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1. Genetic diversity fuels gene discovery for tobacco and alcohol use

Author

Saunders, Gretchen RB, Wang, Xingyan, Chen, Fang, Jang, Seon-Kyeong, Liu, Mengzhen, Wang, Chen, Gao, Shuang, Jiang, Yu, Khunsriraksakul, Chachrit, Otto, Jacqueline M, Addison, Clifton, Akiyama, Masato, Albert, Christine M, Aliev, Fazil, Alonso, Alvaro, Arnett, Donna K, Ashley-Koch, Allison E, Ashrani, Aneel A, Barnes, Kathleen C, Barr, R Graham, Bartz, Traci M, Becker, Diane M, Bielak, Lawrence F, Benjamin, Emelia J, Bis, Joshua C, Bjornsdottir, Gyda, Blangero, John, Bleecker, Eugene R, Boardman, Jason D, Boerwinkle, Eric, Boomsma, Dorret I, Boorgula, Meher Preethi, Bowden, Donald W, Brody, Jennifer A, Cade, Brian E, Chasman, Daniel I, Chavan, Sameer, Chen, Yii-Der Ida, Chen, Zhengming, Cheng, Iona, Cho, Michael H, Choquet, Hélène, Cole, John W, Cornelis, Marilyn C, Cucca, Francesco, Curran, Joanne E, de Andrade, Mariza, Dick, Danielle M, Docherty, Anna R, Duggirala, Ravindranath, Eaton, Charles B, Ehringer, Marissa A, Esko, Tõnu, Faul, Jessica D, Fernandes Silva, Lilian, Fiorillo, Edoardo, Fornage, Myriam, Freedman, Barry I, Gabrielsen, Maiken E, Garrett, Melanie E, Gharib, Sina A, Gieger, Christian, Gillespie, Nathan, Glahn, David C, Gordon, Scott D, Gu, Charles C, Gu, Dongfeng, Gudbjartsson, Daniel F, Guo, Xiuqing, Haessler, Jeffrey, Hall, Michael E, Haller, Toomas, Harris, Kathleen Mullan, He, Jiang, Herd, Pamela, Hewitt, John K, Hickie, Ian, Hidalgo, Bertha, Hokanson, John E, Hopfer, Christian, Hottenga, JoukeJan, Hou, Lifang, Huang, Hongyan, Hung, Yi-Jen, Hunter, David J, Hveem, Kristian, Hwang, Shih-Jen, Hwu, Chii-Min, Iacono, William, Irvin, Marguerite R, Jee, Yon Ho, Johnson, Eric O, Joo, Yoonjung Y, Jorgenson, Eric, Justice, Anne E, Kamatani, Yoichiro, Kaplan, Robert C, Kaprio, Jaakko, Kardia, Sharon LR, and Keller, Matthew C

Subjects
Genetics, Alcoholism, Alcohol Use and Health, Prevention, Human Genome, Substance Misuse, Aetiology, 2.1 Biological and endogenous factors, Cancer, Good Health and Well Being, Humans, Genetic Predisposition to Disease, Genetic Variation, Genome-Wide Association Study, Multifactorial Inheritance, Risk Factors, Tobacco Use, Alcohol Drinking, Transcriptome, Sample Size, Genetic Loci, Internationality, Europe, 23andMe Research Team, Biobank Japan Project, General Science & Technology
Abstract

Tobacco and alcohol use are heritable behaviours associated with 15% and 5.3% of worldwide deaths, respectively, due largely to broad increased risk for disease and injury1-4. These substances are used across the globe, yet genome-wide association studies have focused largely on individuals of European ancestries5. Here we leveraged global genetic diversity across 3.4 million individuals from four major clines of global ancestry (approximately 21% non-European) to power the discovery and fine-mapping of genomic loci associated with tobacco and alcohol use, to inform function of these loci via ancestry-aware transcriptome-wide association studies, and to evaluate the genetic architecture and predictive power of polygenic risk within and across populations. We found that increases in sample size and genetic diversity improved locus identification and fine-mapping resolution, and that a large majority of the 3,823 associated variants (from 2,143 loci) showed consistent effect sizes across ancestry dimensions. However, polygenic risk scores developed in one ancestry performed poorly in others, highlighting the continued need to increase sample sizes of diverse ancestries to realize any potential benefit of polygenic prediction.

Published
2022

2. Adherence to MIND Diet, Genetic Susceptibility, and Incident Dementia in Three US Cohorts

Author

Vu, Thanh Huyen T, Beck, Todd, Bennett, David A, Schneider, Julie A, Hayden, Kathleen M, Shadyab, Aladdin H, Rajan, Kumar B, Morris, Martha Clare, and Cornelis, Marilyn C

Subjects
Health Services and Systems, Health Sciences, Neurodegenerative, Behavioral and Social Science, Neurosciences, Dementia, Genetics, Aging, Nutrition, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), Acquired Cognitive Impairment, Prevention, Alzheimer's Disease, Clinical Research, Brain Disorders, Neurological, Alzheimer Disease, Diet, Mediterranean, Dietary Approaches To Stop Hypertension, Female, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Male, Prospective Studies, diet pattern, dementia, genotype, interaction, Food Sciences, Nutrition and Dietetics, Clinical sciences, Nutrition and dietetics, Public health
Abstract

Adherence to Mediterranean-DASH Diet Intervention for Neurodegenerative Delay (MIND) may lower the risk of dementia by impacting immunity and cholesterol, which are pathways also implicated by genome-wide association studies of Alzheimer’s Dementia (AD). We examined whether adherence to the MIND diet could modify the association of genetic risk for AD with incident dementia. We used three ongoing US cohorts: Chicago Health and Aging Project (CHAP, n = 2449), Rush Memory and Aging Project (MAP, n = 725), and Women’s Health Initiative Memory Study (WHIMS, n = 5308). Diagnosis of dementia was based on clinical neurological examination and standardized criteria. Repeated measures of global cognitive function were available in MAP and CHAP. Self-reported adherence to MIND was estimated using food-frequency questionnaires. Global and pathway-specific genetic scores (GS) for AD were derived. Cox proportional hazard, logistic regression, and mixed models were used to examine associations of MIND, GS, and GS-MIND interactions with incident dementia and cognitive decline. Higher adherence to MIND and lower GS were associated with a lower risk of dementia in MAP and WHIMS and a slower rate of cognitive decline in MAP (p < 0.05). MIND or GS were not associated with incident dementia or cognitive decline in CHAP. No gene−diet interaction was replicated across cohorts. Genetic risk and MIND adherence are independently associated with dementia among older US men and women.

Published
2022

3. Genetic insights into resting heart rate and its role in cardiovascular disease

Author

van de Vegte, Yordi J., Eppinga, Ruben N., van der Ende, M. Yldau, Hagemeijer, Yanick P., Mahendran, Yuvaraj, Salfati, Elias, Smith, Albert V., Tan, Vanessa Y., Arking, Dan E., Ntalla, Ioanna, Appel, Emil V., Schurmann, Claudia, Brody, Jennifer A., Rueedi, Rico, Polasek, Ozren, Sveinbjornsson, Gardar, Lecoeur, Cecile, Ladenvall, Claes, Zhao, Jing Hua, Isaacs, Aaron, Wang, Lihua, Luan, Jian’an, Hwang, Shih-Jen, Mononen, Nina, Auro, Kirsi, Jackson, Anne U., Bielak, Lawrence F., Zeng, Linyao, Shah, Nabi, Nethander, Maria, Campbell, Archie, Rankinen, Tuomo, Pechlivanis, Sonali, Qi, Lu, Zhao, Wei, Rizzi, Federica, Tanaka, Toshiko, Robino, Antonietta, Cocca, Massimiliano, Lange, Leslie, Müller-Nurasyid, Martina, Roselli, Carolina, Zhang, Weihua, Kleber, Marcus E., Guo, Xiuqing, Lin, Henry J., Pavani, Francesca, Galesloot, Tessel E., Noordam, Raymond, Milaneschi, Yuri, Schraut, Katharina E., den Hoed, Marcel, Degenhardt, Frauke, Trompet, Stella, van den Berg, Marten E., Pistis, Giorgio, Tham, Yih-Chung, Weiss, Stefan, Sim, Xueling S., Li, Hengtong L., van der Most, Peter J., Nolte, Ilja M., Lyytikäinen, Leo-Pekka, Said, M. Abdullah, Witte, Daniel R., Iribarren, Carlos, Launer, Lenore, Ring, Susan M., de Vries, Paul S., Sever, Peter, Linneberg, Allan, Bottinger, Erwin P., Padmanabhan, Sandosh, Psaty, Bruce M., Sotoodehnia, Nona, Kolcic, Ivana, Arnar, David O., Gudbjartsson, Daniel F., Holm, Hilma, Balkau, Beverley, Silva, Claudia T., Newton-Cheh, Christopher H., Nikus, Kjell, Salo, Perttu, Mohlke, Karen L., Peyser, Patricia A., Schunkert, Heribert, Lorentzon, Mattias, Lahti, Jari, Rao, Dabeeru C., Cornelis, Marilyn C., Faul, Jessica D., Smith, Jennifer A., Stolarz-Skrzypek, Katarzyna, Bandinelli, Stefania, Concas, Maria Pina, Sinagra, Gianfranco, Meitinger, Thomas, Waldenberger, Melanie, Sinner, Moritz F., Strauch, Konstantin, Delgado, Graciela E., Taylor, Kent D., Yao, Jie, Foco, Luisa, Melander, Olle, de Graaf, Jacqueline, de Mutsert, Renée, de Geus, Eco J. C., Johansson, Åsa, Joshi, Peter K., Lind, Lars, Franke, Andre, Macfarlane, Peter W., Tarasov, Kirill V., Tan, Nicholas, Felix, Stephan B., Tai, E-Shyong, Quek, Debra Q., Snieder, Harold, Ormel, Johan, Ingelsson, Martin, Lindgren, Cecilia, Morris, Andrew P., Raitakari, Olli T., Hansen, Torben, Assimes, Themistocles, Gudnason, Vilmundur, Timpson, Nicholas J., Morrison, Alanna C., Munroe, Patricia B., Strachan, David P., Grarup, Niels, Loos, Ruth J. F., Heckbert, Susan R., Vollenweider, Peter, Hayward, Caroline, Stefansson, Kari, Froguel, Philippe, Groop, Leif, Wareham, Nicholas J., van Duijn, Cornelia M., Feitosa, Mary F., O’Donnell, Christopher J., Kähönen, Mika, Perola, Markus, Boehnke, Michael, Kardia, Sharon L. R., Erdmann, Jeanette, Palmer, Colin N. A., Ohlsson, Claes, Porteous, David J., Eriksson, Johan G., Bouchard, Claude, Moebus, Susanne, Kraft, Peter, Weir, David R., Cusi, Daniele, Ferrucci, Luigi, Ulivi, Sheila, Girotto, Giorgia, Correa, Adolfo, Kääb, Stefan, Peters, Annette, Chambers, John C., Kooner, Jaspal S., März, Winfried, Rotter, Jerome I., Hicks, Andrew A., Smith, J. Gustav, Kiemeney, Lambertus A. L. M., Mook-Kanamori, Dennis O., Penninx, Brenda W. J. H., Gyllensten, Ulf, Wilson, James F., Burgess, Stephen, Sundström, Johan, Lieb, Wolfgang, Jukema, J. Wouter, Eijgelsheim, Mark, Lakatta, Edward L. M., Cheng, Ching-Yu, Dörr, Marcus, Wong, Tien-Yin, Sabanayagam, Charumathi, Oldehinkel, Albertine J., Riese, Harriette, Lehtimäki, Terho, Verweij, Niek, and van der Harst, Pim

Published
2023
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4. Genome-wide association analyses of physical activity and sedentary behavior provide insights into underlying mechanisms and roles in disease prevention

Author

Wang, Zhe, Emmerich, Andrew, Pillon, Nicolas J., Moore, Tim, Hemerich, Daiane, Cornelis, Marilyn C., Mazzaferro, Eugenia, Broos, Siacia, Ahluwalia, Tarunveer S., Bartz, Traci M., Bentley, Amy R., Bielak, Lawrence F., Chong, Mike, Chu, Audrey Y., Berry, Diane, Dorajoo, Rajkumar, Dueker, Nicole D., Kasbohm, Elisa, Feenstra, Bjarke, Feitosa, Mary F., Gieger, Christian, Graff, Mariaelisa, Hall, Leanne M., Haller, Toomas, Hartwig, Fernando P., Hillis, David A., Huikari, Ville, Heard-Costa, Nancy, Holzapfel, Christina, Jackson, Anne U., Johansson, Åsa, Jørgensen, Anja Moltke, Kaakinen, Marika A., Karlsson, Robert, Kerr, Kathleen F., Kim, Boram, Koolhaas, Chantal M., Kutalik, Zoltan, Lagou, Vasiliki, Lind, Penelope A., Lorentzon, Mattias, Lyytikäinen, Leo-Pekka, Mangino, Massimo, Metzendorf, Christoph, Monroe, Kristine R., Pacolet, Alexander, Pérusse, Louis, Pool, Rene, Richmond, Rebecca C., Rivera, Natalia V., Robiou-du-Pont, Sebastien, Schraut, Katharina E., Schulz, Christina-Alexandra, Stringham, Heather M., Tanaka, Toshiko, Teumer, Alexander, Turman, Constance, van der Most, Peter J., Vanmunster, Mathias, van Rooij, Frank J. A., van Vliet-Ostaptchouk, Jana V., Zhang, Xiaoshuai, Zhao, Jing-Hua, Zhao, Wei, Balkhiyarova, Zhanna, Balslev-Harder, Marie N., Baumeister, Sebastian E., Beilby, John, Blangero, John, Boomsma, Dorret I., Brage, Soren, Braund, Peter S., Brody, Jennifer A., Bruinenberg, Marcel, Ekelund, Ulf, Liu, Ching-Ti, Cole, John W., Collins, Francis S., Cupples, L. Adrienne, Esko, Tõnu, Enroth, Stefan, Faul, Jessica D., Fernandez-Rhodes, Lindsay, Fohner, Alison E., Franco, Oscar H., Galesloot, Tessel E., Gordon, Scott D., Grarup, Niels, Hartman, Catharina A., Heiss, Gerardo, Hui, Jennie, Illig, Thomas, Jago, Russell, James, Alan, Joshi, Peter K., Jung, Taeyeong, Kähönen, Mika, Kilpeläinen, Tuomas O., Koh, Woon-Puay, Kolcic, Ivana, Kraft, Peter P., Kuusisto, Johanna, Launer, Lenore J., Li, Aihua, Linneberg, Allan, Luan, Jian’an, Vidal, Pedro Marques, Medland, Sarah E., Milaneschi, Yuri, Moscati, Arden, Musk, Bill, Nelson, Christopher P., Nolte, Ilja M., Pedersen, Nancy L., Peters, Annette, Peyser, Patricia A., Power, Christine, Raitakari, Olli T., Reedik, Mägi, Reiner, Alex P., Ridker, Paul M., Rudan, Igor, Ryan, Kathy, Sarzynski, Mark A., Scott, Laura J., Scott, Robert A., Sidney, Stephen, Siggeirsdottir, Kristin, Smith, Albert V., Smith, Jennifer A., Sonestedt, Emily, Strøm, Marin, Tai, E. Shyong, Teo, Koon K., Thorand, Barbara, Tönjes, Anke, Tremblay, Angelo, Uitterlinden, Andre G., Vangipurapu, Jagadish, van Schoor, Natasja, Völker, Uwe, Willemsen, Gonneke, Williams, Kayleen, Wong, Quenna, Xu, Huichun, Young, Kristin L., Yuan, Jian Min, Zillikens, M. Carola, Zonderman, Alan B., Ameur, Adam, Bandinelli, Stefania, Bis, Joshua C., Boehnke, Michael, Bouchard, Claude, Chasman, Daniel I., Smith, George Davey, de Geus, Eco J. C., Deldicque, Louise, Dörr, Marcus, Evans, Michele K., Ferrucci, Luigi, Fornage, Myriam, Fox, Caroline, Garland, Jr, Theodore, Gudnason, Vilmundur, Gyllensten, Ulf, Hansen, Torben, Hayward, Caroline, Horta, Bernardo L., Hyppönen, Elina, Jarvelin, Marjo-Riitta, Johnson, W. Craig, Kardia, Sharon L. R., Kiemeney, Lambertus A., Laakso, Markku, Langenberg, Claudia, Lehtimäki, Terho, Marchand, Loic Le, Magnusson, Patrik K. E., Martin, Nicholas G., Melbye, Mads, Metspalu, Andres, Meyre, David, North, Kari E., Ohlsson, Claes, Oldehinkel, Albertine J., Orho-Melander, Marju, Pare, Guillaume, Park, Taesung, Pedersen, Oluf, Penninx, Brenda W. J. H., Pers, Tune H., Polasek, Ozren, Prokopenko, Inga, Rotimi, Charles N., Samani, Nilesh J., Sim, Xueling, Snieder, Harold, Sørensen, Thorkild I. A., Spector, Tim D., Timpson, Nicholas J., van Dam, Rob M., van der Velde, Nathalie, van Duijn, Cornelia M., Vollenweider, Peter, Völzke, Henry, Voortman, Trudy, Waeber, Gérard, Wareham, Nicholas J., Weir, David R., Wichmann, Heinz-Erich, Wilson, James F., Hevener, Andrea L., Krook, Anna, Zierath, Juleen R., Thomis, Martine A. I., Loos, Ruth J. F., and Hoed, Marcel den

Published
2022
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5. Applying Mendelian randomization to appraise causality in relationships between nutrition and cancer

Author

Wade, Kaitlin H., Yarmolinsky, James, Giovannucci, Edward, Lewis, Sarah J., Millwood, Iona Y., Munafò, Marcus R., Meddens, Fleur, Burrows, Kimberley, Bell, Joshua A., Davies, Neil M., Mariosa, Daniela, Kanerva, Noora, Vincent, Emma E., Smith-Byrne, Karl, Guida, Florence, Gunter, Marc J., Sanderson, Eleanor, Dudbridge, Frank, Burgess, Stephen, Cornelis, Marilyn C., Richardson, Tom G., Borges, Maria Carolina, Bowden, Jack, Hemani, Gibran, Cho, Yoonsu, Spiller, Wes, Richmond, Rebecca C., Carter, Alice R., Langdon, Ryan, Lawlor, Deborah A., Walters, Robin G., Vimaleswaran, Karani Santhanakrishnan, Anderson, Annie, Sandu, Meda R., Tilling, Kate, Davey Smith, George, Martin, Richard M., and Relton, Caroline L.

Published
2022
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6. Assessment of moderate coffee consumption and risk of epithelial ovarian cancer: a Mendelian randomization study

Author

Ong, Jue-Sheng, Hwang, Liang-Dar, Cuellar-Partida, Gabriel, Martin, Nicholas G, Chenevix-Trench, Georgia, Quinn, Michael CJ, Cornelis, Marilyn C, Gharahkhani, Puya, Webb, Penelope M, MacGregor, Stuart, Bryne, Enda, Fasching, Peter A, Hein, Alexander, Burghaus, Stefanie, Beckmann, Matthias W, Lambrechts, Diether, Van Nieuwenhuysen, Els, Vergote, Ignace, Vanderstichele, Adriaan, Swerdlow, Anthony J, Jones, Michael, Orr, Nicholas, Schoemaker, Minouk, Edwards, Digna Velez, Brenton, James, Benítez, Javier, García, María J, Rodriguez-Antona, Cristina, Rossing, Mary Anne, Fortner, Renée T, Riboli, Elio, Chang-Claude, Jenny, Eilber, Ursula, Wang-Gohrke, Shan, Yannoukakos, Drakoulis, Goodman, Marc T, Bogdanova, Natalia, Dörk, Thilo, Duerst, Matthias, Hillemanns, Peter, Runnebaum, Ingo B, Antonenkova, Natalia, Butzow, Ralf, Nevanlinna, Heli, Pelttari, Liisa M, Edwards, Robert P, Kelley, Joseph L, Modugno, Francesmary, Moysich, Kirsten B, Ness, Roberta B, Cannioto, Rikki, Heitz, Florian, Karlan, Beth, Olsson, Håkan, Kjaer, Susanne K, Jensen, Allan, Giles, Graham G, Bruinsma, Fiona, Hildebrandt, Michelle AT, Liang, Dong, Wu, Xifeng, Le Marchand, Loic, Setiawan, V Wendy, Permuth, Jennifer B, Bisogna, Maria, Dao, Fanny, Levine, Douglas A, Cramer, Daniel W, Terry, Kathryn L, Tworoger, Shelley S, Stampfer, Meir, Willet, Walter, Missmer, Stacey, Bjorge, Line, Kopperud, Reidun K, Bischof, Katharina, Thomsen, Liv Cecilie Vestrheim, Kiemeney, Lambertus A, Massuger, Leon FAG, Pejovic, Tanja, Brooks-Wilson, Angela, Olson, Sara H, McGuire, Valerie, Rothstein, Joseph H, Sieh, Weiva, Whittemore, Alice S, Cook, Linda S, Le, Nhu D, Gilks, C Blake, Gronwald, Jacek, Jakubowska, Anna, Lubiński, Jan, Kluz, Tomasz, Wentzensen, Nicolas, Brinton, Louise, Trabert, Britton, and Lissowska, Jolanta

Subjects
Epidemiology, Health Sciences, Clinical Research, Ovarian Cancer, Nutrition, Rare Diseases, Prevention, Cancer, Genetics, 2.1 Biological and endogenous factors, Aetiology, Carcinoma, Ovarian Epithelial, Coffee, Female, Humans, Mendelian Randomization Analysis, Odds Ratio, Ovarian Neoplasms, Polymorphism, Single Nucleotide, Risk Factors, Ovarian Cancer Association Consortium, Statistics, Public Health and Health Services, Public health
Abstract

BackgroundCoffee consumption has been shown to be associated with various health outcomes in observational studies. However, evidence for its association with epithelial ovarian cancer (EOC) is inconsistent and it is unclear whether these associations are causal.MethodsWe used single nucleotide polymorphisms associated with (i) coffee and (ii) caffeine consumption to perform Mendelian randomization (MR) on EOC risk. We conducted a two-sample MR using genetic data on 44 062 individuals of European ancestry from the Ovarian Cancer Association Consortium (OCAC), and combined instrumental variable estimates using a Wald-type ratio estimator.ResultsFor all EOC cases, the causal odds ratio (COR) for genetically predicted consumption of one additional cup of coffee per day was 0.92 [95% confidence interval (CI): 0.79, 1.06]. The COR was 0.90 (95% CI: 0.73, 1.10) for high-grade serous EOC. The COR for genetically predicted consumption of an additional 80 mg caffeine was 1.01 (95% CI: 0.92, 1.11) for all EOC cases and 0.90 (95% CI: 0.73, 1.10) for high-grade serous cases.ConclusionsWe found no evidence indicative of a strong association between EOC risk and genetically predicted coffee or caffeine levels. However, our estimates were not statistically inconsistent with earlier observational studies and we were unable to rule out small protective associations.

Published
2018

9. An Expanded Genome-Wide Association Study of Type 2 Diabetes in Europeans

Author

Scott, Robert A, Scott, Laura J, Mägi, Reedik, Marullo, Letizia, Gaulton, Kyle J, Kaakinen, Marika, Pervjakova, Natalia, Pers, Tune H, Johnson, Andrew D, Eicher, John D, Jackson, Anne U, Ferreira, Teresa, Lee, Yeji, Ma, Clement, Steinthorsdottir, Valgerdur, Thorleifsson, Gudmar, Qi, Lu, Van Zuydam, Natalie R, Mahajan, Anubha, Chen, Han, Almgren, Peter, Voight, Ben F, Grallert, Harald, Müller-Nurasyid, Martina, Ried, Janina S, Rayner, William N, Robertson, Neil, Karssen, Lennart C, van Leeuwen, Elisabeth M, Willems, Sara M, Fuchsberger, Christian, Kwan, Phoenix, Teslovich, Tanya M, Chanda, Pritam, Li, Man, Lu, Yingchang, Dina, Christian, Thuillier, Dorothee, Yengo, Loic, Jiang, Longda, Sparso, Thomas, Kestler, Hans A, Chheda, Himanshu, Eisele, Lewin, Gustafsson, Stefan, Frånberg, Mattias, Strawbridge, Rona J, Benediktsson, Rafn, Hreidarsson, Astradur B, Kong, Augustine, Sigurðsson, Gunnar, Kerrison, Nicola D, Luan, Jian'an, Liang, Liming, Meitinger, Thomas, Roden, Michael, Thorand, Barbara, Esko, Tõnu, Mihailov, Evelin, Fox, Caroline, Liu, Ching-Ti, Rybin, Denis, Isomaa, Bo, Lyssenko, Valeriya, Tuomi, Tiinamaija, Couper, David J, Pankow, James S, Grarup, Niels, Have, Christian T, Jørgensen, Marit E, Jørgensen, Torben, Linneberg, Allan, Cornelis, Marilyn C, van Dam, Rob M, Hunter, David J, Kraft, Peter, Sun, Qi, Edkins, Sarah, Owen, Katharine R, Perry, John RB, Wood, Andrew R, Zeggini, Eleftheria, Tajes-Fernandes, Juan, Abecasis, Goncalo R, Bonnycastle, Lori L, Chines, Peter S, Stringham, Heather M, Koistinen, Heikki A, Kinnunen, Leena, Sennblad, Bengt, Mühleisen, Thomas W, Nöthen, Markus M, Pechlivanis, Sonali, Baldassarre, Damiano, Gertow, Karl, Humphries, Steve E, Tremoli, Elena, Klopp, Norman, Meyer, Julia, and Steinbach, Gerald

Subjects
Human Genome, Diabetes, Obesity, Genetics, 2.1 Biological and endogenous factors, Aetiology, Metabolic and endocrine, Diabetes Mellitus, Type 2, Gene Expression Regulation, Genetic Variation, Genome-Wide Association Study, Humans, White People, DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium, Medical and Health Sciences, Endocrinology & Metabolism
Abstract

To characterize type 2 diabetes (T2D)-associated variation across the allele frequency spectrum, we conducted a meta-analysis of genome-wide association data from 26,676 T2D case and 132,532 control subjects of European ancestry after imputation using the 1000 Genomes multiethnic reference panel. Promising association signals were followed up in additional data sets (of 14,545 or 7,397 T2D case and 38,994 or 71,604 control subjects). We identified 13 novel T2D-associated loci (P < 5 × 10-8), including variants near the GLP2R, GIP, and HLA-DQA1 genes. Our analysis brought the total number of independent T2D associations to 128 distinct signals at 113 loci. Despite substantially increased sample size and more complete coverage of low-frequency variation, all novel associations were driven by common single nucleotide variants. Credible sets of potentially causal variants were generally larger than those based on imputation with earlier reference panels, consistent with resolution of causal signals to common risk haplotypes. Stratification of T2D-associated loci based on T2D-related quantitative trait associations revealed tissue-specific enrichment of regulatory annotations in pancreatic islet enhancers for loci influencing insulin secretion and in adipocytes, monocytes, and hepatocytes for insulin action-associated loci. These findings highlight the predominant role played by common variants of modest effect and the diversity of biological mechanisms influencing T2D pathophysiology.

Published
2017

10. Genome-wide association meta-analysis of fish and EPA+DHA consumption in 17 US and European cohorts

Author

Mozaffarian, Dariush, Dashti, Hassan S, Wojczynski, Mary K, Chu, Audrey Y, Nettleton, Jennifer A, Männistö, Satu, Kristiansson, Kati, Reedik, Mägi, Lahti, Jari, Houston, Denise K, Cornelis, Marilyn C, van Rooij, Frank JA, Dimitriou, Maria, Kanoni, Stavroula, Mikkilä, Vera, Steffen, Lyn M, de Oliveira Otto, Marcia C, Qi, Lu, Psaty, Bruce, Djousse, Luc, Rotter, Jerome I, Harald, Kennet, Perola, Markus, Rissanen, Harri, Jula, Antti, Krista, Fischer, Mihailov, Evelin, Feitosa, Mary F, Ngwa, Julius S, Xue, Luting, Jacques, Paul F, Perälä, Mia-Maria, Palotie, Aarno, Liu, Yongmei, Nalls, Nike A, Ferrucci, Luigi, Hernandez, Dena, Manichaikul, Ani, Tsai, Michael Y, Jong, Jessica C Kiefte-de, Hofman, Albert, Uitterlinden, André G, Rallidis, Loukianos, Ridker, Paul M, Rose, Lynda M, Buring, Julie E, Lehtimäki, Terho, Kähönen, Mika, Viikari, Jorma, Lemaitre, Rozenn, Salomaa, Veikko, Knekt, Paul, Metspalu, Andres, Borecki, Ingrid B, Cupples, L Adrienne, Eriksson, Johan G, Kritchevsky, Stephen B, Bandinelli, Stefania, Siscovick, David, Franco, Oscar H, Deloukas, Panos, Dedoussis, George, Chasman, Daniel I, Raitakari, Olli, and Tanaka, Toshiko

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Epidemiology, Health Sciences, Nutrition and Dietetics, Complementary and Integrative Health, Human Genome, Nutrition, Aging, Prevention, Obesity, Stroke, Cardiovascular, Oral and gastrointestinal, Adult, Aged, Cohort Studies, Docosahexaenoic Acids, Eicosapentaenoic Acid, Europe, Female, Genome-Wide Association Study, Humans, Male, Middle Aged, Seafood, United States, White People, General Science & Technology
Abstract

BackgroundRegular fish and omega-3 consumption may have several health benefits and are recommended by major dietary guidelines. Yet, their intakes remain remarkably variable both within and across populations, which could partly owe to genetic influences.ObjectiveTo identify common genetic variants that influence fish and dietary eicosapentaenoic acid plus docosahexaenoic acid (EPA+DHA) consumption.DesignWe conducted genome-wide association (GWA) meta-analysis of fish (n = 86,467) and EPA+DHA (n = 62,265) consumption in 17 cohorts of European descent from the CHARGE (Cohorts for Heart and Aging Research in Genomic Epidemiology) Consortium Nutrition Working Group. Results from cohort-specific GWA analyses (additive model) for fish and EPA+DHA consumption were adjusted for age, sex, energy intake, and population stratification, and meta-analyzed separately using fixed-effect meta-analysis with inverse variance weights (METAL software). Additionally, heritability was estimated in 2 cohorts.ResultsHeritability estimates for fish and EPA+DHA consumption ranged from 0.13-0.24 and 0.12-0.22, respectively. A significant GWA for fish intake was observed for rs9502823 on chromosome 6: each copy of the minor allele (FreqA = 0.015) was associated with 0.029 servings/day (~1 serving/month) lower fish consumption (P = 1.96x10-8). No significant association was observed for EPA+DHA, although rs7206790 in the obesity-associated FTO gene was among top hits (P = 8.18x10-7). Post-hoc calculations demonstrated 95% statistical power to detect a genetic variant associated with effect size of 0.05% for fish and 0.08% for EPA+DHA.ConclusionsThese novel findings suggest that non-genetic personal and environmental factors are principal determinants of the remarkable variation in fish consumption, representing modifiable targets for increasing intakes among all individuals. Genes underlying the signal at rs72838923 and mechanisms for the association warrant further investigation.

Published
2017

13. Transforming Big Data into AI‐ready data for nutrition and obesity research

Author

Thomas, Diana M., primary, Knight, Rob, additional, Gilbert, Jack A., additional, Cornelis, Marilyn C., additional, Gantz, Marie G., additional, Burdekin, Kate, additional, Cummiskey, Kevin, additional, Sumner, Susan C. J., additional, Pathmasiri, Wimal, additional, Sazonov, Edward, additional, Gabriel, Kelley Pettee, additional, Dooley, Erin E., additional, Green, Mark A., additional, Pfluger, Andrew, additional, and Kleinberg, Samantha, additional

Published
2024
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14. Control Function Assisted IPW Estimation with a Secondary Outcome in Case-Control Studies

Author

Sofer, Tamar, Cornelis, Marilyn C., Kraft, Peter, and Tchetgen, Eric J. Tchetgen

Subjects
Statistics - Methodology
Abstract

Case-control studies are designed towards studying associations between risk factors and a single, primary outcome. Information about additional, secondary outcomes is also collected, but association studies targeting such secondary outcomes should account for the case-control sampling scheme, or otherwise results may be biased. Often, one uses inverse probability weighted (IPW) estimators to estimate population effects in such studies. However, these estimators are inefficient relative to estimators that make additional assumptions about the data generating mechanism. We propose a class of estimators for the effect of risk factors on a secondary outcome in case-control studies, when the mean is modeled using either the identity or the log link. The proposed estimator combines IPW with a mean zero control function that depends explicitly on a model for the primary disease outcome. The efficient estimator in our class of estimators reduces to standard IPW when the model for the primary disease outcome is unrestricted, and is more efficient than standard IPW when the model is either parametric or semiparametric.

Published
2014

16. Genetic fine mapping and genomic annotation defines causal mechanisms at type 2 diabetes susceptibility loci

Author

Gaulton, Kyle J, Ferreira, Teresa, Lee, Yeji, Raimondo, Anne, Mägi, Reedik, Reschen, Michael E, Mahajan, Anubha, Locke, Adam, William Rayner, N, Robertson, Neil, Scott, Robert A, Prokopenko, Inga, Scott, Laura J, Green, Todd, Sparso, Thomas, Thuillier, Dorothee, Yengo, Loic, Grallert, Harald, Wahl, Simone, Frånberg, Mattias, Strawbridge, Rona J, Kestler, Hans, Chheda, Himanshu, Eisele, Lewin, Gustafsson, Stefan, Steinthorsdottir, Valgerdur, Thorleifsson, Gudmar, Qi, Lu, Karssen, Lennart C, van Leeuwen, Elisabeth M, Willems, Sara M, Li, Man, Chen, Han, Fuchsberger, Christian, Kwan, Phoenix, Ma, Clement, Linderman, Michael, Lu, Yingchang, Thomsen, Soren K, Rundle, Jana K, Beer, Nicola L, van de Bunt, Martijn, Chalisey, Anil, Kang, Hyun Min, Voight, Benjamin F, Abecasis, Gonçalo R, Almgren, Peter, Baldassarre, Damiano, Balkau, Beverley, Benediktsson, Rafn, Blüher, Matthias, Boeing, Heiner, Bonnycastle, Lori L, Bottinger, Erwin P, Burtt, Noël P, Carey, Jason, Charpentier, Guillaume, Chines, Peter S, Cornelis, Marilyn C, Couper, David J, Crenshaw, Andrew T, van Dam, Rob M, Doney, Alex SF, Dorkhan, Mozhgan, Edkins, Sarah, Eriksson, Johan G, Esko, Tonu, Eury, Elodie, Fadista, João, Flannick, Jason, Fontanillas, Pierre, Fox, Caroline, Franks, Paul W, Gertow, Karl, Gieger, Christian, Gigante, Bruna, Gottesman, Omri, Grant, George B, Grarup, Niels, Groves, Christopher J, Hassinen, Maija, Have, Christian T, Herder, Christian, Holmen, Oddgeir L, Hreidarsson, Astradur B, Humphries, Steve E, Hunter, David J, Jackson, Anne U, Jonsson, Anna, Jørgensen, Marit E, Jørgensen, Torben, Kao, Wen-Hong L, Kerrison, Nicola D, Kinnunen, Leena, Klopp, Norman, Kong, Augustine, Kovacs, Peter, Kraft, Peter, Kravic, Jasmina, and Langford, Cordelia

Subjects
Biological Sciences, Genetics, Liver Disease, Diabetes, Human Genome, Digestive Diseases, 2.1 Biological and endogenous factors, Aetiology, Metabolic and endocrine, Binding Sites, Case-Control Studies, Chromatin Immunoprecipitation, Chromosome Mapping, Diabetes Mellitus, Type 2, Gene Expression Regulation, Genetic Loci, Genetic Predisposition to Disease, Genome-Wide Association Study, Genomics, Hepatocyte Nuclear Factor 3-beta, Humans, Islets of Langerhans, Liver, Molecular Sequence Annotation, Polymorphism, Single Nucleotide, Receptor, Melatonin, MT2, DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

We performed fine mapping of 39 established type 2 diabetes (T2D) loci in 27,206 cases and 57,574 controls of European ancestry. We identified 49 distinct association signals at these loci, including five mapping in or near KCNQ1. 'Credible sets' of the variants most likely to drive each distinct signal mapped predominantly to noncoding sequence, implying that association with T2D is mediated through gene regulation. Credible set variants were enriched for overlap with FOXA2 chromatin immunoprecipitation binding sites in human islet and liver cells, including at MTNR1B, where fine mapping implicated rs10830963 as driving T2D association. We confirmed that the T2D risk allele for this SNP increases FOXA2-bound enhancer activity in islet- and liver-derived cells. We observed allele-specific differences in NEUROD1 binding in islet-derived cells, consistent with evidence that the T2D risk allele increases islet MTNR1B expression. Our study demonstrates how integration of genetic and genomic information can define molecular mechanisms through which variants underlying association signals exert their effects on disease.

Published
2015

17. Directional dominance on stature and cognition in diverse human populations

Author

Joshi, Peter K, Esko, Tonu, Mattsson, Hannele, Eklund, Niina, Gandin, Ilaria, Nutile, Teresa, Jackson, Anne U, Schurmann, Claudia, Smith, Albert V, Zhang, Weihua, Okada, Yukinori, Stančáková, Alena, Faul, Jessica D, Zhao, Wei, Bartz, Traci M, Concas, Maria Pina, Franceschini, Nora, Enroth, Stefan, Vitart, Veronique, Trompet, Stella, Guo, Xiuqing, Chasman, Daniel I, O'Connel, Jeffrey R, Corre, Tanguy, Nongmaithem, Suraj S, Chen, Yuning, Mangino, Massimo, Ruggiero, Daniela, Traglia, Michela, Farmaki, Aliki-Eleni, Kacprowski, Tim, Bjonnes, Andrew, van der Spek, Ashley, Wu, Ying, Giri, Anil K, Yanek, Lisa R, Wang, Lihua, Hofer, Edith, Rietveld, Cornelius A, McLeod, Olga, Cornelis, Marilyn C, Pattaro, Cristian, Verweij, Niek, Baumbach, Clemens, Abdellaoui, Abdel, Warren, Helen R, Vuckovic, Dragana, Mei, Hao, Bouchard, Claude, Perry, John RB, Cappellani, Stefania, Mirza, Saira S, Benton, Miles C, Broeckel, Ulrich, Medland, Sarah E, Lind, Penelope A, Malerba, Giovanni, Drong, Alexander, Yengo, Loic, Bielak, Lawrence F, Zhi, Degui, van der Most, Peter J, Shriner, Daniel, Mägi, Reedik, Hemani, Gibran, Karaderi, Tugce, Wang, Zhaoming, Liu, Tian, Demuth, Ilja, Zhao, Jing Hua, Meng, Weihua, Lataniotis, Lazaros, van der Laan, Sander W, Bradfield, Jonathan P, Wood, Andrew R, Bonnefond, Amelie, Ahluwalia, Tarunveer S, Hall, Leanne M, Salvi, Erika, Yazar, Seyhan, Carstensen, Lisbeth, de Haan, Hugoline G, Abney, Mark, Afzal, Uzma, Allison, Matthew A, Amin, Najaf, Asselbergs, Folkert W, Bakker, Stephan JL, Barr, R Graham, Baumeister, Sebastian E, Benjamin, Daniel J, Bergmann, Sven, Boerwinkle, Eric, Bottinger, Erwin P, Campbell, Archie, Chakravarti, Aravinda, Chan, Yingleong, Chanock, Stephen J, Chen, Constance, and Chen, Y-D Ida

Subjects
Biological Sciences, Genetics, Clinical Research, Human Genome, Biological Evolution, Blood Pressure, Body Height, Cholesterol, LDL, Cognition, Cohort Studies, Educational Status, Female, Forced Expiratory Volume, Genome, Human, Homozygote, Humans, Lung Volume Measurements, Male, Phenotype, General Science & Technology
Abstract

Homozygosity has long been associated with rare, often devastating, Mendelian disorders, and Darwin was one of the first to recognize that inbreeding reduces evolutionary fitness. However, the effect of the more distant parental relatedness that is common in modern human populations is less well understood. Genomic data now allow us to investigate the effects of homozygosity on traits of public health importance by observing contiguous homozygous segments (runs of homozygosity), which are inferred to be homozygous along their complete length. Given the low levels of genome-wide homozygosity prevalent in most human populations, information is required on very large numbers of people to provide sufficient power. Here we use runs of homozygosity to study 16 health-related quantitative traits in 354,224 individuals from 102 cohorts, and find statistically significant associations between summed runs of homozygosity and four complex traits: height, forced expiratory lung volume in one second, general cognitive ability and educational attainment (P < 1 × 10(-300), 2.1 × 10(-6), 2.5 × 10(-10) and 1.8 × 10(-10), respectively). In each case, increased homozygosity was associated with decreased trait value, equivalent to the offspring of first cousins being 1.2 cm shorter and having 10 months' less education. Similar effect sizes were found across four continental groups and populations with different degrees of genome-wide homozygosity, providing evidence that homozygosity, rather than confounding, directly contributes to phenotypic variance. Contrary to earlier reports in substantially smaller samples, no evidence was seen of an influence of genome-wide homozygosity on blood pressure and low density lipoprotein cholesterol, or ten other cardio-metabolic traits. Since directional dominance is predicted for traits under directional evolutionary selection, this study provides evidence that increased stature and cognitive function have been positively selected in human evolution, whereas many important risk factors for late-onset complex diseases may not have been.

Published
2015

18. Revisiting mendelian randomization studies of the effect of body mass index on depression

Author

Walter, Stefan, Kubzansky, Laura D, Koenen, Karestan C, Liang, Liming, Tchetgen, Eric J Tchetgen, Cornelis, Marilyn C, Chang, Shun‐Chiao, Rimm, Eric, Kawachi, Ichiro, and Glymour, M Maria

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Clinical Sciences, Neurosciences, Clinical Research, Depression, Prevention, Mental Health, Aetiology, 2.1 Biological and endogenous factors, Mental health, Good Health and Well Being, Adult, Body Mass Index, Female, Genotype, Humans, Mendelian Randomization Analysis, Middle Aged, Models, Genetic, Polymorphism, Single Nucleotide, Risk Factors, obesity, adiposity, genetic, FTO, causation, instrumental variable analysis, Adiposity, Causation, Genetic, Instrumental variable analysis, Obesity, Clinical sciences
Abstract

Mendelian Randomization studies, which use genetic instrumental variables (IVs) as quasi-experiments to estimate causal effects, report inconsistent findings regarding effects of body mass index (BMI) on mental health. We used genetic IV to estimate effects of BMI on depression and evaluated validity of a commonly used IV. Female Nurse's Health Study participants (n=6989, average age 56.4, [Standard Deviation 6.91] years at first depression assessment) self-reported BMI, which was averaged across eight reports prior to depression assessment (mean=24.96, SD 4.50). Genetic instruments included fat mass and obesity-associated protein (FTO) alleles, melanocortin receptor 4 (MC4R) alleles, and polygenic risk scores based on 32 established polymorphisms for BMI. Depression was assessed using multiple symptom measures, scaled to the Geriatric Depression Scale 15, averaged across up to 7 biennial waves. We used over-identification tests to assess the validity of genetic IVs. In conventional estimates, each additional BMI point predicted 0.024 (95% Confidence Interval (CI): 0.020-0.029) higher average depression scores. Genetic IV estimates were not significant when based on FTO (beta: 0.064, CI: -0.014, 0.142), MC4R (beta: 0.005, CI: -0.146, 0.156), polygenic score excluding FTO (beta=-0.003, 95%-CI -0.051, 0.045), or mechanism-specific scores. The over-identification test comparing IV estimates based on FTO to estimates based on the polygenic score excluding FTO rejected equality of estimated effects (P=0.014). Results provide no evidence against a null effect of BMI on depression and call into question validity of FTO as an instrument for BMI in Mendelian Randomization studies.

Published
2015

20. Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility

Author

Mahajan, Anubha, Go, Min Jin, Zhang, Weihua, Below, Jennifer E, Gaulton, Kyle J, Ferreira, Teresa, Horikoshi, Momoko, Johnson, Andrew D, Ng, Maggie CY, Prokopenko, Inga, Saleheen, Danish, Wang, Xu, Zeggini, Eleftheria, Abecasis, Goncalo R, Adair, Linda S, Almgren, Peter, Atalay, Mustafa, Aung, Tin, Baldassarre, Damiano, Balkau, Beverley, Bao, Yuqian, Barnett, Anthony H, Barroso, Ines, Basit, Abdul, Been, Latonya F, Beilby, John, Bell, Graeme I, Benediktsson, Rafn, Bergman, Richard N, Boehm, Bernhard O, Boerwinkle, Eric, Bonnycastle, Lori L, Burtt, Noël, Cai, Qiuyin, Campbell, Harry, Carey, Jason, Cauchi, Stephane, Caulfield, Mark, Chan, Juliana CN, Chang, Li-Ching, Chang, Tien-Jyun, Chang, Yi-Cheng, Charpentier, Guillaume, Chen, Chien-Hsiun, Chen, Han, Chen, Yuan-Tsong, Chia, Kee-Seng, Chidambaram, Manickam, Chines, Peter S, Cho, Nam H, Cho, Young Min, Chuang, Lee-Ming, Collins, Francis S, Cornelis, Marilyn C, Couper, David J, Crenshaw, Andrew T, van Dam, Rob M, Danesh, John, Das, Debashish, de Faire, Ulf, Dedoussis, George, Deloukas, Panos, Dimas, Antigone S, Dina, Christian, Doney, Alex SF, Donnelly, Peter J, Dorkhan, Mozhgan, van Duijn, Cornelia, Dupuis, Josée, Edkins, Sarah, Elliott, Paul, Emilsson, Valur, Erbel, Raimund, Eriksson, Johan G, Escobedo, Jorge, Esko, Tonu, Eury, Elodie, Florez, Jose C, Fontanillas, Pierre, Forouhi, Nita G, Forsen, Tom, Fox, Caroline, Fraser, Ross M, Frayling, Timothy M, Froguel, Philippe, Frossard, Philippe, Gao, Yutang, Gertow, Karl, Gieger, Christian, Gigante, Bruna, Grallert, Harald, Grant, George B, Groop, Leif C, Groves, Christopher J, Grundberg, Elin, Guiducci, Candace, Hamsten, Anders, Han, Bok-Ghee, Hara, Kazuo, and Hassanali, Neelam

Subjects
Biological Sciences, Genetics, Human Genome, Diabetes, Metabolic and endocrine, Alleles, Asian People, Case-Control Studies, Diabetes Mellitus, Type 2, Genetic Predisposition to Disease, Genome-Wide Association Study, Hispanic or Latino, Humans, Polymorphism, Single Nucleotide, Risk Factors, White People, DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium, Asian Genetic Epidemiology Network Type 2 Diabetes (AGEN-T2D) Consortium, South Asian Type 2 Diabetes (SAT2D) Consortium, Mexican American Type 2 Diabetes (MAT2D) Consortium, Type 2 Diabetes Genetic Exploration by Nex-generation sequencing in muylti-Ethnic Samples (T2D-GENES) Consortium, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

To further understanding of the genetic basis of type 2 diabetes (T2D) susceptibility, we aggregated published meta-analyses of genome-wide association studies (GWAS), including 26,488 cases and 83,964 controls of European, east Asian, south Asian and Mexican and Mexican American ancestry. We observed a significant excess in the directional consistency of T2D risk alleles across ancestry groups, even at SNPs demonstrating only weak evidence of association. By following up the strongest signals of association from the trans-ethnic meta-analysis in an additional 21,491 cases and 55,647 controls of European ancestry, we identified seven new T2D susceptibility loci. Furthermore, we observed considerable improvements in the fine-mapping resolution of common variant association signals at several T2D susceptibility loci. These observations highlight the benefits of trans-ethnic GWAS for the discovery and characterization of complex trait loci and emphasize an exciting opportunity to extend insight into the genetic architecture and pathogenesis of human diseases across populations of diverse ancestry.

Published
2014

21. A Genome-Wide Association Study of Depressive Symptoms

Author

Hek, Karin, Demirkan, Ayse, Lahti, Jari, Terracciano, Antonio, Teumer, Alexander, Cornelis, Marilyn C, Amin, Najaf, Bakshis, Erin, Baumert, Jens, Ding, Jingzhong, Liu, Yongmei, Marciante, Kristin, Meirelles, Osorio, Nalls, Michael A, Sun, Yan V, Vogelzangs, Nicole, Yu, Lei, Bandinelli, Stefania, Benjamin, Emelia J, Bennett, David A, Boomsma, Dorret, Cannas, Alessandra, Coker, Laura H, de Geus, Eco, De Jager, Philip L, Diez-Roux, Ana V, Purcell, Shaun, Hu, Frank B, Rimm, Eric B, Hunter, David J, Jensen, Majken K, Curhan, Gary, Rice, Kenneth, Penman, Alan D, Rotter, Jerome I, Sotoodehnia, Nona, Emeny, Rebecca, Eriksson, Johan G, Evans, Denis A, Ferrucci, Luigi, Fornage, Myriam, Gudnason, Vilmundur, Hofman, Albert, Illig, Thomas, Kardia, Sharon, Kelly-Hayes, Margaret, Koenen, Karestan, Kraft, Peter, Kuningas, Maris, Massaro, Joseph M, Melzer, David, Mulas, Antonella, Mulder, Cornelis L, Murray, Anna, Oostra, Ben A, Palotie, Aarno, Penninx, Brenda, Petersmann, Astrid, Pilling, Luke C, Psaty, Bruce, Rawal, Rajesh, Reiman, Eric M, Schulz, Andrea, Shulman, Joshua M, Singleton, Andrew B, Smith, Albert V, Sutin, Angelina R, Uitterlinden, André G, Völzke, Henry, Widen, Elisabeth, Yaffe, Kristine, Zonderman, Alan B, Cucca, Francesco, Harris, Tamara, Ladwig, Karl-Heinz, Llewellyn, David J, Räikkönen, Katri, Tanaka, Toshiko, van Duijn, Cornelia M, Grabe, Hans J, Launer, Lenore J, Lunetta, Kathryn L, Mosley, Thomas H, Newman, Anne B, Tiemeier, Henning, and Murabito, Joanne

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Mental Illness, Clinical Research, Brain Disorders, Depression, Human Genome, Mental Health, 2.1 Biological and endogenous factors, Aged, Aged, 80 and over, Chromosomes, Human, Pair 5, Female, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Male, Middle Aged, Polymorphism, Single Nucleotide, Center for Epidemiologic Studies Depression Scale, CHARGE consortium, depression, depressive symptoms, genetics, genome-wide association study, meta-analysis, Medical and Health Sciences, Psychology and Cognitive Sciences, Psychiatry, Biological sciences, Biomedical and clinical sciences, Psychology
Abstract

BackgroundDepression is a heritable trait that exists on a continuum of varying severity and duration. Yet, the search for genetic variants associated with depression has had few successes. We exploit the entire continuum of depression to find common variants for depressive symptoms.MethodsIn this genome-wide association study, we combined the results of 17 population-based studies assessing depressive symptoms with the Center for Epidemiological Studies Depression Scale. Replication of the independent top hits (p

Published
2013

22. A genome-wide association study of early menopause and the combined impact of identified variants

Author

Perry, John RB, Corre, Tanguy, Esko, Tõnu, Chasman, Daniel I, Fischer, Krista, Franceschini, Nora, He, Chunyan, Kutalik, Zoltan, Mangino, Massimo, Rose, Lynda M, Smith, Albert Vernon, Stolk, Lisette, Sulem, Patrick, Weedon, Michael N, Zhuang, Wei V, Arnold, Alice, Ashworth, Alan, Bergmann, Sven, Buring, Julie E, Burri, Andrea, Chen, Constance, Cornelis, Marilyn C, Couper, David J, Goodarzi, Mark O, Gudnason, Vilmundur, Harris, Tamara, Hofman, Albert, Jones, Michael, Kraft, Peter, Launer, Lenore, Laven, Joop SE, Li, Guo, McKnight, Barbara, Masciullo, Corrado, Milani, Lili, Orr, Nicholas, Psaty, Bruce M, Ridker, Paul M, Rivadeneira, Fernando, Sala, Cinzia, Salumets, Andres, Schoemaker, Minouk, Traglia, Michela, Waeber, Gérard, Chanock, Stephen J, Demerath, Ellen W, Garcia, Melissa, Hankinson, Susan E, Hu, Frank B, Hunter, David J, Lunetta, Kathryn L, Metspalu, Andres, Montgomery, Grant W, Murabito, Joanne M, Newman, Anne B, Ong, Ken K, Spector, Tim D, Stefansson, Kari, Swerdlow, Anthony J, Thorsteinsdottir, Unnur, Van Dam, Rob M, Uitterlinden, André G, Visser, Jenny A, Vollenweider, Peter, Toniolo, Daniela, and Murray, Anna

Subjects
Biotechnology, Contraception/Reproduction, Infertility, Genetics, Human Genome, Aging, Estrogen, Prevention, Aetiology, 2.1 Biological and endogenous factors, Reproductive health and childbirth, Good Health and Well Being, Case-Control Studies, Female, Gene Frequency, Genome-Wide Association Study, Humans, Menopause, Premature, Polymorphism, Single Nucleotide, Primary Ovarian Insufficiency, Quantitative Trait Loci, Risk, ReproGen Consortium, Biological Sciences, Medical and Health Sciences, Genetics & Heredity
Abstract

Early menopause (EM) affects up to 10% of the female population, reducing reproductive lifespan considerably. Currently, it constitutes the leading cause of infertility in the western world, affecting mainly those women who postpone their first pregnancy beyond the age of 30 years. The genetic aetiology of EM is largely unknown in the majority of cases. We have undertaken a meta-analysis of genome-wide association studies (GWASs) in 3493 EM cases and 13 598 controls from 10 independent studies. No novel genetic variants were discovered, but the 17 variants previously associated with normal age at natural menopause as a quantitative trait (QT) were also associated with EM and primary ovarian insufficiency (POI). Thus, EM has a genetic aetiology which overlaps variation in normal age at menopause and is at least partly explained by the additive effects of the same polygenic variants. The combined effect of the common variants captured by the single nucleotide polymorphism arrays was estimated to account for ∼30% of the variance in EM. The association between the combined 17 variants and the risk of EM was greater than the best validated non-genetic risk factor, smoking.

Published
2013

33. Measuring alcohol consumption for genomic meta-analyses of alcohol intake: opportunities and challenges

Author

Agrawal, Arpana, Freedman, Neal D, Cheng, Yu-Ching, Lin, Peng, Shaffer, John R, Sun, Qi, Taylor, Kira, Yaspan, Brian, Cole, John W, Cornelis, Marilyn C, DeSensi, Rebecca S, Fitzpatrick, Annette, Heiss, Gerardo, Kang, Jae H, O’Connell, Jeffrey, Bennett, Siiri, Bookman, Ebony, Bucholz, Kathleen K, Caporaso, Neil, Crout, Richard, Dick, Danielle M, Edenberg, Howard J, Goate, Alison, Hesselbrock, Victor, Kittner, Steven, Kramer, John, Nurnberger, John I, Jr, Qi, Lu, Rice, John P, Schuckit, Marc, van Dam, Rob M, Boerwinkle, Eric, Hu, Frank, Levy, Steven, Marazita, Mary, Mitchell, Braxton D, Pasquale, Louis R, and Bierut, Laura J

Published
2012
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34. 1000 Genomes-based meta-analysis identifies 10 novel loci for kidney function

Author

Gorski, Mathias, van der Most, Peter J., Teumer, Alexander, Chu, Audrey Y., Li, Man, Mijatovic, Vladan, Nolte, Ilja M., Cocca, Massimiliano, Taliun, Daniel, Gomez, Felicia, Li, Yong, Tayo, Bamidele, Tin, Adrienne, Feitosa, Mary F., Aspelund, Thor, Attia, John, Biffar, Reiner, Bochud, Murielle, Boerwinkle, Eric, Borecki, Ingrid, Bottinger, Erwin P., Chen, Ming-Huei, Chouraki, Vincent, Ciullo, Marina, Coresh, Josef, Cornelis, Marilyn C., Curhan, Gary C., d’Adamo, Adamo Pio, Dehghan, Abbas, Dengler, Laura, Ding, Jingzhong, Eiriksdottir, Gudny, Endlich, Karlhans, Enroth, Stefan, Esko, Tõnu, Franco, Oscar H., Gasparini, Paolo, Gieger, Christian, Girotto, Giorgia, Gottesman, Omri, Gudnason, Vilmundur, Gyllensten, Ulf, Hancock, Stephen J., Harris, Tamara B., Helmer, Catherine, Höllerer, Simon, Hofer, Edith, Hofman, Albert, Holliday, Elizabeth G., Homuth, Georg, Hu, Frank B., Huth, Cornelia, Hutri-Kähönen, Nina, Hwang, Shih-Jen, Imboden, Medea, Johansson, Åsa, Kähönen, Mika, König, Wolfgang, Kramer, Holly, Krämer, Bernhard K., Kumar, Ashish, Kutalik, Zoltan, Lambert, Jean-Charles, Launer, Lenore J., Lehtimäki, Terho, de Borst, Martin H., Navis, Gerjan, Swertz, Morris, Liu, Yongmei, Lohman, Kurt, Loos, Ruth J. F., Lu, Yingchang, Lyytikäinen, Leo-Pekka, McEvoy, Mark A., Meisinger, Christa, Meitinger, Thomas, Metspalu, Andres, Metzger, Marie, Mihailov, Evelin, Mitchell, Paul, Nauck, Matthias, Oldehinkel, Albertine J., Olden, Matthias, WJH Penninx, Brenda, Pistis, Giorgio, Pramstaller, Peter P., Probst-Hensch, Nicole, Raitakari, Olli T., Rettig, Rainer, Ridker, Paul M., Rivadeneira, Fernando, Robino, Antonietta, Rosas, Sylvia E., Ruderfer, Douglas, Ruggiero, Daniela, Saba, Yasaman, Sala, Cinzia, Schmidt, Helena, Schmidt, Reinhold, Scott, Rodney J., Sedaghat, Sanaz, Smith, Albert V., Sorice, Rossella, Stengel, Benedicte, Stracke, Sylvia, Strauch, Konstantin, Toniolo, Daniela, Uitterlinden, Andre G., Ulivi, Sheila, Viikari, Jorma S., Völker, Uwe, Vollenweider, Peter, Völzke, Henry, Vuckovic, Dragana, Waldenberger, Melanie, Jin Wang, Jie, Yang, Qiong, Chasman, Daniel I., Tromp, Gerard, Snieder, Harold, Heid, Iris M., Fox, Caroline S., Köttgen, Anna, Pattaro, Cristian, Böger, Carsten A., and Fuchsberger, Christian

Published
2017
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39. MIND Dietary Pattern and Its Association with Cognition and Incident Dementia in the UK Biobank.

Author

Cornelis, Marilyn C., Agarwal, Puja, Holland, Thomas M., and van Dam, Rob M.

Abstract

A high adherence to the Mediterranean-Dietary Approaches to Stop Hypertension Diet Intervention for Neurodegenerative Delay (MIND) has been associated with better cognition and a lower risk of dementia in some but not all studies. We measured adherence to MIND and its association with cognitive health in the UK Biobank (UKB). A MIND score was derived from 24 h diet recall questionnaires for 120,661 participants who completed at least one of seven self-administered cognitive function tests. In a subset of 78,663 participants aged 55+, diagnosis of dementia was determined by linked hospital and death records. Multivariable regression and Cox proportional hazard ratio (HR) models were used to examine associations of MIND with cognitive ability and incident dementia. Higher adherence to MIND was associated with a small but significant worsening in performance on five of seven cognitive tests (p < 0.002). Associations were strongest among highly educated participants (p < 0.002 for MIND × education interaction). After a mean follow-up time of 10.5 years, 842 participants developed dementia. Overall, MIND adherence was not associated with incident dementia. An inverse association was observed among females (HR = 0.87 per score standard deviation (SD), p = 0.008) but not males (HR = 1.09, p = 0.11) (p = 0.008 for MIND × sex interaction). Similar associations with cognitive ability and dementia were observed for the Alternative Healthy Eating Index-2010 (AHEI-2010) dietary pattern. Associations were not modified by genetic susceptibility. In UKB, the MIND diet was not associated with better cognitive test scores and only with lower dementia risk in women. [ABSTRACT FROM AUTHOR]

Published
2023
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41. Using genetics to test the causal relationship of total adiposity and periodontitis: Mendelian randomization analyses in the Gene-Lifestyle Interactions and Dental Endpoints (GLIDE) Consortium

Author

Shungin, Dmitry, Cornelis, Marilyn C, Divaris, Kimon, Holtfreter, Birte, Shaffer, John R, Yu, Yau-Hua, Barros, Silvana P, Beck, James D, Biffar, Reiner, Boerwinkle, Eric A, Crout, Richard J., Ganna, Andrea, Hallmans, Goran, Hindy, George, Hu, Frank B, Kraft, Peter, McNeil, Daniel W, Melander, Olle, Moss, Kevin L, North, Kari E, Orho-Melander, Marju, Pedersen, Nancy L, Ridker, Paul M, Rimm, Eric B, Rose, Lynda M, Rukh, Gull, Teumer, Alexander, Weyant, Robert J, Chasman, Daniel I, Joshipura, Kaumudi, Kocher, Thomas, Magnusson, Patrik KE, Marazita, Mary L, Nilsson, Peter, Offenbacher, Steve, Davey Smith, George, Lundberg, Pernilla, Palmer, Tom M, Timpson, Nicholas J, Johansson, Ingegerd, and Franks, Paul W

Published
2015
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47. Applying Mendelian randomization to appraise causality in relationships between nutrition and cancer

Author

Wade, Kaitlin, primary, Yarmolinsky, James, additional, Giovannucci, Edward, additional, Lewis, Sarah J., additional, Millwood, Iona Y, additional, Munafo, Marcus Robert, additional, Meddens, Fleur, additional, Burrows, Kimberley, additional, Bell, Joshua A, additional, Davies, Neil Martin, additional, Mariosa, Daniela, additional, Kanerva, Noora, additional, Vincent, Emma E, additional, Smith-Byrne, Karl, additional, Guida, Florence, additional, Gunter, Marc J., additional, Sanderson, Eleanor, additional, Dudbridge, Frank, additional, Burgess, Stephen, additional, Cornelis, Marilyn C, additional, Richardson, Tom, additional, Borges, Maria Carolina, additional, Bowden, Jack, additional, Hemani, Gibran, additional, Cho, Yoonsu, additional, Spiller, Wes, additional, Richmond, Rebecca, additional, Carter, Alice, additional, Langdon, Ryan, additional, Lawlor, Deborah A, additional, Walters, Robin G, additional, Vimaleswaran, Karani Santhanakrishnan, additional, Anderson, Annie, additional, Sandu, Meda, additional, Tilling, Kate, additional, Smith, George Davey, additional, Martin, Richard, additional, Relton, Caroline, additional, and group, in Nutrition and Cancer working, additional

Published
2021
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48. Model-based assessment of replicability for genome-wide association meta-analysis

Author

McGuire, Daniel, Jiang, Yu, Liu, Mengzhen, Weissenkampen, J. Dylan, Eckert, Scott, Yang, Lina, Chen, Fang, Liu, MengZhen, Wedow, Robbee, Li, Yue, Brazel, David M., Datta, Gargi, Davila-Velderrain, Jose, Tian, Chao, Zhan, Xiaowei, Choquet, H. éléne, Docherty, Anna R., Faul, Jessica D., Foerster, Johanna R., Fritsche, Lars, Gabrielsen, Maiken Elvestad, Gordon, Scott D., Haessler, Jeffrey, Hottenga, Jouke-Jan, Huang, Hongyan, Jang, Seon-Kyeong, Jansen, Philip R., Ling, Yueh, Ma ̈gi, Reedik, Matoba, Nana, McMahon, George, Mulas, Antonella, Orru, Valeria, Palviainen, Teemu, Pandit, Anita, Reginsson, Gunnar W., Skogholt, Anne Heidi, Smith, Jennifer A., Taylor, Amy E., Turman, Constance, Willemsen, Gonneke, Young, Hannah, Young, Kendra A., Zajac, Gregory J. M., Zhao, Wei, Zhou, Wei, Bjornsdottir, Gyda, Boardman, Jason D., Boehnke, Michael, Boomsma, Dorret I., Chen, Chu, Cucca, Francesco, Davies, Gareth E., Eaton, Charles B., Ehringer, Marissa A., Esko, Tõnu, Fiorillo, Edoardo, Gillespie, Nathan A., Gudbjartsson, Daniel F., Haller, Toomas, Harris, Kathleen Mullan, Heath, Andrew C., Hewitt, John K., Hickie, Ian B., Hokanson, John E., Hopfer, Christian J., Hunter, David J., Iacono, William G., Johnson, Eric O., Kamatani, Yoichiro, Kardia, Sharon L. R., Keller, Matthew C., Kellis, Manolis, Kooperberg, Charles, Kraft, Peter, Krauter, Kenneth S., Laakso, Markku, Lind, Penelope A., Loukola, Anu, Lutz, Sharon M., Madden, Pamela A. F., Martin, Nicholas G., McGue, Matt, McQueen, Matthew B., Medland, Sarah E., Metspalu, Andres, Mohlke, Karen L., Nielsen, Jonas B., Okada, Yukinori, Peters, Ulrike, Polderman, Tinca J. C., Posthuma, Danielle, Reiner, Alexander P., Rice, JP, Rimm, Eric, Rose, Richard J., Runarsdottir, Valgerdur, Stallings, Michael C., Stanˇca ́kova, Alena, Stefansson, Hreinn, Thai, Khanh K., Tindle, Hilary A., Tyrfingsson, Thorarinn, Wall, Tamara L., Weir, David R., Weisner, Constance M, Whitfield, John B., Winsvold, Bendik K S, Yin, Jie, Zuccolo, Luisa, Bierut, Laura J., Hveem, Kristian, Lee, James J., Munafo, Marcus R., Saccone, Nancy L., Willer, Cristen J, Cornelis, Marilyn C., David, Sean P., Hinds, David, Jorgenson, Eric, Kaprio, Jaakko, Stitzel, Jerry A., Stefansson, Kari, Thorgeirsson, Thorgeir E., Abecasis, Goncalo, Liu, Dajiang J., Vrieze, Scott, Berg, Arthur, Jiang, Bibo, Li, Qunhua, Technology Centre, Institute for Molecular Medicine Finland, Genetic Epidemiology, HUSLAB, Centre of Excellence in Complex Disease Genetics, Jaakko Kaprio / Principal Investigator, Department of Public Health, Human genetics, Amsterdam Neuroscience - Complex Trait Genetics, Amsterdam Neuroscience - Compulsivity, Impulsivity & Attention, APH - Aging & Later Life, APH - Mental Health, Child and Adolescent Psychiatry / Psychology, Biological Psychology, APH - Health Behaviors & Chronic Diseases, APH - Personalized Medicine, Complex Trait Genetics, APH - Methodology, and Clinical Developmental Psychology

Subjects
0301 basic medicine, Genotype, Computer science, Science, General Physics and Astronomy, Genome-wide association study, Genomics, Computational biology, Genome-wide association studies, Polymorphism, Single Nucleotide, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, Consistency (database systems), 0302 clinical medicine, Meta-Analysis as Topic, Replication (statistics), Genetic Association Studies, Multidisciplinary, biology, Models, Genetic, Statistics, Mamba, Computational Biology, Reproducibility of Results, General Chemistry, Replicate, biology.organism_classification, 030104 developmental biology, Phenotype, Sample size determination, Sample Size, 1182 Biochemistry, cell and molecular biology, 3111 Biomedicine, 030217 neurology & neurosurgery, Imputation (genetics), Software, Algorithms, Genome-Wide Association Study
Abstract

Genome-wide association meta-analysis (GWAMA) is an effective approach to enlarge sample sizes and empower the discovery of novel associations between genotype and phenotype. Independent replication has been used as a gold-standard for validating genetic associations. However, as current GWAMA often seeks to aggregate all available datasets, it becomes impossible to find a large enough independent dataset to replicate new discoveries. Here we introduce a method, MAMBA (Meta-Analysis Model-based Assessment of replicability), for assessing the “posterior-probability-of-replicability” for identified associations by leveraging the strength and consistency of association signals between contributing studies. We demonstrate using simulations that MAMBA is more powerful and robust than existing methods, and produces more accurate genetic effects estimates. We apply MAMBA to a large-scale meta-analysis of addiction phenotypes with 1.2 million individuals. In addition to accurately identifying replicable common variant associations, MAMBA also pinpoints novel replicable rare variant associations from imputation-based GWAMA and hence greatly expands the set of analyzable variants., In genome-wide association meta-analysis, it is often difficult to find an independent dataset of sufficient size to replicate associations. Here, the authors have developed MAMBA to calculate the probability of replicability based on consistency between datasets within the meta-analysis.

Published
2021
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