Identification of Sex-Specific Genetic Polymorphisms Associated with Asthma in Middle-Aged and Older Canadian Adults: An Analysis of CLSA Data

Figures & data

Table 1 Characteristics of the Study Population

Characteristics	Males (n=13,343)	Females (n= 13,279)	p-value*
	(%)	(%)
Asthma
Yes	10.6	14	<0.0001
Age, mean ± SEM	59.1 ± 0.10	60.0 ± 0.10	<0.0001
Lifestyle and Health Behavior
Smoking Status			<0.0001
Current Smoker	10	8.5
Never Smoker	47.6	51.4
Former Smoker	42.4	40.1
Socio-Demographic and Economic Factors
Marital status			<0.0001
Single/never married	8.1	8.2
Married/Living in common law	82.3	70.2
Widowed/Separated/Divorced	9.6	21.6
Urban or Rural Dwelling			0.003
Urban core	86.6	85
Rural/not Urban core	13.4	15
Homeownership			0.0008
Owned	86.7	85
Rented/Others	13.3	15
Total household income			<0.0001
Less than $20,000	3.4	5.6
$20,000 to less than $50,000	15	22.2
$50,000 to less than $100,000	32.5	34.2
$100,000 or more	49.1	38
Total personal income			<0.0001
Less than $20,000	7.8	22.9
$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			<0.0001
Retired completely	29	38
Not retired/partly retired	71	62
Province of recruitment			<0.0001
Prairies	22.2	19.1
British Columbia	28.9	30
Eastern provinceᵃ	5.2	6.2
Ontario	13.5	13.6
Quebec	30.2	31.1
Highest Education Status			<0.0001
No post-secondary Education	7.2	8.4
Non-university post-secondary	31.4	34.8
University post-secondary	61.4	56.8

Notes: *p-values for overall comparison between males and females; ᵃNewfoundland and Labrador, Nova Scotia.

Table 2 49 Signals of the SNP-by-Sex Interactions with p-value Less Than 10⁻⁵ for Asthma

CHR	SNP	A1/A2	MAF	Gene/Nearest Gene	OR (95% CI)	Interaction p-value	Functional Consequence
4	rs7676077	T/C	0.308	SLC34A2	0.73 (0.641, 0.821)	3.84E-07	Intergenic variant
1	rs6701638	G/A	0.493	KIF26B	1.33 (1.188, 1.492)	7.88E-07	Intron variant
2	rs2968822	T/C	0.403	RTN4	1.33 (1.184, 1.489)	1.24E-06	Intron variant
2	rs2968801	G/A	0.297	RTN4	1.35 (1.190, 1.521)	2.14E-06	Intergenic variant
14	rs10467731	G/A	0.014	SLC38A6	0.27 (0.158, 0.473)	3.52E-06	Regulatory region variant
20	rs11699160	C/T	0.353	RPS21	0.76 (0.671, 0.852)	4.40E-06	Intergenic variant
18	rs4800396	C/T	0.169	CTAGE1	0.70 (0.602, 0.817)	4.94E-06	Intergenic variant
18	rs3911730	A/C	0.079	RTTN	0.62 (0.503, 0.766)	8.95E-06	Missense variant
2	rs2006878	A/G	0.271	EML6	1.33 (1.173, 1.510)	9.06E-06	Intron variant
1	rs3737247	G/A	0.384	SMYD3	0.77 (0.687, 0.869)	1.53E-05	Intron varint
1	rs7519461	T/C	0.331	KIF26B	1.30 (1.154, 1.468)	1.84E-05	Intron variant
13	rs117190915	C/T	0.034	LINC00408	0.48 (0.338, 0.669)	1.94E-05	Intron variant
21	rs34026679	A/C	0.041	APP	1.88 (1.405, 2.506)	1.99E-05	Intergenic variant
20	rs79496646	C/T	0.038	KIF16B	1.87 (1.403, 2.504)	2.12E-05	Intergenic variant
7	rs62442915	T/C	0.039	MAD1L1	1.88 (1.406, 2.520)	2.13E-05	Intron variant
6	rs17071077	G/A	0.278	NMBR	0.76 (0.664, 0.860)	2.21E-05	Intergenic variant
5	rs75073573	A/C	0.199	FGF18	0.73 (0.631, 0.845)	2.37E-05	Intron variant
13	rs9525931	G/A	0.245	SERP2	1.33 (1.166, 1.523)	2.50E-05	Intergenic variant
13	rs628778	T/C	0.066	FARP1	0.61 (0.481, 0.767)	2.78E-05	Synonymous variant
19	rs254804	G/T	0.181	PEPD	1.37 (1.180, 1.578)	2.83E-05	Intergenic variant
10	rs72804487	T/C	0.018	BICC1	0.38 (0.238, 0.595)	2.85E-05	Intergenic variant
5	rs61027918	G/A	0.173	TENM2	0.72 (0.622, 0.842)	3.00E-05	Intron variant
3	rs35644024	A/G	0.073	TGFBR2	0.61 (0.487, 0.772)	3.07E-05	Intergenic variant
13	rs74438452	G/T	0.019	DACH1	2.67 (1.680, 4.237)	3.21E-05	Intron variant
16	rs111933452	A/G	0.049	CDH5	1.75 (1.342, 2.272)	3.31E-05	Intergenic variant
8	rs73191549	A/C	0.087	MSRA	1.52 (1.243, 1.848)	3.93E-05	Intron variant
7	rs4718733	G/A	0.317	NA	1.29 (1.141, 1.457)	4.51E-05	Intergenic variant
6	rs1416037	A/G	0.086	HACE1	1.54 (1.250, 1.887)	4.51E-05	Intergenic variant
15	rs16974494	C/G	0.231	SEC11A	1.32 (1.155, 1.509)	4.64E-05	Intron variant
21	rs382583	T/C	0.109	RBM11	0.68 (0.562, 0.818)	5.08E-05	Intron variant
3	rs1488342	T/G	0.368	LOC101927394	0.78 (0.694, 0.881)	5.27E-05	Intron variant
3	rs36213	G/C	0.487	EPHB1	1.26 (1.128, 1.414)	5.43E-05	Intron variant
5	rs6893959	A/G	0.439	CD180	1.26 (1.128, 1.416)	5.63E-05	Intergenic variant
16	rs7200747	C/G	0.396	ZNF598	0.79 (0.700, 0.884)	5.74E-05	Intron variant
20	rs6013213	A/G	0.445	NFATC2	0.79 (0.704, 0.886)	6.06E-05	Intron variant
2	rs10205651	C/T	0.131	NA	0.71 (0.605, 0.841)	6.10E-05	Regulatory region variant
2	rs2864052	A/G	0.239	RTN4	1.31 (1.147, 1.493)	6.11E-05	Intron variant
7	rs59889022	T/C	0.122	LOC100507642	0.69 (0.582, 0.831)	6.53E-05	Intergenic variant
2	rs3821261	C/A	0.075	TGFA	0.64 (0.515, 0.799)	7.35E-05	Intron variant
20	rs117107888	T/C	0.054	RALGAPA2	1.68 (1.300, 2.178)	7.67E-05	Intron variant
16	rs4513116	G/A	0.019	RBFOX1	0.37 (0.226, 0.606)	7.92E-05	Intergenic variant
2	rs1527243	C/T	0.160	TSN	0.73 (0.629, 0.856)	8.18E-05	Intergenic variant
15	rs837132	C/T	0.262	MEIS2	1.29 (1.137, 1.467)	8.30E-05	Intron variant
13	rs7998573	T/C	0.012	SLITRK6	0.29 (0.163, 0.545)	8.38E-05	Intron variant
1	rs868376	T/C	0.279	PBX1	0.77 (0.679, 0.879)	8.56E-05	Intergenic variant
3	rs73877940	T/A	0.033	ARL14	0.49 (0.348, 0.704)	8.92E-05	Regulatory region variant
16	rs72799714	G/T	0.054	NA	0.58 (0.436, 0.759)	9.11E-05	Intergenic variant
6	rs6926101	T/C	0.057	SLC18B1	0.61 (0.477, 0.782)	9.25E-05	Missense variant
20	rs6041383	T/C	0.029	LOC101929486	0.46 (0.314, 0.681)	9.47E-05	Intergenic variant

Notes: SNP-by-Sex Interaction GWAS on Asthma controlling for Age, Sex, smoking status, and top 4 principal components. Genes contain variants or are located within 500kb of variants.

Abbreviations: Chr, Chromosome; SNP, Single Nucleotide Polymorphism; MAF, Minor allele frequency; OR, Odds ratio; A1/A2, Minor/Major allele; NA, No Annotation.

Figure 1 (A) Manhattan plot for the SNP-by-sex interaction GWAS. The X-axis indicates the chromosomal positions of each variant and the Y-axis shows the negative Log p-values. The blue horizontal line indicates the suggestive significance threshold (1x10⁻⁵),and the red horizontal line shows the genome-wide signficance threshold (5x10⁻⁸). (B) Quantile-Quantile plot showing the distribution of observed versus expected p-values. The genomic inflation factor, lambda (λ) = 1.025.

Table 3 Result of Sex Stratified Analysis for Asthma

Chr	Gene /Nearest Gene	SNP (A1/A2) [Functional Consequence]	Male		Female
			OR (95% CI)	p-value	OR (95% CI)	p-value
1	KIF26B	rs6701638 (G/A) [Intron variant]	1.24 (1.11, 1.38)^A	0.0001*	0.91 (0.83, 1.00)^A	0.0503
6	NMBR	rs17071077 (G/A) [Intergenic variant]	0.79 (0.70, 0.91)^A	0.0006*	PM: 1.05 (0.92, 1.19)^D WT: 1	0.5095
19	PEPD	rs254804 (G/T) [Intergenic variant]	1.27 (1.11, 1.45)^A	0.0005*	PM: 0.89 (0.77, 1.03)^D WT: 1	0.1167
20	NFATC2	rs6013213 (A/G) [Intron variant]	0.77 (0.69, 0.86)^A	<0.0001*	PM: 1.04 (0.89, 1.19)^D WT: 1	0.6293
2	RTN4	rs2968822 (T/C) [Intron variant]	1.22 (1.09, 1.36)^A	0.0004*	PM: 0.85 (0.74, 0.97)^D WT: 1	0.0174
2	RTN4	rs2968801 (G/A) [Intergenic variant]	1.12 (0.99, 1.25)^A	0.0587	PM: 0.79 (0.69, 0.91)^D WT: 1	0.0007*
2	RTN4	rs2864052 (A/G) [Intron Variant]	1.09 (0.96, 1.23)^A	0.1843	PM: 0.77 (0.67, 0.89)^D WT: 1	0.0003*
13	SERP2	rs9525931 (G/A) [Intergenic variant]	1.07 (0.95, 1.21)^A	0.2716	0.80 (0.72, 0.89)^A	<0.0001*
3	EPHB1	rs36213 (G/C) [Intron variant]	PM: 1.35 (1.14, 1.60)^R WT: 1	0.0004*	0.84 (0.76, 0.92)^A	0.0003*

Notes: Sex-stratified multivariate survey logistic regression of top interaction single nucleotide polymorphisms for asthma, adjusting for age, smoking status, province of recruitment, marital status, total personal income, retirement status, and first four principal components. *Statistically significant after adjusting for multiple comparisons (0.05/49 =p ≤ 0.001), Functional consequence of each variant is presented in bold. Genes contain variants or are located within 500kb of variants.

Abbreviations: A, Additive; D, Dominant; R, Recessive; PM, Polymorphism; WT, Wild type; Chr, Chromosome; SNP, Single Nucleotide Polymorphism; A1/A2, Minor/Major Allele; OR, Odds ratio; CI, Confidence Interval.

Figure 2 Regional plots for the nine sex-specific SNPs show their respective locations. (A) SNP rs6701638 in KIF26B gene. (B) SNP rs17071077 near NMBR gene. (C) SNP rs254804 near PEPD gene. (D) SNP rs6013213 in NFATC2 gene. (E) SNP rs2968822 in RTN4 gene. (F) SNP rs2968801 near RTN4 gene. (G) SNP rs2864052 in RTN4 gene. (H) SNP rs9525931 near SERP2 gene. (I) SNP rs36213 in EPHB1 gene.

Figure 3 The forest plots show the odds ratio distribution for the sex-specific variants associated with asthma from the sex-stratified analysis. (A) Males. (B) Females. Only significant SNPs after Bonferroni adjustment were plotted. The blue diamonds represent effect sizes (Odds ratio), and the lines extending from the blue diamonds are the 95% confidence intervals.