Smoking and blood DNA methylation: an epigenome-wide association study and assessment of reversibility

Figures & data

Table 1. Characteristics of study participants from the Melbourne Collaborative Cohort Study (MCCS) at baseline (1990–1994) and follow-up (2003–2007).

	Cross-sectional analysis (N = 5,044)	Longitudinal analysis (N = 1,024)
	Baseline data	Baseline data	Wave 2 data
Age in years, median, interquartile range [IQR]	60.7 [53.9–65.4]	58.5 [51.1–64.1]	69.8 [62.7–75.5]
Sex, male	3,408 (68%)		701 (68%)
Country of birth
AU/NZ/Other	3,411 (68%)		799 (78%)
Greece	382 (8%)		36 (4%)
Italy	714 (14%)		75 (7%)
UK	537 (11%)		114 (11%)
BMI (kg/m^2), median [range]	26.9 [24.5–29.5]	26.3 [24.1–29.0]	26.7 [24.2–29.3]
Alcohol intake^a (g/day), median [IQR]	4.3 [0.0–18.7]	7.1 [0.0–19.0]	8.8 [0.0–22.5]
Smoking status
Never	2,379 (47%)
Former ≥15 years ago	1059 (21%)
Former <15 years ago	951 (19%)
Current <20 cig/day	269 (5%)
Current ≥20 cig/day	386 (8%)
Smoking status at baseline and follow-up
Never-Never			518 (51%)
Former-Former			400 (39%)
Current-Former			50 (5%)
Current-Current			56 (5%)

^a Alcohol consumption was assessed ‘in the previous week’ at baseline and ‘in the previous year’ at follow-up.

Figure 1. Relationship^a between smoking status and comprehensive smoking indices (equation (1)) for various values of half-life parameter τ.

Smoking categories:1: Current smoker; 20 cigarettes or more per day; 2: Current smoker; between 10 and 20 cigarettes per day; 3: Current smoker; less than 10 cigarettes per day; 4: Former smokers for less than 15 years; 20 cigarettes or more per day; 5: Former smokers for less than 15 years; less than 20 cigarettes per day; 6: Former smokers for more than 15 years; 20 cigarettes or more per day; 5: Former smokers for more than 15 years; less than 20 cigarettes per day; $\left(1\right)CSI=ln\left(1+\left(1-{0.5}^{\frac{T}{\tau }}\right).\left({0.5}^{\frac{tsc}{\tau }}\right).N\right)$

Table 2. Replication of previously reported associations (P < 10⁻⁷ in six large studies) using the ‘Current vs Never’ smoker comparison, and for 3 comprehensive smoking indices (τ = 1.5, τ = 2.75 or τ = 5.25).

			Current smokers P < 10^−7	Current smokers P < 0.05	P < 10^−7 for any CSI	P < 0.05 for any CSI
CpG identified in Current vs Never smokers	N current smokers	N reported associations (P < 10^−7)	% replicated	% replicated	% replicated	% replicated
Ambatipudi et al. ^a	193	196	90%	99%	91%	100%
Besingi et al.	117	39	95%	95%	95%	95%
Guida et al.	177	447	77%	99%	83%	99%
Joehanes et al.	2,433	2,641	31%	86%	39%	90%
Wilson et al.	280	584	71%	97%	78%	98%
Zeilinger et al.	262	972	39%	82%	46%	87%
All studies		3,327	28%	84%	36%	89%
In one study only		2,500	15%	79%	23%	85%
In two studies		439	51%	95%	61%	96%
In three or more studies		389	98%	99.5%	97%	99.5%
			Former smokers P < 10^−7	Former smokers P < 0.05
CpG identified in Former vs Never smokers		N (P < 10^−7)	% replicated	% replicated
All studies		172^a	48%	90%
In one study only		146	41%	88%
In two studies		18	83%	100%
In three or more studies		8	100%	100%

^aWe assumed the coefficients from the Ambatipudi study were in the same direction as in our study, which might only slightly overestimate the replication rate (90% of associations had P < 10⁻⁷ in both studies).

^a Of the 172 associations, 30 were identified in Ambatipudi et al., 3 in Guida et al, 161 in Joehanes et al, and 14 in Zeilinger et al.

Figure 2. Estimated values of half-life parameter τ according to other features of smoking-associated CpG sites^a.

^a Values of τ above 40 (N = 44 CpGs) were omitted for graphical presentation