. Author manuscript; available in PMC: 2012 Mar 1.

Published in final edited form as: Ann Rheum Dis. 2010 Dec 3;70(3):454–462. doi: 10.1136/ard.2010.130138

Table 4.

Distribution of PTPN22 genetic variants according with scleroderma-specific autoantibody status

SNP	Population		GG	GA	AA	G	A	p Value^*	OR	(95% CI)
rs33996649	Spain	ACA (n=253)	0.964	0.036	0	0.982	0.0178	0.06	0.51	0.26 to 1.03
		ATA (n=112)	0.964	0.036	0	0.982	0.0179	0.19	0.52	0.19 to 1.42
		Controls (n=1128)	0.932	0.068	0	0.966	0.0341
	Belgium	ACA (n=40)	0.950	0.050	0	0.975	0.0250	0.98	0.98	0.22 to 4.48
		ATA (n=32)	0.938	0.063	0	0.969	0.0313	0.78	1.24	0.27 to 5.66
		Controls (n=236)	0.949	0.051	0	0.975	0.0254
	England	ACA (n=133)	0.962	0.038	0	0.981	0.0188	0.73	1.20	0.42 to 3.44
		ATA (n=56)	0.982	0.018	0	0.991	0.0089	0.58	0.56	0.07 to 4.38
		Controls (n=382)	0.969	0.031	0	0.984	0.0157
	Germany	ACA (n=127)	0.953	0.047	0	0.976	0.0236	0.82	1.13	0.42 to 3.03
		ATA (n=97)	0.979	0.021	0	0.990	0.0103	0.34	0.48	0.11 to 2.18
		Controls (n=285)	0.958	0.042	0	0.979	0.0211
	Netherlands	ACA (n=37)	0.946	0.054	0	0.973	0.0270	0.91	1.10	0.24 to 4.96
		ATA (n=32)	0.938	0.063	0	0.969	0.0313	0.58	0.79	0.35 to 1.81
		Controls (n=263)	0.951	0.049	0	0.975	0.0247
	Italy	ACA (n=177)	0.944	0.056	0	0.972	0.0282	0.80	0.91	0.43 to 1.93
		ATA (n=114)	0.939	0.061	0	0.969	0.0307	0.98	0.99	0.42 to 2.34
		Controls (n=371)	0.938	0.062	0	0.969	0.0310
	USA	ACA (n=296)	0.956	0.044	0	0.978	0.0220	0.18	1.39	0.86 to 2.23
		ATA (n=174)	0.954	0.046	0	0.977	0.0230	0.15	1.49	0.86 to 2.58
		Controls (n=693)	0.958	0.042	0	0.979	0.0209
	Sweden	ACA (n=51)	0.980	0.020	0	0.990	0.0098	0.30	0.36	0.05 to 2.75
		ATA (n=33)	0.939	0.061	0	0.970	0.0303	0.87	1.14	0.25 to 5.08
		Controls (n=280)	0.946	0.054	0	0.973	0.0268
	Pooled^†^‡	ACA (n=1114)	0.957	0.043	0	0.978	0.0225	0.46	0.87	0.63 to 1.21
		ATA (n=650)	0.957	0.043	0	0.978	0.0215	0.48	0.85	0.56 to 1.27
		Controls (n=3638)	0.947	0.053	0	0.973	0.0265

SNP	Population		CC	CT	TT	C	T	p Value^*	OR	(95% CI)

rs2476601	Spain	ACA (n=266)	0.853	0.139	0.008	0.923	0.0771	0.87	1.03	0.72 to 1.47
		ATA (n=126)	0.881	0.111	0.008	0.937	0.0635	0.51	0.84	0.49 to 1.42
		Controls (n=1128)	0.857	0.136	0.007	0.925	0.0749
	Belgium	ACA (n=41)	0.805	0.195	0.000	0.902	0.0976	0.43	1.38	0.62 to 3.08
		ATA (n=32)	0.750	0.250	0.000	0.875	0.1250	0.14	1.83	0.81 to 4.12
		Controls (n=255)	0.863	0.129	0.008	0.927	0.0725
	England	ACA (n=130)	0.777	0.223	0.000	0.888	0.1115	0.06	1.58	0.98 to 2.53
		ATA (n=55)	0.891	0.091	0.018	0.936	0.0636	0.70	0.85	0.38 to 1.93
		Controls (n=373)	0.853	0.147	0.000	0.926	0.0737
	Germany	ACA (n=127)	0.787	0.157	0.055	0.866	0.1339	0.57	1.14	0.73 to 1.76
		ATA (n=92)	0.804	0.196	0.000	0.902	0.0978	0.42	0.80	0.46 to 1.38
		Controls (n=288)	0.774	0.212	0.014	0.880	0.1198
	Netherlands	ACA (n=43)	0.791	0.209	0.000	0.895	0.1047	0.71	1.15	0.55 to 2.44
		ATA (n=47)	0.851	0.149	0.000	0.926	0.0745	0.58	0.79	0.35 to 1.81
		Controls (n=277)	0.819	0.177	0.004	0.908	0.0921
	Italy	ACA (n=161)	0.888	0.106	0.006	0.941	0.0590	0.07	1.73	0.94 to 3.17
		ATA (n=97)	0.907	0.093	0.000	0.954	0.0464	0.46	1.34	0.62 to 2.91
		Controls (n=371)	0.935	0.059	0.005	0.965	0.0350
	Sweden	ACA (n=48)	0.792	0.188	0.021	0.885	0.1146	0.96	0.98	0.50 to 1.94
		ATA (n=31)	0.613	0.355	0.032	0.790	0.2097	0.08^††	2.01	1.04 to 3.91
		Controls (n=279)	0.789	0.190	0.022	0.884	0.1165
	Dieudé et al¹⁹^§	ACA (n=372)	0.812	0.183	0.005	0.903	0.0968	0.62	1.08	0.81 to 1.44
		ATA (n=247)	0.834	0.158	0.008	0.913	0.0870	0.80	0.97	0.69 to 1.37
		Controls (n=1004)	0.828	0.163	0.009	0.909	0.0906
	Gourh et al²⁰^§	ACA (n=188)	0.761	0.229	0.011	0.875	0.1250	0.04^††	1.60	1.08 to 2.35
		ATA (n=107)	0.710	0.271	0.019	0.846	0.1542	0.005^††	2.05	1.32 to 3.19
		Controls (n=430)	0.844	0.147	0.009	0.917	0.0826
	Pooled^¶^**	ACA (n=1376)	0.815	0.174	0.011	0.902	0.0981	0.02^††	1.22	1.05 to 1.42
		ATA (n=834)	0.824	0.168	0.008	0.908	0.0923	0.26	1.17	0.89 to 1.55
		Controls (n=4126)	0.847	0.145	0.007	0.920	0.0800

p Value for the minor allele.

^†

Heterogeneity for systemic sclerosis (SSc) patients with anticentromere antibody (ACA)-positive and healthy controls analysis I²=0%, Breslow–Day p=0.61 Q=5.01 p=0.66. The statistical power for this pooled analysis was 69%.

^‡

Heterogeneity for SSc patients with antitopoisomerase antibody (ATA)-positive and healthy controls analysis I²=0.0%, Breslow–Day p=0.89 Q=2.82 p=0.90. The statistical power for this pooled analysis was 42%.

^§

These data were provided by personal communication by the authors, because they did not showed the complete frequencies in the previous work.

^¶

Heterogeneity for SSc patients with ACA-positive and healthy controls analysis I²=0%, Breslow–Day p=0.60 Q=6.36 p=0.61. The statistical power for this pooled analysis was 99%.

^**

Heterogeneity for SSc patients with ATA-positive and healthy controls analysis I²=49.9%, Breslow–Day p=0.04 Q=15.96 p=0.04. The values showed for the ATA-positive status correspond to the random effects model. The statistical power for this pooled analysis was 90%, in this case the values correspond to the random effect model.

^††

False discovery rate correction p value.

SNP, single nucleotide polymorphism.