Association of insertion-deletions polymorphisms with colorectal cancer risk and clinical features

Table 1 Potential biological effects of insertion-deletions polymorphism selected in this study

Gene	dbSNP	Localization1	INDEL	Region	Potential biological effect[84]				Potential impact on carcinogenesis
			lenght		mRNA splicing	mRNA stability	Gene expression	Protein function
ACE	rs4646994	17:63488539	289	Intron	X	X		X	Angiogenesis, proliferation, progression and metastases[85]
CASP8	rs3834129	2:201232809	6	Promoter			X		Apoptosis[86-88]
SGSM3	rs56228771	22:40410092	4	3'-UTR		X	X		Proliferation and apoptosis [83,89-91]
CYP2E1	-	-	96	5'-Flanking			X		Metabolism of endo- and exogenous[92-97]
CYP19A1	rs11575899	15:51227749	3	Intron	X	X		X	Metabolism of endo- and exogenous[92-97]
HLAG	rs371194629	6:29830804	14	3'-UTR		X	X		Immune surveillance[98-102]
IL1A	rs3783553	2:112774138	4	3'-UTR		X	X		Induce chronic inflammation and proliferation[103,104]
IL4	rs79071878	5:132680584	70	Intron	X	X		X	Immune surveillance and proliferation[40,39,43,105,106]
MDM2	rs3730485	12:68807065	40	Promoter			X		Proliferation and apoptosis[107,108]
NFKB1	rs28362491	4:102500998	4	Promoter			X		Differentiation, proliferation and apoptosis [109,110]
TP53	rs17878362	17:7676372	16	Intron	X	X		X	Proliferation, apoptosis, repair, differentiation[111-114]
TP53	rs17880560	17:7668169	6	3'-Flanking		X	X		Proliferation, apoptosis, repair, differentiation[111-114]
TYMS	rs151264360	18:673444	6	3'-UTR		X	X		Differentiation, replication and repair[50,105]
UCP2	-	-	45	3'-UTR		X	X		Tumor aggressiveness and metastasis[56]
UGT1A1	rs8175347	2:233760235	2	3'-UTR		X	X		Metabolism of endo- and exogenous[92-97]
XRCC1	rs3213239	19:43576907	4	5'- Flanking			X		Repair[115-117]

¹According to the single nucleotide polymorphism database (dbSNP); UTR: Untranslated region; INDEL: Insertion-deletions.

Table 2 Participant demographic and clinical characteristics and their stratification by case and control groups

Characteristic	Total, n = 280	Cases, n = 140	Controls, n = 140	P value
Age (yr)	48 (21-93)	59 (23-93)	37 (21-81)	< 0.001
< 45	136 (48.7)	23 (16.5)	113 (80.7)
≥ 45	144 (51.3)	116 (83.5)	27 (19.3)
Gender				< 0.001
Male	172 (61.6)	62 (44.6)	110 (78.6)
Female	108 (38.4)	78 (55.4)	30 (21.4)
Alcohol consumption				< 0.001
No	180 (65.1)	118 (85.5)	62 (44.9)
Yes	96 (34.9)	20 (14.5)	76 (55.1)
Eventually	56 (20.4)	11 (8.0)	45 (32.6)
Frequently	40 (14.5)	9 (6.5)	31 (22.5)
Tobacco consumption				< 0.001
Never	182 (65.4)	68 (48.9)	114 (82.0)
Already	96 (24.6)	71 (48.1)	25 (18.0)
Former	66 (23.8)	55 (39.6)	11 (7.9)
Current	30 (10.8)	16 (11.5)	14 (10.1)

Categorized data are presented by absolute numbers of individuals (percentage) and analyzed by Chi-square test. Continuous data are presented by mean (min-max) and analyzed by Mann-Whitney test.

Table 3 Genetic ancestry distribution between case and control groups

Genetic ancestry (%)	Total, n = 280	Cases, n = 140	Controls, n = 140	OR (95%CI)	P value
European	65.3 ± 15.5	64.2 ± 15.6	66.4 ± 15.3		0.243
95-80	50 (17.9)	21 (15.1)	29 (20.7)	1.0 (Reference)
80-70	70 (25.1)	33 (23.7)	37 (26.4)	1.23 (0.59-2.56)	0.577
70-60	67 (24.0)	38 (27.3)	29 (20.7)	1.81 (0.86-3.80)	0.117
60-50	47 (16.8)	22 (15.8)	25 (17.9)	1.21 (0.54-2.71)	0.634
50-40	26 (9.3)	14 (10.1)	12 (8.6)	1.61 (0.62-4.18)	0.327
40-30	11 (3.9)	6 (4.3)	5 (3.6)	1.66 (0.45-6.16)	0.451
30-20	7 (2.5)	5 (3.6)	2 (1.4)	3.45 (0.61-19.54)	0.161
20-10	1 (0.4)	-	1 (0.7)	-
Amerindian	16.2 ± 10.1	16.0 ± 10.3	16.3 ± 9.9		0.645
02-10	90 (32.3)	45 (32.4)	45 (32.1)	1.0 (Reference)
10-20	113 (40.5)	60 (43.2)	53 (37.9)	1.13 (0.65-1.97)	0.661
20-30	47 (16.8)	18 (12.9)	29 (20.7)	0.62 (0.30-1.27)	0.193
30-40	21 (7.5)	11 (7.9)	10 (7.1)	1.10 (0.42-2.85)	0.844
40-50	7 (2.5)	4 (2.9)	2 (2.1)	2.00 (0.35-11.47)	0.437
50-60	1 (0.4)	1 (0.7)	-	-
African	18.6 ± 12.0	19.8 ± 12.3	17.3 ± 11.7		0.049
02-10	81 (29.0)	36 (25.9)	45 (32.1)	1.0 (Reference)
10-20	89 (31.9)	41 (29.5)	48 (34.3)	1.07 (0.58-1.95)	0.832
20-30	66 (23.7)	38 (27.3)	28 (20.0)	1.70 (0.88-3.27)	0.114
30-40	28 (10.0)	15 (10.8)	13 (9.3)	1.44 (0.61-3.42)	0.405
40-50	8 (2.9)	5 (3.6)	3 (2.1)	2.08 (0.47-9.31)	0.337
50-60	5 (1.8)	3 (2.2)	2 (1.4)	1.87 (0.30-11.83)	0.504
60-70	2 (0.7)	1 (0.7)	1 (0.7)	1.25 (0.07-20.68)	0.876

Categorized data are presented by absolute numbers of individuals (percentage) and analyzed by Chi-square test. Continuous data are presented by mean ± standard variation and analyzed by Mann-Whitney test.

Table 4 Genotype and allele frequency in percentage of patients with colorectal cancer and controls

Gene	dbSNP	Case/control (n = 140/140)
		Genotype frequency				Allele frequency		HWE
		II	ID	DD	P value	I	D	P value
ACE	rs4646994	21.0/14.3	49.3/54.3	29.7/31.4	0.335	45.7/41.4	54.3/58.6	0.161
CASP8	rs3834129	34.5/30.0	46.0/46.4	19.4/23.6	0.605	57.6/53.2	42.4/46.8	0.424
SGSM3	rs56228771	7.2/3.6	30.2/36.4	62.6/60.0	0.274	22.3/21.8	77.7/78.2	0.415
CYP19A1	rs11575899	35.8/37.9	49.6/50.0	14.6/12.1	0.82	60.3/62.9	39.7/37.1	0.402
CYP2E1	-	0.7/0.7	17.3/12.9	82.0/86.4	0.588	9.4/7.1	90.6/92.6	0.716
HLAG	rs371194629	14.7/13.6	43.4/50.0	41.9/36.4	0.538	36.4/38.6	63.6/61.4	0.514
IL1A	rs3783553	46.0/52.1	38.8/37.9	15.1/10.0	0.368	65.5/71.1	34.5/28.9	0.348
IL4	rs79071878	48.9/60.0	40.3/37.1	10.8/2.9	0.017	69.1/78.6	30.9/21.4	0.223
MDM2	rs3730485	50.4/50.7	43.2/37.1	6.5/12.1	0.219	71.9/69.3	28.1/30.7	0.132
NFKB1	rs28362491	38.1/40.7	46.0/42.1	15.8/17.1	0.806	61.2/61.8	38.8/38.2	0.203
TP53	rs17878362	3.6/1.4	27.3/32.1	69.1/66.4	0.383	17.3/17.5	82.7/82.5	0.181
TP53	rs17880560	7.2/7.1	39.6/32.9	53.2/60.0	0.489	27.0/23.6	73.0/76.4	0.297
TYMS	rs151264360	46.0/42.9	43.9/42.1	10.1/15.0	0.459	68.0/63.9	32.0/36.1	0.308
UCP2	-	6.6/9.3	35.3/44.3	58.1/46.4	0.149	24.3/31.4	75.7/68.6	0.745
UGT1A1	rs8175347	11.5/10.8	44.6/46.0	43.9/43.2	0.785	33.8/33.8	66.2/66.2	0.735
XRCC1	rs3213239	41.7/42.9	47.5/45.0	10.8/12.1	0.894	65.5/65.4	34.5/34.6	0.941

Genotype frequencies are presented as the percentage of patients with colorectal cancer/percentage of controls, and analysis by Chi-square test. dbSNP: Register of genetic variation on NCBI database; bp: Base pairs of DNA sequence; HWE: Hardy-Weinberg Equilibrium.

Table 5 The logistic regression analyses between case-control and insertion-deletions polymorphism

Gene	Model	OR (95%CI)	P-value
IL4	Ins/Ins vs Del/Ins + Del/Del	2.26 (1.20-4.31)	0.0110
TYMS	Ins/Ins + Del/Ins vs Del/Del	0.26 (0.08-0.75)	0.0120
UCP2	Del/Del vs Del/Ins + Ins/Ins	0.48 (0.25-0.90)	0.0210

Adjusted by age at diagnosis, gender, alcohol consumption, tobacco consumption and ancestry distribution. The Supplementary Table 2 shows the genotype frequency and all logistic regression.

Table 6 Clinical characteristics of patients with colorectal cancer at diagnosis and follow-up

Characteristics	Cases (n = 140)
Tumor localization
Colon	25 (17.9)
Rectosigmoid	115 (82.1)
Tumor grade
G1, G2	130 (92.9)
G3, G4	10 (7.1)
Depth of invasion
T1, T2	37 (26.6)
T3, T4	89 (64.0)
Tx	13 (9.4)
Lymph node involvement
N0	77 (55.4)
N1, N2	47 (33.8)
Nx	15 (10.8)
Distant metastasis
M0	109 (78.4)
M1	13 (9.4)
Mx	17 (12.2)
AJCC stage
StageI	31 (22.3)
Stage II	43 (30.9)
Stage III	43 (30.9)
Stage IV	15 (10.8)
Unknown	7 (5.1)
Relapse, Yes	48 (34.5)
Death, Yes	18 (12.9)

Categorized data are presented by absolute numbers (percentage) and continuous data are presented as median (min-max). Tumors were classified according to the guidelines of the American Joint Committee on Cancer (AJCC) staging system.

Table 7 The significant insertion-deletions associations with anatomic localization

Gene	Model	OR (95%CI)	P value
CASP8	Ins/Ins vs Del/Ins + Del/Del	0.28 (0.08-0.97)	0.0303
NFKB1	Ins/Ins vs Del/Ins+Del/Del	0.31 (0.10-0.93)	0.0276

Logistic regression adjusted for confounders. The Supplementary Table 3 shows the genotype frequency and all logistic regression.

Table 8 The significant insertion-deletions associations with tumor node metastasis stage risks

Gene	Model	OR (95%CI)	P value
ACE	Del/Del vs Del/Ins + Ins/Ins	2.82 (1.26-6.31)	0.0092
HLAG	Del/Del + Del/Ins vs Ins/Ins	2.74 (1.01-7.42)	0.0416
TP53 06 bp	Del/Del vs Del/Ins + Ins/Ins	2.50 (1.23-5.06)	0.0099

Logistic regression adjusted for confounders. The Supplementary Table 3 shows the genotype frequency and all logistic regression.

Table 9 The significant insertion-deletions associations with relapse risks

Gene	Model	Time of follow-up	OR (95%CI)	P value
ACE	Del/Del vs Del/Ins + Ins/Ins	2 yr	0.32 (0.13-0.77)	0.0113
ACE	Del/Del vs Del/Ins + Ins/Ins	3 yr	0.37 (0.15-0.91)	0.0298
HLAG	Del/Del vs Del/Ins + Ins/Ins	2 yr	2.75 (1.07-7.08)	0.0281
HLAG	Del/Del vs Del/Ins + Ins/Ins	4 yr	2.83 (1.07-7.52)	0.0332
HLAG	Del/Del vs Del/Ins + Ins/Ins	5 yr	3.47 (1.20-9.99)	0.0194
TYMS	Ins/Ins vs Del/Ins + Del/Del	2 yr	3.35 (1.36-8.28)	0.0058
TYMS	Ins/Ins vs Del/Ins + Del/Del	3 yr	3.42 (1.41-8.28)	0.0046
UGT1A1	Del/Del vs Del/Ins + Ins/Ins	4 yr	3.23 (1.27-8.22)	0.0116
UGT1A1	Del/Del vs Del/Ins + Ins/Ins	5 yr	3.50 (1.24-9.84)	0.0145

Logistic regression adjusted for confounders. The Supplementary Table 4 shows the genotype frequency of all insertion-deletions polymorphism.

Table 10 The significant insertion-deletions associations with death risks

Gene	Model	Time of follow-up	OR (95%CI)	P value
SGSM3	Del/Del vs Del/Ins + Ins/Ins	6 yr	3.61 (1.01-12.92)	0.0487
SGSM3	Del/Del vs Del/Ins + Ins/Ins	7 yr	4.60 (1.16-18.23)	0.0260
UGT1A1	Del/Del vs Del/Ins + Ins/Ins	6 yr	5.30 (1.43-19.73)	0.0084
UGT1A1	Del/Del vs Del/Ins + Ins/Ins	7 yr	4.64 (1.19-18.10)	0.0202
UGT1A1	Del/Del vs Del/Ins + Ins/Ins	8 yr	6.50 (1.47-28.80)	0.0091

Logistic regression adjusted for confounders. The Supplementary Table 5 shows the genotype frequency of all insertion-deletions polymorphism.