Genome-wide association Scan of dental caries in the permanent dentition

Wang, Xiaojing; Shaffer, John R; Zeng, Zhen; Begum, Ferdouse; Vieira, Alexandre R; Noel, Jacqueline; Anjomshoaa, Ida; Cuenco, Karen T; Lee, Myoung-Keun; Beck, James; Boerwinkle, Eric; Cornelis, Marilyn C; Hu, Frank B; Crosslin, David R; Laurie, Cathy C; Nelson, Sarah C; Doheny, Kimberly F; Pugh, Elizabeth W; Polk, Deborah E; Weyant, Robert J; Crout, Richard; McNeil, Daniel W; Weeks, Daniel E; Feingold, Eleanor; Marazita, Mary L

doi:10.1186/1472-6831-12-57

BMC Oral Health

Table 2 Effect size and P-values for top SNPs in three meta-analyses ^*

From: Genome-wide association Scan of dental caries in the permanent dentition

Gene/SNPs	Chr	Base Pair position	Data Status^†	Effect Size^§					P-value (Meta 1)	P-value (Meta 2)	P-value (Meta 3)
Gene/SNPs	Chr	Base Pair position	Data Status^†	COHRA	DRDR1	DRDR2	ARIC	HPFS	P-value (Meta 1)	P-value (Meta 2)	P-value (Meta 3)
RHOU
rs3936161	1	227336163	Illumina	−1.95	7.17	--	−0.70	--	0.721	1.55E-05	6.76E-05
rs12072775	1	227339176	Affymetrix	−1.94	7.17	--	−0.71	0.007	0.725	4.23E-05	0.001
rs9287022	1	227344972	Imputed	−2.09	7.19	--	−0.61	--	0.673	3.79E-06	1.86E-05
rs9793739	1	227352481	Imputed	−2.08	7.88	--	−0.75	--	0.721	5.27E-07	4.28E-06
rs2988738	1	227427128	Affymetrix	0.67	9.55	--	−1.75	−0.15	0.567	2.02E-05	0.002
ADAMTS3
rs788919	4	73572758	Illumina	−1.40	−4.14	−3.56	−0.47	--	0.026	1.36E-04	1.02E-05
rs4694123	4	73606652	Illumina	−1.31	−2.94	−3.89	−0.46	--	0.038	1.18E-04	1.26E-05
rs10805050	4	73612147	Illumina	1.01	2.93	2.50	0.42	--	0.093	4.88E-06	1.68E-06
rs788911	4	73632087	Illumina	0.99	2.54	3.29	0.38	--	0.084	4.77E-06	1.46E-06
rs1383934	4	73636388	Illumina	1.19	3.20	3.70	0.64	--	0.046	1.77E-06	2.96E-07
RPS6K2
rs505982	6	167095386	Imputed	3.66	8.52	--	−0.35	--	8.93E-06	0.859	0.025
rs635808	6	167097412	Illumina	−4.21	−7.53	−8.30	0.44	--	1.06E-07	0.898	0.010
PTK2B
rs17057381	8	27416801	Affymetrix	16.39	28.98	--	0.47	−0.03	4.02E-07	0.267	0.764
CNIH
rs1953743	14	53722229	Both	−3.08	−6.55	−6.87	0.01	0.04	1.98E-06	0.371	0.027
rs4251631	14	53945934	Illumina	−3.78	−6.32	−10.02	−0.35	--	2.13E-07	0.013	1.80E-06
rs11850320	14	53990173	Illumina	−4.57	−7.93	−6.78	−0.33	--	9.92E-07	0.177	0.0003
rs7150062	14	53997400	Both	4.52	7.93	6.78	0.40	0.01	1.15E-06	0.295	0.001
rs7143579	14	54010435	Illumina	−4.42	−7.15	−7.89	−0.42	--	1.16E-06	0.137	0.0002

* Summarizes genes/regions containing at least one SNP with significant P-values ≤ 10E-7 (bolded); Listed are the first five most significant SNPs if more than five SNPs observed at the corresponding region;
† Illumina/Affymetrix/Both: SNP was genotyped in Illumina 610Quad/Affymetrix 6.0/both chips respectively;
Imputed: SNP data was generated by imputation only. “--" indicating the corresponding SNP was not genotyped in DRDR2 or
HPFS;
§ Effect size can be directly compared ONLY among Meta 1 cohorts (COHRA, DRDR1 and DRDR2).

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ISSN: 1472-6831

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