The power comparison of the haplotype-based collapsing tests and the variant-based collapsing tests for detecting rare variants in pedigrees

Table 3 Power and effects of LD under special haplotype setting

β settings	maxH	hPDT	hPDT-t	maxV	vPDT	vPDT-t
(1) β₁ = β₄ = 3, β₅ = β₆ = β₇ = β₈ = − 3	0.589	0.114	0.394	0.158	0.110	0.065
(2) β₁ = β₄ = 3, β₅ = β₆ = 1, β₇ = β₈ = − 3	0.541	0.088	0.331	0.505	0.258	0.168
(3) β₁ = β₂ = β₃ = β₄ = 2	0.488	0.412	0.230	0.691	0.616	0.391

Note: (1) Other βs are zero if not specified under each β setting; (2) For fifteen haplotypes, 1010000000, 0110000000, 1001000000, 0101000000, 1000000000, 0100000000, 0010000000, 0001000000, 0000100000, 0000010000, 0000001000, 0000000100, 0000000010, 0000000001, 0000000000, the first fourteen rare haplotypes have equal frequencies of 0.01 and the last common haplotype has frequency of 0.86; (3) Simulation results are based on 1000 replicates (10 permutations for each replicate).
Abbreviations: maxH maximal haplotype test, hPDT haplotype-based pedigree disequilibrium test; hPDT-t haplotype-based pedigree disequilibrium test with training data, maxV maximal rare variant test, vPDT variant-based pedigree disequilibrium test, vPDT-t rare variant based pedigree disequilibrium test with training data.

ISSN: 1471-2164