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

Table 4 The significant genes from FHS study with p-values < 0.001 at any test

gene	Chromosome	Nsnp	maxH	hPDT	hPDT-t	maxV	vPDT	vPDT-t
PLG	chr6	10	0.02498	1.05E-05	0.08819	0.43656	0.50666	1
TFPI	Chr2	18	0.00099	0.00146	9.76E-05	0.45654	0.88330	1
TNFRSF4	chr1	7	1	0.71721	0.00056	0.64336	0.37994	1
TGFB3	chr14	10	0.01998	0.00060	1	0.16284	0.62846	1
IL1R2	chr2	21	0.00200	0.19275	0.00067	0.16783	0.91804	1
MMP16	chr8	9	0.09790	0.00090	1	1	0.31731	1
LRP2	chr2	21	0.00100	0.61149	0.00091	0.03197	0.14087	1
LEP	chr7	18	0.05395	0.00093	0.06325	0.66533	0.35130	1

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