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Genome-wide meta-analysis identifies six novel loci associated with habitual coffee consumption

Authors: Consortium, Coffee and Caffeine Genetics; Cornelis, Marilyn C; Renstrom, Frida; Rasheed, Asif; Mason, Marc A; Zonderman, Alan B; Franke, Lude; +193 Authors

Genome-wide meta-analysis identifies six novel loci associated with habitual coffee consumption

Abstract

Coffee, a major dietary source of caffeine, is among the most widely consumed beverages in the world and has received considerable attention regarding health risks and benefits. We conducted a genome-wide (GW) meta-analysis of predominately regular-type coffee consumption (cups per day) among up to 91,462 coffee consumers of European ancestry with top single-nucleotide polymorphisms (SNPs) followed-up in ~30 062 and 7964 coffee consumers of European and African-American ancestry, respectively. Studies from both stages were combined in a trans-ethnic meta-analysis. Confirmed loci were examined for putative functional and biological relevance. Eight loci, including six novel loci, met GW significance (log10Bayes factor (BF)>5.64) with per-allele effect sizes of 0.03-0.14 cups per day. Six are located in or near genes potentially involved in pharmacokinetics (ABCG2, AHR, POR and CYP1A2) and pharmacodynamics (BDNF and SLC6A4) of caffeine. Two map to GCKR and MLXIPL genes related to metabolic traits but lacking known roles in coffee consumption. Enhancer and promoter histone marks populate the regions of many confirmed loci and several potential regulatory SNPs are highly correlated with the lead SNP of each. SNP alleles near GCKR, MLXIPL, BDNF and CYP1A2 that were associated with higher coffee consumption have previously been associated with smoking initiation, higher adiposity and fasting insulin and glucose but lower blood pressure and favorable lipid, inflammatory and liver enzyme profiles (P<5 × 10(-8)).Our genetic findings among European and African-American adults reinforce the role of caffeine in mediating habitual coffee consumption and may point to molecular mechanisms underlying inter-individual variability in pharmacological and health effects of coffee.

Countries
United Kingdom, Germany, Netherlands, Netherlands, Netherlands, Netherlands, United Kingdom, Netherlands, United Kingdom, Australia, Netherlands, Australia, Australia
Keywords

INVOLVEMENT, Netherlands Twin Register (NTR), GCKR protein, human, 2804 Cellular and Molecular Neuroscience, PROTEIN, Coffea, 910, VARIANTS, genetics [Brain-Derived Neurotrophic Factor], genetics [Adaptor Proteins, Signal Transducing], BINDING, BRAIN, EMC MGC-02-96-01, Psychiatry, Basic Helix-Loop-Helix Leucine Zipper Transcription Factors, EMC NIHES-03-30-02, Phenotype, genetics [Polymorphism, Single Nucleotide], /dk/atira/pure/sustainabledevelopmentgoals/good_health_and_well_being, genetics [Cytochrome P-450 CYP1A2], EMC COEUR-09, Biochemistry & Molecular Biology, CAFFEINE, 572, EMC NIHES-01-64-02, 610, Polymorphism, Single Nucleotide, EMC NIHES-04-55-01, SDG 3 - Good Health and Well-being, Cytochrome P-450 CYP1A2, 2738 Psychiatry and Mental health, 1312 Molecular Biology, Humans, genetics [Basic Helix-Loop-Helix Leucine Zipper Transcription Factors], Adaptor Proteins, Signal Transducing, MLXIPL protein, human, EMC ONWAR-01-58-02, RECEPTOR, Brain-Derived Neurotrophic Factor, Neurosciences, ta1182, Radboudumc 3: Disorders of movement DCMN: Donders Center for Medical Neuroscience, Feeding Behavior, ta3124, name=SDG 3 - Good Health and Well-being, BDNF, EMC MM-01-39-09-A, Neurosciences & Neurology, Developmental Psychopathology, metabolism [Coffea], GLUCOKINASE, Genome-Wide Association Study, ddc: ddc:610

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citations
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
247
Top 1%
Top 10%
Top 1%
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