p have average per-allele effect size variance proportional to p (1 − p)α. Simulations used causal SNPs with MAF≥0.1% in UK10K sequencing data and tag SNPs from our PGC2 analyses; error bars, 95% confidence intervals based on 4,000 runs. (b) SNP-heritability (red) and inferred narrow-sense heritability (blue) of schizophrenia liability partitioned across six MAF bins. Point estimates of narrow-sense heritability per bin are based on interpolated values of the ratio hg,MAF2hMAF2 at α=−0.28, which provided the best weighted least-squares fit between observed hg,MAF2 and interpolated hg,MAF2 from the simulations in panel (a) (Supplementary Fig. 12). (c) Inferred narrow-sense heritability of schizophrenia liability explained per SNP in each MAF bin, i.e., hMAF2 in panel (b) normalized by UK10K SNP counts (Supplementary Table 14). Schizophrenia hg,MAF2 error bars, 95% confidence intervals based on REML analytic standard errors. Schizophrenia hMAF2 and σMAF2 error bars, unions of 95% confidence intervals assuming −1≤α≤0.