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Genome-Wide Meta-Analysis Identifies Regions on 7p21 (AHR) and 15q24 (CYP1A2) As Determinants of Habitual Caffeine Consumption
Open accessAbstract
We report the first genome-wide association study of habitual caffeine intake. We included 47,341 individuals of European descent based on five population-based studies within the United States. In a meta-analysis adjusted for age, sex, smoking, and eigenvectors of population variation, two loci achieved genome-wide significance: 7p21 (P = 2.4 × 10(-19)), near AHR, and 15q24 (P = 5.2 × 10(-14)), between CYP1A1 and CYP1A2. Both the AHR and CYP1A2 genes are biologically plausible candidates as CYP1A2 metabolizes caffeine and AHR regulates CYP1A2.
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“Recently, a genome-wide association study (GWAS) found a highly significant association between a variant on CYP1A2 and coffee intake48.”
From Long-Term Coffee Consumption and Risk of Cardiovascular Disease: A Systematic Review and a Dose–Response Meta-Analysis of Prospective Cohort Studies (2014) · cites this paper as [48]
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“However, this variant explains only a very small population variance.”
From Long-Term Coffee Consumption and Risk of Cardiovascular Disease: A Systematic Review and a Dose–Response Meta-Analysis of Prospective Cohort Studies (2014) · cites this paper as [48]
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Walter, S., Kubzansky, L. D., Koenen, K. C., Liang, L., Tchetgen, E. J. T., Cornelis, M. C., Chang, S., Rimm, E. B., Kawachi, I. I., & Glymour, M. M. (2015) · American Journal of Medical Genetics Part B Neuropsychiatric Genetics · doi:10.1002/ajmg.b.32286 · Cited by 47
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“73 Whether or not caffeine’s bitterness can be partly attributed to its ability to antagonize A2B receptors remains unknown.”
Sleep Pharmacogenetics: Personalized Sleep-Wake Therapy
Holst, S. C., Valomon, A., & Landolt, H. (2015) · The Annual Review of Pharmacology and Toxicology · doi:10.1146/annurev-pharmtox-010715-103801 · Cited by 48
“Genetic variation of ADORA2A is an important determinant of wake promotion by caffeine (125, 126).”
InfluentialHuang, T., Zheng, Y., Qi, Q., Xu, M., Ley, S. H., Li, Y., Kang, J. H., Wiggs, J. L., Pasquale, L. R., Chan, A. T., et al. (2015) · Diabetes · doi:10.2337/db15-0264 · Cited by 52
Self-citationDenden, S., Bouden, B., Khelil, A. H., Chibani, J. B., & Hamdaoui, M. H. (2016) · Genetics and Molecular Research · doi:10.4238/gmr.15027487 · Cited by 48
“The following papers were excluded: four GWAS (Cornelis et al., 2011; Sulem et al., 2011; Amin et al., 2012; Rodenburg et al., 2012); four studies lacking coffee intake analysis (Sachse et al., 1999; Basvi et al., 2007; Ghotbi et al., 2007; Gunes et al., 2009); eight studies not providing coffee…”
BackgroundInfluentialSaid, M. A., van de Vegte, Y. J., Verweij, N., & van der Harst, P. (2020) · Journal of the American Heart Association · doi:10.1161/jaha.120.016808 · Cited by 47
“Combined caffeine 0 (0-0) 33 (15-60) 96 (90-120) 159 (150-180) 230 (210-240) 285 (270-300) 345 (330-360) 450 (420-540)”
InfluentialPolymorphic Variants of Cytochrome P450
Daly, A. K. (2015) · Advances in pharmacology · doi:10.1016/bs.apha.2015.03.001 · Cited by 45
Chang, S.-C., Glymour, M. M., Rewak, M., Cornelis, M. C., Walter, S., Koenen, K. C., Kawachi, I. I., Liang, L., Tchetgen, E. J. T., & Kubzansky, L. D. (2013) · Psychoneuroendocrinology · doi:10.1016/j.psyneuen.2013.09.024 · Cited by 47
“Genotyping and quality control have been detailed elsewhere (Cornelis et al., 2011).”
BackgroundSelf-citationNakagawa‐Senda, H., Hachiya, T., Shimizu, A., Hosono, S., Oze, I., Watanabe, M., Matsuo, K., Ito, H. M., Hara, M., Nishida, Y., et al. (2018) · Scientific Reports · doi:10.1038/s41598-018-19914-w · Cited by 43
Coffee Consumption Is Associated with DNA Methylation Levels of Human Blood
Chuang, Y.-H., Quach, A., Absher, D., Assimes, T., Horvath, S., & Ritz, B. (2017) · European Journal of Human Genetics · doi:10.1038/ejhg.2016.175 · Cited by 40
Lowcock, E. C., Cotterchio, M., Anderson, L. N., Boucher, B. A., & El‐Sohemy, A. (2013) · Nutrition and Cancer · doi:10.1080/01635581.2013.768348 · Cited by 40
Li, M., Li, Y., Weeks, O., Mijatovic, V., Teumer, A., Huffman, J. E., Tromp, G., Fuchsberger, C., Gorski, M., Lyytikäinen, L., et al. (2016) · Journal of the American Society of Nephrology · doi:10.1681/asn.2016020131 · Cited by 43
Self-citationToward systems epidemiology of coffee and health
Cornelis, M. C. (2014) · Current Opinion in Lipidology · doi:10.1097/mol.0000000000000143 · Cited by 39
“Two studies identified significant associations upstream of AHR [61,62], and all three identified associations mapping to the CYP1A1–CYP1A2 bidirectional promoter.”
BackgroundMethodInfluentialSelf-citationFast Association Tests for Genes with FAST
Chanda, P., Huang, H., Arking, D. E., & Bader, J. S. (2013) · PLoS ONE · doi:10.1371/journal.pone.0068585 · Cited by 38
Matthaei, J., Tzvetkov, M. V., Strube, J., Sehrt, D. B., Sachse-Seeboth, C., Hjelmborg, J., Möller, S., Halekoh, U., Hofmann, U., Schwab, M. G., et al. (2016) · Clinical Pharmacology & Therapeutics · doi:10.1002/cpt.444 · Cited by 38
Huang, T., Wang, T., Heianza, Y., Zheng, Y., Sun, D., Kang, J. H., Pasquale, L. R., Rimm, E. B., Manson, J. E., Hu, F. B., et al. (2018) · American Journal of Clinical Nutrition · doi:10.1093/ajcn/nqy238 · Cited by 39
Self-citationCoffee consumption and incidence of lung cancer in the NIH-AARP Diet and Health Study
Guertin, K. A., Freedman, N. D., Loftfield, E., Graubard, B. I., Caporaso, N. E., & Sinha, R. R. (2015) · International Journal of Epidemiology · doi:10.1093/ije/dyv104 · Cited by 37
Self-citationPolygenic risk score: use in migraine research
Chalmer, M. A., Esserlind, A.-L., Olesen, J., & Hansen, T. F. (2018) · The Journal of Headache and Pain · doi:10.1186/s10194-018-0856-0 · Cited by 40
“Chang et al. [52] 6989 cases (NHS) 3 of the 4 NHS-GWAS [53] substudies were used as training sets PRS was estimated by 3 different approaches: internal whole-genome scoring and two external PRS weighting algorithms from independent samples.”
MethodKapellou, A., King, A., Graham, C., Pilić, L., & Mavrommatis, Y. (2023) · Nutrition Reviews · doi:10.1093/nutrit/nuad029 · Cited by 41
Jankun, J. (2011) · International Journal of Molecular Medicine · doi:10.3892/ijmm.2011.810 · Cited by 35
“Very recently, Cornelis et al (60) reported the a genome-wide association study of habitual caffeine intake on large number (>47,000) individuals within the United States.”
Caffeine Consumption Contributes to Skin Intrinsic Fluorescence in Type 1 Diabetes
Eny, K. M., Orchard, T. J., Miller, R. G., Maynard, J., Grant, D. M., Costacou, T., Cleary, P. A., Braffett, B. H., & Paterson, A. D. (2015) · Diabetes Technology & Therapeutics · doi:10.1089/dia.2015.0017 · Cited by 33
“Furthermore, a candidate gene approach reported no nominal association of 32 single nucleotdie polymorphisms in NAT2 with caffeine intake using gene-based tests.(30) On the other hand, NAT2 has been associated with 1-methylxanthine:4-acetamidobutanoate, reflecting metabolites of caffeine metabolism in a GWAS of serum…”
Taylor, A. E., Smith, G. D., & Munafo, M. R. (2017) · Addiction · doi:10.1111/add.13975 · Cited by 33
“We also created a genetic risk score using only variants in or near the strongest two loci, AHR (rs4410790) and CYP1A1/2 (rs2470893), which have been identified in multiple GWAS studies of coffee consumption [1,2] and a score with four SNPs from loci that reached genome-wide significance in the European discovery samp…”
MethodResultGenetic determinants of liking and intake of coffee and other bitter foods and beverages
Cornelis, M. C., & van Dam, R. M. (2021) · Scientific Reports · doi:10.1038/s41598-021-03153-7 · Cited by 34
Self-citationGenetic Polymorphisms Affecting Drug Metabolism
Daly, A. K. (2012) · Advances in pharmacology · doi:10.1016/b978-0-12-398339-8.00004-5 · Cited by 33
Liu, G., Jiang, Y., Chen, X., Zhang, R., Ma, G., Feng, R., Zhang, L., Liao, M., Miao, Y., Chen, Z., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0075951 · Cited by 31
“05/17,787 (number of autosomal genes)] [30].”
Pirastu, N., Kooyman, M., Robino, A., van der Spek, A., Navarini, L., Amin, N., Karssen, L. C., van Duijn, C. M., & Gasparini, P. (2016) · Scientific Reports · doi:10.1038/srep31590 · Cited by 31
Genomic analysis of diet composition finds novel loci and associations with health and lifestylePreprint
Meddens, S. F. W., de Vlaming, R., Bowers, P., Burik, C. A. P., Linnér, R. K., Lee, C. W., Okbay, A., Turley, P., Rietveld, C. A., Fontana, M. A., et al. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/383406 · Cited by 32
Metadata
- Authors
- Cornelis, M. C., Monda, K. L., Yu, K., Paynter, N., Azzato, E. M., Bennett, S. N., Berndt, S. I., Boerwinkle, E., Chanock, S., Chatterjee, N., Couper, D., Curhan, G., Heiss, G., Hu, F. B., Hunter, D. J., Jacobs, K., Jensen, M. K., Kraft, P., Landi, M. T., Nettleton, J. A., Purdue, M. P., Rajaraman, P., Rimm, E. B., Rose, L. M., Rothman, N., Silverman, D., Stolzenberg-Solomon, R., Subar, A., Yeager, M., Chasman, D. I., van Dam, R. M., & Caporaso, N. E.
- Affiliations
- Harvard University (US)
- University of North Carolina at Chapel Hill (US)
- National Institutes of Health (US)
- Brigham and Women's Hospital (US)
- University of Washington (US)
- The University of Texas Health Science Center at Houston (US)
- National University of Singapore (SG)
- Corresponding author
- Chasman, Daniel I.
- van Dam, Rob M.
- Caporaso, Neil E.
- ORCID
- Cornelis, Marilyn C.
- Yu, Kai
- Paynter, Nina
- Azzato, Elizabeth M.
- Berndt, Sonja I.
- Boerwinkle, Eric
- Chanock, Stephen
- Chatterjee, Nilanjan
- Couper, David
- Curhan, Gary
- Heiss, Gerardo
- Hu, Frank B.
- Jacobs, Kevin
- Jensen, Majken K.
- Kraft, Peter
- Landi, Maria Teresa
- Purdue, Mark P.
- Rajaraman, Preetha
- Rimm, Eric B.
- Rose, Lynda M.
- Rothman, Nathaniel
- Silverman, Debra
- Yeager, Meredith
- Chasman, Daniel I.
- van Dam, Rob M.
- Caporaso, Neil E.
- Venue
- PLoS Genetics
- Publisher
- Public Library of Science (PLoS)
- Published
- 2011-04-07
- Volume
- 7
- Issue
- 4
- Pages
- e1002033
- ISSN
- 1553-7390 (ISSN-L)
- 1553-7404
- PMC
- PMC3071630
- OpenAlex
- W2147245308
- Cited by
- 228
- References
- 37
- Citations by year
- 2026: 8 · 2025: 8 · 2024: 10 · 2023: 10 · 2022: 8 · 2021: 13 · 2020: 21 · 2019: 15 · 2018: 20 · 2017: 15 · 2016: 21 · 2015: 15 · 2014: 20 · 2013: 18 · 2012: 18
- FWCI
- 14.76
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- PLoS Genetics (publishedVersion, public-domain)
- Europe PMC (PubMed Central) (publishedVersion, public-domain)
- PubMed Central (publishedVersion, public-domain)
- PubMed (publishedVersion)
- Carolina Digital Repository (University of North Carolina at Chapel Hill) (submittedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- National University of Singapore (submittedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- UNC Libraries
- Funders
- U.S. Department of Health and Human Services (R01HL086694, U10AA008401, U01HG004438, R01HL087641, R01HL59367, U01HG004729)
- Donald W. Reynolds Foundation
- Amgen
- Division of Cancer Prevention, National Cancer Institute (CA55075)
- Johns Hopkins University (N01-HC-55020, HHSN268200782096C, U01HG004438)
- Broad Institute
- Fondation Leducq
- National Institutes of Health (HSN268200625226C, n01hc55021-47-0-1, n01hc55020-39-0-0, n01hc55016-37-0-0, n01hc055022-024, 5u01hg004423-02, n01hc55019-35-0-1, 5p01dk070756-05, n01hc55018-38-0-1, 5r01hl043851-10, HHSN268200782096C, N01-HC55020, N01-HC-55021, N01-HC-55019, N01-HC-55022, N01-HC55016, N01-HC55018, CA55075, CA54281, CA63464, N01-HC-55015, HL69757, n01hc55015-48-0-1)
- U.S. Public Health Service (AHG006033)
- Canadian Institutes of Health Research (U10AA008401, CA63464, CA54281)
- National Institute on Alcohol Abuse and Alcoholism (HHSN268200782096C, U10AA008401)
- National Heart, Lung, and Blood Institute (N01-HC55022, HC-55016, N01 HC055016, N01-HC-55018, R01HL087641, R01HL59367 and R01HL086694, HL043851, N01 HC 55020, R01‐HL043851, HC-55021, HC-55018, N01 HC 55019, R01 HL-59367, U19HL069757, HC-55022, N01 HC055020, R01HL035464, HC-55019, N01-HC, N01 HC055018, HC-55015, U01HL069757, HC-55020, N01-HC55016, R01HL087641, N01 HC055022, HL 69757, R01HL059367, HL35464, HHSN268200782096C, N01 HC055019, CA55075, N01‐HC‐55015, N01-HC55021, CA047988, N01 HC055021, N01 HC055015, R01HL086694)
- National Institute on Drug Abuse (01DA013423, R01DA013423, HHSN268200782096C)
- National Human Genome Research Institute (U01HG004735, U01-HG004423, U01HG004726, U01HG04424, U01HG004422, U01HG004738, U01HG004399, U01HG004402, U01HG004728, U01HG004415, U01HG004446, U01HG004729, U01HG004424, U01HG004438, U01HG004436, 01HG004735, HHSN268200782096C)
- National Cancer Institute (R01CA040356, CA63464, CA136792, U01CA063464, CA-55075, R37CA054281, CA-40356, CA98233, P01CA087969, R01CA054281, P01CA089392, CA 047988, R01CA063464, CA 54281, U01 CA 98233, P01CA055075, U01CA098233, R01CA047988, U01CA136792, Z01CP010200)
- National Institute of Diabetes and Digestive and Kidney Diseases (P01-DK-070756, R01DK058845, N01-HC-55016, N01-HC-55018, N01-HC-55021, N01-HC-55020, N01-HC-55015, 5P01DK070756, N01-HC-55019, N01-HC-55022)
- National Institute of Dental and Craniofacial Research (U01DE018993, U01DE018903, HHSN268200782096C)
- National Center for Research Resources (UL1RR025005)
- Topics
- Health Sciences › Medicine › Pharmacology (medical) › Coffee research and impacts
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Keywords
- habitual caffeine consumption, caffeine consumption, CYP1A1, caffeine metabolism, gene expression regulation
- MeSH terms
- Adult, Aged, Caffeine, Chromosomes, Human, Pair 15, Chromosomes, Human, Pair 7, Drinking Behavior, Female, Genotype, Humans, Male, Middle Aged, Quality Control, Sex Factors, United States, Receptors, Aryl Hydrocarbon, Cytochrome P-450 CYP1A2, Polymorphism, Single Nucleotide, White People, Genome-Wide Association Study
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