Fig. 1.

Patterns of breast tumor differential methylation in smokers compared with never smokers. Generalized linear regression models (GLM) (logit link) adjusted for age, race, menopausal status, stage, BMI, and alcohol consumption were used to identify CpG loci differentially methylated in breast tumors in smokers versus never smokers. Volcano plots display array-wide patterns of breast tumor differential methylation in current or ever smokers among: a all cases, b HR+ cases, c HR− cases, d HR− cases according to smoking duration (long-term >20 years or shorter-term ≤20 years) among ever smokers, or e basal-like cases. Each volcano plot displays the negative log of unadjusted p-values for differences in β (proportion DNA methylated) at each probe on the y axis versus the correlation coefficient for methylation at each CpG locus on the x axis. Probes that fall above the broken line are significant at p <0.05. Probes hypomethylated in smokers have negative coefficients, while probes hypermethylated in smokers have positive coefficients. f Bar graph summarizing numbers of differentially hypomethylated or hypermethylated CpG probes at p < 0.05 in ever smokers, current smokers, long-term (>20 year), or shorter-term (<20 year) smokers versus never smokers among all cases or by HR status