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Habitual coffee consumption is an addictive behavior with unknown genetic variations and has raised public health issues about its potential health-related outcomes. We performed exome-wide association studies to identify rare risk variants contributing to habitual coffee consumption utilizing the newly released UK Biobank exome dataset (<i>n</i> = 200,643). A total of 34,761 qualifying variants were imported into SKAT to conduct gene-based burden and robust tests with minor allele frequency <0.01, adjusting the polygenic risk scores (PRS) of coffee intake to exclude the effect of common coffee-related polygenic risk. The gene-based burden and robust test of the exonic variants found seven exome-wide significant associations, such as <i>OR2G2</i> (<i>P_SKAT</i> = 1.88 × 10⁻⁹, <i>P_SKAT-Robust</i> = 2.91 × 10⁻¹⁷), <i>VEZT1</i> (<i>P_SKAT</i> = 3.72 × 10⁻⁷, <i>P_SKAT-Robust</i> = 1.41 × 10⁻⁷), and <i>IRGC</i> (<i>P_SKAT</i> = 2.92 × 10⁻⁵, <i>P_SKAT-Robust</i> = 1.07 × 10⁻⁷). These candidate genes were verified in the GWAS summary data of coffee intake, such as rs12737801 (<i>p</i> = 0.002) in <i>OR2G2</i>, and rs34439296 (<i>p</i> = 0.008) in <i>IRGC</i>. This study could help to extend genetic insights into the pathogenesis of coffee addiction, and may point to molecular mechanisms underlying health effects of habitual coffee consumption.