Whole genome sequence analysis of the simulated systolic blood pressure in Genetic Analysis Workshop 18 family data: long-term average and collapsing methods

Table 4 Empirical power at 0.05 using collapsing and single-marker approaches at all 22 causal genes for long-term average phenotype

	Causal genes	Total SNPs		Causal SNPs¹		% Variance explained²		Empirical Power
		Common	Rare³	Common	Rare	Common	Rare	Collapse all SNPs	Collapse rare SNPs	Best rare⁴
1	MAP4	149	739	3	12	0.01456	0.06336	0.99	0.17	1.00
	FLNB	321	628	1	5	0.00273	0.00007	0.69	0.03	0.20
	ARHGEF3	899	1303	2	8	0.00001	0.00006	0.28	0.07	0.11
	TUSC2	1	9	0	0			0.21	0.04
	ABTB1	7	41	2	0	0.00132		0.18	0.02
	NMNAT3	157	332	3	6	0.00014	0.00017	0.15	0.00	0.09
2	ZBTB38	175	408	5	4	0.00087	0.00003	0.09	0.15	0.14
	DNASE1L3	57	79	4	4	0.00005	0.00026	0.01	0.34	0.08
	LOC152217	3	4	1	0	0.00001		0.04	0.28
	SCAP	31	174	0	2		0.00004	0.03	0.51	0.05
	BTD	72	216	0	8		0.00011	0.03	0.08	0.07
	FBLN2	230	452	1	3	0.00002	0.00006	0.02	0.06	0.04
3	CXCR6	5	18	0	1		<1.0E-5	0.12	0.03	0.28
	PDCD6IP	145	318	2	3	0.00025	0.00003	0.04	0.14	0.15
	SUMF1	236	502	1	2	0.00008	<1.0E-5	0.03	0.06	0.16
	SENP5	130	275	0	5		0.00007	0.02	0.03	0.12
	PTPLB	158	329	1	2	0.00002	0.00004	0.02	0.03	0.10
	PPP2R3A	198	860	1	11	<1.0E-5	0.00010	0.02	0.01	0.12
4	SEMA3F	51	83	0	2		0.00001	0.05	0.03	0.05
	TFDP2	363	852	0	5		0.00005	0.04	0.03	0.04
	PAK2	294	516	0	0			0.04	0.02
	B4GALT4	90	126	1	0	0.00002		0.01	0.00
Overall power								0.139	0.095
Type I error								0.071	0.057

Bold type for % variance indicates 3 largest among common variants and 2 largest among rare variants; bold type for empirical power indicates the highest across three analysis options.
¹Number of causal single-nucleotide polymorphisms (SNPs) is computed based on the used annotation file (not based on the answers).
²% Variance explained is computed by adding the percent variance explained by each SNP based on the used annotation file (not based on the answers).
³Rare SNPs are defined as SNPs with minor allele frequencies (MAFs) less than 0.5.
⁴Best rare is the best power across all rare variants in a gene.

ISSN: 1753-6561