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Table 1 Case study p-values for SNPs flanking the causal loci

From: One-stage design is empirically more powerful than two-stage design for family-based genome-wide association studies

  p-Value (relative rank)
SNP index 185 186 191 192
CMMT 4.0 × 10-2 (457) 8.3 × 10-5 (1) 1.2 × 10-1 (1257) 2.6 × 10-3 (43)
FBAT 9.9 × 10-5 (2) 2.4 × 10-3 (30) 4.4 × 10-4 (5) 5.4 × 10-3 (57)
2-stagea 1.0 2.4 × 10-3 (1) 1.0 1.0
1-stage CSST 6.2 × 10-5 (3) 4.3 × 10-6 (1) 6.1 × 10-4 (16) 2.2 × 10-4 (7)
1-stage CLRT 8.0 × 10-5 (3) 7.7 × 10-6 (1) 6.9 × 10-4 (13) 3.0 × 10-4 (5)
  1. aIf a SNP is not among the top ten SNPs from the CMMT stage, it is not considered in the second stage, so the two-stage method p-value is listed as 1.0, the only p-value for which the null hypothesis will never be rejected, regardless of α.