Sex-Specific Genetic Determinants of Asthma-COPD Phenotype and COPD in Middle-Aged and Older Canadian Adults: An Analysis of CLSA Data

Figures & data

Figure 1. Study flow charts. (A) Workflow for the genome-wide SNP-by-sex interaction and sex-stratified analysis. (B) Flow chart for sample and marker quality control.

Table 1. Descriptive characteristics of the study population.

Variables	Groups	Males (n = 13,343)	Females (n = 13,279)	p-value
Asthma + COPD, N(%)	Yes	218 (1.4)	327 (2.3)	<0.0001
COPD, N(%)	Yes	451 (2.6)	508 (3.0)	<0.0001
Age, mean ± SEM		59.1 ± 0.1	59.9 ± 0.1	<0.0001
Age group (%)	45 to 54	44.3	39.7	<0.0001
	55 to 64	29.8	30.2
	65 to 74	15.8	18.3
	75 and above	10.2	11.7
Smoking Status (%)	Current Smoker	10.0	8.5	<0.0001
	Never Smoker	47.6	51.4
	Former Smoker	42.4	40.1
Marital status (%)	Single/never married	8.1	8.2	<0.0001
	Married/Living in common law	82.3	70.1
	Widowed/Separated/Divorced	9.6	21.6
Urban or Rural Dwelling (%)	Urban core	86.6	85.0	0.0028
	Rural/not Urban core	13.4	15.0
Homeownership (%)	Owned	86.6	84.9	0.0029
	Rented/Others	13.2	15.0
Total household income (%)	Less than $20,000	3.4	5.6	<0.0001
	$20,000 to less than $50,000	15.1	22.2
	$50,000 to less than $100,000	32.5	34.2
	$100,000 or more	49.1	38.0
Total personal income (%)	Less than $20,000	7.8	22.9	<0.0001
	$20,000 to less than $50,000	27.9	39.9
	$50,000 to less than $100,000	40.7	28.9
	$100,000 or more	23.6	8.2
Retirement Status (%)	Retired completely	29.0	38.0	<0.0001
	Not retired/partly retired	71.0	62.0
Province of recruitment (%)	Prairies	22.2	19.1	<0.0001
	British Columbia	28.9	30.0
	Eastern province^a	5.2	6.2
	Ontario	13.5	13.6
	Quebec	30.2	31.1
Highest Education Status (%)	No post-secondary Education	7.4	8.4	<0.0001
	Non-university post-secondary	31.4	34.8
	University post-secondary	61.4	56.8

Number of participants in the unweighted sample: 26622 (13,343 males and 13,279 females).

represent 3,295,958 participants (1,670,060 males and 1,625,898 females) in the weighted sample.

451 males and 508 Females with COPD in the unweighted sample represent 43722 males and 48348 females in the weighted sample.

218 males and 327 Females with asthma + COPD in the unweighted sample represent 24068 males and 38085 females in the weighted sample.

^a: Newfoundland and Labrador, Nova Scotia; COPD: chronic obstructive pulmonary disease; Asthma + COPD: Asthma-COPD phenotype; SEM: standard error of the mean.

Figure 2. Quantile-Quantile plots (Q-Q plot) showing the distribution of observed versus Expected pvalue. (A) Q-Q plot for the genome-wide SNP-by-sex interaction for asthma-COPD phenotype. Genomic inflation factor, lambda (λ) = 1.00. (B) Q-Q plot for the genome-wide SNP-by-sex interaction for COPD. Genomic inflation factor, lambda (λ) = 1.00.

Table 2. 18 Signals of the SNP-by-Sex Interactions with pvalue less than 10^¯5 for asthma-COPD phenotype.

Chr	SNP	Effect Allele	MAF	Major Allele	OR	Interaction P value	Gene/Nearest Gene	Consequence
1	rs619928	A	0.387	G	0.57	5.74E-05	SPSB1	Intron variant
1	rs6666629	T	0.061	C	2.77	8.47E-05	HSD52	Intron variant
1	rs12062324	G	0.059	A	2.99	8.93E-05	RPS6KC1	Intergenic variant
1	rs61140467*	A	0.285	G	1.76	9.78E-05	SMYD3	Intron variant
1	rs11799559*	A	0.458	G	1.68	8.55E-05	SMYD3	Intron variant
2	rs77602394	G	0.064	A	2.96	3.99E-05	RAD51AP2	Intergenic variant
3	rs3821479	C	0.430	T	0.57	4.51E-05	FHIT	Intron variant
4	rs72901492	A	0.107	C	0.40	3.83E-05	NDST4	Intergenic variant
5	rs77800494	T	0.043	G	3.84	6.73E-05	ZNF608	Intergenic variant
7	rs7782108	C	0.190	T	0.48	8.00E-05	CARD11	Intron variant
7	rs34331963	C	0.159	T	2.05	4.52E-05	SDK1	Intergenic variant
8	rs6986253	A	0.254	G	1.81	9.60E-05	LRP12	Intron variant
12	rs11061082	A	0.399	G	1.71	6.16E-05	RIMBP2	Intergenic variant
14	rs2582577	T	0.199	C	1.88	7.47E-05	C14orf79	Intergenic variant
20	rs926718	A	0.374	G	0.55	2.18E-05	ZNF133	Intron variant
20	rs1884882	C	0.282	T	1.82	2.66E-05	BPIFB1	Intergenic variant
20	rs6013630	T	0.122	C	2.34	4.26E-05	TSHZ2	Intron variant
21	rs1051169	C	0.329	G	1.72	9.53E-05	S100B	Synonymous variant

SNP-by-Sex Interaction GWAS on asthma-COPD phenotype, controlling for age, sex, smoking status, and top 4 principal components.

*: SNP rs11799559 was in high linkage disequilibrium (D’=0.99) with rs61140467.

Chr: chromosome; SNP: single nucleotide polymorphism; MAF: minor allele frequency; OR: odds ratio.

Genes contain variant or are located within 500 kb from variants.

Table 3. 28 Signals of the SNP-by-Sex Interactions with pvalue less than 10⁻⁵ for COPD.

Chr	SNP	Effect Allele	MAF	Major Allele	OR	Interaction P value	Gene/Nearest Gene	Consequence
1	rs12025895	C	0.44	T	1.48	6.74E-05	CAMTA1	Intron variant
1	rs6429144	T	0.24	C	1.63	3.17E-05	CHRM3	Intron variant
2	rs10931835	C	0.43	T	1.52	3.01E-05	SATB2	Intergenic variant
2	rs7557339	T	0.39	C	0.65	1.85E-05	SLC19A3	Intergenic variant
3	rs13326145	T	0.05	C	0.32	3.86E-05	MAGI1	Intron variant
3	rs12633737	A	0.31	G	1.57	2.00E-05	ALCAM	Intergenic variant
4	rs56334611	G	0.27	A	0.63	3.69E-05	COX18	Intergenic variant
4	rs6816344	T	0.28	A	0.62	1.65E-05	COX18	Intergenic variant
4	rs73838466^a	T	0.15	C	1.86	9.35E-06	OSTC	Intron variant
4	rs17039240^a	T	0.26	C	1.57	5.84E-05	OSTC	Intergenic variant
4	rs11947441	C	0.03	T	0.19	9.65E-05	FRG1	Intergenic variant
5	rs76189059	A	0.06	G	0.38	8.89E-05	NA	Intergenic variant
6	rs6935314	C	0.33	T	0.64	3.93E-05	ELOVL5	Intergenic variant
6	rs117896837	T	0.02	C	4.80	9.10E-05	FAM46A	Intergenic variant
6	rs220806	T	0.31	C	1.58	2.78E-05	PDE10A	Intron variant
7	rs59794319	G	0.08	A	0.48	9.09E-05	NXPH1	Intergenic variant
7	rs10488084	C	0.08	A	0.48	9.95E-05	PLEKHA8	Intron variant
7	rs1911770	T	0.43	C	1.51	4.81E-05	ZPBP	Intron variant
7	rs13225543	T	0.41	C	0.67	5.48E-05	C7orf72	Intergenic variant
8	rs112593560	T	0.03	C	3.69	8.14E-05	KCNQ3	Intron variant
9	rs4076140	G	0.08	A	2.18	3.39E-05	TRPM3	Intron variant
9	rs74964803	G	0.05	T	0.39	7.95E-05	MED27	Intergenic variant
13	rs66468120	A	0.05	G	2.64	5.02E-05	RNF219-AS1	Intron variant
13	rs12869252	G	0.24	A	0.64	9.73E-05	FGF14	Intron variant
14	rs12879329	G	0.07	A	2.24	3.85E-05	NPAS3	Intron variant
18	rs77625370	T	0.05	C	2.75	7.03E-05	LINC00908	Intergenic variant
20	rs1891778	G	0.48	A	1.52	2.60E-05	CDH4	Intron variant
20	rs6090327	C	0.17	T	0.59	8.39E-05	NKAIN4	3 prime UTR variant

SNP-by-Sex Interaction GWAS on COPD, controlling for age, sex, smoking status, and top 4 principal components.

^aSNP rs17039240 was in high linkage disequilibrium (D’=0.99) with rs73838466,.

Chr: Chromosome; SNP: Single Nucleotide Polymorphism; MAF: Minor allele frequency; OR: Odds ratio NA: No annotation.

Genes contain variants or are located within 500 kb from variants.

Table 4. Result of sex-stratified analysis for asthma-COPD phenotype.

Chr	Gene/Nearest Gene	SNP (A1/A2)	Male		Female
			OR (95% CI)	p-value	OR (95% CI)	p-value
1	SMYD3	rs11799559 (A/G)^a	1.56 (1.18 − 2.07)zz^A	0.0021*	PM: 0.69 (0.50 − 0.94)^DWT: 1	0.0185
3	FHIT	rs3821479 (C/T)	0.55 (0.41 − 0.73)^A	<0.0001*	PM: 0.79 (0.57 − 1.08)^DWT: 1	0.141
5	ZNF608	rs77800494 (T/G)	2.08 (1.30 − 3.34)^A	0.0025*	0.42 (0.20 − 0.86)^A	0.0178
12	RIMBP2	rs11061082 (A/G)	PM: 2.15 (1.37 − 3.37)^RWT: 1	0.0009*	PM: 0.75 (0.48 − 1.16)^RWT: 1	0.199
20	ZNF133	rs926718 (A/G)	0.58 (0.43 − 0.79)^A	0.0005*	1.32 (1.07 − 1.64)^A	0.0101
20	BPIFB1	rs1884882 (C/T)	PM: 2.24 (1.32 − 3.81)^RWT: 1	0.0029*	0.93 (0.73 − 1.20)^A	0.5823
21	S100B	rs1051169 (C/G)	1.56 (1.18 − 2.06)^A	0.0019*	PM: 0.74 (0.55 − 1.01)^DWT: 1	0.0562

Sex-stratified multivariate logistic regression of top interaction single nucleotide polymorphisms for asthma-COPD phenotype, adjusting for age, smoking status, marital status, homeownership, total household income, education level, retirement status, and first four principal components.

^aSNP rs11799559 was in high linkage disequilibrium (D’=0.99) with rs61140467; hence rs61140467 was removed from sex-stratified analysis due to lower polymorphic information content (PIC).

*: statistically significant after adjusting for multiple comparisons (p ≤ 0.003).

^A: Additive; ^D: Dominant; ^R: Recessive; PM: Polymorphism; WT: wild type; Chr: chromosome.

SNP: single nucleotide polymorphism; A1/A2: minor allele/major allele; OR: odds ratio; CI: confidence interval.

Genes contain variants or are located within 500 kb from variants.

Figure 3. Forest plot showing the direction of effects of the male-specific SNPs associated with asthma-COPD phenotype from the sex-stratified analysis.

Table 5. Result of sex-stratified analysis for COPD.

Chr	Gene/Nearest Gene	SNP (A1/A2)	Male		Female
			OR (95% CI)	p-value	OR (95% CI)	p-value
1	CAMTA1	rs12025895 (C/T	PM: 1.29 (0.99 − 1.68)^D WT: 1	0.0622	0.72 (0.61 − 0.84)^A	<0.0001*
2	SATB2	rs10931835 (C/T)	PM: 1.20 (0.92 − 1.57)^D WT: 1	0.1761	PM: 0.64 (0.50 − 0.81)^D WT: 1	0.0002*
3	MAGI1	rs13326145 (T/C)	0.38 (0.22 − 0.65)^A	0.0005*	PM: 0.61 (0.08 − 4.58)^R WT: 1	0.6267
4	COX18	rs56334611 (G/A)	0.69 (0.57 − 0.84)^A	0.0002*	PM: 1.37 (1.09 − 1.73)^D WT: 1	0.0073
4	COX18	rs6816344 (T/A)	0.71 (0.58 − 0.85)^A	0.0003*	1.26 (1.04 − 1.52)^A	0.0176
4	OSTC	rs17039240 (T/C)^a	PM: 2.48 (1.62 − 3.79)^R WT: 1	<0.0001*	0.83 (0.69 − 1.01)^A	0.0571
6	ELOVL5	rs6935314 (C/T)	0.74 (0.61 − 0.89)^A	0.0017*	PM: 1.30 (1.03 − 1.65)^D WT: 1	0.0276
6	PDE10A	rs220806 (T/C)	PM: 1.19 (0.93 − 1.51)^D WT: 1	0.1624	0.70 (0.58 − 0.84)^A	0.0001*
7	ZPBP	rs1911770 (T/C)^b	PM: 1.64 (1.24 − 2.16)^R WT: 1	0.0005*	0.76 (0.64 − 0.91)^A	0.002*
7	C7orf72	rs13225543 (T/C)	PM: 0.65 (0.51 − 0.83)^D WT: 1	0.0005*	PM: 1.36 (1.05 − 1.77)^D WT: 1	0.0196
13	FGF14	rs12869252 (G/A)	PM: 0.68 (0.53 − 0.87)^D WT: 1	0.002*	1.24 (0.99 − 1.56)^A	0.0194
18	LINC00908	rs77625370 (T/C)	1.61 (1.12 − 2.30)^A	0.0094	0.45 (0.28 − 0.74)^A	0.0014*
20	NKAIN4	rs6090327 (C/T)	0.65 (0.51 − 0.84)^A	0.001*	1.38 (1.11 − 1.71)^A	0.0038

Sex-stratified multivariate survey logistic regression of top interaction single nucleotide polymorphisms for COPD, adjusting for age, smoking status, province of recruitment, marital status, homeownership, total personal income, retirement status, and first four principal components.

^a: SNP rs17039240 was in high linkage disequilibrium (D’=0.99) with rs73838466; hence rs73838466 was removed from sex-stratified analysis due to lower polymorphic information content (PIC).

*:statistically significant after adjusting for multiple comparisons (p ≤ 0.002).

^bsignificant in both males and females.

^A: additive; ^D: dominant; ^R: recessive; PM: polymorphism; WT: wild type; Chr: chromosome; SNP: single nucleotide polymorphism; A1/A2: minor allele/major allele; OR: odds ratio; CI: confidence interval.

Genes contain variants or are located within 500 kb from variants.

Figure 4. Forest plots showing the direction of effects for the sex-specific SNPs associated with COPD from the sex-stratified analysis. (A) Males. (B) Females. Only significant SNPs after the Bonferroni adjustment were plotted.

Figure 5. Regional plots for the 7 male-specific SNPs associated with asthma-COPD phenotype showing their respective genomic locations. (A) rs11799559 in SMYD3 gene. (B) rs3821479 in FHIT gene. (C) rs77800494 near ZNF608 gene. (D) rs11061082 near RIMBP2 gene. (E) rs926718 in ZNF133 gene. (F) rs1884882 near BPIFB1 gene. (G) rs1051169 in S100B gene.

Figure 6. Regional plots for the sex-specific SNPs associated with COPD showing their respective genomic locations (A) rs12025895 in CAMTA1 gene. (B) rs10931835 near SATB2 gene. (C) rs13326145 in MAGI1 gene. (D) rs56334611 near COX18 gene. (E) rs6816344 near COX18 gene. (F) rs17039240 near OSTC gene. (G) rs6935314 near ELOVL5 gene. (H) rs220806 in PDE10A gene. (I) rs1911770 in ZPBP gene. (J) rs13225543 near C7orf72 gene. (K) rs12869252 in FGF14 gene. (L) rs77625370 near LINC00908 gene. (M) rs6090327 in NKAIN4 gene.

Data availability statement

The datasets used in this study are not readily available. Data are only available from the Canadian Longitudinal Study on Aging (www.clsa-elcv.ca) for researchers who meet the criteria for access to de-identified CLSA data.