IL-10 and TNF-α promoter haplotypes are associated with childhood Crohn’s disease location

Table 1 Characteristics of IBD patients

Variables	CD (n = 94)
Boys	44
Girls	50
Age of onset (yr)	11.3 ± 3.7
Location of disease1
Terminal ileum	11
Ileocolonic	56
Colon	8
Upper digestive tract2	19
H-B index	5.0 ± 1.5
ESR (mm/h)	39.0 ± 14
Albumin (g/L)	32.0 ± 7
WBC (× 109/L)	9.3 ± 3.4
HgB (g/L)	110.0 ± 14
MCV (fL)	76.3 ± 7.2
PLT (x 109/L)	468 ± 146
ABS polys (%)	6.1 ± 3
ABS lymphs (%)	2.0 ± 2.1
ALT (IU/L)	13.0 ± 8.9
AST (IU/L)	19.5 ± 7.3

¹Vienna classification (1998);

²Always associated with other location. H-B index: Harvey-Bradshaw index; ESR: Erythrocyte sedimentation rate; WBC: White blood cells; HgB: Haemoglobin; MCV: Mean corpuscular value; PLT: Platelet; ABS polys: Absolute value of neutrophils; ABS lymphs: Absolute value of lymphocytes; ALT: Alanine aminotransferase; AST: Aspartate aminotransferase; IBD: Inflammatory bowel disease; CD: Crohn’s disease.

Table 2 Characteristic of the primers used to genotype the SNP in TNF-α, IL-10 and GR genes

Locus	SNP	Amplimers		ASO probe1
TNF-α		F 5'CTAAGGAATGGAGGGAGGGA3'
		R 5'CTTCTGTCTCGGTTTCTTCT3'
	T-1031C		rs1799964	GAGAAGATGAAGGAA
				GAGAAGACGAAGGAA
	C-863A		rs1800630	GACCCCCCCTTAACG
				GACCCCCACTTAACG
	C-857T		rs1799724	CCCTTAATGAAGACA
				CCCTTAACGAAGACA
	G-308A		rs59729336	GGGCATGGGGACGGG
				GGGCATGAGGACGGG
	G-238A		rs361525	CGGAATCGGAGCAGG
				CGGAATCAGAGCAGG
IL-10		F 5'CACTACTAAGGCTTCTTTGGG3'
		R 5'CTGTAGGAAGCCAGTCTCTG3'
	G-1087A		rs1800896	TTTGGGAGGGGGAAG
				TTTGGGAAGGGGAAG
	C-824T		rs1800871	GTGATGTAACATCTCTGTG
				GTGATGTAATATCTCTGTG
	C-597A		rs1800872	CGCCTGTCCTGTAGG
				CGCCTGTACTGTAGG
GR	R23K	F 5'TGTAGGATTGATATTCACTGATG3'	rs6189	GGAGAGGGGAGATGT
	G > A	R 5'CAAAAGTCTTCGCTGCTTGG3'		GGAGAAGGGAGATGT
	N363S	F 5'TCCATGGTGTGAGTACCTCTGG3'	rs6195	CGGTTCCGAAAGTTG
	A > G	R 5'GACCAGGGAAGTTCAGAGTCC3'		CGGTTCCGAAAATTG

ASO: Allele specific oligonucleotide.

¹Boldface characters indicate the polymorphic position.

Table 3 Allele and genotype distribution of the GR polymorphism n (%)

Position	Controls	CD
R23K G > A
GG	79 (94)	106 (94)
GA	5 (6)	7 (6)
AA	-	-
G	163 (97)	219 (97)
A	5 (3)	7 (3)
N363S A > G
AA	-	-
AG	5 (6)	4 (4)
GG	82 (94)	108 (94)
A	5 (3)	4 (2)
G	169 (97)	220 (98)

Table 4 Distribution of GR haplotypes in patients and control groups (%)

Haplotype1	Controls (n = 174)	CD (n = 226)
GG	94	95
GA	3	2
AG	3	3

¹The SNP positions within a haplotype are the following: R23K G > A, N363S A > G. n: Number of chromosomes.

Table 5 Allele and genotype distribution of the IL-10 polymorphisms n (%)

Position	Controls	CD
-1087 G > A1
GG	19 (20)	24 (22)
GA	42 (45)	50 (45)
AA	33 (35)	37 (33)
A	108 (57)	124 (56)
G	80 (43)	98 (44)
-824 T > C
TT	7 (7)	14 (13)
TC	37 (39)	39 (35)
CC	50 (53)	64 (58)
T	51 (27)	55 (25)
C	137 (73)	167 (75)
-597 A > C
AA	1 (1)	8 (7)
AC	37 (39)	40 (36)
CC	50 (53)	63 (57)
A	51 (27)	56 (25)
C	137 (73)	166 (75)

¹The homozygous GG is significantly associated (P = 0.008) with disease location in the colonic region.

Table 6 IL-10 haplotypes inferred in patients and control groups (% )

Haplotype1	Controls (n = 188)	CD (n = 222)
GCC	43	44
ACC	30	30
ACA	-	0.9
ATC	-	0.45
ATA	27	24

¹The SNP positions within a haplotype are the following: -1082 G > A, -819 C > T, -592 C > A. n: Number of chromosomes.

Table 8 TNF-α haplotypes inferred in patients and control groups (%)

Haplotype1	Controls (n = 202)	CD (n = 228)
H1 TCCGG2	56	48
H2 TCCGA	1	-
H3 TCCAG	12	13
H4 TCTGG	8	7
H5 TACGG	0.5	-
H6 CCCGA	4	5
H7 CACGG3	17	25
H8 CACAG	0.5	-
H9 TATGG	-	1
H10 CCCGG	-	0.9
H11 CATGG	-	0.4

¹SNP positions within a haplotype are the following: -1031 T > C, -863 C > A, -857 C > T, -308 G > A, -238 G > A;

²OR = 0.69, 95% CI: 0.49-0.99;

³OR = 1.64, 95% CI: 1.05-2.56. n: Number of chromosomes.

Table 7 Allele and genotype distribution of the TNF-α polymorphisms n (%)

Position2	Controls	CD
-1031 C > T
CC1	1 (1)	12 (11)
CT	39 (47)	45 (40)
TT	43 (52)	55 (49)
C	41 (25)	69 (31)
T	125 (75)	155 (69)
-863 A > C
AA	4 (5)	10 (10)
AC	22 (28)	32 (32)
CC	52 (67)	58 (58)
A	30 (19)	52 (26)
C	126 (81)	148 (74)
-857 T > C
TT	1 (1)	1 (1)
CT	14 (18)	17 (17)
CC	63 (80)	82 (82)
T	16 (10)	19 (10)
C	140 (90)	181 (90)
-308 A > G
AA	1 (1)	-
AG	27 (29)	29 (26)
GG	66 (70)	83 (74)
A	29 (15)	29 (13)
G	159 (85)	195 (87)
-238 A > G
AA	2 (2)	-
AG	7 (8)	11 (10)
GG	80 (90)	97 (90)
A	11 (6)	11 (5)
G	167 (94)	205 (95)

¹The homozygous -1031 CC is associated with an increased risk of disease (OR = 9.9, 95% CI: 1.3-78, P = 0.008);

²The homozygous -1031 CC is associated (P = 0.02) with the colonic region; the heterozygous -1031 CT is associated with the terminal ileum location (P = 0.03); the homozygous -308 GG (P = 0.008) and -238 GG (P = 0.05) with the upper digestive tract.