NOD2, IL23R and ATG16L1 polymorphisms in Lithuanian patients with inflammatory bowel disease

Table 1 Summary of clinical and demographic characteristics of the IBD patients n (%)

Characteristics	CD	UC
Gender (male/female)	27/30	68/55
Age (years ± SD)	40.5 ± 14.9	45.4 ± 16.4
Age at diagnosis (years ± SD)	31.7 ± 16.6	34.3 ± 14.7
Familial IBD	0	0
Surgery treatment	15 (26.3)	3 (2.4)
Disease extension in UC
Proctitis	-	26 (21.1)
Left-sided colitis	-	61 (49.5)
Extended colitis	-	36 (29.3)
Disease localization in CD
Terminal ileum, L1	17 (29.8)	-
Colon, L2	16 (28.1)	-
Ileocolon, L3	23 (40.3)	-
Upper GI, L4	1 (1.8)	-
Disease Behavior in CD
Non-stricturing, non-penetrating, B1	41 (71.9)	-
Stricturing, B2	5 (8.8)	-
Penetrating, B3	11 (19.3)	-
Perianal disease, B4	-	-
Extraintestinal manifestations
Joints	6 (10.5)	13 (10.6)
Cutaneus	3 (5.3)	4 (3.3)
Ocular	1 (1.8)	0
Hepatobiliary	0	2 (1.6)

IBD: Inflammatory bowel diseases; CD: Crohn’s disease; UC: Ulcerative colitis.

Table 2 TaqMan^® primer and probe sequences of NOD2 and IL23R assays

Marker	Primers	Probes
NOD2
rs2066844	5'-TTCCTGGCAGGGCTGTTGTC	TET-CCTGCTCTGGCGCCAGGCC
	5'-AGTGGAAGTGCTTGCGGAGG	FAM-CCTGCTCCGGCGCCAGGC
rs2066845	5'-ACTCACTGACACTGTCTGTTGACTCT	TET-TTCAGATTCTGGCGCAACAGAGTGGGT
	5'-AGCCACCTCAAGCTCTGGTG	FAM-TTTTCAGATTCTGGGGCAACAGAGTGGGT
rs2066847	5'-CCAGGTTGTCCAATAACTGCATC	VIC-TGCAGGCCCCTTG
	5'-CCTTACCAGACTTCCAGGATGGT	FAM-CTGCAGGCCCTTG
IL23R
rs11209026	5'-CGTCTTTGCTGTTATGTTGTCAATTCTT	VIC-CAGATCATTCCAAACTG
	5'-AGAAAACAGAAATTCTGCAAAAACCTACC	FAM-ACAGATCATTCCGAACTG

The examined alleles are highlighted by bold underlined typing.

Table 3 Association statistics for the NOD2, ATG16L1 and IL23R variants in the Lithuanian IBD population

Gene marker	Minor allele	Controls (n = 186)			CD (n = 56)				UC (n = 123)
		GT (11/12/22)	MAF	PHWE	GT (11/12/22)	MAF	PCCA	OR (95% CI)	GT (11/12/22)	MAF	PCCA	OR (95% CI)
NOD2
rs2066844	T	0/9/171	0.025	> 0.99	0/2/54	0.018	> 0.99	0.71 (0.15-3.33)	0/10/113	0.041	0.278	1.65 (0.66-4.13)
rs2066845	C	1/7/169	0.025	0.099	0/3/53	0.027	> 0.99	1.06 (0.28-3.97)	0/1/121	0.004	0.055	0.16 (0.02-1.25)
rs2066847	insC	2/13/166	0.047	0.048	4/16/36	0.214	3.687 × 10-8a	5.54 (2.85-10.75)	1/8/114	0.041	0.711	0.86 (0.39-1.91)
ATG16L1
rs2241880	G	44/89/53	0.476	0.560	16/28/11	0.546	0.199	1.32 (0.86-2.03)	33/61/25	0.534	0.164	1.26 (0.91-1.75)
IL23R
rs11209026	A	3/16/167	0.059	0.017	0/4/52	0.036	0.335	0.59 (0.20-1.75)	0/11/109	0.045	0.477	0.76 (0.36-1.61)

Minor allele frequencies (MAF), genotype counts (GT; 11 = homozygous for minor allele; 12 = heterozygous for common allele; 22 = homozygote for common allele), allelic test P values (^aP_CCA < 0.05), and odds ratios (OR, shown for the minor allele) with 95% confidence intervals (CI) are depicted for both the CD and UC case-control population.