Over the last decade, the introduction of microarray technology has had a profound impact on gene expression research. The publication of studies with dissimilar or altogether contradictory results, obtained using different microarray platforms to analyze identical RNA samples, has raised concerns about the reliability of this technology. The MicroArray Quality Control (MAQC) project was initiated to address these concerns, as well as other performance and data analysis issues. Expression data on four titration pools from two distinct reference RNA samples were generated at multiple test sites using a variety of microarray-based and alternative technology platforms. Here we describe the experimental design and probe mapping efforts behind the MAQC project. We show intraplatform consistency across test sites as well as a high level of interplatform concordance in terms of genes identified as differentially expressed. This study provides a resource that represents an important first step toward establishing a framework for the use of microarrays in clinical and regulatory settings.

Alcoholism has a profound impact on millions of people throughout the world. However, the ability to determine if a patient needs treatment is hindered by reliance on self-reporting and the clinician’s capability to monitor the patient’s response to treatment is challenged by the lack of reliable biomarkers. Using a genome-wide approach, we have previously shown that chronic alcohol use is associated with methylation changes in DNA from human cell lines. In this pilot study, we now examine DNA methylation in peripheral mononuclear cell DNA gathered from subjects as they enter and leave short-term alcohol treatment. When compared with abstinent controls, subjects with heavy alcohol use show widespread changes in DNA methylation that have a tendency to reverse with abstinence. Pathway analysis demonstrates that these changes map to gene networks involved in apoptosis. There is no significant overlap of the alcohol signature with the methylation signature previously derived for smoking. We conclude that DNA methylation may have future clinical utility in assessing acute alcohol use status and monitoring treatment response.

Smoking is the largest preventable cause of morbidity and mortality in the world. Although there are effective pharmacologic and behavioral treatments for smoking cessation, our inability to objectively quantify smokers’ progress in decreasing smoking has been a barrier to both clinical and research efforts. In prior work, we and others have shown that DNA methylation at cg05575921, a CpG residue in the aryl hydrocarbon receptor repressor (AHRR), can be used to determine smoking status and infer cigarette consumption history. In this study, we serially assessed self-report and existing objective markers of cigarette consumption in 35 subjects undergoing smoking cessation therapy, then quantified DNA methylation at cg05575921 at study entry and three subsequent time points. Five subjects who reported serum cotinine and exhaled carbon monoxide verified smoking abstinence for the 3 months prior to study exit averaged a 5.9% increase in DNA methylation at cg05575921 (p < 0.004) over the 6-month study. Although the other 30 subjects did not achieve smoking cessation at the 6-month time point, their self-reported reduction of cigarette consumption (mean = 6 cigarettes/day) was associated with a 2.8% increase DNA methylation at cg05575921 (p < 0.05). Finally, a survey of subjects as they exited the study demonstrated strong support for the clinical use of epigenetic biomarkers. We conclude that AHRR methylation status is a quantifiable biomarker for progress in smoking cessation that could have substantial impact on both smoking cessation treatment and research.

Smoking is the largest preventable cause of morbidity and mortality in the world. Despite the development of numerous preventive and treatment interventions, the rate of daily smoking in the United States is still approximately 22%. Effective psychosocial interventions and pharmacologic agents exist for the prevention and treatment of smoking. Unfortunately, both approaches are hindered by our inability to accurately quantify amount of cigarette consumption from the point of initial experimentation to the point of total dependency. Recently, we and others have demonstrated that smoking is associated with genome-wide changes in DNA methylation. However, whether this advance in basic science can be employed as a reliable assay that is useful for clinical diagnosis and treatment has not been shown. In this communication, we determine the sensitivity and specificity of five of the most consistently replicated CpG loci with respect to smoking status using data from a publically available dataset. We show that methylation status at a CpG locus in the aryl hydrocarbon receptor repressor, cg05575921, is both sensitive and specific for smoking status in adults with a receiver operated curve characteristic area under the curve of 0.99. Given recent demonstrations that methylation at this locus reflects both intensity of smoking and the degree of smoking cessation, we conclude that a methylation-based diagnostic at this locus could have a prominent role in understanding the impact of new products, such as e-cigarettes on initiation of cigarette smoking among adolescents, while improving the prevention and treatment of smoking, and smoking related disorders.

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