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Table 3 Comparison of power between GCDH and single-SNP approaches in analysis of exome-sequencing data from the Rotterdam Study

From: CollapsABEL: an R library for detecting compound heterozygote alleles in genome-wide association studies

  Causal SNPs available Causal SNPs excluded
β MAF Single-SNP GCDH Single-SNP GCDH
1 (0.00, 0.02) 0.09 0.09 0.08 0.08
1 (0.02, 0.04) 0.17 0.23 0.13 0.14
1 (0.04, 0.06) 0.18 0.28 0.11 0.15
1 (0.06, 0.08) 0.29 0.43 0.19 0.22
1 (0.08, 0.10) 0.20 0.44 0.14 0.18
2 (0.00, 0.02) 0.13 0.16 0.10 0.11
2 (0.02, 0.04) 0.29 0.56 0.19 0.29
2 (0.04, 0.06) 0.28 0.69 0.18 0.32
2 (0.06, 0.08) 0.41 0.75 0.31 0.41
2 (0.08, 0.10) 0.41 0.83 0.28 0.46
3 (0.00, 0.02) 0.18 0.19 0.12 0.12
3 (0.02, 0.04) 0.47 0.72 0.32 0.41
3 (0.04, 0.06) 0.45 0.86 0.32 0.49
3 (0.06, 0.08) 0.55 0.89 0.41 0.58
3 (0.08, 0.10) 0.65 0.94 0.46 0.63
4 (0.00, 0.02) 0.23 0.26 0.13 0.15
4 (0.02, 0.04) 0.55 0.83 0.41 0.53
4 (0.04, 0.06) 0.56 0.94 0.43 0.62
4 (0.06, 0.08) 0.70 0.97 0.54 0.71
4 (0.08, 0.10) 0.75 0.98 0.58 0.76
  1. The simulation analyses are conducted based on the exom sequencing data from Rotterdam Study 1 (RS1), consisting of 1037 individuals and 167,209 SNPs. Power estimates are calculated from 10,000 simulations. Type-I error rate for single-SNP and GCDH analyses are controlled at 5 %