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Table 1 Parameter specification in the simulated examples

From: GLOSSI: a method to assess the association of genetic loci-sets with complex diseases

Scenario Number of causal SNPs RR (OR)* MAF of causal SNPs Whether causal SNPs were 'genotyped'
1–3 1, 5 or 20 1.07 (1.10) 0.25 Yes
4–6 1, 5 or 20 1.34 (1.52) 0.05 Yes
7–9 1, 5 or 20 1.34 (1.50) 0.25 Yes
10–12 1, 5, or 20 1.61 (2.00) 0.05 Yes
13–15 1, 5, or 20 1.61 (1.94) 0.25 Yes
16–18 1 or 5 2.00 (2.67) 0.25 Yes
19–21 1, 5, or 17 1.61 (~1.94) ~0.25 No
  1. *RR (OR) = relative risks (odds ratio) when a loci carries two disease alleles, assuming an additive model; MAF = minor allele frequency of the Utah samples in the HapMap project. Three out of the 20 original causal SNPs, generated under the case where MAF equals 0.25, are not in high LD with any SNP genotyped in the HapMap phase I/II project. Disease prevalence and crossover rate are fixed at 25% and 1.0 centiMorgan, respectively, in all simulations.