Table 2.

Power Comparisons of Sequencing-Based and Variant-Based Replication under Variable Effect Model

	Ratesa				Power for Replicationb
Number of Cases/Controls in Stage 1 and 2 Samples	False Positive	False Negative	Assay Succes	Error Ratio	Sequence-Based	Variant-Based
250/250c	0	0	1	1	0.542	0.507
	1%	4%	0.9	0.5	0.521	0.458
				1		0.452
	6.3%	1%	0.9	0.5	0.520	0.466
				1		0.461
	10%	5%	0.9	0.5	0.503	0.459
				1		0.447
500/500c	0	0	1	1	0.731	0.708
	1%	4%	0.9	0.5	0.719	0.675
				1		0.667
	6.3%	1%	0.9	0.5	0.718	0.674
				1		0.674
	10%	5%	0.9	0.5	0.701	0.672
				1		0.661
2000/2000d	0	0	1	1	0.827	0.825
	1%	4%	0.9	0.5	0.816	0.780
				1		0.766
	6.3%	1%	0.9	0.5	0.814	0.781
				1		0.769
	10%	5%	0.9	0.5	0.802	0.781
				1		0.755
3500/3500d	0	0	1	1	0.899	0.898
	1%	4%	0.9	0.5	0.893	0.870
				1		0.863
	6.3%	1%	0.9	0.5	0.893	0.868
				1		0.865
	10%	5%	0.9	0.5	0.886	0.874
				1		0.858

^aSignificance levels for small-scale study: α_S1 = 0.05 and α_S2 = 0.05.

^bSignificance levels for large-scale study: α_S1 = 2.5 × 10⁻⁶ and α_S2 = 2.5 × 10⁻⁶.

^cThe impact of different combinations of false-positive/false-negative rate, assay success rate, and genotyping and sequencing error rate ratio on the replication power is examined.

^dThe power was empirically estimated based upon 10,000 replicates.