TABLE 3.

Impact of family size, family information, and parental haplotype distribution on estimated haplotype frequencies, as measured by the discrepancy statistic (top) and on phase reconstruction error (bottom)

	Family size		UN	P	PS	PSD
Haplotype frequency discrepancies
APOE1	1	0.116 A	0.116 A, B, F	0.078 B	0.063 B
2	0.123	0.117	0.095	0.070
5	G	0.143	0.119	0.109 F	0.077
10	0.162	0.119 E	0.116 E	0.081
25	0.212	0.122 C	0.122 C, D	0.082 D
APOE2	1	0.082	0.082	0.061	0.049
2	0.091	0.088	0.077	0.060
5	0.110	0.097	0.090	0.065
10	0.132	0.103	0.099	0.066
25	0.180	0.104	0.104	0.070
IL8E	1	0.047	0.047	0.037	0.032
2	0.054	0.054	0.051	0.040
5	0.065	0.060	0.058	0.043
10	0.085	0.065	0.063	0.046
25	0.110	0.068	0.068	0.047
Phase reconstruction error rate
APOE1	1	0.21 A′	0.21 B′, F′	0.12 B′, H	0.06 B′, I
2	0.20	0.17	0.10	0.03
5	G′	0.19	0.12 H	0.06 F′, I	0.02
10	0.18 J	0.07 J	0.05	0.02
25	0.15 J	0.06 J	0.06	0.02
APOE2	1	0.13	0.13	0.08	0.04
2	0.13	0.11	0.07	0.03
5	0.13	0.09	0.05	0.02
10	0.11	0.06	0.05	0.02
25	0.11	0.05	0.04	0.02
IL8E	1	0.00	0.00	0.00	0.00
2	0.00	0.00	0.00	0.00
5	0.00	0.00	0.00	0.00
10	0.00	0.00	0.00	0.00
	25		0.00	0.00	0.00	0.00

Each entry for a given metric corresponds to the average value for 100 replicates. Italic entries denote estimates that were obtained using the standard EM algorithm for unrelated individuals, and underlined italic entries denote estimates obtained by treating related individuals as unrelated. Letters are referenced in the text. See Table 1 for category definitions.