Markup | Genome Research

Table 3.

Haplotype Frequency Estimates and Significance Levels of Case-control Comparison from Permutation Tests

Chromosome 19 APOE Gene Region
*Configuration 1[i]: M1 M2 M3 M4^ M5 M6 M7 M8 ↓ ↓ ↓ ↓ ↓ ↓ ↓ ↓ ^part of ɛ4 allele determination*			*Configuration 2[i]: M1 M2 M3 M4^ M5 M6 M7 M8 ↓ ↓ ↓ ↓ ↓ ↓ ↓ ↓**
(APOEɛ4 SNP included in haplotypes)			(Loci flank the APOEɛ4 SNP)
Haplotype	Overall	Case	Control	χ²	P value[ii]	Haplotype	Overall	Case	Control	χ²	P value[ii]
TCCA	0.007	0.012	0.000	1.83	0.243	TACA	0.207	0.192	0.220	0.42	0.357
CCCA	0.013	0.022	0.000	3.34	0.025	CACA	0.057	0.050	0.069	0.60	0.357
TTCA	0.009	0.009	0.007	0.04	0.884	TGCA	0.015	0.003	0.034	5.53	0.002
CTCA	0.031	0.049	0.000	7.41	0.014	CGCA	0.166	0.190	0.132	2.10	0.044
TCTA	0.224	0.197	0.258	1.81	0.072	TATA	0.021	0.019	0.023	0.06	0.810
CCTA	0.198	0.189	0.219	0.47	0.285	CATA	0.005	0.009	0.004	0.27	0.776
TTTA	0.000	0.000	0.000	0.00	0.116	TGTA	0.000	0.000	0.000	0.00	0.395
CTTA	0.004	0.006	0.002	0.26	0.837	CGTA	0.008	0.009	0.008	0.02	0.896
TCCG	0.002	0.003	0.000	0.44	0.664	TACG	0.232	0.262	0.195	2.21	0.055
CCCG	0.002	0.004	0.000	0.64	0.562	CACG	0.066	0.049	0.092	2.57	0.061
TTCG	0.088	0.115	0.056	3.56	0.023	TGCG	0.013	0.000	0.032	6.67	0.000
CTCG	0.079	0.110	0.042	5.22	0.023	CGCG	0.176	0.189	0.152	0.83	0.209
TCTG	0.138	0.124	0.159	0.85	0.276	TATG	0.000	0.000	0.000	0.00	0.285
CCTG	0.180	0.135	0.228	5.01	0.008	CATG	0.018	0.014	0.022	0.33	0.606
TTTG	0.017	0.14	0.017	0.04	0.780	TGTG	0.000	0.000	0.000	0.00	0.619
CTTG	0.010	0.010	0.012	0.04	0.846	CGTG	0.016	0.015	0.018	0.05	0.804
Log (ln) Likelihoods:	−1117.2	−668.7	−4.16.9	63.12[iii]	0.0001		−1149.7	−621.6	−511.5	33.34[iii]	0.0041
Other Haplotype Configuration[i] and Significance Levels
Chromosome 19 region		LRT[iii]	P value[ii]
Configuration 3: M1 M2 M3 M4^* M5 M6 M7 M8 Haplotypes contain ɛ4 locus		93.66	0.0001
Configuration 4: M1 M2 *M3 M4^ M5 M6** M7 M8 Haplotypes contain ɛ4 locus		57.39	0.0001
Configuration 5: M1 M2 M3 M4^* M5 M6 M7 M8 Haplotypes flank ɛ4 locus		45.64	0.0001
Configuration 6: M1 M2 M3 M4^* M5 M6 M7 M8 Haplotypes do not contain or flank ɛ4 locus		13.48	0.2401
Chromosome 13 region
Configuration 7: M1 M2 M3 M4 M5 Haplotypes in control region		17.29	0.0940
Configuration 8: M1 M2 M3 M4 M5 Haplotypes in control region		6.49	0.4930

[i] Markers indicated in bold define the haplotype configuration.

[ii] P values based on 10000 permutations.

[iii] Likelihood ratio test statistic values for omnibus test.