Expanding the phenotypic boundaries of alcohol and nicotine consumption: A search for rare genetic variants in in a general population sample of 16,000 subjects

Background: Alcohol and nicotine consumption are two of the most important preventable causes of morbidity and premature death worldwide. In western populations, alcohol and nicotine consumption are highly correlated which further increases medical costs as co-use is associated with even worse health outcomes than either of the substances used alone. In order to improve the efficacy of prevention and treatment strategies, we need a better understanding of risk factors contributing to harmful alcohol and nicotine consumption. Phenotypic correlations between alcohol and nicotine consumption are at least partly explained by overlap in genetic risk factors. Therefore, we aim to investigate the genetic architecture of multiple phenotypes associated with alcohol and nicotine consumption, including the number of alcoholic beverages, heavy vs. non heavy drinking, number of cigarettes smoked per day (CPD), age of smoking initiation, ever vs. never smoker, and heavy vs. non-heavy smoker. Methods: Phenotypes have been assessed in a general population sample including 16,000 subjects from the Netherlands. All subjects have been genotyped on the Illumina Human Exome BeadChip v1.1 that interrogates 250,000 nonsense, missense, and splice site variants with an allele frequency >=1% allowing us to evaluate the role of functional, rare variants. Genotyping and calling was conducted at a single laboratory according to uniform procedures which facilitates comparison of genotype frequencies between groups. Results: Preliminary analysis of a single phenotype (i.e., number of alcoholic drinks per week) in a subset of the total sample (N=1,491) revealed several promising findings (see Figure 1). Interestingly, the genetic variant most strongly associated with alcohol consumption (beta=0.11; p=4*10-6) was located at chromosome 11 in the tumor P53-Regulated Apoptosis-Inducing Protein 1 (TP53AIP1). Mutations in a gene from the same P53 gene family were previously found to be associated with alcohol consumption. In this relatively small pilot study, no findings were statistically significant, but power analysis of the top finding (minor allele frequency=0.20, p=0.11) shows that increasing the sample size to ~16,000 will provide enough statistical power (0.83) to detect this particular variant. Discussion: This work will be extended to the full sample and will focus on the detection of rare genetic variants involved in different alcohol and nicotine phenotypes. Since all phenotypes have been assessed in the same subjects, we will also be able to determine genetic variants that explain the phenotypic concordance across multiple traits using multivariate genetic analyses. Methodological challenges specific to population-based association analysis of rare variants and quantitative behavioral traits will be discussed.