Combinatorial Mismatch Scan (CMS) for loci associated with dementia in the Amish

McCauley, Jacob L; Hahs, Daniel W; Jiang, Lan; Scott, William K; Welsh-Bohmer, Kathleen A; Jackson, Charles E; Vance, Jeffery M; Pericak-Vance, Margaret A; Haines, Jonathan L

doi:10.1186/1471-2350-7-19

BMC Medical Genetics

Table 2 Microsatellite markers demonstrating nominally significant (p ≤ 0.05) empiric p-values for allele and genotype frequency differences between dementia cases and controls. Microsatellite markers in close proximity to those demonstrating significance in this study and found to be either linked (lod ≥ 1) or associated (p ≤ 0.05) in previous studies are also listed.

From: Combinatorial Mismatch Scan (CMS) for loci associated with dementia in the Amish

Chromosome	Map Position (cM)	Mb Location	Marker	Fisher's Exact p-value		Empiric p-value		Max Lod Score	Study
				Allele	Genotype	Allele	Genotype
1	25	11.4	D1S2667	0.162	0.007	0.170	0.015
1	64	32.1	D1S396	0.043	0.449	0.050	0.407
2	38	17.4	D2S1360	0.028	0.243	0.035	0.228
2	74	50.7	D2S1352	0.200	0.026	0.208	0.032
2	252	237.9	D2S2968	0.688	0.018	0.684	0.025
3	119	103.7	D3S2459	0.223	0.007	0.231	0.014
3	153	140.7	D3S1764	0.029	0.271	0.035	0.248
3	177	168.7	D3S1763					1.69	Hahs et al.
3	201	187.5	D3S1602			0.007**			Hiltunen et al.
3	201	187.7	*D3S1262*	0.001	0.019	*0.003*	0.026
3	209	191	D3S2398					2.16	Hahs et al.
3	216	193.8	D3S2418					1.18	Hahs et al.
4	78		D4S2367	0.557	0.015	0.557	0.022
4	130	130.7	D4S2394					2.12	Hahs et al.
4	146	143.9	D4S1625	0.032	0.013	0.038	0.020
4	154	152.5	D4S1548					3.01	Hahs et al.
4	158	158.7	D4S1629					1.32	Pericak-Vance et al. (2000)
5	8		D5S2849	0.590	0.031	0.589	0.038
5	92	82.3	D5S1347	0.060	0.002	0.068	0.007
5	98	89.2	D5S1725					1.47	Hahs et al.
5	147	144.1	D5S1480	0.465	0.001	0.467	0.005
5	175	168.4	D5S400	0.04*					Farrer et al.
5	183	173.2	*D5S211*	0.001	0.001	*0.002*	*0.004*
5	183	173.2	D5S211					1.3	Blacker et al.
6	89	77.5	D6S1031	0.024	0.046	0.030	0.051
6	160	158	D6S1007	0.933	0.017	0.923	0.025
8	60	32.2	D8S1477	0.004	0.018	0.007	0.026
8	125	118.5	D8S592	0.387	0.032	0.391	0.038
8	154	137.8	D8S272	0.007	0.021	0.010	0.028
9	14		D9S2169	0.022	0.394	0.027	0.362
10	63	35.3	D10S1208	0.013	0.247	0.018	0.231
10	76	57.2	D10S1221	0.028	0.054	0.034	0.059
12	78	66.2	D12S1294	0.220	0.045	0.228	0.050
13	39	42.1	D13S325	0.027	0.070	0.033	0.072
13	76	96.7	D13S892	0.040	0.224	0.047	0.210
14	44	37.4	D14S306	0.020	0.104	0.026	0.103
14	94	86.3	D14S612	0.016	0.166	0.021	0.156
15	101	92.8	D15S816	0.046	0.158	0.053	0.150
15	116	98.9	D15S87	0.031	0.083	0.037	0.084
16	64	49.7	D16S3396	0.039	0.450	0.046	0.409
16	130		D16S2621	0.227	0.036	0.235	0.042
17	36	14.2	D17S921	0.024	0.026	0.030	0.032
17	126	77.8	D17S928	0.024	0.201	0.029	0.186
18	7	3.1	D18S481	0.017	0.006	0.022	0.013
18	109		D18S1362	0.431	0.021	0.434	0.028
19	21	6.1	D19S1034			0.013**			Hiltunen et al.
19	33	9.7	D19S586					2.06	Hahs et al.
19	36	12.2	D19S1165	0.002	0.066	0.004	0.069
20	39	17.3	D20S470	0.027	0.206	0.033	0.191
21	27	30.6	D21S1270	0.245	0.010	0.253	0.018

Bold denotes markers nominally significant (p ≤ 0.05) in both allele and genotype comparisions
Italics highlights markers empirically significant at p ≤ 0.005
*SAS software was used to measure significant differences in allele frequency between DAT cases and controls
**Pearson's chi-square was calculated and then empirical significance was determined through examination of 1000 replicated datasets.

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