Table 1. Fraction of simulated local heritability explained in WTCCC2 genotypes.
| # Low-frequency typed causals: | |||||
| A: | 1 | 2 | 3 | 5 | 10 |
|
100% | 82% | 69% | 55% | 37% |
|
100% | 85% | 74% | 59% | 44% |
|
61% (1%) | 65% (1%) | 61% (1%) | 58% (2%) | 60% (1%) |
|
94% (2%) | 92% (2%) | 97% (3%) | 95% (2%) | 90% (2%) |
|
0.94 | 1.13 | 1.40 | 1.71 | 2.37 |
Analysis of simulated disease architecture with 180 causal 1Mbp loci yielding a true 
. In each locus, 1–10 causal variants were sampled from either low-frequency (
) of common (MAF
) WTCCC2 SNPs. For each of four methods tested, the fraction of local heritability identified by the method is reported over 50 simulations (with standard error in parenthesis). Top two panels correspond to experiments with observed causal variants and bottom two panels to experiments with causal variants hidden. In A and B only (where causals are typed), bold-faced 
and 
represents significant difference from 100% by z-score at 
(accounting for 5 architectures tested). The ratio of 
to 
is reported in the bottom row of each panel (with bold-face indicating significance by t-test at 
).