Systemic lupus erythematosus and rheumatoid arthritis

Allele Patients 
Controls 
OR 
95% 
CI 
P-value 
Mid-Sweden 
C 
335 (83.3) 
492 (88.5) 
T 
67 (16.7) 
64 (11.5) 
1.54 
1.06-2.22 
0.022 
South Sweden 
C 
197 (84.9) 
324 (86.2) 
T 
35 (15.1) 
52 (13.8) 
1.11 
0.69-1.76 
0.667 
North Sweden 
C 
421 (82.9) 
1012 (87.8) 
T 
87 (17.1) 
140 (12.2) 
1.49 
1.11-1.99 
0.007 
Combined 
C 
953 (83.5) 
1828 (87.7) 
T 
189 (16.5) 
256 (12.3) 
1.42 
1.15-1.73 
0.0007 
Table 13.
Comparison of the frequencies of the 
PTPN22
1858C/T polymorphism in
SLE patients having or not having renal disorder. 
Genotype 
Renal
disorder 
No renal
disorder 
OR 95% 
CI P-value 
South and mid-Sweden
CT+TT 
25 (38.5) 
38 (24.5) 
1.92 
1.03-3.57 
0.037 
CC 
40 (61.5) 
117 (75.5) 
North Sweden 
CT+TT 
31 (38.3) 
40 (24.2) 
1.94 
1.09-3.43 
0.022 
CC 
50 (61.7) 
125 (75.8) 
Combined 
CT+TT 
56 (38.4) 
78 (24.4) 
1.93 
1.26-2.93 
0.002 
CC 
90 (61.6) 
242 (75.6) 
- 47 -

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There was a north to south gradient in allele frequency in Sweden, however, the 
number of patients from southern Sweden was quite small, which could explain 
the relatively high allele frequency of 1858T in the control group. There was an 
increased frequency of renal disorder in patients carrying the risk allele 
compared with patients homozygous for the major allele (Table 13).
It was shown in paper II that the 
PD-1.3A
allele was associated with renal 
disorder as was the case for the 
PTPN22
1858T allele. A combined analysis of 
the two risk alleles was performed in patients with renal disorder (n = 142) and 
compared to those without either allele and to controls. The strongest 
association was between individuals negative for both 
PTPN22
1858T and 
PD-
1.3A
compared with the control group (P = 0.000008) (Table 14). This 
suggested a strong protective effect of the non-risk alleles. The test for 
independence was more significantly associated in the 
PTPN22
positive and 
PDCD1
negative group (P = 0.004) than in the 
PDCD1
positive and 
PTPN22
negative group (P = 0.0710) when patients with renal disorder were compared 
with patients without renal disorder. This suggests that 
PTPN22
1858T confers 
a stronger risk for renal disorder than 
PD-1.3A
and that they may be 
independently associated (Table 14). There was some degree of interaction, 
although weak, and was based on only 9 individuals (P = 0.02) (Table 14). 
Table 14.
PTPN22
1858T and 
PD-1.3A
are independent genetic susceptibility factors in SLE. 
PDCD1 +ve = positive for 
PD-1.3A
; PTPN22 +ve = positive for 
PTPN22
1858T; PDCD1 -ve = 
negative for 
PD-1.3A
; PTPN22 -ve = negative for 
PTPN22
1858T.