A generic research paradigm for identification and validation of early molecular diagnostics and new therapeutics in common disorders

Determination of genetic correlation between tobacco smoking and coronary artery disease

Backgrounds

Tobacco smoking is an important risk factor for coronary artery disease (CAD), but the genetic mechanisms linking smoking to CAD remain largely unknown.

Methods

We analyzed summary data from the genome-wide association study (GWAS) of the UK Biobank for CAD, plasma lipid concentrations (n = 184,305), and smoking (n = 337,030) using different biostatistical methods, which included LD score regression and Mendelian randomization (MR).

Results

We identified SNPs shared by CAD and at least one smoking behavior, the genes where these SNPs are located were found to be significantly enriched in the processes related to lipoprotein metabolic, chylomicron-mediated lipid transport, lipid digestion, mobilization, and transport. The MR analysis revealed a positive correlation between smoking cessation and decreased risk for CAD when smoking cessation was considered as exposure (p = 0.001), and a negative correlation between the increased risk for CAD and smoking cessation when CAD was considered as exposure (p = 2.95E-08). This analysis further indicated that genetic liability for smoking cessation increased the risk of CAD.

Conclusion

These findings inform the concomitant conditions of CAD and smoking and support the idea that genetic liabilities for smoking behaviors are strongly associated with the risk of CAD.

A decade in psychiatric GWAS research

After more than 10 years of accumulated efforts, genome-wide association studies (GWAS) have led to many findings, most of which have been deposited into the GWAS Catalog. Between GWAS's inception and March 2017, the GWAS Catalog has collected 2429 studies, 1818 phenotypes, and 28,462 associated SNPs. We reclassified the psychology-related phenotypes into 217 reclassified phenotypes, which accounted for 514 studies and 7052 SNPs. In total, 1223 of the SNPs reached genome-wide significance. Of these, 147 were replicated for the same psychological trait in different studies. Another 305 SNPs were replicated within one original study. The SNPs rs2075650 and rs4420638 were linked to the most replications within a single reclassified phenotype or very similar reclassified phenotypes; both were associated with Alzheimer's disease (AD). Schizophrenia was associated with 74 within-phenotype SNPs reported in independents studies. Alzheimer's disease and schizophrenia were both linked to some physical phenotypes, including cholesterol and body mass index, through common GWAS signals. Alzheimer's disease also shared risk SNPs with age-related phenotypes such as age-related macular degeneration and longevity. Smoking-related SNPs were linked to lung cancer and respiratory function. Alcohol-related SNPs were associated with cardiovascular and digestive system phenotypes and disorders. Two separate studies also identified a shared risk SNP for bipolar disorder and educational attainment. This review revealed a list of reproducible SNPs worthy of future functional investigation. Additionally, by identifying SNPs associated with multiple phenotypes, we illustrated the importance of studying the relationships among phenotypes to resolve the nature of their causal links. The insights within this review will hopefully pave the way for future evidence-based genetic studies.

Genomic medicine and lung diseases

The recent explosion of genomic data and technology points to opportunities to redefine lung diseases at the molecular level; to apply integrated genomic approaches to elucidate mechanisms of lung pathophysiology; and to improve early detection, diagnosis, and treatment of lung diseases. Research is needed to translate genomic discoveries into clinical applications, such as detecting preclinical disease, predicting patient outcomes, guiding treatment choices, and most of all identifying potential therapeutic targets for lung diseases. The Division of Lung Diseases in the National Heart, Lung, and Blood Institute convened a workshop, "Genomic Medicine and Lung Diseases," to discuss the potential for integrated genomics and systems approaches to advance 21st century pulmonary medicine and to evaluate the most promising opportunities for this next phase of genomics research to yield clinical benefit. Workshop sessions included (1) molecular phenotypes, molecular biomarkers, and therapeutics; (2) new technology and opportunity; (3) integrative genomics; (4) molecular anatomy of the lung; (5) novel data and information platforms; and (6) recommendations for exceptional research opportunities in lung genomics research.