Identification of genetic variants in the TNF promoter associated with COPD secondary to tobacco smoking and its severity

Figures & data

Table 1 Demographic and lung function variables

Variables	First stage		Second stage		P-value
	COPD (n=165)	SNC (n=165)	COPD (n=260)	SNC (n=506)
Sex
Male (%)	112 (67.87)	107 (64.84)	181 (69.62)	340 (67.19)	NS
Female (%)	53 (32.12)	58 (35.15)	79 (30.38)	166 (32.80)	NS
Agea	63.96±2.92	60.07±4.63	66.8±3.21	63.5±5.02	NS
Tobacco indexa	55.16±4.8	51.87±1.7	52±4.1	48±2.2	NS
GOLD grades (%)
I	27 (16.36)		44 (16.92)		NS
II	74 (44.84)		104 (41.15)		NS
III	47 (28.48)		71 (27.30)		NS
IV	17 (10.30)		38 (14.61)		NS
Measures of lung functionb,c
FEV1 ref (%)	58.70 (14–129)	97.54 (58–140)	65 (15–78)	95 (83–160)	<0.001
FVC ref (%)	85.06 (31–160)	97.53 (61–140)	81 (18–90)	90 (80–156)	<0.001
FEV1/FVC (%)	51.82 (22–70)	79.88 (71–91)	57 (19–62)	84 (73–108)	<0.001

Notes:

a Mean ± SD;

b Postbronchodilator values;

c minimum and maximum values are shown.

Abbreviations: COPD, chronic obstructive pulmonary disease; SNC, smokers without COPD; NS, Not significant; GOLD, Global Initiative for COPD; FEV₁, forced expiratory volume in 1 second; FVC, forced vital capacity; SD, standard deviation.

Table 2 Frequencies of the TNF alignment assemblies

TNF contig	COPD		SNC		P-value	OR	95% CI
	n=165	CF (%)	n=165	CF (%)
10	57	34.55	21	12.65	5.0E-04	3.64	2.03–6.71
2	22	13.33	23	13.86
1	21	12.73	28	16.87
3	21	12.73	22	13.25
6	18	10.91	28	16.87
Others	26	<10	43	<10

Note: Only those contigs that had a frequency >10% are shown.

Abbreviations: COPD, chronic obstructive pulmonary disease; SNC, smokers without COPD; CF, “contig” frequency; OR, odds ratio; 95% CI, 95% confidence intervals.

Table 3 Contig frequencies in the GOLD stratification

TNF contig	G1		G2		SNC		P-value
	n=101	CF (%)	n=64	CF (%)	n=165	CF (%)
10	36	35.6	19	29.7	21	12.7	1.8E-05a, 4.2E-05b
1	8	7.92	15	23.4	22	13.3	1.0E-02c
2	13	12.9	8	12.5	23	13.9
3	15	14.9	8	12.5	28	16.9
Others	29	<10	14	<10	71	<10

Notes:

a Association between G1 and SNC, OR =3.82, 95% CI =1.99–7.43;

b association between G2 and SNC, OR =2.92, 95% CI =1.35–6.24;

c association between G2 and G1, OR =3.56, 95% CI =1.30–10.33. Only those contigs that had a frequency >10% are shown.

Abbreviations: GOLD, Global Initiative for chronic obstructive pulmonary disease; G1, GOLD I + II; G2, GOLD III + IV; SNC, smokers without COPD; CF, “contig” frequency; OR, odds ratio; CI, confidence intervals.

Table 4 Genotype frequencies of the SNPs identified by sequencing (FS) and allelic discrimination (SS)

SNP	FS				SS				P-value		OR		95% CI
	COPD		SNC		COPD		SNC		FS	SS	FS	SS	FS	SS
	n=165	GF (%)	n=165	GF (%)	n=260	GF (%)	n=506	GF (%)
rs1800629
GG	133	80.60	148	89.70	233	89.6	479	94.74
GA	30	18.18	16	9.70	27	10.4	25	4.84	3.8E−02	6.00E-03	2.07	2.26	1.04–4.25	1.23–4.15
AA	2	1.22	1	0.60	0		2	0.42
rs56036015
GG	142	86.06	157	95.15	230	88.61	482	95.2
GA	23	13.94	8	4.85	30	11.39	24	4.8	8.2E−03	1.10E-03	3.18	2.54	1.32–8.46	1.40–4.61
AA	0		0		0		0
rs4987027
AA	162	98.18	162	98.18	250	96.06	494	97.6
CA	2	1.21	3	1.82	5	1.97	6	1.2
CC	1	0.61	0		5	1.97	6	1.2
rs673
GG	158	95.76	162	98.18	243	93.46	483	95.38
GA	7	4.24	3	1.82	17	6.92	23	4.62
AA	0		0		0		0
rs361525
GG	136	82.42	155	93.94	237	91.24	464	91.79
GA	26	15.76	7	4.24	22	8.37	41	8.01	1.0E−03		4.220		1.71–11.84
AA	3	1.82	3	1.82	1	0.4	1	0.21
rs41297589
TT	145	87.88	147	89.09	247	94.95	494	97.59
TA	17	10.30	18	10.91	13	5.05	12	2.41
AA	3	1.82	0		0		0

Abbreviations: FS, first stage; SS, second stage; COPD, chronic obstructive pulmonary disease; SNC, smokers without COPD; GF, genotype frequency; OR, odds ratio; 95% CI, 95% confidence intervals.

Table 5 Localization of SNP identified

SNP	Chr P	Change	NP
rs1800629	31543031	G/A	−308
rs56036015	31543065	G/A	−274
rs4987027	31543094	G/A	−245
rs673	31543095	G/C	−244
rs361525	31543101	G/A	−238
rs41297589	31543262	T/A	−77

Abbreviations: SNP, single nucleotide polymorphisms; Chr P, chromosome position; NP, nucleotide position.

Table S1 Sequence of contigs identified

Contig	Sequence
1	GAAATGGAGGCAATAGGTTTTGAGGGGCATGAGGACGGGGTTCAGCCTCCAGGGTCCTACACACAAATCAGTCAGTGGCCCAGAAGACCCCCCTCGGAATCGGAGCAGGGAGGATGGGGAGTGTGAGGGGTATCCTTGATGCTTGTGTGTCCCCAACTTTCCAAATCCCCGCCCCCGCGATGGAGAAGAAACCGAGACAGAAGGTGCAGGGCCCACTACCGCTTCCTCCAGATGAGCTCATGGGTTTCTCCACCAAGGAAGTTTTCCGCTGGTTGAATGATTCTTTCCCCGCCCTCCTCTCGCCCCAGGGACATATAAAGGCAGTTGTTGGCACACCCAGCCAGCAGACG
2	GAAATGGAGGCAATAGGTTTTTGAGGGCATGGGGACGGGGTTCAGCCTCCAGGGTCCTACACACAATCAGTCAGTGGCCCAGAAGACCCCCCTCGCAATCGGAGCAGGGAGGATGGGGAGTGTGAGGGGTATCCTTGATGCTTGTGTGTCCCCAACTTTCCAAATCCCCGCCCCCGCGATGGAGAAGAAACCGAGACAGAAGGTGCAGGGCCCACTACCGCTTCCTCCAGATGAGCTCATGGGTTTCTCCACCAAGGAAGTTTTCCGCTGGTTGAATGATTCTTTCCCCCCCTCCTCTCGCCCCAGGGACATATAAAGGCAGTTGTTGGCACACCCAGCCAGCAGACG
3	GAAATGGAGGCAATAGGTTTTGAGGGGCATGGGGACGGGGTTCAGCCTCCAGGGTCCTACACACAAATCAGTCAGTGGCCCAGAAGACCCCCCTCAGAATCGGAGCAGGGAGGATGGGGAGTGTGAGGGGTATCCTTGATGCTTGTGTGTCCCCAACTTTCCAAATCCCCGCCCCCGCGATGGAGAAGAAACCGAGACAGAAGGTGCAGGGCCCACTACCGCTTCCTCCAGATGAGCTCATGGGTTTCTCCACCAAGGAAGTTTTCCGCTGGTTGAATGATTCTTTCCCCGCCCTCCTCTCGCCCCAGGGACATATAAAGGCAGTTGTTGGCACACCCAGCCAGCAGACG
4	GAAATGGAGGCAATAGGTTTTGAGGGGCATGGGGACGGGGTTCAGCCTCCAGGGTCCTACACACAAATCAGTCAGTGGCCCAGAAGACCCCCCTCGGAATCGGAGCAGGGAGGATGGGGAGTGTGAGGGGTATCCTTGATGCTTGTGTGTCCCCAACTTTCCAAATCCCCGCCCCCGCGATGGAGAAGAAACCGAGACAGAAGGTGCAGGGCCCACTACCGCTTCCTCCAGATGAGCTCATGGGTTTCTCCACCAAGGAAGTTTACCGCTGGTTGAATGATTCTTTCCCCGCCCTCCTCTCGCCCCAGGGACATATAAAGGCAGTTGTTGGCACACCCAGCCAGCAGACG
5	GAAATGGAGGCAATAGGTTTTTGAGGGCATGGGGACGGGGTTCAGCCTCCAGGGTCCTACACACAGAACAGTCAGTGGCCCAGAAGACCCCCCTCGCAATCGGAGCAGGGAGGATGGGGAGTGTGAGGGGTATCCTTGATGCTTGTGTGTCCCCAACTTTCCAAATCCCCGCCCCCGCGATGGAGAAGAAACCGAGACAGAAGGTGCAGGGCCCACTACCGCTTCCTCCAGATGAGCTCATGGGTTTCTCCACCAAGGAAGTTTTCCGCTGGTTGAATGATTCTTTCCCCCCCTCCTCTCGCCCCAGGGACATATAAAGGCAGTTGTTGGCACACCCAGCCAGCAGACG
6	GAAATGGAGGCAATAGGTTTTGAGGGGCATGGGGACGGGGTTCAGCCTCCAGGGTCCTACACACAAATCAGTCAGTGGCCCAGAAGACCCCCCTCGGAATCGGAGCAGGGAGGATGGGGAGTGTGAGGGGTATCCTTGATGCTTGTGTGTCCCCAACTTTCCAAATCCCCGCCCCCGCGATGGAGAAGAAACCGAGACAGAAGGTGCAGGGCCCACTACCGCTTCCTCCAGATGAGCTCATGGGTTTCTCCACCAAGGAAGTTTTCCGCTGGTTGAATGATTCTTTCCCCGCCCTCCTCTCGCCCCAGGGACATATAAAGGCAGTTGTTGGCACACCCAGCCAGCAGACG
7	GAAATGGAGGCAATAGGTTTTGAGGGGCATGGGGACGGGGTTCAGCCTCCAGGGTCCTACACACAAATCAGTCAGTGGCCCAGAAGACCCCCCTCGGAATCGGAGCAGGGAGGATGGGGAGTGTGAGGGGTATCCTTGATGCTTGTGTGTCCCCAACTTTCCAAATCCCCGCCCCCGCGATGGAGAAGAAACCGAGACAGAAGGTGCAGGGCCCACTACCGCTTCCTCCAGATGAGCTCATGGGTTTCTCCACCAAGGAAGTTTTCCGCTGGTTGAATGATTCTTTCCCCGCCCTCCTCTCGCCCCAGGGACATATAAAGGCAGTTGTTGGCACACCCAGCCAGCAGACG
8	GAAATGGAGGCAATAGGTTTTGAGGGGCATGAGGACGGGGTTCAGCCTCCAGGGTCCTACACACAAATCAGTCAGTGGCCCAGAAGACCCCCCTCGAAATCGGAGCAGGGAGGATGGGGAGTGTGAGGGGTATCCTTGATGCTTGTGTGTCCCCAACTTTCCAAATCCCCGCCCCCGCGATGGAGAAGAAACCGAGACAGAAGGTGCAGGGCCCACTACCGCTTCCTCCAGATGAGCTCATGGGTTTCTCCACCAAGGAAGTTTTCCGCTGGTTGAATGATTCTTTCCCCGCCCTCCTCTCGCCCCAGGGACATATAAAGGCAGTTGTTGGCACACCCAGCCAGCAGACG
9	GAAATGGAGGCAATAGGTTTTGAGGGGCATGGGGACGGGGTTCAGCCTCCAGGGTCCTACACACAAATCAGTCAGTGGCCCAGAAGACCCCCCTCGGAATCGAAGCAGGGAGGATGGGGAGTGTGAGGGGTATCCTTGATGCTTGTGTGTCCCCAACTTTCCAAATCCCCGCCCCCGCGATGGAGAAGAAACCGAGACAGAAGGTGCAGGGCCCACTACCGCTTCCTCCAGATGAGCTCATGGGTTTCTCCACCAAGGAAGTTTTCCGCTGGTTGAATGATTCTTTCCCCGCCCTCCTCTCGCCCCAGGGACATATAAAGGCAGTTGTTGGCACACCCAGCCAGCAGACG
10	GAAATGGAGGCAATAGGTTTTGAGGGGCATGGGGACGGGGTTCAGCCTCCAGGGTCCTACACACAGATCAGTCAGTGGCCCAGAAGACCCCCCTCGCAATCGGAGCAGGGAGGATGGGGAGTGTGAGGGGTATCCTTGATGCTTGTGTGTCCCCAACTTTCCAAATCCCCGCCCCCGCGATGGAGAAGAAACCGAGACAGAAGGTGCAGGGCCCACTACCGCTTCCTCCAGATGAGCTCATGGGTTTCTCCACCAAGGAAGTTTTCCGCTGGTTGAATGATTCTTTCCCCGCCCTCCTCTCGCCCCAGGGACATATAAAGGCAGTTGTTGGCACACCCAGCCAGCAGACG
11	GAAATGGAGGCAATAGGTTTTGAGGGGCATGAGACGGGGTTCAGCCTCCAGGGTCCTACACACAAATCAGTCAGTGGCCCAGAAGACCCCCCTCACAATCGGAGCAGGGAGGATGGGGAGTGTGAGGGGTATCCTTGATGCTTGTGTGTCCCCAACTTTCCAAATCCCCGCCCCCGCGATGGAGAAGAAACCGAGACAGAAGGTGCAGGGCCCACTACCGCTTCCTCCAGATGAGCTCATGGGTTTCTCCACCAAGGAAGTTTTCCGCTGGTTGAATGATTCTTTCCCCGCCCTCCTCTCGCCCCAGGGACATATAAAGGCAGTTGTTGGCACACCCAGCCAGCAGACG

Notes: Reference Sequence: NC_000006.12 >gi|224589818:31543000-31543350 Homo sapiens chromosome 6, GRCh37.p5 Primary Assembly, NCBI Reference Sequence: NC_000006.12 GAAATGGAGGCAATAGTTTTGAGGGGCATGGGGACGGGGTTCAGCCTCCAGGGTCCTACACACAAATCAGTCAGTGGCCCAGAAGACCCCCCTCGGAATCGGAGCAGGGAGGATGGGGAGTGTGAGGGGTATCCTTGATGCTTGTGTGTCCCCAACTTTCCAAATCCCCGCCCCCGCGATGGAGAAGAAACCGAGACAGAAGGTGCAGGGCCCACTACCGCTTCCTCCAGATGAGCTCATGGGTTTCTCCACCAAGGAAGTTTTCCGCTGGTTGAATGATTCTTTCCCCGCCCTCCTCTCGCCCCAGGGACATATAAAGGCAGTTGTTGGCACACCCAGCCAGCAGACG.