Author: "Ruth J" / Topic: humans - Searchworks@Jio Institute Digital Library Search Results

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869 results on '"Ruth J"'

1. Predicting alcohol dependence from multi‐site brain structural measures

Author: Hahn, Sage, Mackey, Scott, Cousijn, Janna, Foxe, John J, Heinz, Andreas, Hester, Robert, Hutchinson, Kent, Kiefer, Falk, Korucuoglu, Ozlem, Lett, Tristram, Li, Chiang‐Shan R, London, Edythe, Lorenzetti, Valentina, Maartje, Luijten, Momenan, Reza, Orr, Catherine, Paulus, Martin, Schmaal, Lianne, Sinha, Rajita, Sjoerds, Zsuzsika, Stein, Dan J, Stein, Elliot, Holst, Ruth J, Veltman, Dick, Walter, Henrik, Wiers, Reinout W, Yucel, Murat, Thompson, Paul M, Conrod, Patricia, Allgaier, Nicholas, and Garavan, Hugh
Subjects: Biological Psychology, Psychology, Brain Disorders, Neurosciences, Substance Misuse, Alcoholism, Alcohol Use and Health, Neurological, Good Health and Well Being, Alcoholism, Cerebral Cortex, Humans, Machine Learning, Magnetic Resonance Imaging, Multicenter Studies as Topic, Neuroimaging, Putamen, Reproducibility of Results, addiction, alcohol dependence, genetic algorithm, machine learning, multi-site, prediction, structural MRI, Cognitive Sciences, Experimental Psychology, Biological psychology, Cognitive and computational psychology
Abstract: To identify neuroimaging biomarkers of alcohol dependence (AD) from structural magnetic resonance imaging, it may be useful to develop classification models that are explicitly generalizable to unseen sites and populations. This problem was explored in a mega-analysis of previously published datasets from 2,034 AD and comparison participants spanning 27 sites curated by the ENIGMA Addiction Working Group. Data were grouped into a training set used for internal validation including 1,652 participants (692 AD, 24 sites), and a test set used for external validation with 382 participants (146 AD, 3 sites). An exploratory data analysis was first conducted, followed by an evolutionary search based feature selection to site generalizable and high performing subsets of brain measurements. Exploratory data analysis revealed that inclusion of case- and control-only sites led to the inadvertent learning of site-effects. Cross validation methods that do not properly account for site can drastically overestimate results. Evolutionary-based feature selection leveraging leave-one-site-out cross-validation, to combat unintentional learning, identified cortical thickness in the left superior frontal gyrus and right lateral orbitofrontal cortex, cortical surface area in the right transverse temporal gyrus, and left putamen volume as final features. Ridge regression restricted to these features yielded a test-set area under the receiver operating characteristic curve of 0.768. These findings evaluate strategies for handling multi-site data with varied underlying class distributions and identify potential biomarkers for individuals with current AD.
Published: 2022

2. Mapping cortical and subcortical asymmetries in substance dependence: Findings from the ENIGMA Addiction Working Group

Author: Cao, Zhipeng, Ottino‐Gonzalez, Jonatan, Cupertino, Renata B, Schwab, Nathan, Hoke, Colin, Catherine, Orr, Cousijn, Janna, Dagher, Alain, Foxe, John J, Goudriaan, Anna E, Hester, Robert, Hutchison, Kent, Li, Chiang‐Shan R, London, Edythe D, Lorenzetti, Valentina, Luijten, Maartje, Martin‐Santos, Rocio, Momenan, Reza, Paulus, Martin P, Schmaal, Lianne, Sinha, Rajita, Sjoerds, Zsuzsika, Solowij, Nadia, Stein, Dan J, Stein, Elliot A, Uhlmann, Anne, Holst, Ruth J, Veltman, Dick J, Wiers, Reinout W, Yücel, Murat, Zhang, Sheng, Jahanshad, Neda, Thompson, Paul M, Conrod, Patricia, Mackey, Scott, and Garavan, Hugh
Subjects: Biological Psychology, Pharmacology and Pharmaceutical Sciences, Biomedical and Clinical Sciences, Psychology, Substance Misuse, Drug Abuse (NIDA only), Neurosciences, Brain Disorders, Mental health, Good Health and Well Being, Adult, Alcoholism, Behavior, Addictive, Brain, Brain Cortical Thickness, Cerebellar Cortex, Female, Humans, Magnetic Resonance Imaging, Male, Middle Aged, Neuroimaging, Nucleus Accumbens, Substance-Related Disorders, Tobacco Use Disorder, Young Adult, brain asymmetry, mega-analysis, substance dependence, Medical and Health Sciences, Psychology and Cognitive Sciences, Substance Abuse, Biomedical and clinical sciences, Health sciences
Abstract: Brain asymmetry reflects left-right hemispheric differentiation, which is a quantitative brain phenotype that develops with age and can vary with psychiatric diagnoses. Previous studies have shown that substance dependence is associated with altered brain structure and function. However, it is unknown whether structural brain asymmetries are different in individuals with substance dependence compared with nondependent participants. Here, a mega-analysis was performed using a collection of 22 structural brain MRI datasets from the ENIGMA Addiction Working Group. Structural asymmetries of cortical and subcortical regions were compared between individuals who were dependent on alcohol, nicotine, cocaine, methamphetamine, or cannabis (n = 1,796) and nondependent participants (n = 996). Substance-general and substance-specific effects on structural asymmetry were examined using separate models. We found that substance dependence was significantly associated with differences in volume asymmetry of the nucleus accumbens (NAcc; less rightward; Cohen's d = 0.15). This effect was driven by differences from controls in individuals with alcohol dependence (less rightward; Cohen's d = 0.10) and nicotine dependence (less rightward; Cohen's d = 0.11). These findings suggest that disrupted structural asymmetry in the NAcc may be a characteristic of substance dependence.
Published: 2021

3. Is (poly-) substance use associated with impaired inhibitory control? A mega-analysis controlling for confounders.

Author: Liu, Yang, van den Wildenberg, Wery PM, de Graaf, Ysanne, Ames, Susan L, Baldacchino, Alexander, Bø, Ragnhild, Cadaveira, Fernando, Campanella, Salvatore, Christiansen, Paul, Claus, Eric D, Colzato, Lorenza S, Filbey, Francesca M, Foxe, John J, Garavan, Hugh, Hendershot, Christian S, Hester, Robert, Jester, Jennifer M, Karoly, Hollis C, Kräplin, Anja, Kreusch, Fanny, Landrø, Nils Inge, Littel, Marianne, Loeber, Sabine, London, Edythe D, López-Caneda, Eduardo, Lubman, Dan I, Luijten, Maartje, Marczinski, Cecile A, Metrik, Jane, Montgomery, Catharine, Papachristou, Harilaos, Mi Park, Su, Paz, Andres L, Petit, Géraldine, Prisciandaro, James J, Quednow, Boris B, Ray, Lara A, Roberts, Carl A, Roberts, Gloria MP, de Ruiter, Michiel B, Rupp, Claudia I, Steele, Vaughn R, Sun, Delin, Takagi, Michael, Tapert, Susan F, van Holst, Ruth J, Verdejo-Garcia, Antonio, Vonmoos, Matthias, Wojnar, Marcin, Yao, Yuanwei, Yücel, Murat, Zack, Martin, Zucker, Robert A, Huizenga, Hilde M, and Wiers, Reinout W
Subjects: Humans, Substance-Related Disorders, Psychomotor Performance, Executive Function, Inhibition, Psychological, Go/No-Go task, Mega-analysis, Polysubstance use, Response inhibition, Stop-signal task, Prevention, Behavioral and Social Science, Clinical Research, Substance Misuse, Drug Abuse (NIDA only), Mental health, Good Health and Well Being, Medical and Health Sciences, Psychology and Cognitive Sciences, Behavioral Science & Comparative Psychology
Abstract: Many studies have reported that heavy substance use is associated with impaired response inhibition. Studies typically focused on associations with a single substance, while polysubstance use is common. Further, most studies compared heavy users with light/non-users, though substance use occurs along a continuum. The current mega-analysis accounted for these issues by aggregating individual data from 43 studies (3610 adult participants) that used the Go/No-Go (GNG) or Stop-signal task (SST) to assess inhibition among mostly "recreational" substance users (i.e., the rate of substance use disorders was low). Main and interaction effects of substance use, demographics, and task-characteristics were entered in a linear mixed model. Contrary to many studies and reviews in the field, we found that only lifetime cannabis use was associated with impaired response inhibition in the SST. An interaction effect was also observed: the relationship between tobacco use and response inhibition (in the SST) differed between cannabis users and non-users, with a negative association between tobacco use and inhibition in the cannabis non-users. In addition, participants' age, education level, and some task characteristics influenced inhibition outcomes. Overall, we found limited support for impaired inhibition among substance users when controlling for demographics and task-characteristics.
Published: 2019

4. Association between persistent endocrine-disrupting chemicals (PBDEs, OH-PBDEs, PCBs, and PFASs) and biomarkers of inflammation and cellular aging during pregnancy and postpartum

Author: Zota, Ami R, Geller, Ruth J, Romano, Laura E, Coleman-Phox, Kimberly, Adler, Nancy E, Parry, Emily, Wang, Miaomiao, Park, June-Soo, Elmi, Angelo F, Laraia, Barbara A, and Epel, Elissa S
Subjects: Reproductive Medicine, Biomedical and Clinical Sciences, Environmental Sciences, Pollution and Contamination, Clinical Research, Obesity, Estrogen, Prevention, Aetiology, 2.1 Biological and endogenous factors, Inflammatory and immune system, Reproductive health and childbirth, Good Health and Well Being, Biomarkers, Cellular Senescence, Cohort Studies, Endocrine Disruptors, Female, Humans, Inflammation, Interleukins, Maternal Exposure, Postpartum Period, Pregnancy, San Francisco, Polybrominated diphenyl ethers, Per- and polyfluorochemicals, Leukocyte telomere length, Environmental chemicals, Prenatal exposures
Abstract: BackgroundEndocrine-disrupting chemicals (EDCs) can target immune and metabolic pathways. However, few epidemiologic studies have examined the influence of EDCs on measures of inflammation and cellular aging during pregnancy and postpartum.ObjectiveWe investigated associations between prenatal exposures to polybrominated diphenyl ethers (PBDEs), hydroxylated PBDE metabolites (OH-PBDEs), polychlorinated biphenyls (PCBs), and per- and polyfluorochemicals (PFASs) with repeated biomarker measurements of inflammation and cellular aging in women during pregnancy and the postpartum period.MethodologyOverweight or obese pregnant women were recruited from the San Francisco Bay area (n = 103) during their first or second trimester of pregnancy. Blood samples were collected from participants at baseline (median 16 weeks gestation) and at three and nine months postpartum. Serum concentrations of PBDEs, OH-PBDEs, PCBs, and PFASs were measured at baseline. Inflammation biomarkers (interleukin 6 [IL-6], interleukin 10 [IL-10], and tumor necrosis factor [TNF-α]) and leukocyte telomere length (LTL), a biomarker of cellular aging, were measured at all three time points. Associations between serum chemical concentrations and repeated measures of IL-6, IL-10, TNF-α, and LTL were examined using linear mixed models. We also examined the potential for effect modification by time (visit) and obesity.ResultsIn adjusted models, we observed positive relationships between PBDEs and pro-inflammatory cytokines (IL-6 and TNF-α). A doubling in ∑PBDEs was associated with a 15.26% (95% CI 1.24, 31.22) and 3.74% (95% CI -0.19, 7.82) increase in IL-6 and TNF-α, respectively. Positive associations were also observed for PFASs and IL-6. A two-fold increase in ∑PFASs was associated with a 20.87% (95% CI 3.46, 41.22) increase in IL-6. 5-OHBDE-47 was inversely associated with anti-inflammatory cytokine IL-10. Some EDC-outcome associations, including those of PBDEs with TNF-α, were stronger during pregnancy (compared to three or nine months postpartum) and among obese (compared to overweight) women (p-interaction
Published: 2018

5. Increased Striatal Dopamine Synthesis Capacity in Gambling Addiction

Author: van Holst, Ruth J, Sescousse, Guillaume, Janssen, Lieneke K, Janssen, Marcel, Berry, Anne S, Jagust, William J, and Cools, Roshan
Subjects: Biological Psychology, Pharmacology and Pharmaceutical Sciences, Biomedical and Clinical Sciences, Psychology, Neurosciences, Good Health and Well Being, Adult, Brain Mapping, Corpus Striatum, Dihydroxyphenylalanine, Dopamine, Dopamine Agents, Female, Fluorine Radioisotopes, Gambling, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Male, Middle Aged, Positron-Emission Tomography, Psychiatric Status Rating Scales, Self Report, Addiction, [F-18]DOPA, Neuroimaging, Reward, [(18)F]DOPA, Biological Sciences, Medical and Health Sciences, Psychology and Cognitive Sciences, Psychiatry, Biological sciences, Biomedical and clinical sciences
Abstract: BackgroundThe hypothesis that dopamine plays an important role in the pathophysiology of pathological gambling is pervasive. However, there is little to no direct evidence for a categorical difference between pathological gamblers and healthy control subjects in terms of dopamine transmission in a drug-free state. Here we provide evidence for this hypothesis by comparing dopamine synthesis capacity in the dorsal and ventral parts of the striatum in 13 pathological gamblers and 15 healthy control subjects.MethodsThis was achieved using [18F]fluoro-levo-dihydroxyphenylalanine dynamic positron emission tomography scans and striatal regions of interest that were hand-drawn based on visual inspection of individual structural magnetic resonance imaging scans.ResultsOur results show that dopamine synthesis capacity was increased in pathological gamblers compared with healthy control subjects. Dopamine synthesis was 16% higher in the caudate body, 17% higher in the dorsal putamen, and 17% higher in the ventral striatum in pathological gamblers compared with control subjects. Moreover, dopamine synthesis capacity in the dorsal putamen and caudate head was positively correlated with gambling distortions in pathological gamblers.ConclusionsTaken together, these results provide empirical evidence for increased striatal dopamine synthesis in pathological gambling.
Published: 2018

6. Spontaneous eye blink rate and dopamine synthesis capacity: preliminary evidence for an absence of positive correlation

Author: Sescousse, Guillaume, Ligneul, Romain, Holst, Ruth J, Janssen, Lieneke K, Boer, Femke, Janssen, Marcel, Berry, Anne S, Jagust, William J, and Cools, Roshan
Subjects: Biological Psychology, Pharmacology and Pharmaceutical Sciences, Biomedical and Clinical Sciences, Psychology, Neurosciences, Clinical Research, Biomedical Imaging, Neurological, Mental health, Adult, Blinking, Corpus Striatum, Dopamine, Eye, Gambling, Humans, Male, Middle Aged, Positron-Emission Tomography, Receptors, Dopamine D2, [F-18]DOPA, dopamine, eye blink rate, PET, proxy measure, PET, [18F]DOPA, Cognitive Sciences, Neurology & Neurosurgery, Biological psychology, Cognitive and computational psychology
Abstract: Dopamine is central to a number of cognitive functions and brain disorders. Given the cost of neurochemical imaging in humans, behavioural proxy measures of dopamine have gained in popularity in the past decade, such as spontaneous eye blink rate (sEBR). Increased sEBR is commonly associated with increased dopamine function based on pharmacological evidence and patient studies. Yet, this hypothesis has not been validated using in vivo measures of dopamine function in humans. To fill this gap, we measured sEBR and striatal dopamine synthesis capacity using [18 F]DOPA PET in 20 participants (nine healthy individuals and 11 pathological gamblers). Our results, based on frequentist and Bayesian statistics, as well as region-of-interest and voxel-wise analyses, argue against a positive relationship between sEBR and striatal dopamine synthesis capacity. They show that, if anything, the evidence is in favour of a negative relationship. These results, which complement findings from a recent study that failed to observe a relationship between sEBR and dopamine D2 receptor availability, suggest that caution and nuance are warranted when interpreting sEBR in terms of a proxy measure of striatal dopamine.
Published: 2018

7. A multi-layer functional genomic analysis to understand noncoding genetic variation in lipids

Author: Ramdas, Shweta, Judd, Jonathan, Graham, Sarah E, Kanoni, Stavroula, Wang, Yuxuan, Surakka, Ida, Wenz, Brandon, Clarke, Shoa L, Chesi, Alessandra, Wells, Andrew, Bhatti, Konain Fatima, Vedantam, Sailaja, Winkler, Thomas W, Locke, Adam E, Marouli, Eirini, Zajac, Greg J M, Wu, Kuan-Han H, Ntalla, Ioanna, Hui, Qin, Klarin, Derek, Hilliard, Austin T, Wang, Zeyuan, Xue, Chao, Thorleifsson, Gudmar, Helgadottir, Anna, Gudbjartsson, Daniel F, Holm, Hilma, Olafsson, Isleifur, Hwang, Mi Yeong, Han, Sohee, Akiyama, Masato, Sakaue, Saori, Terao, Chikashi, Kanai, Masahiro, Zhou, Wei, Brumpton, Ben M, Rasheed, Humaira, Havulinna, Aki S, Veturi, Yogasudha, Pacheco, Jennifer Allen, Rosenthal, Elisabeth A, Lingren, Todd, Feng, QiPing, Kullo, Iftikhar J, Narita, Akira, Takayama, Jun, Martin, Hilary C, Hunt, Karen A, Trivedi, Bhavi, Haessler, Jeffrey, Giulianini, Franco, Bradford, Yuki, Miller, Jason E, Campbell, Archie, Lin, Kuang, Millwood, Iona Y, Rasheed, Asif, Hindy, George, Faul, Jessica D, Zhao, Wei, Weir, David R, Turman, Constance, Huang, Hongyan, Graff, Mariaelisa, Choudhury, Ananyo, Sengupta, Dhriti, Mahajan, Anubha, Brown, Michael R, Zhang, Weihua, Yu, Ketian, Schmidt, Ellen M, Pandit, Anita, Gustafsson, Stefan, Yin, Xianyong, Luan, Jian'an, Zhao, Jing-Hua, Matsuda, Fumihiko, Jang, Hye-Mi, Yoon, Kyungheon, Medina-Gomez, Carolina, Pitsillides, Achilleas, Hottenga, Jouke Jan, Wood, Andrew R, Ji, Yingji, Gao, Zishan, Haworth, Simon, Mitchell, Ruth E, Chai, Jin Fang, Aadahl, Mette, Bjerregaard, Anne A, Yao, Jie, Manichaikul, Ani, Lee, Wen-Jane, Hsiung, Chao Agnes, Warren, Helen R, Ramirez, Julia, Bork-Jensen, Jette, Kårhus, Line L, Goel, Anuj, Sabater-Lleal, Maria, Noordam, Raymond, Mauro, Pala, Matteo, Floris, McDaid, Aaron F, Marques-Vidal, Pedro, Wielscher, Matthias, Trompet, Stella, Sattar, Naveed, Møllehave, Line T, Munz, Matthias, Zeng, Lingyao, Huang, Jianfeng, Yang, Bin, Poveda, Alaitz, Kurbasic, Azra, Schönherr, Sebastian, Forer, Lukas, Scholz, Markus, Galesloot, Tessel E, Bradfield, Jonathan P, Ruotsalainen, Sanni E, Daw, E Warwick, Zmuda, Joseph M, Mitchell, Jonathan S, Fuchsberger, Christian, Christensen, Henry, Brody, Jennifer A, Le, Phuong, Feitosa, Mary F, Wojczynski, Mary K, Hemerich, Daiane, Preuss, Michael, Mangino, Massimo, Christofidou, Paraskevi, Verweij, Niek, Benjamins, Jan W, Engmann, Jorgen, Noah, Tsao L, Verma, Anurag, Slieker, Roderick C, Lo, Ken Sin, Zilhao, Nuno R, Kleber, Marcus E, Delgado, Graciela E, Huo, Shaofeng, Ikeda, Daisuke D, Iha, Hiroyuki, Yang, Jian, Liu, Jun, Demirkan, Ayşe, Leonard, Hampton L, Marten, Jonathan, Emmel, Carina, Schmidt, Börge, Smyth, Laura J, Cañadas-Garre, Marisa, Wang, Chaolong, Nakatochi, Masahiro, Wong, Andrew, Hutri-Kähönen, Nina, Sim, Xueling, Xia, Rui, Huerta-Chagoya, Alicia, Fernandez-Lopez, Juan Carlos, Lyssenko, Valeriya, Nongmaithem, Suraj S, Sankareswaran, Alagu, Irvin, Marguerite R, Oldmeadow, Christopher, Kim, Han-Na, Ryu, Seungho, Timmers, Paul R H J, Arbeeva, Liubov, Dorajoo, Rajkumar, Lange, Leslie A, Prasad, Gauri, Lorés-Motta, Laura, Pauper, Marc, Long, Jirong, Li, Xiaohui, Theusch, Elizabeth, Takeuchi, Fumihiko, Spracklen, Cassandra N, Loukola, Anu, Bollepalli, Sailalitha, Warner, Sophie C, Wang, Ya Xing, Wei, Wen B, Nutile, Teresa, Ruggiero, Daniela, Sung, Yun Ju, Chen, Shufeng, Liu, Fangchao, Yang, Jingyun, Kentistou, Katherine A, Banas, Bernhard, Morgan, Anna, Meidtner, Karina, Bielak, Lawrence F, Smith, Jennifer A, Hebbar, Prashantha, Farmaki, Aliki-Eleni, Hofer, Edith, Lin, Maoxuan, Concas, Maria Pina, Vaccargiu, Simona, van der Most, Peter J, Pitkänen, Niina, Cade, Brian E, van der Laan, Sander W, Chitrala, Kumaraswamy Naidu, Weiss, Stefan, Bentley, Amy R, Doumatey, Ayo P, Adeyemo, Adebowale A, Lee, Jong Young, Petersen, Eva R B, Nielsen, Aneta A, Choi, Hyeok Sun, Nethander, Maria, Freitag-Wolf, Sandra, Southam, Lorraine, Rayner, Nigel W, Wang, Carol A, Lin, Shih-Yi, Wang, Jun-Sing, Couture, Christian, Lyytikäinen, Leo-Pekka, Nikus, Kjell, Cuellar-Partida, Gabriel, Vestergaard, Henrik, Hidalgo, Bertha, Giannakopoulou, Olga, Cai, Qiuyin, Obura, Morgan O, van Setten, Jessica, He, Karen Y, Tang, Hua, Terzikhan, Natalie, Shin, Jae Hun, Jackson, Rebecca D, Reiner, Alexander P, Martin, Lisa Warsinger, Chen, Zhengming, Li, Liming, Kawaguchi, Takahisa, Thiery, Joachim, Bis, Joshua C, Launer, Lenore J, Li, Huaixing, Nalls, Mike A, Raitakari, Olli T, Ichihara, Sahoko, Wild, Sarah H, Nelson, Christopher P, Campbell, Harry, Jäger, Susanne, Nabika, Toru, Al-Mulla, Fahd, Niinikoski, Harri, Braund, Peter S, Kolcic, Ivana, Kovacs, Peter, Giardoglou, Tota, Katsuya, Tomohiro, de Kleijn, Dominique, de Borst, Gert J, Kim, Eung Kweon, Adams, Hieab H H, Ikram, M Arfan, Zhu, Xiaofeng, Asselbergs, Folkert W, Kraaijeveld, Adriaan O, Beulens, Joline W J, Shu, Xiao-Ou, Rallidis, Loukianos S, Pedersen, Oluf, Hansen, Torben, Mitchell, Paul, Hewitt, Alex W, Kähönen, Mika, Pérusse, Louis, Bouchard, Claude, Tönjes, Anke, Ida Chen, Yii-Der, Pennell, Craig E, Mori, Trevor A, Lieb, Wolfgang, Franke, Andre, Ohlsson, Claes, Mellström, Dan, Cho, Yoon Shin, Lee, Hyejin, Yuan, Jian-Min, Koh, Woon-Puay, Rhee, Sang Youl, Woo, Jeong-Taek, Heid, Iris M, Stark, Klaus J, Zimmermann, Martina E, Völzke, Henry, Homuth, Georg, Evans, Michele K, Zonderman, Alan B, Polasek, Ozren, Pasterkamp, Gerard, Hoefer, Imo E, Redline, Susan, Pahkala, Katja, Oldehinkel, Albertine J, Snieder, Harold, Biino, Ginevra, Schmidt, Reinhold, Schmidt, Helena, Bandinelli, Stefania, Dedoussis, George, Thanaraj, Thangavel Alphonse, Peyser, Patricia A, Kato, Norihiro, Schulze, Matthias B, Girotto, Giorgia, Böger, Carsten A, Jung, Bettina, Joshi, Peter K, Bennett, David A, De Jager, Philip L, Lu, Xiangfeng, Mamakou, Vasiliki, Brown, Morris, Caulfield, Mark J, Munroe, Patricia B, Guo, Xiuqing, Ciullo, Marina, Jonas, Jost B, Samani, Nilesh J, Kaprio, Jaakko, Pajukanta, Päivi, Tusié-Luna, Teresa, Aguilar-Salinas, Carlos A, Adair, Linda S, Bechayda, Sonny Augustin, de Silva, H Janaka, Wickremasinghe, Ananda R, Krauss, Ronald M, Wu, Jer-Yuarn, Zheng, Wei, den Hollander, Anneke I, Bharadwaj, Dwaipayan, Correa, Adolfo, Wilson, James G, Lind, Lars, Heng, Chew-Kiat, Nelson, Amanda E, Golightly, Yvonne M, Wilson, James F, Penninx, Brenda, Kim, Hyung-Lae, Attia, John, Scott, Rodney J, Rao, D C, Arnett, Donna K, Walker, Mark, Scott, Laura J, Koistinen, Heikki A, Chandak, Giriraj R, Mercader, Josep M, Villalpando, Clicerio Gonzalez, Orozco, Lorena, Fornage, Myriam, Tai, E Shyong, van Dam, Rob M, Lehtimäki, Terho, Chaturvedi, Nish, Yokota, Mitsuhiro, Liu, Jianjun, Reilly, Dermot F, McKnight, Amy Jayne, Kee, Frank, Jöckel, Karl-Heinz, McCarthy, Mark I, Palmer, Colin N A, Vitart, Veronique, Hayward, Caroline, Simonsick, Eleanor, van Duijn, Cornelia M, Jin, Zi-Bing, Lu, Fan, Hishigaki, Haretsugu, Lin, Xu, März, Winfried, Gudnason, Vilmundur, Tardif, Jean-Claude, Lettre, Guillaume, T Hart, Leen M, Elders, Petra J M, Rader, Daniel J, Damrauer, Scott M, Kumari, Meena, Kivimaki, Mika, van der Harst, Pim, Spector, Tim D, Loos, Ruth J F, Province, Michael A, Parra, Esteban J, Cruz, Miguel, Psaty, Bruce M, Brandslund, Ivan, Pramstaller, Peter P, Rotimi, Charles N, Christensen, Kaare, Ripatti, Samuli, Widén, Elisabeth, Hakonarson, Hakon, Grant, Struan F A, Kiemeney, Lambertus, de Graaf, Jacqueline, Loeffler, Markus, Kronenberg, Florian, Gu, Dongfeng, Erdmann, Jeanette, Schunkert, Heribert, Franks, Paul W, Linneberg, Allan, Jukema, J Wouter, Khera, Amit V, Männikkö, Minna, Jarvelin, Marjo-Riitta, Kutalik, Zoltan, Francesco, Cucca, Mook-Kanamori, Dennis O, Willems van Dijk, Ko, Watkins, Hugh, Strachan, David P, Grarup, Niels, Sever, Peter, Poulter, Neil, Huey-Herng Sheu, Wayne, Rotter, Jerome I, Dantoft, Thomas M, Karpe, Fredrik, Neville, Matt J, Timpson, Nicholas J, Cheng, Ching-Yu, Wong, Tien-Yin, Khor, Chiea Chuen, Li, Hengtong, Sabanayagam, Charumathi, Peters, Annette, Gieger, Christian, Hattersley, Andrew T, Pedersen, Nancy L, Magnusson, Patrik K E, Boomsma, Dorret I, de Geus, Eco J C, Cupples, L Adrienne, van Meurs, Joyce B J, Ikram, Arfan, Ghanbari, Mohsen, Gordon-Larsen, Penny, Huang, Wei, Kim, Young Jin, Tabara, Yasuharu, Wareham, Nicholas J, Langenberg, Claudia, Zeggini, Eleftheria, Tuomilehto, Jaakko, Kuusisto, Johanna, Laakso, Markku, Ingelsson, Erik, Abecasis, Goncalo, Chambers, John C, Kooner, Jaspal S, de Vries, Paul S, Morrison, Alanna C, Hazelhurst, Scott, Ramsay, Michèle, North, Kari E, Daviglus, Martha, Kraft, Peter, Martin, Nicholas G, Whitfield, John B, Abbas, Shahid, Saleheen, Danish, Walters, Robin G, Holmes, Michael V, Black, Corri, Smith, Blair H, Baras, Aris, Justice, Anne E, Buring, Julie E, Ridker, Paul M, Chasman, Daniel I, Kooperberg, Charles, Tamiya, Gen, Yamamoto, Masayuki, van Heel, David A, Trembath, Richard C, Wei, Wei-Qi, Jarvik, Gail P, Namjou, Bahram, Hayes, M Geoffrey, Ritchie, Marylyn D, Jousilahti, Pekka, Salomaa, Veikko, Hveem, Kristian, Åsvold, Bjørn Olav, Kubo, Michiaki, Kamatani, Yoichiro, Okada, Yukinori, Murakami, Yoshinori, Kim, Bong-Jo, Thorsteinsdottir, Unnur, Stefansson, Kari, Zhang, Jifeng, Chen, Y Eugene, Ho, Yuk-Lam, Lynch, Julie A, Tsao, Philip S, Chang, Kyong-Mi, Cho, Kelly, O'Donnell, Christopher J, Gaziano, John M, Wilson, Peter, Mohlke, Karen L, Frayling, Timothy M, Hirschhorn, Joel N, Kathiresan, Sekar, Boehnke, Michael, Million Veterans Program, Global Lipids Genetics Consortium, Struan Grant, Natarajan, Pradeep, Sun, Yan V, Morris, Andrew P, Deloukas, Panos, Peloso, Gina, Assimes, Themistocles L, Willer, Cristen J, Zhu, Xiang, Brown, Christopher D, Interdisciplinary Centre Psychopathology and Emotion regulation (ICPE), Life Course Epidemiology (LCE), Cardiovascular Centre (CVC), Tampere University, Clinical Medicine, Department of Clinical Chemistry, TAYS Heart Centre, Department of Clinical Physiology and Nuclear Medicine, Ramdas, Shweta, Judd, Jonathan, Graham, Sarah E, Kanoni, Stavroula, Wang, Yuxuan, Surakka, Ida, Wenz, Brandon, Clarke, Shoa L, Chesi, Alessandra, Wells, Andrew, Bhatti, Konain Fatima, Vedantam, Sailaja, Winkler, Thomas W, Locke, Adam E, Marouli, Eirini, Zajac, Greg J M, Wu, Kuan-Han H, Ntalla, Ioanna, Hui, Qin, Klarin, Derek, Hilliard, Austin T, Wang, Zeyuan, Xue, Chao, Thorleifsson, Gudmar, Helgadottir, Anna, Gudbjartsson, Daniel F, Holm, Hilma, Olafsson, Isleifur, Hwang, Mi Yeong, Han, Sohee, Akiyama, Masato, Sakaue, Saori, Terao, Chikashi, Kanai, Masahiro, Zhou, Wei, Brumpton, Ben M, Rasheed, Humaira, Havulinna, Aki S, Veturi, Yogasudha, Pacheco, Jennifer Allen, Rosenthal, Elisabeth A, Lingren, Todd, Feng, Qiping, Kullo, Iftikhar J, Narita, Akira, Takayama, Jun, Martin, Hilary C, Hunt, Karen A, Trivedi, Bhavi, Haessler, Jeffrey, Giulianini, Franco, Bradford, Yuki, Miller, Jason E, Campbell, Archie, Lin, Kuang, Millwood, Iona Y, Rasheed, Asif, Hindy, George, Faul, Jessica D, Zhao, Wei, Weir, David R, Turman, Constance, Huang, Hongyan, Graff, Mariaelisa, Choudhury, Ananyo, Sengupta, Dhriti, Mahajan, Anubha, Brown, Michael R, Zhang, Weihua, Yu, Ketian, Schmidt, Ellen M, Pandit, Anita, Gustafsson, Stefan, Yin, Xianyong, Luan, Jian'An, Zhao, Jing-Hua, Matsuda, Fumihiko, Jang, Hye-Mi, Yoon, Kyungheon, Medina-Gomez, Carolina, Pitsillides, Achillea, Hottenga, Jouke Jan, Wood, Andrew R, Ji, Yingji, Gao, Zishan, Haworth, Simon, Mitchell, Ruth E, Chai, Jin Fang, Aadahl, Mette, Bjerregaard, Anne A, Yao, Jie, Manichaikul, Ani, Lee, Wen-Jane, Hsiung, Chao Agne, Warren, Helen R, Ramirez, Julia, Bork-Jensen, Jette, Kårhus, Line L, Goel, Anuj, Sabater-Lleal, Maria, Noordam, Raymond, Mauro, Pala, Matteo, Flori, Mcdaid, Aaron F, Marques-Vidal, Pedro, Wielscher, Matthia, Trompet, Stella, Sattar, Naveed, Møllehave, Line T, Munz, Matthia, Zeng, Lingyao, Huang, Jianfeng, Yang, Bin, Poveda, Alaitz, Kurbasic, Azra, Schönherr, Sebastian, Forer, Luka, Scholz, Marku, Galesloot, Tessel E, Bradfield, Jonathan P, Ruotsalainen, Sanni E, Daw, E Warwick, Zmuda, Joseph M, Mitchell, Jonathan S, Fuchsberger, Christian, Christensen, Henry, Brody, Jennifer A, Le, Phuong, Feitosa, Mary F, Wojczynski, Mary K, Hemerich, Daiane, Preuss, Michael, Mangino, Massimo, Christofidou, Paraskevi, Verweij, Niek, Benjamins, Jan W, Engmann, Jorgen, Noah, Tsao L, Verma, Anurag, Slieker, Roderick C, Lo, Ken Sin, Zilhao, Nuno R, Kleber, Marcus E, Delgado, Graciela E, Huo, Shaofeng, Ikeda, Daisuke D, Iha, Hiroyuki, Yang, Jian, Liu, Jun, Demirkan, Ayşe, Leonard, Hampton L, Marten, Jonathan, Emmel, Carina, Schmidt, Börge, Smyth, Laura J, Cañadas-Garre, Marisa, Wang, Chaolong, Nakatochi, Masahiro, Wong, Andrew, Hutri-Kähönen, Nina, Sim, Xueling, Xia, Rui, Huerta-Chagoya, Alicia, Fernandez-Lopez, Juan Carlo, Lyssenko, Valeriya, Nongmaithem, Suraj S, Sankareswaran, Alagu, Irvin, Marguerite R, Oldmeadow, Christopher, Kim, Han-Na, Ryu, Seungho, Timmers, Paul R H J, Arbeeva, Liubov, Dorajoo, Rajkumar, Lange, Leslie A, Prasad, Gauri, Lorés-Motta, Laura, Pauper, Marc, Long, Jirong, Li, Xiaohui, Theusch, Elizabeth, Takeuchi, Fumihiko, Spracklen, Cassandra N, Loukola, Anu, Bollepalli, Sailalitha, Warner, Sophie C, Wang, Ya Xing, Wei, Wen B, Nutile, Teresa, Ruggiero, Daniela, Sung, Yun Ju, Chen, Shufeng, Liu, Fangchao, Yang, Jingyun, Kentistou, Katherine A, Banas, Bernhard, Morgan, Anna, Meidtner, Karina, Bielak, Lawrence F, Smith, Jennifer A, Hebbar, Prashantha, Farmaki, Aliki-Eleni, Hofer, Edith, Lin, Maoxuan, Concas, Maria Pina, Vaccargiu, Simona, van der Most, Peter J, Pitkänen, Niina, Cade, Brian E, van der Laan, Sander W, Chitrala, Kumaraswamy Naidu, Weiss, Stefan, Bentley, Amy R, Doumatey, Ayo P, Adeyemo, Adebowale A, Lee, Jong Young, Petersen, Eva R B, Nielsen, Aneta A, Choi, Hyeok Sun, Nethander, Maria, Freitag-Wolf, Sandra, Southam, Lorraine, Rayner, Nigel W, Wang, Carol A, Lin, Shih-Yi, Wang, Jun-Sing, Couture, Christian, Lyytikäinen, Leo-Pekka, Nikus, Kjell, Cuellar-Partida, Gabriel, Vestergaard, Henrik, Hidalgo, Bertha, Giannakopoulou, Olga, Cai, Qiuyin, Obura, Morgan O, van Setten, Jessica, He, Karen Y, Tang, Hua, Terzikhan, Natalie, Shin, Jae Hun, Jackson, Rebecca D, Reiner, Alexander P, Martin, Lisa Warsinger, Chen, Zhengming, Li, Liming, Kawaguchi, Takahisa, Thiery, Joachim, Bis, Joshua C, Launer, Lenore J, Li, Huaixing, Nalls, Mike A, Raitakari, Olli T, Ichihara, Sahoko, Wild, Sarah H, Nelson, Christopher P, Campbell, Harry, Jäger, Susanne, Nabika, Toru, Al-Mulla, Fahd, Niinikoski, Harri, Braund, Peter S, Kolcic, Ivana, Kovacs, Peter, Giardoglou, Tota, Katsuya, Tomohiro, de Kleijn, Dominique, de Borst, Gert J, Kim, Eung Kweon, Adams, Hieab H H, Ikram, M Arfan, Zhu, Xiaofeng, Asselbergs, Folkert W, Kraaijeveld, Adriaan O, Beulens, Joline W J, Shu, Xiao-Ou, Rallidis, Loukianos S, Pedersen, Oluf, Hansen, Torben, Mitchell, Paul, Hewitt, Alex W, Kähönen, Mika, Pérusse, Loui, Bouchard, Claude, Tönjes, Anke, Ida Chen, Yii-Der, Pennell, Craig E, Mori, Trevor A, Lieb, Wolfgang, Franke, Andre, Ohlsson, Clae, Mellström, Dan, Cho, Yoon Shin, Lee, Hyejin, Yuan, Jian-Min, Koh, Woon-Puay, Rhee, Sang Youl, Woo, Jeong-Taek, Heid, Iris M, Stark, Klaus J, Zimmermann, Martina E, Völzke, Henry, Homuth, Georg, Evans, Michele K, Zonderman, Alan B, Polasek, Ozren, Pasterkamp, Gerard, Hoefer, Imo E, Redline, Susan, Pahkala, Katja, Oldehinkel, Albertine J, Snieder, Harold, Biino, Ginevra, Schmidt, Reinhold, Schmidt, Helena, Bandinelli, Stefania, Dedoussis, George, Thanaraj, Thangavel Alphonse, Peyser, Patricia A, Kato, Norihiro, Schulze, Matthias B, Girotto, Giorgia, Böger, Carsten A, Jung, Bettina, Joshi, Peter K, Bennett, David A, De Jager, Philip L, Lu, Xiangfeng, Mamakou, Vasiliki, Brown, Morri, Caulfield, Mark J, Munroe, Patricia B, Guo, Xiuqing, Ciullo, Marina, Jonas, Jost B, Samani, Nilesh J, Kaprio, Jaakko, Pajukanta, Päivi, Tusié-Luna, Teresa, Aguilar-Salinas, Carlos A, Adair, Linda S, Bechayda, Sonny Augustin, de Silva, H Janaka, Wickremasinghe, Ananda R, Krauss, Ronald M, Wu, Jer-Yuarn, Zheng, Wei, den Hollander, Anneke I, Bharadwaj, Dwaipayan, Correa, Adolfo, Wilson, James G, Lind, Lar, Heng, Chew-Kiat, Nelson, Amanda E, Golightly, Yvonne M, Wilson, James F, Penninx, Brenda, Kim, Hyung-Lae, Attia, John, Scott, Rodney J, Rao, D C, Arnett, Donna K, Walker, Mark, Scott, Laura J, Koistinen, Heikki A, Chandak, Giriraj R, Mercader, Josep M, Villalpando, Clicerio Gonzalez, Orozco, Lorena, Fornage, Myriam, Tai, E Shyong, van Dam, Rob M, Lehtimäki, Terho, Chaturvedi, Nish, Yokota, Mitsuhiro, Liu, Jianjun, Reilly, Dermot F, Mcknight, Amy Jayne, Kee, Frank, Jöckel, Karl-Heinz, Mccarthy, Mark I, Palmer, Colin N A, Vitart, Veronique, Hayward, Caroline, Simonsick, Eleanor, van Duijn, Cornelia M, Jin, Zi-Bing, Lu, Fan, Hishigaki, Haretsugu, Lin, Xu, März, Winfried, Gudnason, Vilmundur, Tardif, Jean-Claude, Lettre, Guillaume, T Hart, Leen M, Elders, Petra J M, Rader, Daniel J, Damrauer, Scott M, Kumari, Meena, Kivimaki, Mika, van der Harst, Pim, Spector, Tim D, Loos, Ruth J F, Province, Michael A, Parra, Esteban J, Cruz, Miguel, Psaty, Bruce M, Brandslund, Ivan, Pramstaller, Peter P, Rotimi, Charles N, Christensen, Kaare, Ripatti, Samuli, Widén, Elisabeth, Hakonarson, Hakon, Grant, Struan F A, Kiemeney, Lambertu, de Graaf, Jacqueline, Loeffler, Marku, Kronenberg, Florian, Gu, Dongfeng, Erdmann, Jeanette, Schunkert, Heribert, Franks, Paul W, Linneberg, Allan, Jukema, J Wouter, Khera, Amit V, Männikkö, Minna, Jarvelin, Marjo-Riitta, Kutalik, Zoltan, Francesco, Cucca, Mook-Kanamori, Dennis O, Willems van Dijk, Ko, Watkins, Hugh, Strachan, David P, Grarup, Niel, Sever, Peter, Poulter, Neil, Huey-Herng Sheu, Wayne, Rotter, Jerome I, Dantoft, Thomas M, Karpe, Fredrik, Neville, Matt J, Timpson, Nicholas J, Cheng, Ching-Yu, Wong, Tien-Yin, Khor, Chiea Chuen, Li, Hengtong, Sabanayagam, Charumathi, Peters, Annette, Gieger, Christian, Hattersley, Andrew T, Pedersen, Nancy L, Magnusson, Patrik K E, Boomsma, Dorret I, de Geus, Eco J C, Cupples, L Adrienne, van Meurs, Joyce B J, Ikram, Arfan, Ghanbari, Mohsen, Gordon-Larsen, Penny, Huang, Wei, Kim, Young Jin, Tabara, Yasuharu, Wareham, Nicholas J, Langenberg, Claudia, Zeggini, Eleftheria, Tuomilehto, Jaakko, Kuusisto, Johanna, Laakso, Markku, Ingelsson, Erik, Abecasis, Goncalo, Chambers, John C, Kooner, Jaspal S, de Vries, Paul S, Morrison, Alanna C, Hazelhurst, Scott, Ramsay, Michèle, North, Kari E, Daviglus, Martha, Kraft, Peter, Martin, Nicholas G, Whitfield, John B, Abbas, Shahid, Saleheen, Danish, Walters, Robin G, Holmes, Michael V, Black, Corri, Smith, Blair H, Baras, Ari, Justice, Anne E, Buring, Julie E, Ridker, Paul M, Chasman, Daniel I, Kooperberg, Charle, Tamiya, Gen, Yamamoto, Masayuki, van Heel, David A, Trembath, Richard C, Wei, Wei-Qi, Jarvik, Gail P, Namjou, Bahram, Hayes, M Geoffrey, Ritchie, Marylyn D, Jousilahti, Pekka, Salomaa, Veikko, Hveem, Kristian, Åsvold, Bjørn Olav, Kubo, Michiaki, Kamatani, Yoichiro, Okada, Yukinori, Murakami, Yoshinori, Kim, Bong-Jo, Thorsteinsdottir, Unnur, Stefansson, Kari, Zhang, Jifeng, Chen, Y Eugene, Ho, Yuk-Lam, Lynch, Julie A, Tsao, Philip S, Chang, Kyong-Mi, Cho, Kelly, O'Donnell, Christopher J, Gaziano, John M, Wilson, Peter, Mohlke, Karen L, Frayling, Timothy M, Hirschhorn, Joel N, Kathiresan, Sekar, Boehnke, Michael, Struan Grant, Null, Natarajan, Pradeep, Sun, Yan V, Morris, Andrew P, Deloukas, Pano, Peloso, Gina, Assimes, Themistocles L, Willer, Cristen J, Zhu, Xiang, Brown, Christopher D, Epidemiology and Data Science, ACS - Diabetes & metabolism, ACS - Heart failure & arrhythmias, APH - Health Behaviors & Chronic Diseases, Psychiatry, APH - Mental Health, Amsterdam Neuroscience - Complex Trait Genetics, Amsterdam Neuroscience - Mood, Anxiety, Psychosis, Stress & Sleep, General practice, APH - Aging & Later Life, APH - Digital Health, Million Veterans Program, Global Lipids Genetics Consortium, Radiology & Nuclear Medicine, Internal Medicine, Epidemiology, Biological Psychology, APH - Personalized Medicine, APH - Methodology, AMS - Ageing & Vitality, and AMS - Sports
Subjects: regulatory mechanism, Vascular damage Radboud Institute for Health Sciences [Radboudumc 16], post-GWAS, Medizin, complex traits, fine-mapping, functional genomics, lipid biology, variant prioritization, Medical and Health Sciences, Polymorphism, Single Nucleotide, Sensory disorders Donders Center for Medical Neuroscience [Radboudumc 12], Article, INTEGRATIVE ANALYSIS, WIDE ASSOCIATION, 3D GENOME, VARIANTS, CHOLESTEROL, ANNOTATION, OBESITY, COMMON, LOCI, EXPRESSION, functional genomic, Genetics, 2.1 Biological and endogenous factors, Humans, Genetics(clinical), Polymorphism, Aetiology, Genetics (clinical), Genetics & Heredity, Chromatin/genetics, Genome-Wide Association Study, Genomics, Lipids/genetics, Polymorphism, Single Nucleotide/genetics, Human Genome, Million Veterans Program, Global Lipids Genetics Consortium, Single Nucleotide, Biological Sciences, Lipids, Chromatin, complex trait, Urological cancers Radboud Institute for Health Sciences [Radboudumc 15], 3111 Biomedicine, Biotechnology
Abstract: A major challenge of genome-wide association studies (GWASs) is to translate phenotypic associations into biological insights. Here, we integrate a large GWAS on blood lipids involving 1.6 million individuals from five ancestries with a wide array of functional genomic datasets to discover regulatory mechanisms underlying lipid associations. We first prioritize lipid-associated genes with expression quantitative trait locus (eQTL) colocalizations and then add chromatin interaction data to narrow the search for functional genes. Polygenic enrichment analysis across 697 annotations from a host of tissues and cell types confirms the central role of the liver in lipid levels and highlights the selective enrichment of adipose-specific chromatin marks in high-density lipoprotein cholesterol and triglycerides. Overlapping transcription factor (TF) binding sites with lipid-associated loci identifies TFs relevant in lipid biology. In addition, we present an integrative framework to prioritize causal variants at GWAS loci, producing a comprehensive list of candidate causal genes and variants with multiple layers of functional evidence. We highlight two of the prioritized genes, CREBRF and RRBP1, which show convergent evidence across functional datasets supporting their roles in lipid biology. Xiang Zhu is supported by the Stein Fellowship from Stanford University and Institute for Computational and Data Sciences Seed Grant from The Pennsylvania State University. C.D.B. is supported by the NIH (R01-HL133218). Funding for the Global Lipids Genetics Consortium was provided by the NIH (R01-HL127564). This research was conducted using the UK Biobank Resource under application number 24460. This research is based on data from the Million Veteran Program, Office of Research and Development, Veterans Health Administration, and was supported by awards 2I01BX003362-03A1 and 1I01BX004821-01A1. This publication does not represent the views of the Department of Veteran Affairs or the United States Government. We thank Bethany Klunder for administrative support. Study-specific acknowledgments are provided in the supplemental information.
Published: 2022
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8. Non-invasive tissue temperature measurements based on quantitative diffuse optical spectroscopy (DOS) of water

Author: Chung, SH, Cerussi, AE, Merritt, SI, Ruth, J, and Tromberg, BJ
Subjects: Clinical Research, Hematology, Bioengineering, Absorption, Algorithms, Body Temperature, Cold Temperature, Forearm, Hemoglobins, Humans, Male, Muscle, Skeletal, Optics and Photonics, Oxyhemoglobins, Phantoms, Imaging, Scattering, Radiation, Spectroscopy, Near-Infrared, Spectrum Analysis, Stress, Physiological, Temperature, Thermography, Water, Young Adult, Other Physical Sciences, Biomedical Engineering, Clinical Sciences, Nuclear Medicine & Medical Imaging
Abstract: We describe the development of a non-invasive method for quantitative tissue temperature measurements using Broadband diffuse optical spectroscopy (DOS). Our approach is based on well-characterized opposing shifts in near-infrared (NIR) water absorption spectra that appear with temperature and macromolecular binding state. Unlike conventional reflectance methods, DOS is used to generate scattering-corrected tissue water absorption spectra. This allows us to separate the macromolecular bound water contribution from the thermally induced spectral shift using the temperature isosbestic point at 996 nm. The method was validated in intralipid tissue phantoms by correlating DOS with thermistor measurements (R=0.96) with a difference of 1.1+/-0.91 degrees C over a range of 28-48 degrees C. Once validated, thermal and hemodynamic (i.e. oxy- and deoxy-hemoglobin concentration) changes were measured simultaneously and continuously in human subjects (forearm) during mild cold stress. DOS-measured arm temperatures were consistent with previously reported invasive deep tissue temperature studies. These results suggest that DOS can be used for non-invasive, co-registered measurements of absolute temperature and hemoglobin parameters in thick tissues, a potentially important approach for optimizing thermal diagnostics and therapeutics.
Published: 2010

9. Cross-Ancestry Investigation of Venous Thromboembolism Genomic Predictors

Author: Florian, Thibord, Derek, Klarin, Jennifer A, Brody, Ming-Huei, Chen, Michael G, Levin, Daniel I, Chasman, Ellen L, Goode, Kristian, Hveem, Maris, Teder-Laving, Angel, Martinez-Perez, Dylan, Aïssi, Delphine, Daian-Bacq, Kaoru, Ito, Pradeep, Natarajan, Pamela L, Lutsey, Girish N, Nadkarni, Paul S, de Vries, Gabriel, Cuellar-Partida, Brooke N, Wolford, Jack W, Pattee, Charles, Kooperberg, Sigrid K, Braekkan, Ruifang, Li-Gao, Noemie, Saut, Corriene, Sept, Marine, Germain, Renae L, Judy, Kerri L, Wiggins, Darae, Ko, Christopher J, O'Donnell, Kent D, Taylor, Franco, Giulianini, Mariza, De Andrade, Therese H, Nøst, Anne, Boland, Jean-Philippe, Empana, Satoshi, Koyama, Thomas, Gilliland, Ron, Do, Jennifer E, Huffman, Xin, Wang, Wei, Zhou, Jose, Manuel Soria, Juan, Carlos Souto, Nathan, Pankratz, Jeffery, Haessler, Kristian, Hindberg, Frits R, Rosendaal, Constance, Turman, Robert, Olaso, Rachel L, Kember, Traci M, Bartz, Julie A, Lynch, Susan R, Heckbert, Sebastian M, Armasu, Ben, Brumpton, David M, Smadja, Xavier, Jouven, Issei, Komuro, Katharine R, Clapham, Ruth J F, Loos, Cristen J, Willer, Maria, Sabater-Lleal, James S, Pankow, Alexander P, Reiner, Vania M, Morelli, Paul M, Ridker, Astrid van Hylckama, Vlieg, Jean-François, Deleuze, Peter, Kraft, Daniel J, Rader, Kyung, Min Lee, Bruce M, Psaty, Anne, Heidi Skogholt, Joseph, Emmerich, Pierre, Suchon, Stephen S, Rich, Ha My T, Vy, Weihong, Tang, Rebecca D, Jackson, John-Bjarne, Hansen, Pierre-Emmanuel, Morange, Christopher, Kabrhel, David-Alexandre, Trégouët, Scott M, Damrauer, Andrew D, Johnson, Nicholas L, Smith, Bordeaux population health (BPH), Université de Bordeaux (UB)-Institut de Santé Publique, d'Épidémiologie et de Développement (ISPED)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre recherche en CardioVasculaire et Nutrition = Center for CardioVascular and Nutrition research (C2VN), and Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: genome-wide association study, venous thromboembolism, Quantitative Trait Loci, Thrombosis, Genomics, Venous Thromboembolism, Polymorphism, Single Nucleotide, meta-analysis, Meta-analysis, Physiology (medical), Venous thrombosis, Genetics, Humans, genetics, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Genetic Predisposition to Disease, venous thrombosis, Cardiology and Cardiovascular Medicine, Genome-Wide Association Study
Abstract: Background: Venous thromboembolism (VTE) is a life-threatening vascular event with environmental and genetic determinants. Recent VTE genome-wide association studies (GWAS) meta-analyses involved nearly 30 000 VTE cases and identified up to 40 genetic loci associated with VTE risk, including loci not previously suspected to play a role in hemostasis. The aim of our research was to expand discovery of new genetic loci associated with VTE by using cross-ancestry genomic resources. Methods: We present new cross-ancestry meta-analyzed GWAS results involving up to 81 669 VTE cases from 30 studies, with replication of novel loci in independent populations and loci characterization through in silico genomic interrogations. Results: In our genetic discovery effort that included 55 330 participants with VTE (47 822 European, 6320 African, and 1188 Hispanic ancestry), we identified 48 novel associations, of which 34 were replicated after correction for multiple testing. In our combined discovery-replication analysis (81 669 VTE participants) and ancestry-stratified meta-analyses (European, African, and Hispanic), we identified another 44 novel associations, which are new candidate VTE-associated loci requiring replication. In total, across all GWAS meta-analyses, we identified 135 independent genomic loci significantly associated with VTE risk. A genetic risk score of the significantly associated loci in Europeans identified a 6-fold increase in risk for those in the top 1% of scores compared with those with average scores. We also identified 31 novel transcript associations in transcriptome-wide association studies and 8 novel candidate genes with protein quantitative-trait locus Mendelian randomization analyses. In silico interrogations of hemostasis and hematology traits and a large phenome-wide association analysis of the 135 GWAS loci provided insights to biological pathways contributing to VTE, with some loci contributing to VTE through well-characterized coagulation pathways and others providing new data on the role of hematology traits, particularly platelet function. Many of the replicated loci are outside of known or currently hypothesized pathways to thrombosis. Conclusions: Our cross-ancestry GWAS meta-analyses identified new loci associated with VTE. These findings highlight new pathways to thrombosis and provide novel molecules that may be useful in the development of improved antithrombosis treatments.
Published: 2022
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10. Insights From a Large-Scale Whole-Genome Sequencing Study of Systolic Blood Pressure, Diastolic Blood Pressure, and Hypertension

Author: Tanika N, Kelly, Xiao, Sun, Karen Y, He, Michael R, Brown, Sarah A Gagliano, Taliun, Jacklyn N, Hellwege, Marguerite R, Irvin, Xuenan, Mi, Jennifer A, Brody, Nora, Franceschini, Xiuqing, Guo, Shih-Jen, Hwang, Paul S, de Vries, Yan, Gao, Arden, Moscati, Girish N, Nadkarni, Lisa R, Yanek, Tali, Elfassy, Jennifer A, Smith, Ren-Hua, Chung, Amber L, Beitelshees, Amit, Patki, Stella, Aslibekyan, Brandon M, Blobner, Juan M, Peralta, Themistocles L, Assimes, Walter R, Palmas, Chunyu, Liu, Adam P, Bress, Zhijie, Huang, Lewis C, Becker, Chii-Min, Hwa, Jeffrey R, O'Connell, Jenna C, Carlson, Helen R, Warren, Sayantan, Das, Ayush, Giri, Lisa W, Martin, W, Craig Johnson, Ervin R, Fox, Erwin P, Bottinger, Alexander C, Razavi, Dhananjay, Vaidya, Lee-Ming, Chuang, Yen-Pei C, Chang, Take, Naseri, Deepti, Jain, Hyun Min, Kang, Adriana M, Hung, Vinodh, Srinivasasainagendra, Beverly M, Snively, Dongfeng, Gu, May E, Montasser, Muagututi'a Sefuiva, Reupena, Benjamin D, Heavner, Jonathon, LeFaive, James E, Hixson, Kenneth M, Rice, Fei Fei, Wang, Jonas B, Nielsen, Jianfeng, Huang, Alyna T, Khan, Wei, Zhou, Jovia L, Nierenberg, Cathy C, Laurie, Nicole D, Armstrong, Mengyao, Shi, Yang, Pan, Adrienne M, Stilp, Leslie, Emery, Quenna, Wong, Nicola L, Hawley, Ryan L, Minster, Joanne E, Curran, Patricia B, Munroe, Daniel E, Weeks, Kari E, North, Russell P, Tracy, Eimear E, Kenny, Daichi, Shimbo, Aravinda, Chakravarti, Stephen S, Rich, Alex P, Reiner, John, Blangero, Susan, Redline, Braxton D, Mitchell, Dabeeru C, Rao, Yii-Der, Ida Chen, Sharon L R, Kardia, Robert C, Kaplan, Rasika A, Mathias, Jiang, He, Bruce M, Psaty, Myriam, Fornage, Ruth J F, Loos, Adolfo, Correa, Eric, Boerwinkle, Jerome I, Rotter, Charles, Kooperberg, Todd L, Edwards, Gonçalo R, Abecasis, Xiaofeng, Zhu, Daniel, Levy, Donna K, Arnett, and Alanna C, Morrison
Subjects: Hypertension, Internal Medicine, Humans, Blood Pressure, Genomics, Precision Medicine, Polymorphism, Single Nucleotide, Genome-Wide Association Study
Abstract: Background: The availability of whole-genome sequencing data in large studies has enabled the assessment of coding and noncoding variants across the allele frequency spectrum for their associations with blood pressure. Methods: We conducted a multiancestry whole-genome sequencing analysis of blood pressure among 51 456 Trans-Omics for Precision Medicine and Centers for Common Disease Genomics program participants (stage-1). Stage-2 analyses leveraged array data from UK Biobank (N=383 145), Million Veteran Program (N=318 891), and Reasons for Geographic and Racial Differences in Stroke (N=10 643) participants, along with whole-exome sequencing data from UK Biobank (N=199 631) participants. Results: Two blood pressure signals achieved genome-wide significance in meta-analyses of stage-1 and stage-2 single variant findings ( P -8 ). Among them, a rare intergenic variant at novel locus, LOC100506274 , was associated with lower systolic blood pressure in stage-1 (beta [SE]=−32.6 [6.0]; P =4.99×10 -8 ) but not stage-2 analysis ( P =0.11). Furthermore, a novel common variant at the known INSR locus was suggestively associated with diastolic blood pressure in stage-1 (beta [SE]=−0.36 [0.07]; P =4.18×10 -7 ) and attained genome-wide significance in stage-2 (beta [SE]=−0.29 [0.03]; P =7.28×10 -23 ). Nineteen additional signals suggestively associated with blood pressure in meta-analysis of single and aggregate rare variant findings ( P -6 and P -4 , respectively). Discussion: We report one promising but unconfirmed rare variant for blood pressure and, more importantly, contribute insights for future blood pressure sequencing studies. Our findings suggest promise of aggregate analyses to complement single variant analysis strategies and the need for larger, diverse samples, and family studies to enable robust rare variant identification.
Published: 2023

11. African-specific molecular taxonomy of prostate cancer

Author: Weerachai Jaratlerdsiri, Jue Jiang, Tingting Gong, Sean M. Patrick, Cali Willet, Tracy Chew, Ruth J. Lyons, Anne-Maree Haynes, Gabriela Pasqualim, Melanie Louw, James G. Kench, Raymond Campbell, Lisa G. Horvath, Eva K. F. Chan, David C. Wedge, Rosemarie Sadsad, Ilma Simoni Brum, Shingai B. A. Mutambirwa, Phillip D. Stricker, M. S. Riana Bornman, and Vanessa M. Hayes
Subjects: Male, China, Multidisciplinary, Black People, Nuclear Proteins, Prostatic Neoplasms, Europe, Nuclear Receptor Coactivator 2, Asian People, Africa, Mutation, Ethnicity, Humans, RNA, Long Noncoding, Carrier Proteins, Africa South of the Sahara, RNA Helicases
Abstract: Prostate cancer is characterized by considerable geo-ethnic disparity. African ancestry is a significant risk factor, with mortality rates across sub-Saharan Africa of 2.7-fold higher than global averages1. The contributing genetic and non-genetic factors, and associated mutational processes, are unknown2,3. Here, through whole-genome sequencing of treatment-naive prostate cancer samples from 183 ancestrally (African versus European) and globally distinct patients, we generate a large cancer genomics resource for sub-Saharan Africa, identifying around 2 million somatic variants. Significant African-ancestry-specific findings include an elevated tumour mutational burden, increased percentage of genome alteration, a greater number of predicted damaging mutations and a higher total of mutational signatures, and the driver genes NCOA2, STK19, DDX11L1, PCAT1 and SETBP1. Examining all somatic mutational types, we describe a molecular taxonomy for prostate cancer differentiated by ancestry and defined as global mutational subtypes (GMS). By further including Chinese Asian data, we confirm that GMS-B (copy-number gain) and GMS-D (mutationally noisy) are specific to African populations, GMS-A (mutationally quiet) is universal (all ethnicities) and the African–European-restricted subtype GMS-C (copy-number losses) predicts poor clinical outcomes. In addition to the clinical benefit of including individuals of African ancestry, our GMS subtypes reveal different evolutionary trajectories and mutational processes suggesting that both common genetic and environmental factors contribute to the disparity between ethnicities. Analogous to gene–environment interaction—defined here as a different effect of an environmental surrounding in people with different ancestries or vice versa—we anticipate that GMS subtypes act as a proxy for intrinsic and extrinsic mutational processes in cancers, promoting global inclusion in landmark studies.
Published: 2022
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12. Monogenic and Polygenic Contributions to QTc Prolongation in the Population

Author: Victor, Nauffal, Valerie N, Morrill, Sean J, Jurgens, Seung Hoan, Choi, Amelia W, Hall, Lu-Chen, Weng, Jennifer L, Halford, Christina, Austin-Tse, Christopher M, Haggerty, Stephanie L, Harris, Eugene K, Wong, Alvaro, Alonso, Dan E, Arking, Emelia J, Benjamin, Eric, Boerwinkle, Yuan-I, Min, Adolfo, Correa, Brandon K, Fornwalt, Susan R, Heckbert, Charles, Kooperberg, Henry J, Lin, Ruth, J F Loos, Kenneth M, Rice, Namrata, Gupta, Thomas W, Blackwell, Braxton D, Mitchell, Alanna C, Morrison, Bruce M, Psaty, Wendy S, Post, Susan, Redline, Heidi L, Rehm, Stephen S, Rich, Jerome I, Rotter, Elsayed Z, Soliman, Nona, Sotoodehnia, Kathryn L, Lunetta, Patrick T, Ellinor, Steven A, Lubitz, Cardiology, and Graduate School
Subjects: QT interval, Heterozygote, Multifactorial Inheritance, Whole Genome Sequencing, polygenic, sudden cardiac death, Article, Electrocardiography, Long QT Syndrome, Physiology (medical), monogenic, Humans, Cardiology and Cardiovascular Medicine, Genome-Wide Association Study
Abstract: Background: Rare sequence variation in genes underlying cardiac repolarization and common polygenic variation influence QT interval duration. However, current clinical genetic testing of individuals with unexplained QT prolongation is restricted to examination of monogenic rare variants. The recent emergence of large-scale biorepositories with sequence data enables examination of the joint contribution of rare and common variations to the QT interval in the population. Methods: We performed a genome-wide association study of the QTc in 84 630 UK Biobank participants and created a polygenic risk score (PRS). Among 26 976 participants with whole-genome sequencing and ECG data in the TOPMed (Trans-Omics for Precision Medicine) program, we identified 160 carriers of putative pathogenic rare variants in 10 genes known to be associated with the QT interval. We examined QTc associations with the PRS and with rare variants in TOPMed. Results: Fifty-four independent loci were identified by genome-wide association study in the UK Biobank. Twenty-one loci were novel, of which 12 were replicated in TOPMed. The PRS composed of 1 110 494 common variants was significantly associated with the QTc in TOPMed (ΔQTc /decile of PRS =1.4 ms [95% CI, 1.3 to 1.5]; P =1.1×10 -196 ). Carriers of putative pathogenic rare variants had longer QTc than noncarriers (ΔQTc=10.9 ms [95% CI, 7.4 to 14.4]). Of individuals with QTc>480 ms, 23.7% carried either a monogenic rare variant or had a PRS in the top decile (3.4% monogenic, 21% top decile of PRS). Conclusions: QTc duration in the population is influenced by both rare variants in genes underlying cardiac repolarization and polygenic risk, with a sizeable contribution from polygenic risk. Comprehensive assessment of the genetic determinants of QTc prolongation includes incorporation of both polygenic and monogenic risk.
Published: 2023

13. Identifying Phenotypically Distinct Fibroblast Subsets in Type 2 Diabetes-Associated Iatrogenic Laryngotracheal Stenosis

Author: Alexander T. Hillel, Kevin M. Motz, Samuel L. Collins, Ioan A. Lina, Hsiu-Wen Tsai, Ruth J. Davis, Rafael Ospino, and Alexandra J. Berges
Subjects: 0301 basic medicine, Pathology, medicine.medical_specialty, Iatrogenic Disease, CD34, Constriction, Pathologic, Stem cell marker, Article, Flow cytometry, Cohort Studies, 03 medical and health sciences, 0302 clinical medicine, Biopsy, medicine, Humans, CD90, 030223 otorhinolaryngology, Fibroblast, Subglottis, medicine.diagnostic_test, business.industry, Laryngostenosis, Fibroblasts, medicine.disease, 030104 developmental biology, medicine.anatomical_structure, Otorhinolaryngology, Diabetes Mellitus, Type 2, Surgery, business, Laryngotracheal stenosis
Abstract: Objective Iatrogenic laryngotracheal stenosis (iLTS) is the pathologic narrowing of the glottis, subglottis, and/or trachea secondary to intubation or tracheostomy related injury. Patients with type 2 diabetes mellitus (T2DM) are more likely to develop iLTS. To date, the metabolomics and phenotypic expression of cell markers in fibroblasts derived from patients with T2DM and iLTS are largely unknown. Study design Controlled in vitro cohort study. Setting Tertiary referral center (2017-2020). Methods This in vitro study assessed samples from 6 patients with iLTS who underwent surgery at a single institution. Fibroblasts were isolated from biopsy specimens of laryngotracheal scar and normal-appearing trachea and compared with controls obtained from the trachea of rapid autopsy specimens. Patients with iLTS were subcategorized into those with and without T2DM. Metabolic substrates were identified by mass spectrometry, and cell protein expression was measured by flow cytometry. Results T2DM iLTS-scar fibroblasts had a metabolically distinct profile and clustered tightly on a Pearson correlation heat map as compared with non-T2DM iLTS-scar fibroblasts. Levels of itaconate were elevated in T2DM iLTS-scar fibroblasts. Flow cytometry demonstrated that T2DM iLTS-scar fibroblasts were associated with higher CD90 expression (Thy-1; mean, 95%) when compared with non-T2DM iLTS-scar (mean, 83.6%; P = .0109) or normal tracheal fibroblasts (mean, 81.1%; P = .0042). Conclusions Scar-derived fibroblasts from patients with T2DM and iLTS have a metabolically distinct profile. These fibroblasts are characterized by an increase in itaconate, a metabolite related to immune-induced scar remodeling, and can be identified by elevated expression of CD90 (Thy-1) in vitro.
Published: 2023

14. Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis

Author: Stavroula Kanoni, Sarah E. Graham, Yuxuan Wang, Ida Surakka, Shweta Ramdas, Xiang Zhu, Shoa L. Clarke, Konain Fatima Bhatti, Sailaja Vedantam, Thomas W. Winkler, Adam E. Locke, Eirini Marouli, Greg J. M. Zajac, Kuan-Han H. Wu, Ioanna Ntalla, Qin Hui, Derek Klarin, Austin T. Hilliard, Zeyuan Wang, Chao Xue, Gudmar Thorleifsson, Anna Helgadottir, Daniel F. Gudbjartsson, Hilma Holm, Isleifur Olafsson, Mi Yeong Hwang, Sohee Han, Masato Akiyama, Saori Sakaue, Chikashi Terao, Masahiro Kanai, Wei Zhou, Ben M. Brumpton, Humaira Rasheed, Aki S. Havulinna, Yogasudha Veturi, Jennifer Allen Pacheco, Elisabeth A. Rosenthal, Todd Lingren, QiPing Feng, Iftikhar J. Kullo, Akira Narita, Jun Takayama, Hilary C. Martin, Karen A. Hunt, Bhavi Trivedi, Jeffrey Haessler, Franco Giulianini, Yuki Bradford, Jason E. Miller, Archie Campbell, Kuang Lin, Iona Y. Millwood, Asif Rasheed, George Hindy, Jessica D. Faul, Wei Zhao, David R. Weir, Constance Turman, Hongyan Huang, Mariaelisa Graff, Ananyo Choudhury, Dhriti Sengupta, Anubha Mahajan, Michael R. Brown, Weihua Zhang, Ketian Yu, Ellen M. Schmidt, Anita Pandit, Stefan Gustafsson, Xianyong Yin, Jian’an Luan, Jing-Hua Zhao, Fumihiko Matsuda, Hye-Mi Jang, Kyungheon Yoon, Carolina Medina-Gomez, Achilleas Pitsillides, Jouke Jan Hottenga, Andrew R. Wood, Yingji Ji, Zishan Gao, Simon Haworth, Noha A. Yousri, Ruth E. Mitchell, Jin Fang Chai, Mette Aadahl, Anne A. Bjerregaard, Jie Yao, Ani Manichaikul, Chii-Min Hwu, Yi-Jen Hung, Helen R. Warren, Julia Ramirez, Jette Bork-Jensen, Line L. Kårhus, Anuj Goel, Maria Sabater-Lleal, Raymond Noordam, Pala Mauro, Floris Matteo, Aaron F. McDaid, Pedro Marques-Vidal, Matthias Wielscher, Stella Trompet, Naveed Sattar, Line T. Møllehave, Matthias Munz, Lingyao Zeng, Jianfeng Huang, Bin Yang, Alaitz Poveda, Azra Kurbasic, Claudia Lamina, Lukas Forer, Markus Scholz, Tessel E. Galesloot, Jonathan P. Bradfield, Sanni E. Ruotsalainen, EWarwick Daw, Joseph M. Zmuda, Jonathan S. Mitchell, Christian Fuchsberger, Henry Christensen, Jennifer A. Brody, Miguel Vazquez-Moreno, Mary F. Feitosa, Mary K. Wojczynski, Zhe Wang, Michael H. Preuss, Massimo Mangino, Paraskevi Christofidou, Niek Verweij, Jan W. Benjamins, Jorgen Engmann, Noah L. Tsao, Anurag Verma, Roderick C. Slieker, Ken Sin Lo, Nuno R. Zilhao, Phuong Le, Marcus E. Kleber, Graciela E. Delgado, Shaofeng Huo, Daisuke D. Ikeda, Hiroyuki Iha, Jian Yang, Jun Liu, Ayşe Demirkan, Hampton L. Leonard, Jonathan Marten, Mirjam Frank, Börge Schmidt, Laura J. Smyth, Marisa Cañadas-Garre, Chaolong Wang, Masahiro Nakatochi, Andrew Wong, Nina Hutri-Kähönen, Xueling Sim, Rui Xia, Alicia Huerta-Chagoya, Juan Carlos Fernandez-Lopez, Valeriya Lyssenko, Suraj S. Nongmaithem, Swati Bayyana, Heather M. Stringham, Marguerite R. Irvin, Christopher Oldmeadow, Han-Na Kim, Seungho Ryu, Paul R. H. J. Timmers, Liubov Arbeeva, Rajkumar Dorajoo, Leslie A. Lange, Gauri Prasad, Laura Lorés-Motta, Marc Pauper, Jirong Long, Xiaohui Li, Elizabeth Theusch, Fumihiko Takeuchi, Cassandra N. Spracklen, Anu Loukola, Sailalitha Bollepalli, Sophie C. Warner, Ya Xing Wang, Wen B. Wei, Teresa Nutile, Daniela Ruggiero, Yun Ju Sung, Shufeng Chen, Fangchao Liu, Jingyun Yang, Katherine A. Kentistou, Bernhard Banas, Giuseppe Giovanni Nardone, Karina Meidtner, Lawrence F. Bielak, Jennifer A. Smith, Prashantha Hebbar, Aliki-Eleni Farmaki, Edith Hofer, Maoxuan Lin, Maria Pina Concas, Simona Vaccargiu, Peter J. van der Most, Niina Pitkänen, Brian E. Cade, Sander W. van der Laan, Kumaraswamy Naidu Chitrala, Stefan Weiss, Amy R. Bentley, Ayo P. Doumatey, Adebowale A. Adeyemo, Jong Young Lee, Eva R. B. Petersen, Aneta A. Nielsen, Hyeok Sun Choi, Maria Nethander, Sandra Freitag-Wolf, Lorraine Southam, Nigel W. Rayner, Carol A. Wang, Shih-Yi Lin, Jun-Sing Wang, Christian Couture, Leo-Pekka Lyytikäinen, Kjell Nikus, Gabriel Cuellar-Partida, Henrik Vestergaard, Bertha Hidalgo, Olga Giannakopoulou, Qiuyin Cai, Morgan O. Obura, Jessica van Setten, Xiaoyin Li, Jingjing Liang, Hua Tang, Natalie Terzikhan, Jae Hun Shin, Rebecca D. Jackson, Alexander P. Reiner, Lisa Warsinger Martin, Zhengming Chen, Liming Li, Takahisa Kawaguchi, Joachim Thiery, Joshua C. Bis, Lenore J. Launer, Huaixing Li, Mike A. Nalls, Olli T. Raitakari, Sahoko Ichihara, Sarah H. Wild, Christopher P. Nelson, Harry Campbell, Susanne Jäger, Toru Nabika, Fahd Al-Mulla, Harri Niinikoski, Peter S. Braund, Ivana Kolcic, Peter Kovacs, Tota Giardoglou, Tomohiro Katsuya, Dominique de Kleijn, Gert J. de Borst, Eung Kweon Kim, Hieab H. H. Adams, M. Arfan Ikram, Xiaofeng Zhu, Folkert W. Asselbergs, Adriaan O. Kraaijeveld, Joline W. J. Beulens, Xiao-Ou Shu, Loukianos S. Rallidis, Oluf Pedersen, Torben Hansen, Paul Mitchell, Alex W. Hewitt, Mika Kähönen, Louis Pérusse, Claude Bouchard, Anke Tönjes, Yii-Der Ida Chen, Craig E. Pennell, Trevor A. Mori, Wolfgang Lieb, Andre Franke, Claes Ohlsson, Dan Mellström, Yoon Shin Cho, Hyejin Lee, Jian-Min Yuan, Woon-Puay Koh, Sang Youl Rhee, Jeong-Taek Woo, Iris M. Heid, Klaus J. Stark, Martina E. Zimmermann, Henry Völzke, Georg Homuth, Michele K. Evans, Alan B. Zonderman, Ozren Polasek, Gerard Pasterkamp, Imo E. Hoefer, Susan Redline, Katja Pahkala, Albertine J. Oldehinkel, Harold Snieder, Ginevra Biino, Reinhold Schmidt, Helena Schmidt, Stefania Bandinelli, George Dedoussis, Thangavel Alphonse Thanaraj, Sharon L. R. Kardia, Patricia A. Peyser, Norihiro Kato, Matthias B. Schulze, Giorgia Girotto, Carsten A. Böger, Bettina Jung, Peter K. Joshi, David A. Bennett, Philip L. De Jager, Xiangfeng Lu, Vasiliki Mamakou, Morris Brown, Mark J. Caulfield, Patricia B. Munroe, Xiuqing Guo, Marina Ciullo, Jost B. Jonas, Nilesh J. Samani, Jaakko Kaprio, Päivi Pajukanta, Teresa Tusié-Luna, Carlos A. Aguilar-Salinas, Linda S. Adair, Sonny Augustin Bechayda, H. Janaka de Silva, Ananda R. Wickremasinghe, Ronald M. Krauss, Jer-Yuarn Wu, Wei Zheng, Anneke Iden Hollander, Dwaipayan Bharadwaj, Adolfo Correa, James G. Wilson, Lars Lind, Chew-Kiat Heng, Amanda E. Nelson, Yvonne M. Golightly, James F. Wilson, Brenda Penninx, Hyung-Lae Kim, John Attia, Rodney J. Scott, D. C. Rao, Donna K. Arnett, Steven C. Hunt, Mark Walker, Heikki A. Koistinen, Giriraj R. Chandak, Josep M. Mercader, Maria C. Costanzo, Dongkeun Jang, Noël P. Burtt, Clicerio Gonzalez Villalpando, Lorena Orozco, Myriam Fornage, EShyong Tai, Rob M. van Dam, Terho Lehtimäki, Nish Chaturvedi, Mitsuhiro Yokota, Jianjun Liu, Dermot F. Reilly, Amy Jayne McKnight, Frank Kee, Karl-Heinz Jöckel, Mark I. McCarthy, Colin N. A. Palmer, Veronique Vitart, Caroline Hayward, Eleanor Simonsick, Cornelia M. van Duijn, Zi-Bing Jin, Jia Qu, Haretsugu Hishigaki, Xu Lin, Winfried März, Vilmundur Gudnason, Jean-Claude Tardif, Guillaume Lettre, Leen M.‘t Hart, Petra J. M. Elders, Scott M. Damrauer, Meena Kumari, Mika Kivimaki, Pim van der Harst, Tim D. Spector, Ruth J. F. Loos, Michael A. Province, Esteban J. Parra, Miguel Cruz, Bruce M. Psaty, Ivan Brandslund, Peter P. Pramstaller, Charles N. Rotimi, Kaare Christensen, Samuli Ripatti, Elisabeth Widén, Hakon Hakonarson, Struan F. A. Grant, Lambertus A. L. M. Kiemeney, Jacqueline de Graaf, Markus Loeffler, Florian Kronenberg, Dongfeng Gu, Jeanette Erdmann, Heribert Schunkert, Paul W. Franks, Allan Linneberg, J. Wouter Jukema, Amit V. Khera, Minna Männikkö, Marjo-Riitta Jarvelin, Zoltan Kutalik, Cucca Francesco, Dennis O. Mook-Kanamori, Ko Willems van Dijk, Hugh Watkins, David P. Strachan, Niels Grarup, Peter Sever, Neil Poulter, Lee-Ming Chuang, Jerome I. Rotter, Thomas M. Dantoft, Fredrik Karpe, Matt J. Neville, Nicholas J. Timpson, Ching-Yu Cheng, Tien-Yin Wong, Chiea Chuen Khor, Hengtong Li, Charumathi Sabanayagam, Annette Peters, Christian Gieger, Andrew T. Hattersley, Nancy L. Pedersen, Patrik K. E. Magnusson, Dorret I. Boomsma, Allegonda H. M. Willemsen, LAdrienne Cupples, Joyce B. J. van Meurs, Mohsen Ghanbari, Penny Gordon-Larsen, Wei Huang, Young Jin Kim, Yasuharu Tabara, Nicholas J. Wareham, Claudia Langenberg, Eleftheria Zeggini, Johanna Kuusisto, Markku Laakso, Erik Ingelsson, Goncalo Abecasis, John C. Chambers, Jaspal S. Kooner, Paul S. de Vries, Alanna C. Morrison, Scott Hazelhurst, Michèle Ramsay, Kari E. North, Martha Daviglus, Peter Kraft, Nicholas G. Martin, John B. Whitfield, Shahid Abbas, Danish Saleheen, Robin G. Walters, Michael V. Holmes, Corri Black, Blair H. Smith, Aris Baras, Anne E. Justice, Julie E. Buring, Paul M. Ridker, Daniel I. Chasman, Charles Kooperberg, Gen Tamiya, Masayuki Yamamoto, David A. van Heel, Richard C. Trembath, Wei-Qi Wei, Gail P. Jarvik, Bahram Namjou, M. Geoffrey Hayes, Marylyn D. Ritchie, Pekka Jousilahti, Veikko Salomaa, Kristian Hveem, Bjørn Olav Åsvold, Michiaki Kubo, Yoichiro Kamatani, Yukinori Okada, Yoshinori Murakami, Bong-Jo Kim, Unnur Thorsteinsdottir, Kari Stefansson, Jifeng Zhang, YEugene Chen, Yuk-Lam Ho, Julie A. Lynch, Daniel J. Rader, Philip S. Tsao, Kyong-Mi Chang, Kelly Cho, Christopher J. O’Donnell, John M. Gaziano, Peter W. F. Wilson, Timothy M. Frayling, Joel N. Hirschhorn, Sekar Kathiresan, Karen L. Mohlke, Yan V. Sun, Andrew P. Morris, Michael Boehnke, Christopher D. Brown, Pradeep Natarajan, Panos Deloukas, Cristen J. Willer, Themistocles L. Assimes, Gina M. Peloso, Biological Psychology, APH - Health Behaviors & Chronic Diseases, APH - Personalized Medicine, Amsterdam Reproduction & Development, APH - Mental Health, APH - Methodology, Interdisciplinary Centre Psychopathology and Emotion regulation (ICPE), Life Course Epidemiology (LCE), Cardiovascular Centre (CVC), Medicum, Institute for Molecular Medicine Finland, Complex Disease Genetics, Samuli Olli Ripatti / Principal Investigator, HUSLAB, Epigenetics of Complex Diseases and Traits, Department of Medicine, Helsinki University Hospital Area, Centre of Excellence in Complex Disease Genetics, Department of Public Health, Faculty Common Matters (Faculty of Social Sciences), Elisabeth Ingrid Maria Widen / Principal Investigator, Genomic Discoveries and Clinical Translation, Tampere University, Primary Health Care, Clinical Medicine, Department of Clinical Chemistry, TAYS Heart Centre, Department of Clinical Physiology and Nuclear Medicine, Epidemiology and Data Science, APH - Aging & Later Life, ACS - Diabetes & metabolism, ACS - Heart failure & arrhythmias, Psychiatry, Amsterdam Neuroscience - Complex Trait Genetics, Amsterdam Neuroscience - Mood, Anxiety, Psychosis, Stress & Sleep, General practice, APH - Digital Health, Lee Kong Chian School of Medicine (LKCMedicine), Peloso, Gina M [0000-0002-5355-8636], Apollo - University of Cambridge Repository, Epidemiology, Department of Marketing Management, Erasmus MC other, Radiology & Nuclear Medicine, Kanoni, Stavroula, Graham, Sarah E, Wang, Yuxuan, Surakka, Ida, Ramdas, Shweta, Zhu, Xiang, Clarke, Shoa L, Bhatti, Konain Fatima, Vedantam, Sailaja, Winkler, Thomas W, Locke, Adam E, Marouli, Eirini, Zajac, Greg J M, Wu, Kuan-Han H, Ntalla, Ioanna, Hui, Qin, Klarin, Derek, Hilliard, Austin T, Wang, Zeyuan, Xue, Chao, Thorleifsson, Gudmar, Helgadottir, Anna, Gudbjartsson, Daniel F, Holm, Hilma, Olafsson, Isleifur, Hwang, Mi Yeong, Han, Sohee, Akiyama, Masato, Sakaue, Saori, Terao, Chikashi, Kanai, Masahiro, Zhou, Wei, Brumpton, Ben M, Rasheed, Humaira, Havulinna, Aki S, Veturi, Yogasudha, Pacheco, Jennifer Allen, Rosenthal, Elisabeth A, Lingren, Todd, Feng, Qiping, Kullo, Iftikhar J, Narita, Akira, Takayama, Jun, Martin, Hilary C, Hunt, Karen A, Trivedi, Bhavi, Haessler, Jeffrey, Giulianini, Franco, Bradford, Yuki, Miller, Jason E, Campbell, Archie, Lin, Kuang, Millwood, Iona Y, Rasheed, Asif, Hindy, George, Faul, Jessica D, Zhao, Wei, Weir, David R, Turman, Constance, Huang, Hongyan, Graff, Mariaelisa, Choudhury, Ananyo, Sengupta, Dhriti, Mahajan, Anubha, Brown, Michael R, Zhang, Weihua, Yu, Ketian, Schmidt, Ellen M, Pandit, Anita, Gustafsson, Stefan, Yin, Xianyong, Luan, Jian'An, Zhao, Jing-Hua, Matsuda, Fumihiko, Jang, Hye-Mi, Yoon, Kyungheon, Medina-Gomez, Carolina, Pitsillides, Achillea, Hottenga, Jouke Jan, Wood, Andrew R, Ji, Yingji, Gao, Zishan, Haworth, Simon, Yousri, Noha A, Mitchell, Ruth E, Chai, Jin Fang, Aadahl, Mette, Bjerregaard, Anne A, Yao, Jie, Manichaikul, Ani, Hwu, Chii-Min, Hung, Yi-Jen, Warren, Helen R, Ramirez, Julia, Bork-Jensen, Jette, Kårhus, Line L, Goel, Anuj, Sabater-Lleal, Maria, Noordam, Raymond, Mauro, Pala, Matteo, Flori, Mcdaid, Aaron F, Marques-Vidal, Pedro, Wielscher, Matthia, Trompet, Stella, Sattar, Naveed, Møllehave, Line T, Munz, Matthia, Zeng, Lingyao, Huang, Jianfeng, Yang, Bin, Poveda, Alaitz, Kurbasic, Azra, Lamina, Claudia, Forer, Luka, Scholz, Marku, Galesloot, Tessel E, Bradfield, Jonathan P, Ruotsalainen, Sanni E, Daw, Ewarwick, Zmuda, Joseph M, Mitchell, Jonathan S, Fuchsberger, Christian, Christensen, Henry, Brody, Jennifer A, Vazquez-Moreno, Miguel, Feitosa, Mary F, Wojczynski, Mary K, Wang, Zhe, Preuss, Michael H, Mangino, Massimo, Christofidou, Paraskevi, Verweij, Niek, Benjamins, Jan W, Engmann, Jorgen, Tsao, Noah L, Verma, Anurag, Slieker, Roderick C, Lo, Ken Sin, Zilhao, Nuno R, Le, Phuong, Kleber, Marcus E, Delgado, Graciela E, Huo, Shaofeng, Ikeda, Daisuke D, Iha, Hiroyuki, Yang, Jian, Liu, Jun, Demirkan, Ayşe, Leonard, Hampton L, Marten, Jonathan, Frank, Mirjam, Schmidt, Börge, Smyth, Laura J, Cañadas-Garre, Marisa, Wang, Chaolong, Nakatochi, Masahiro, Wong, Andrew, Hutri-Kähönen, Nina, Sim, Xueling, Xia, Rui, Huerta-Chagoya, Alicia, Fernandez-Lopez, Juan Carlo, Lyssenko, Valeriya, Nongmaithem, Suraj S, Bayyana, Swati, Stringham, Heather M, Irvin, Marguerite R, Oldmeadow, Christopher, Kim, Han-Na, Ryu, Seungho, Timmers, Paul R H J, Arbeeva, Liubov, Dorajoo, Rajkumar, Lange, Leslie A, Prasad, Gauri, Lorés-Motta, Laura, Pauper, Marc, Long, Jirong, Li, Xiaohui, Theusch, Elizabeth, Takeuchi, Fumihiko, Spracklen, Cassandra N, Loukola, Anu, Bollepalli, Sailalitha, Warner, Sophie C, Wang, Ya Xing, Wei, Wen B, Nutile, Teresa, Ruggiero, Daniela, Sung, Yun Ju, Chen, Shufeng, Liu, Fangchao, Yang, Jingyun, Kentistou, Katherine A, Banas, Bernhard, Nardone, Giuseppe Giovanni, Meidtner, Karina, Bielak, Lawrence F, Smith, Jennifer A, Hebbar, Prashantha, Farmaki, Aliki-Eleni, Hofer, Edith, Lin, Maoxuan, Concas, Maria Pina, Vaccargiu, Simona, van der Most, Peter J, Pitkänen, Niina, Cade, Brian E, van der Laan, Sander W, Chitrala, Kumaraswamy Naidu, Weiss, Stefan, Bentley, Amy R, Doumatey, Ayo P, Adeyemo, Adebowale A, Lee, Jong Young, Petersen, Eva R B, Nielsen, Aneta A, Choi, Hyeok Sun, Nethander, Maria, Freitag-Wolf, Sandra, Southam, Lorraine, Rayner, Nigel W, Wang, Carol A, Lin, Shih-Yi, Wang, Jun-Sing, Couture, Christian, Lyytikäinen, Leo-Pekka, Nikus, Kjell, Cuellar-Partida, Gabriel, Vestergaard, Henrik, Hidalgo, Bertha, Giannakopoulou, Olga, Cai, Qiuyin, Obura, Morgan O, van Setten, Jessica, Li, Xiaoyin, Liang, Jingjing, Tang, Hua, Terzikhan, Natalie, Shin, Jae Hun, Jackson, Rebecca D, Reiner, Alexander P, Martin, Lisa Warsinger, Chen, Zhengming, Li, Liming, Kawaguchi, Takahisa, Thiery, Joachim, Bis, Joshua C, Launer, Lenore J, Li, Huaixing, Nalls, Mike A, Raitakari, Olli T, Ichihara, Sahoko, Wild, Sarah H, Nelson, Christopher P, Campbell, Harry, Jäger, Susanne, Nabika, Toru, Al-Mulla, Fahd, Niinikoski, Harri, Braund, Peter S, Kolcic, Ivana, Kovacs, Peter, Giardoglou, Tota, Katsuya, Tomohiro, de Kleijn, Dominique, de Borst, Gert J, Kim, Eung Kweon, Adams, Hieab H H, Ikram, M Arfan, Zhu, Xiaofeng, Asselbergs, Folkert W, Kraaijeveld, Adriaan O, Beulens, Joline W J, Shu, Xiao-Ou, Rallidis, Loukianos S, Pedersen, Oluf, Hansen, Torben, Mitchell, Paul, Hewitt, Alex W, Kähönen, Mika, Pérusse, Loui, Bouchard, Claude, Tönjes, Anke, Chen, Yii-Der Ida, Pennell, Craig E, Mori, Trevor A, Lieb, Wolfgang, Franke, Andre, Ohlsson, Clae, Mellström, Dan, Cho, Yoon Shin, Lee, Hyejin, Yuan, Jian-Min, Koh, Woon-Puay, Rhee, Sang Youl, Woo, Jeong-Taek, Heid, Iris M, Stark, Klaus J, Zimmermann, Martina E, Völzke, Henry, Homuth, Georg, Evans, Michele K, Zonderman, Alan B, Polasek, Ozren, Pasterkamp, Gerard, Hoefer, Imo E, Redline, Susan, Pahkala, Katja, Oldehinkel, Albertine J, Snieder, Harold, Biino, Ginevra, Schmidt, Reinhold, Schmidt, Helena, Bandinelli, Stefania, Dedoussis, George, Thanaraj, Thangavel Alphonse, Kardia, Sharon L R, Peyser, Patricia A, Kato, Norihiro, Schulze, Matthias B, Girotto, Giorgia, Böger, Carsten A, Jung, Bettina, Joshi, Peter K, Bennett, David A, De Jager, Philip L, Lu, Xiangfeng, Mamakou, Vasiliki, Brown, Morri, Caulfield, Mark J, Munroe, Patricia B, Guo, Xiuqing, Ciullo, Marina, Jonas, Jost B, Samani, Nilesh J, Kaprio, Jaakko, Pajukanta, Päivi, Tusié-Luna, Teresa, Aguilar-Salinas, Carlos A, Adair, Linda S, Bechayda, Sonny Augustin, de Silva, H Janaka, Wickremasinghe, Ananda R, Krauss, Ronald M, Wu, Jer-Yuarn, Zheng, Wei, Hollander, Anneke Iden, Bharadwaj, Dwaipayan, Correa, Adolfo, Wilson, James G, Lind, Lar, Heng, Chew-Kiat, Nelson, Amanda E, Golightly, Yvonne M, Wilson, James F, Penninx, Brenda, Kim, Hyung-Lae, Attia, John, Scott, Rodney J, Rao, D C, Arnett, Donna K, Hunt, Steven C, Walker, Mark, Koistinen, Heikki A, Chandak, Giriraj R, Mercader, Josep M, Costanzo, Maria C, Jang, Dongkeun, Burtt, Noël P, Villalpando, Clicerio Gonzalez, Orozco, Lorena, Fornage, Myriam, Tai, Eshyong, van Dam, Rob M, Lehtimäki, Terho, Chaturvedi, Nish, Yokota, Mitsuhiro, Liu, Jianjun, Reilly, Dermot F, Mcknight, Amy Jayne, Kee, Frank, Jöckel, Karl-Heinz, Mccarthy, Mark I, Palmer, Colin N A, Vitart, Veronique, Hayward, Caroline, Simonsick, Eleanor, van Duijn, Cornelia M, Jin, Zi-Bing, Qu, Jia, Hishigaki, Haretsugu, Lin, Xu, März, Winfried, Gudnason, Vilmundur, Tardif, Jean-Claude, Lettre, Guillaume, Hart, Leen M 't, Elders, Petra J M, Damrauer, Scott M, Kumari, Meena, Kivimaki, Mika, van der Harst, Pim, Spector, Tim D, Loos, Ruth J F, Province, Michael A, Parra, Esteban J, Cruz, Miguel, Psaty, Bruce M, Brandslund, Ivan, Pramstaller, Peter P, Rotimi, Charles N, Christensen, Kaare, Ripatti, Samuli, Widén, Elisabeth, Hakonarson, Hakon, Grant, Struan F A, Kiemeney, Lambertus A L M, de Graaf, Jacqueline, Loeffler, Marku, Kronenberg, Florian, Gu, Dongfeng, Erdmann, Jeanette, Schunkert, Heribert, Franks, Paul W, Linneberg, Allan, Jukema, J Wouter, Khera, Amit V, Männikkö, Minna, Jarvelin, Marjo-Riitta, Kutalik, Zoltan, Francesco, Cucca, Mook-Kanamori, Dennis O, van Dijk, Ko Willem, Watkins, Hugh, Strachan, David P, Grarup, Niel, Sever, Peter, Poulter, Neil, Chuang, Lee-Ming, Rotter, Jerome I, Dantoft, Thomas M, Karpe, Fredrik, Neville, Matt J, Timpson, Nicholas J, Cheng, Ching-Yu, Wong, Tien-Yin, Khor, Chiea Chuen, Li, Hengtong, Sabanayagam, Charumathi, Peters, Annette, Gieger, Christian, Hattersley, Andrew T, Pedersen, Nancy L, Magnusson, Patrik K E, Boomsma, Dorret I, Willemsen, Allegonda H M, Cupples, Ladrienne, van Meurs, Joyce B J, Ghanbari, Mohsen, Gordon-Larsen, Penny, Huang, Wei, Kim, Young Jin, Tabara, Yasuharu, Wareham, Nicholas J, Langenberg, Claudia, Zeggini, Eleftheria, Kuusisto, Johanna, Laakso, Markku, Ingelsson, Erik, Abecasis, Goncalo, Chambers, John C, Kooner, Jaspal S, de Vries, Paul S, Morrison, Alanna C, Hazelhurst, Scott, Ramsay, Michèle, North, Kari E, Daviglus, Martha, Kraft, Peter, Martin, Nicholas G, Whitfield, John B, Abbas, Shahid, Saleheen, Danish, Walters, Robin G, Holmes, Michael V, Black, Corri, Smith, Blair H, Baras, Ari, Justice, Anne E, Buring, Julie E, Ridker, Paul M, Chasman, Daniel I, Kooperberg, Charle, Tamiya, Gen, Yamamoto, Masayuki, van Heel, David A, Trembath, Richard C, Wei, Wei-Qi, Jarvik, Gail P, Namjou, Bahram, Hayes, M Geoffrey, Ritchie, Marylyn D, Jousilahti, Pekka, Salomaa, Veikko, Hveem, Kristian, Åsvold, Bjørn Olav, Kubo, Michiaki, Kamatani, Yoichiro, Okada, Yukinori, Murakami, Yoshinori, Kim, Bong-Jo, Thorsteinsdottir, Unnur, Stefansson, Kari, Zhang, Jifeng, Chen, Yeugene, Ho, Yuk-Lam, Lynch, Julie A, Rader, Daniel J, Tsao, Philip S, Chang, Kyong-Mi, Cho, Kelly, O'Donnell, Christopher J, Gaziano, John M, Wilson, Peter W F, Frayling, Timothy M, Hirschhorn, Joel N, Kathiresan, Sekar, Mohlke, Karen L, Sun, Yan V, Morris, Andrew P, Boehnke, Michael, Brown, Christopher D, Natarajan, Pradeep, Deloukas, Pano, Willer, Cristen J, Assimes, Themistocles L, and Peloso, Gina M
Subjects: Genome-wide association study, Medizin, Polymorphism, Single Nucleotide, Humans, Genome-Wide Association Study, Genetic Predisposition to Disease, Sex Characteristics, Phenotype, Lipids/genetics, Genetic Pleiotropy, Cholesterol, GWAS, Genetics, Lipids, Genetic, SDG 3 - Good Health and Well-being, Medicine [Science], 112 Statistics and probability, Medicinsk genetik, Genome-wide Association Study, Gwas, 1184 Genetics, developmental biology, physiology, 3126 Surgery, anesthesiology, intensive care, radiology, 3142 Public health care science, environmental and occupational health, 3141 Health care science, FOS: Biological sciences, Urological cancers Radboud Institute for Health Sciences [Radboudumc 15], 3111 Biomedicine, Medical Genetics
Abstract: Background: Genetic variants within nearly 1000 loci are known to contribute to modulation of blood lipid levels. However, the biological pathways underlying these associations are frequently unknown, limiting understanding of these findings and hindering downstream translational efforts such as drug target discovery. Results: To expand our understanding of the underlying biological pathways and mechanisms controlling blood lipid levels, we leverage a large multi-ancestry metaanalysis (N = 1,654,960) of blood lipids to prioritize putative causal genes for 2286 lipid associations using six gene prediction approaches. Using phenome-wide association (PheWAS) scans, we identify relationships of genetically predicted lipid levels to other diseases and conditions. We confirm known pleiotropic associations with cardiovascular phenotypes and determine novel associations, notably with cholelithiasis risk. We perform sex-stratified GWAS meta-analysis of lipid levels and show that 3–5% of autosomal lipid-associated loci demonstrate sex-biased effects. Finally, we report 21 novel lipid loci identified on the X chromosome. Many of the sex-biased autosomal and X chromosome lipid loci show pleiotropic associations with sex hormones, emphasizing the role of hormone regulation in lipid metabolism. Conclusions: Taken together, our findings provide insights into the biological mechanisms through which associated variants lead to altered lipid levels and potentially cardiovascular disease risk., United States Department of Health & Human Services National Institutes of Health (NIH) - USA NIH National Heart Lung & Blood Institute (NHLBI) R01HL127564 R01HL142711, Wellcome Trust 201543/B/16/Z 202802/Z/16/Z, European Commission HEALTH-F2-2013-601456 608765 786833, TriPartite Immunometabolism Consortium [TrIC]-Novo Nordisk Foundation NNF15CC0018486, American Diabetes Association 1-19-ICTS-068, Academy of Finland 312062 Finnish Foundation for Cardiovascular Research, Sigrid Juselius Foundation, Finnish innovation fund Sitra (EW) Finska Lakaresallskapet, American Heart Association 15POST24470131 17POST33650016, University of Bristol NIHR Biomedical Research Centre BRC-1215-2001, MRC & WT 217065/Z/19/Z, UK Research & Innovation (UKRI), Medical Research Council UK (MRC) MC_UU_00011, CRUK Integrative Cancer Epidemiology Programme C18281/A19169, Medical Research Council UK (MRC) MC_UU_00011/1, UK National Institute for Health Research Academic Clinical Fellowship, American Heart Association 18CDA34110116, Miguel Servet contract from the ISCIII Spanish Health Institute CP17/00142, European Social Fund (ESF), Westlake Education Foundation, British Heart Foundation FS/14/66/3129 Z01HG200362 R01HL142302 R01HL105756
Published: 2022
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15. Genetic analyses of the electrocardiographic QT interval and its components identify additional loci and pathways

Author: William J. Young, Najim Lahrouchi, Aaron Isaacs, ThuyVy Duong, Luisa Foco, Farah Ahmed, Jennifer A. Brody, Reem Salman, Raymond Noordam, Jan-Walter Benjamins, Jeffrey Haessler, Leo-Pekka Lyytikäinen, Linda Repetto, Maria Pina Concas, Marten E. van den Berg, Stefan Weiss, Antoine R. Baldassari, Traci M. Bartz, James P. Cook, Daniel S. Evans, Rebecca Freudling, Oliver Hines, Jonas L. Isaksen, Honghuang Lin, Hao Mei, Arden Moscati, Martina Müller-Nurasyid, Casia Nursyifa, Yong Qian, Anne Richmond, Carolina Roselli, Kathleen A. Ryan, Eduardo Tarazona-Santos, Sébastien Thériault, Stefan van Duijvenboden, Helen R. Warren, Jie Yao, Dania Raza, Stefanie Aeschbacher, Gustav Ahlberg, Alvaro Alonso, Laura Andreasen, Joshua C. Bis, Eric Boerwinkle, Archie Campbell, Eulalia Catamo, Massimiliano Cocca, Michael J. Cutler, Dawood Darbar, Alessandro De Grandi, Antonio De Luca, Jun Ding, Christina Ellervik, Patrick T. Ellinor, Stephan B. Felix, Philippe Froguel, Christian Fuchsberger, Martin Gögele, Claus Graff, Mariaelisa Graff, Xiuqing Guo, Torben Hansen, Susan R. Heckbert, Paul L. Huang, Heikki V. Huikuri, Nina Hutri-Kähönen, M. Arfan Ikram, Rebecca D. Jackson, Juhani Junttila, Maryam Kavousi, Jan A. Kors, Thiago P. Leal, Rozenn N. Lemaitre, Henry J. Lin, Lars Lind, Allan Linneberg, Simin Liu, Peter W. MacFarlane, Massimo Mangino, Thomas Meitinger, Massimo Mezzavilla, Pashupati P. Mishra, Rebecca N. Mitchell, Nina Mononen, May E. Montasser, Alanna C. Morrison, Matthias Nauck, Victor Nauffal, Pau Navarro, Kjell Nikus, Guillaume Pare, Kristen K. Patton, Giulia Pelliccione, Alan Pittman, David J. Porteous, Peter P. Pramstaller, Michael H. Preuss, Olli T. Raitakari, Alexander P. Reiner, Antonio Luiz P. Ribeiro, Kenneth M. Rice, Lorenz Risch, David Schlessinger, Ulrich Schotten, Claudia Schurmann, Xia Shen, M. Benjamin Shoemaker, Gianfranco Sinagra, Moritz F. Sinner, Elsayed Z. Soliman, Monika Stoll, Konstantin Strauch, Kirill Tarasov, Kent D. Taylor, Andrew Tinker, Stella Trompet, André Uitterlinden, Uwe Völker, Henry Völzke, Melanie Waldenberger, Lu-Chen Weng, Eric A. Whitsel, James G. Wilson, Christy L. Avery, David Conen, Adolfo Correa, Francesco Cucca, Marcus Dörr, Sina A. Gharib, Giorgia Girotto, Niels Grarup, Caroline Hayward, Yalda Jamshidi, Marjo-Riitta Järvelin, J. Wouter Jukema, Stefan Kääb, Mika Kähönen, Jørgen K. Kanters, Charles Kooperberg, Terho Lehtimäki, Maria Fernanda Lima-Costa, Yongmei Liu, Ruth J. F. Loos, Steven A. Lubitz, Dennis O. Mook-Kanamori, Andrew P. Morris, Jeffrey R. O’Connell, Morten Salling Olesen, Michele Orini, Sandosh Padmanabhan, Cristian Pattaro, Annette Peters, Bruce M. Psaty, Jerome I. Rotter, Bruno Stricker, Pim van der Harst, Cornelia M. van Duijn, Niek Verweij, James F. Wilson, Dan E. Arking, Julia Ramirez, Pier D. Lambiase, Nona Sotoodehnia, Borbala Mifsud, Christopher Newton-Cheh, Patricia B. Munroe, Cardiology, ACS - Heart failure & arrhythmias, Epidemiology, Radiology & Nuclear Medicine, Medical Informatics, Internal Medicine, Young, William J, Lahrouchi, Najim, Isaacs, Aaron, Duong, Thuyvy, Foco, Luisa, Ahmed, Farah, Brody, Jennifer A, Salman, Reem, Noordam, Raymond, Benjamins, Jan-Walter, Haessler, Jeffrey, Lyytikäinen, Leo-Pekka, Repetto, Linda, Concas, Maria Pina, van den Berg, Marten E, Weiss, Stefan, Baldassari, Antoine R, Bartz, Traci M, Cook, James P, Evans, Daniel S, Freudling, Rebecca, Hines, Oliver, Isaksen, Jonas L, Lin, Honghuang, Mei, Hao, Moscati, Arden, Müller-Nurasyid, Martina, Nursyifa, Casia, Qian, Yong, Richmond, Anne, Roselli, Carolina, Ryan, Kathleen A, Tarazona-Santos, Eduardo, Thériault, Sébastien, van Duijvenboden, Stefan, Warren, Helen R, Yao, Jie, Raza, Dania, Aeschbacher, Stefanie, Ahlberg, Gustav, Alonso, Alvaro, Andreasen, Laura, Bis, Joshua C, Boerwinkle, Eric, Campbell, Archie, Catamo, Eulalia, Cocca, Massimiliano, Cutler, Michael J, Darbar, Dawood, De Grandi, Alessandro, De Luca, Antonio, Ding, Jun, Ellervik, Christina, Ellinor, Patrick T, Felix, Stephan B, Froguel, Philippe, Fuchsberger, Christian, Gögele, Martin, Graff, Clau, Graff, Mariaelisa, Guo, Xiuqing, Hansen, Torben, Heckbert, Susan R, Huang, Paul L, Huikuri, Heikki V, Hutri-Kähönen, Nina, Ikram, M Arfan, Jackson, Rebecca D, Junttila, Juhani, Kavousi, Maryam, Kors, Jan A, Leal, Thiago P, Lemaitre, Rozenn N, Lin, Henry J, Lind, Lar, Linneberg, Allan, Liu, Simin, Macfarlane, Peter W, Mangino, Massimo, Meitinger, Thoma, Mezzavilla, Massimo, Mishra, Pashupati P, Mitchell, Rebecca N, Mononen, Nina, Montasser, May E, Morrison, Alanna C, Nauck, Matthia, Nauffal, Victor, Navarro, Pau, Nikus, Kjell, Pare, Guillaume, Patton, Kristen K, Pelliccione, Giulia, Pittman, Alan, Porteous, David J, Pramstaller, Peter P, Preuss, Michael H, Raitakari, Olli T, Reiner, Alexander P, Ribeiro, Antonio Luiz P, Rice, Kenneth M, Risch, Lorenz, Schlessinger, David, Schotten, Ulrich, Schurmann, Claudia, Shen, Xia, Shoemaker, M Benjamin, Sinagra, Gianfranco, Sinner, Moritz F, Soliman, Elsayed Z, Stoll, Monika, Strauch, Konstantin, Tarasov, Kirill, Taylor, Kent D, Tinker, Andrew, Trompet, Stella, Uitterlinden, André, Völker, Uwe, Völzke, Henry, Waldenberger, Melanie, Weng, Lu-Chen, Whitsel, Eric A, Wilson, James G, Avery, Christy L, Conen, David, Correa, Adolfo, Cucca, Francesco, Dörr, Marcu, Gharib, Sina A, Girotto, Giorgia, Grarup, Niel, Hayward, Caroline, Jamshidi, Yalda, Järvelin, Marjo-Riitta, Jukema, J Wouter, Kääb, Stefan, Kähönen, Mika, Kanters, Jørgen K, Kooperberg, Charle, Lehtimäki, Terho, Lima-Costa, Maria Fernanda, Liu, Yongmei, Loos, Ruth J F, Lubitz, Steven A, Mook-Kanamori, Dennis O, Morris, Andrew P, O'Connell, Jeffrey R, Olesen, Morten Salling, Orini, Michele, Padmanabhan, Sandosh, Pattaro, Cristian, Peters, Annette, Psaty, Bruce M, Rotter, Jerome I, Stricker, Bruno, van der Harst, Pim, van Duijn, Cornelia M, Verweij, Niek, Wilson, James F, Arking, Dan E, Ramirez, Julia, Lambiase, Pier D, Sotoodehnia, Nona, Mifsud, Borbala, Newton-Cheh, Christopher, Munroe, Patricia B, Cardiovascular Centre (CVC), Tampere University, Department of Clinical Chemistry, Clinical Medicine, Department of Paediatrics, TAYS Heart Centre, Department of Clinical Physiology and Nuclear Medicine, Fysiologie, RS: Carim - B01 Blood proteins & engineering, RS: Carim - H08 Experimental atrial fibrillation, and Biochemie
Subjects: Male, Electrocardiography/methods, General Physics and Astronomy, 610 Medicine & health, Arrhythmias, 3121 Internal medicine, Genome-wide association studies, General Biochemistry, Genetics and Molecular Biology, Electrocardiography, Humans, Arrhythmias, Cardiac/genetics, Genetic Testing, Medicinsk genetik, Multidisciplinary, Death, Sudden, Cardiac, Arrhythmias, Cardiac, General Chemistry, Sudden, Electrocardiogram, Death, Genetic markers, 3111 Biomedicine, 610 Medizin und Gesundheit, Cardiac, Medical Genetics
Abstract: The QT interval is a heritable electrocardiographic measure associated with arrhythmia risk when prolonged. Here, the authors used a series of genetic analyses to identify genetic loci, pathways, therapeutic targets, and relationships with cardiovascular disease. The QT interval is an electrocardiographic measure representing the sum of ventricular depolarization and repolarization, estimated by QRS duration and JT interval, respectively. QT interval abnormalities are associated with potentially fatal ventricular arrhythmia. Using genome-wide multi-ancestry analyses (>250,000 individuals) we identify 177, 156 and 121 independent loci for QT, JT and QRS, respectively, including a male-specific X-chromosome locus. Using gene-based rare-variant methods, we identify associations with Mendelian disease genes. Enrichments are observed in established pathways for QT and JT, and previously unreported genes indicated in insulin-receptor signalling and cardiac energy metabolism. In contrast for QRS, connective tissue components and processes for cell growth and extracellular matrix interactions are significantly enriched. We demonstrate polygenic risk score associations with atrial fibrillation, conduction disease and sudden cardiac death. Prioritization of druggable genes highlight potential therapeutic targets for arrhythmia. Together, these results substantially advance our understanding of the genetic architecture of ventricular depolarization and repolarization.
Published: 2022
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16. Differential and shared genetic effects on kidney function between diabetic and non-diabetic individuals

Author: Winkler, Thomas W., Rasheed, Humaira, Teumer, Alexander, Gorski, Mathias, Rowan, Bryce X., Stanzick, Kira J., Thomas, Laurent F., Tin, Adrienne, Hoppmann, Anselm, Chu, Audrey Y., Tayo, Bamidele, Thio, Chris H. L., Cusi, Daniele, Chai, Jin-Fang, Sieber, Karsten B., Horn, Katrin, Li, Man, Scholz, Markus, Cocca, Massimiliano, Wuttke, Matthias, van der Most, Peter J., Yang, Qiong, Ghasemi, Sahar, Nutile, Teresa, Li, Yong, Pontali, Giulia, Günther, Felix, Dehghan, Abbas, Correa, Adolfo, Parsa, Afshin, Feresin, Agnese, de Vries, Aiko P. J., Zonderman, Alan B., Smith, Albert V., Oldehinkel, Albertine J., De Grandi, Alessandro, Rosenkranz, Alexander R., Franke, Andre, Teren, Andrej, Metspalu, Andres, Hicks, Andrew A., Morris, Andrew P., Tönjes, Anke, Morgan, Anna, Podgornaia, Anna I., Peters, Annette, Körner, Antje, Mahajan, Anubha, Campbell, Archie, Freedman, Barry I., Spedicati, Beatrice, Ponte, Belen, Schöttker, Ben, Brumpton, Ben, Banas, Bernhard, Krämer, Bernhard K., Jung, Bettina, Åsvold, Bjørn Olav, Smith, Blair H., Ning, Boting, Penninx, Brenda W. J. H., Vanderwerff, Brett R., Psaty, Bruce M., Kammerer, Candace M., Langefeld, Carl D., Hayward, Caroline, Spracklen, Cassandra N., Robinson-Cohen, Cassianne, Hartman, Catharina A., Lindgren, Cecilia M., Wang, Chaolong, Sabanayagam, Charumathi, Heng, Chew-Kiat, Lanzani, Chiara, Khor, Chiea-Chuen, Cheng, Ching-Yu, Fuchsberger, Christian, Gieger, Christian, Shaffer, Christian M., Schulz, Christina-Alexandra, Willer, Cristen J., Chasman, Daniel I., Gudbjartsson, Daniel F., Ruggiero, Daniela, Toniolo, Daniela, Czamara, Darina, Porteous, David J., Waterworth, Dawn M., Mascalzoni, Deborah, Mook-Kanamori, Dennis O., Reilly, Dermot F., Daw, E. Warwick, Hofer, Edith, Boerwinkle, Eric, Salvi, Erika, Bottinger, Erwin P., Tai, E-Shyong, Catamo, Eulalia, Rizzi, Federica, Guo, Feng, Rivadeneira, Fernando, Guilianini, Franco, Sveinbjornsson, Gardar, Ehret, Georg, Waeber, Gerard, Biino, Ginevra, Girotto, Giorgia, Pistis, Giorgio, Nadkarni, Girish N., Delgado, Graciela E., Montgomery, Grant W., Snieder, Harold, Campbell, Harry, White, Harvey D., Gao, He, Stringham, Heather M., Schmidt, Helena, Li, Hengtong, Brenner, Hermann, Holm, Hilma, Kirsten, Holger, Kramer, Holly, Rudan, Igor, Nolte, Ilja M., Tzoulaki, Ioanna, Olafsson, Isleifur, Martins, Jade, Cook, James P., Wilson, James F., Halbritter, Jan, Felix, Janine F., Divers, Jasmin, Kooner, Jaspal S., Lee, Jeannette Jen-Mai, O’Connell, Jeffrey, Rotter, Jerome I., Liu, Jianjun, Xu, Jie, Thiery, Joachim, Ärnlöv, Johan, Kuusisto, Johanna, Jakobsdottir, Johanna, Tremblay, Johanne, Chambers, John C., Whitfield, John B., Gaziano, John M., Marten, Jonathan, Coresh, Josef, Jonas, Jost B., Mychaleckyj, Josyf C., Christensen, Kaare, Eckardt, Kai-Uwe, Mohlke, Karen L., Endlich, Karlhans, Dittrich, Katalin, Ryan, Kathleen A., Rice, Kenneth M., Taylor, Kent D., Ho, Kevin, Nikus, Kjell, Matsuda, Koichi, Strauch, Konstantin, Miliku, Kozeta, Hveem, Kristian, Lind, Lars, Wallentin, Lars, Yerges-Armstrong, Laura M., Raffield, Laura M., Phillips, Lawrence S., Launer, Lenore J., Lyytikäinen, Leo-Pekka, Lange, Leslie A., Citterio, Lorena, Klaric, Lucija, Ikram, M. Arfan, Ising, Marcus, Kleber, Marcus E., Francescatto, Margherita, Concas, Maria Pina, Ciullo, Marina, Piratsu, Mario, Orho-Melander, Marju, Laakso, Markku, Loeffler, Markus, Perola, Markus, de Borst, Martin H., Gögele, Martin, Bianca, Martina La, Lukas, Mary Ann, Feitosa, Mary F., Biggs, Mary L., Wojczynski, Mary K., Kavousi, Maryam, Kanai, Masahiro, Akiyama, Masato, Yasuda, Masayuki, Nauck, Matthias, Waldenberger, Melanie, Chee, Miao-Li, Chee, Miao-Ling, Boehnke, Michael, Preuss, Michael H., Stumvoll, Michael, Province, Michael A., Evans, Michele K., O’Donoghue, Michelle L., Kubo, Michiaki, Kähönen, Mika, Kastarinen, Mika, Nalls, Mike A., Kuokkanen, Mikko, Ghanbari, Mohsen, Bochud, Murielle, Josyula, Navya Shilpa, Martin, Nicholas G., Tan, Nicholas Y. Q., Palmer, Nicholette D., Pirastu, Nicola, Schupf, Nicole, Verweij, Niek, Hutri-Kähönen, Nina, Mononen, Nina, Bansal, Nisha, Devuyst, Olivier, Melander, Olle, Raitakari, Olli T., Polasek, Ozren, Manunta, Paolo, Gasparini, Paolo, Mishra, Pashupati P., Sulem, Patrick, Magnusson, Patrik K. E., Elliott, Paul, Ridker, Paul M., Hamet, Pavel, Svensson, Per O., Joshi, Peter K., Kovacs, Peter, Pramstaller, Peter P., Rossing, Peter, Vollenweider, Peter, van der Harst, Pim, Dorajoo, Rajkumar, Sim, Ralene Z. H., Burkhardt, Ralph, Tao, Ran, Noordam, Raymond, Mägi, Reedik, Schmidt, Reinhold, de Mutsert, Renée, Rueedi, Rico, van Dam, Rob M., Carroll, Robert J., Gansevoort, Ron T., Loos, Ruth J. F., Felicita, Sala Cinzia, Sedaghat, Sanaz, Padmanabhan, Sandosh, Freitag-Wolf, Sandra, Pendergrass, Sarah A., Graham, Sarah E., Gordon, Scott D., Hwang, Shih-Jen, Kerr, Shona M., Vaccargiu, Simona, Patil, Snehal B., Hallan, Stein, Bakker, Stephan J. L., Lim, Su-Chi, Lucae, Susanne, Vogelezang, Suzanne, Bergmann, Sven, Corre, Tanguy, Ahluwalia, Tarunveer S., Lehtimäki, Terho, Boutin, Thibaud S., Meitinger, Thomas, Wong, Tien-Yin, Bergler, Tobias, Rabelink, Ton J., Esko, Tõnu, Haller, Toomas, Thorsteinsdottir, Unnur, Völker, Uwe, Foo, Valencia Hui Xian, Salomaa, Veikko, Vitart, Veronique, Giedraitis, Vilmantas, Gudnason, Vilmundur, Jaddoe, Vincent W. V., Huang, Wei, Zhang, Weihua, Wei, Wen Bin, Kiess, Wieland, März, Winfried, Koenig, Wolfgang, Lieb, Wolfgang, Gao, Xin, Sim, Xueling, Wang, Ya Xing, Friedlander, Yechiel, Tham, Yih-Chung, Kamatani, Yoichiro, Okada, Yukinori, Milaneschi, Yuri, Yu, Zhi, Hung, Adriana M., Stark, Klaus J., Stefansson, Kari, Böger, Carsten A., Kronenberg, Florian, Köttgen, Anna, Pattaro, Cristian, Heid, Iris M., Psychiatry, APH - Mental Health, Amsterdam Neuroscience - Complex Trait Genetics, Amsterdam Neuroscience - Mood, Anxiety, Psychosis, Stress & Sleep, APH - Digital Health, University of Helsinki, CAMM - Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, Research Programs Unit, Tampere University, Clinical Medicine, TAYS Heart Centre, Department of Clinical Chemistry, Department of Clinical Physiology and Nuclear Medicine, Internal Medicine, Pediatrics, Epidemiology, Radiology & Nuclear Medicine, Erasmus MC other, Home Office, Imperial College Healthcare NHS Trust- BRC Funding, Medical Research Council (MRC), UK DRI Ltd, Interdisciplinary Centre Psychopathology and Emotion regulation (ICPE), Life Course Epidemiology (LCE), Groningen Institute for Organ Transplantation (GIOT), Groningen Kidney Center (GKC), Cardiovascular Centre (CVC), Winkler, Thomas W, Rasheed, Humaira, Teumer, Alexander, Gorski, Mathia, Rowan, Bryce X, Stanzick, Kira J, Thomas, Laurent F, Tin, Adrienne, Hoppmann, Anselm, Chu, Audrey Y, Tayo, Bamidele, Thio, Chris H L, Cusi, Daniele, Chai, Jin-Fang, Sieber, Karsten B, Horn, Katrin, Li, Man, Scholz, Marku, Cocca, Massimiliano, Wuttke, Matthia, van der Most, Peter J, Yang, Qiong, Ghasemi, Sahar, Nutile, Teresa, Li, Yong, Pontali, Giulia, Günther, Felix, Dehghan, Abba, Correa, Adolfo, Parsa, Afshin, Feresin, Agnese, de Vries, Aiko P J, Zonderman, Alan B, Smith, Albert V, Oldehinkel, Albertine J, De Grandi, Alessandro, Rosenkranz, Alexander R, Franke, Andre, Teren, Andrej, Metspalu, Andre, Hicks, Andrew A, Morris, Andrew P, Tönjes, Anke, Morgan, Anna, Podgornaia, Anna I, Peters, Annette, Körner, Antje, Mahajan, Anubha, Campbell, Archie, Freedman, Barry I, Spedicati, Beatrice, Ponte, Belen, Schöttker, Ben, Brumpton, Ben, Banas, Bernhard, Krämer, Bernhard K, Jung, Bettina, Åsvold, Bjørn Olav, Smith, Blair H, Ning, Boting, Penninx, Brenda W J H, Vanderwerff, Brett R, Psaty, Bruce M, Kammerer, Candace M, Langefeld, Carl D, Hayward, Caroline, Spracklen, Cassandra N, Robinson-Cohen, Cassianne, Hartman, Catharina A, Lindgren, Cecilia M, Wang, Chaolong, Sabanayagam, Charumathi, Heng, Chew-Kiat, Lanzani, Chiara, Khor, Chiea-Chuen, Cheng, Ching-Yu, Fuchsberger, Christian, Gieger, Christian, Shaffer, Christian M, Schulz, Christina-Alexandra, Willer, Cristen J, Chasman, Daniel I, Gudbjartsson, Daniel F, Ruggiero, Daniela, Toniolo, Daniela, Czamara, Darina, Porteous, David J, Waterworth, Dawn M, Mascalzoni, Deborah, Mook-Kanamori, Dennis O, Reilly, Dermot F, Daw, E Warwick, Hofer, Edith, Boerwinkle, Eric, Salvi, Erika, Bottinger, Erwin P, Tai, E-Shyong, Catamo, Eulalia, Rizzi, Federica, Guo, Feng, Rivadeneira, Fernando, Guilianini, Franco, Sveinbjornsson, Gardar, Ehret, Georg, Waeber, Gerard, Biino, Ginevra, Girotto, Giorgia, Pistis, Giorgio, Nadkarni, Girish N, Delgado, Graciela E, Montgomery, Grant W, Snieder, Harold, Campbell, Harry, White, Harvey D, Gao, He, Stringham, Heather M, Schmidt, Helena, Li, Hengtong, Brenner, Hermann, Holm, Hilma, Kirsten, Holgen, Kramer, Holly, Rudan, Igor, Nolte, Ilja M, Tzoulaki, Ioanna, Olafsson, Isleifur, Martins, Jade, Cook, James P, Wilson, James F, Halbritter, Jan, Felix, Janine F, Divers, Jasmin, Kooner, Jaspal S, Lee, Jeannette Jen-Mai, O'Connell, Jeffrey, Rotter, Jerome I, Liu, Jianjun, Xu, Jie, Thiery, Joachim, Ärnlöv, Johan, Kuusisto, Johanna, Jakobsdottir, Johanna, Tremblay, Johanne, Chambers, John C, Whitfield, John B, Gaziano, John M, Marten, Jonathan, Coresh, Josef, Jonas, Jost B, Mychaleckyj, Josyf C, Christensen, Kaare, Eckardt, Kai-Uwe, Mohlke, Karen L, Endlich, Karlhan, Dittrich, Katalin, Ryan, Kathleen A, Rice, Kenneth M, Taylor, Kent D, Ho, Kevin, Nikus, Kjell, Matsuda, Koichi, Strauch, Konstantin, Miliku, Kozeta, Hveem, Kristian, Lind, Lar, Wallentin, Lar, Yerges-Armstrong, Laura M, Raffield, Laura M, Phillips, Lawrence S, Launer, Lenore J, Lyytikäinen, Leo-Pekka, Lange, Leslie A, Citterio, Lorena, Klaric, Lucija, Ikram, M Arfan, Ising, Marcu, Kleber, Marcus E, Francescatto, Margherita, Concas, Maria Pina, Ciullo, Marina, Piratsu, Mario, Orho-Melander, Marju, Laakso, Markku, Loeffler, Marku, Perola, Marku, de Borst, Martin H, Gögele, Martin, Bianca, Martina La, Lukas, Mary Ann, Feitosa, Mary F, Biggs, Mary L, Wojczynski, Mary K, Kavousi, Maryam, Kanai, Masahiro, Akiyama, Masato, Yasuda, Masayuki, Nauck, Matthia, Waldenberger, Melanie, Chee, Miao-Li, Chee, Miao-Ling, Boehnke, Michael, Preuss, Michael H, Stumvoll, Michael, Province, Michael A, Evans, Michele K, O'Donoghue, Michelle L, Kubo, Michiaki, Kähönen, Mika, Kastarinen, Mika, Nalls, Mike A, Kuokkanen, Mikko, Ghanbari, Mohsen, Bochud, Murielle, Josyula, Navya Shilpa, Martin, Nicholas G, Tan, Nicholas Y Q, Palmer, Nicholette D, Pirastu, Nicola, Schupf, Nicole, Verweij, Niek, Hutri-Kähönen, Nina, Mononen, Nina, Bansal, Nisha, Devuyst, Olivier, Melander, Olle, Raitakari, Olli T, Polasek, Ozren, Manunta, Paolo, Gasparini, Paolo, Mishra, Pashupati P, Sulem, Patrick, Magnusson, Patrik K E, Elliott, Paul, Ridker, Paul M, Hamet, Pavel, Svensson, Per O, Joshi, Peter K, Kovacs, Peter, Pramstaller, Peter P, Rossing, Peter, Vollenweider, Peter, van der Harst, Pim, Dorajoo, Rajkumar, Sim, Ralene Z H, Burkhardt, Ralph, Tao, Ran, Noordam, Raymond, Mägi, Reedik, Schmidt, Reinhold, de Mutsert, Renée, Rueedi, Rico, van Dam, Rob M, Carroll, Robert J, Gansevoort, Ron T, Loos, Ruth J F, Felicita, Sala Cinzia, Sedaghat, Sanaz, Padmanabhan, Sandosh, Freitag-Wolf, Sandra, Pendergrass, Sarah A, Graham, Sarah E, Gordon, Scott D, Hwang, Shih-Jen, Kerr, Shona M, Vaccargiu, Simona, Patil, Snehal B, Hallan, Stein, Bakker, Stephan J L, Lim, Su-Chi, Lucae, Susanne, Vogelezang, Suzanne, Bergmann, Sven, Corre, Tanguy, Ahluwalia, Tarunveer S, Lehtimäki, Terho, Boutin, Thibaud S, Meitinger, Thoma, Wong, Tien-Yin, Bergler, Tobia, Rabelink, Ton J, Esko, Tõnu, Haller, Tooma, Thorsteinsdottir, Unnur, Völker, Uwe, Foo, Valencia Hui Xian, Salomaa, Veikko, Vitart, Veronique, Giedraitis, Vilmanta, Gudnason, Vilmundur, Jaddoe, Vincent W V, Huang, Wei, Zhang, Weihua, Wei, Wen Bin, Kiess, Wieland, März, Winfried, Koenig, Wolfgang, Lieb, Wolfgang, Gao, Xin, Sim, Xueling, Wang, Ya Xing, Friedlander, Yechiel, Tham, Yih-Chung, Kamatani, Yoichiro, Okada, Yukinori, Milaneschi, Yuri, Yu, Zhi, Stark, Klaus J, Stefansson, Kari, Böger, Carsten A, Hung, Adriana M, Kronenberg, Florian, Köttgen, Anna, Pattaro, Cristian, Heid, Iris M, and Lee Kong Chian School of Medicine (LKCMedicine)
Subjects: Life Sciences & Biomedicine - Other Topics, EXPRESSION, Diabetic Nephropathies/genetics, 610 Medizin, LOCI, Medicine (miscellaneous), EFFICIENT, Lifelines cohort study, Kidney, General Biochemistry, Genetics and Molecular Biology, DISEASE, QUALITY-CONTROL, SDG 3 - Good Health and Well-being, Diabetic Nephropathy, Diabetes Mellitus, Humans, Medicine [Science], Diabetic Nephropathies, GENOME-WIDE ASSOCIATION, Biology, DiscovEHR/MyCode study, METAANALYSIS, Glomerular Filtration Rate/genetics, Medicinsk genetik, ddc:610, Science & Technology, genetic, effects, kidney, diabetic, JOINT, Klinisk medicin, Diabetes Mellitu, 3126 Surgery, anesthesiology, intensive care, radiology, Multidisciplinary Sciences, ENVIRONMENT INTERACTION, Creatinine, VA Million Veteran Program, Science & Technology - Other Topics, 3111 Biomedicine, Clinical Medicine, SMOKING, General Agricultural and Biological Sciences, Life Sciences & Biomedicine, Medical Genetics, Human, Genome-Wide Association Study, Glomerular Filtration Rate
Abstract: Reduced glomerular filtration rate (GFR) can progress to kidney failure. Risk factors include genetics and diabetes mellitus (DM), but little is known about their interaction. We conducted genome-wide association meta-analyses for estimated GFR based on serum creatinine (eGFR), separately for individuals with or without DM (nDM = 178,691, nnoDM = 1,296,113). Our genome-wide searches identified (i) seven eGFR loci with significant DM/noDM-difference, (ii) four additional novel loci with suggestive difference and (iii) 28 further novel loci (including CUBN) by allowing for potential difference. GWAS on eGFR among DM individuals identified 2 known and 27 potentially responsible loci for diabetic kidney disease. Gene prioritization highlighted 18 genes that may inform reno-protective drug development. We highlight the existence of DM-only and noDM-only effects, which can inform about the target group, if respective genes are advanced as drug targets. Largely shared effects suggest that most drug interventions to alter eGFR should be effective in DM and noDM. Published version The Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) supported the meta-analysis—Project-ID 387509280—SFB1350 (Subproject C6 to I.M.H.). A.M.H., B.R., and R.T. were supported by VACSR&D MVP grant CX001897. This research is based on data from the Million Veteran Program, Office of Research and Development, Veterans Health Administration, and was supported by VACSR&D MVP grant CX001897 (A.M.H.). This publication does not represent the views of the Department of Veteran Affairs or the United States Government. We conducted this research using the UK Biobank resource under the application number 20272.
Published: 2022
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17. A single center experience of prenatal parent‐fetus trio exome sequencing for pregnancies with congenital anomalies

Author: Andreas Dufke, Markus Hoopmann, Stephan Waldmüller, Natalia Carmen Prodan, Stefanie Beck‐Wödl, Ute Grasshoff, Tilman Heinrich, Angelika Riess, Martin Kehrer, Ruth J. Falb, Alexandra Liebmann, Cristiana Roggia, Miriam Stampfer, Malou Schadeck, Amelie J. Müller, Mona Grimmel, Petra Stöbe, Darja Gauck, Rebecca Buchert‐Lo, Sarah Baumann, Karin Schäferhoff, Miriam Bertrand, Benita Menden, Marc Sturm, Leon Schütz, Olaf Riess, Stephan Ossowski, Tobias B. Haack, and Karl Oliver Kagan
Subjects: Adult, Parents, Fetus, Pregnancy, Hydrops Fetalis, Prenatal Diagnosis, Exome Sequencing, Humans, Obstetrics and Gynecology, Exome, Female, Ultrasonography, Prenatal, Genetics (clinical)
Abstract: To examine the diagnostic yield of trio exome sequencing in fetuses with multiple structural defects with no pathogenic findings in cytogenetic and microarray analyses.We recruited 51 fetuses with two or more defects, non-immune fetal hydrops or fetal akinesia deformation syndrome|or fetal akinesia deformation sequence (FADS). Trio exome sequencing was performed on DNA from chorionic villi samples and parental blood. Detection of genomic variation and prioritization of clinically relevant variants was performed according to in-house standard operating procedures.Median maternal and gestational age was 32.0 years and 21.0 weeks, respectively. Forty-three (84.3%) fetuses had two or more affected organ systems. The remaining fetuses had isolated fetal hydrops or FADS. In total, the exome analysis established the genetic cause for the clinical abnormalities in 22 (43.1%, 95% CI 29.4%-57.8%) pregnancies.In fetuses with multiple defects, hydrops or FADS and normal standard genetic results, trio exome sequencing has the potential to identify genetic anomalies in more than 40% of cases.
Published: 2022
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18. Predicted gene expression in ancestrally diverse populations leads to discovery of susceptibility loci for lifestyle and cardiometabolic traits

Author: Heather M. Highland, Genevieve L. Wojcik, Mariaelisa Graff, Katherine K. Nishimura, Chani J. Hodonsky, Antoine R. Baldassari, Alanna C. Cote, Iona Cheng, Christopher R. Gignoux, Ran Tao, Yuqing Li, Eric Boerwinkle, Myriam Fornage, Jeffrey Haessler, Lucia A. Hindorff, Yao Hu, Anne E. Justice, Bridget M. Lin, Danyu Lin, Daniel O. Stram, Christopher A. Haiman, Charles Kooperberg, Loic Le Marchand, Tara C. Matise, Eimear E. Kenny, Christopher S. Carlson, Eli A. Stahl, Christy L. Avery, Kari E. North, Jose Luis Ambite, Steven Buyske, Ruth J. Loos, Ulrike Peters, Kristin L. Young, Stephanie A. Bien, and Laura M. Huckins
Subjects: Cardiovascular Diseases, Genetics, Humans, Genetic Predisposition to Disease, Transcriptome, Life Style, Polymorphism, Single Nucleotide, Article, Genetics (clinical), Genome-Wide Association Study
Abstract: One mechanism by which genetic factors influence complex traits and diseases is altering gene expression. Direct measurement of gene expression in relevant tissues is rarely tenable; however, genetically regulated gene expression (GReX) can be estimated using prediction models derived from large multi-omic datasets. These approaches have led to the discovery of many gene-trait associations, but whether models derived from predominantly European ancestry (EA) reference panels can map novel associations in ancestrally diverse populations remains unclear. We applied PrediXcan to impute GReX in 51,520 ancestrally diverse Population Architecture using Genomics and Epidemiology (PAGE) participants (35% African American, 45% Hispanic/Latino, 10% Asian, and 7% Hawaiian) across 25 key cardiometabolic traits and relevant tissues to identify 102 novel associations. We then compared associations in PAGE to those in a random subset of 50,000 White British participants from UK Biobank (UKBB(50k)) for height and body mass index (BMI). We identified 517 associations across 47 tissues in PAGE but not UKBB(50k), demonstrating the importance of diverse samples in identifying trait-associated GReX. We observed that variants used in PrediXcan models were either more or less differentiated across continental-level populations than matched-control variants depending on the specific population reflecting sampling bias. Additionally, variants from identified genes specific to either PAGE or UKBB(50k) analyses were more ancestrally differentiated than those in genes detected in both analyses, underlining the value of population-specific discoveries. This suggests that while EA-derived transcriptome imputation models can identify new associations in non-EA populations, models derived from closely matched reference panels may yield further insights. Our findings call for more diversity in reference datasets of tissue-specific gene expression.
Published: 2022
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19. Whole-Genome Sequencing Association Analyses of Stroke and Its Subtypes in Ancestrally Diverse Populations From Trans-Omics for Precision Medicine Project

Author: Regina Manansala, Jeffrey Haessler, Sandro Marini, Rebecca D. Jackson, Tanika N. Kelly, Ruth J. F. Loos, Quenna Wong, Jonathan Rosand, Sudha Seshadri, Charles Kooperberg, Adolfo Correa, Stephen S. Rich, Ron Do, Paul L. Auer, Xiao Sun, Kerri L. Wiggins, Bruce M. Psaty, Jerome I. Rotter, Alexander P. Reiner, Jaeyoon Chung, Arden Moscati, Chloé Sarnowski, Laura M. Raffield, William T. Longstreth, Themistocles L. Assimes, Christopher D. Anderson, Yao Hu, David L. Tirschwell, Joshua C. Bis, Braxton D. Mitchell, Simin Liu, Leslie A. Lange, Alexa S. Beiser, Brian Silver, Ramachandran S. Vasan, Huichun Xu, Nancy L. Heard-Costa, Sylvia Wassertheil-Smoller, and Myriam Fornage
Subjects: Male, Bioinformatics, Polymorphism, Single Nucleotide, Article, medicine, Humans, Genetic Predisposition to Disease, Precision Medicine, Stroke, Aged, Genetic association, Cause of death, Aged, 80 and over, Advanced and Specialized Nursing, Whole genome sequencing, Whole Genome Sequencing, business.industry, Racial Groups, Middle Aged, medicine.disease, Omics, Precision medicine, Embolic stroke, Genetic Loci, Female, Neurology (clinical), Cardiology and Cardiovascular Medicine, business, Genome-Wide Association Study
Abstract: Background and Purpose: Stroke is the leading cause of death and long-term disability worldwide. Previous genome-wide association studies identified 51 loci associated with stroke (mostly ischemic) and its subtypes among predominantly European populations. Using whole-genome sequencing in ancestrally diverse populations from the Trans-Omics for Precision Medicine (TOPMed) Program, we aimed to identify novel variants, especially low-frequency or ancestry-specific variants, associated with all stroke, ischemic stroke and its subtypes (large artery, cardioembolic, and small vessel), and hemorrhagic stroke and its subtypes (intracerebral and subarachnoid). Methods: Whole-genome sequencing data were available for 6833 stroke cases and 27 116 controls, including 22 315 European, 7877 Black, 2616 Hispanic/Latino, 850 Asian, 54 Native American, and 237 other ancestry participants. In TOPMed, we performed single variant association analysis examining 40 million common variants and aggregated association analysis focusing on rare variants. We also combined TOPMed European populations with over 28 000 additional European participants from the UK BioBank genome-wide array data through meta-analysis. Results: In the single variant association analysis in TOPMed, we identified one novel locus 13q33 for large artery at whole-genome-wide significance ( P −9 ) and 4 novel loci at genome-wide significance ( P −8 ), all of which need confirmation in independent studies. Lead variants in all 5 loci are low-frequency but are more common in non-European populations. An aggregation of synonymous rare variants within the gene C6orf26 demonstrated suggestive evidence of association for hemorrhagic stroke ( P −6 ). By meta-analyzing European ancestry samples in TOPMed and UK BioBank, we replicated several previously reported stroke loci including PITX2 , HDAC9 , ZFHX3 , and LRCH1 . Conclusions: We represent the first association analysis for stroke and its subtypes using whole-genome sequencing data from ancestrally diverse populations. While our findings suggest the potential benefits of combining whole-genome sequencing data with populations of diverse genetic backgrounds to identify possible low-frequency or ancestry-specific variants, they also highlight the need to increase genome coverage and sample sizes.
Published: 2022
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20. Phenotypic Epithelial Changes in Laryngotracheal Stenosis

Author: Ioan A. Lina, Hsiu‐Wen Tsai, Alexandra J. Berges, Rafael A. Ospino, Ruth J. Davis, Kevin M. Motz, Samuel Collins, Baishakhi Ghosh, Venkataramana Sidhaye, Alexander Gelbard, and Alexander T. Hillel
Subjects: Cohort Studies, Cicatrix, Otorhinolaryngology, Tubulin, Keratin-14, Humans, Laryngostenosis, Constriction, Pathologic, RNA, Messenger, Mucin 5AC, Tracheal Stenosis
Abstract: Characterize and quantify epithelium in multiple etiologies of laryngotracheal stenosis (LTS) to better understand its role in pathogenesis.Controlled in vitro cohort study.Endoscopic brush biopsy samples of both normal (non-scar) and scar were obtained in four patients with idiopathic subglottic stenosis (iSGS) and four patients with iatrogenic LTS (iLTS). mRNA expression of basal, ciliary, and secretory cell markers were evaluated using quantitative PCR. Cricotracheal resection tissue samples (n = 5 per group) were also collected, analyzed using quantitative immunohistochemistry, and compared with rapid autopsy tracheal samples.Both iSGS and iLTS-scar epithelium had reduced epithelial thickness compared with non-scar control epithelium (P = .0009 and P = .0011, respectively). Basal cell gene and protein expression for cytokeratin 14 was increased in iSGS-scar epithelium compared with iLTS or controls. Immunohistochemical expression of ciliary tubulin alpha 1, but not gene expression, was reduced in both iSGS and iLTS-scar epithelium compared with controls (P = .0184 and P = .0125, respectively). Both iSGS and iLTS-scar had reductions in Mucin 5AC gene expression (P = .0007 and P = .0035, respectively), an epithelial goblet cell marker, with reductions in secretory cells histologically (P.0001).Compared with non-scar epithelium, the epithelium within iSGS and iLTS is morphologically abnormal. Although both iSGS and iLTS have reduced epithelial thickness, ciliary cells, and secretory cells, only iSGS had significant increases in pathological basal cell expression. These data suggest that the epithelium in iSGS and iLTS play a common role in the pathogenesis of fibrosis in these two etiologies of laryngotracheal stenosis.Tertiary referral center (2017-2020).NA Laryngoscope, 132:2194-2201, 2022.
Published: 2022
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21. Predicting alcohol dependence from multi-site brain structural measures

Author: Chiang-Shan R. Li, Sage Hahn, Robert Hester, Martin P. Paulus, Luijten Maartje, Valentina Lorenzetti, Catherine Orr, Kent Hutchinson, Nicholas Allgaier, Falk Kiefer, Henrik Walter, Patricia J. Conrod, Elliot A. Stein, Rajita Sinha, Scott Mackey, Dan J. Stein, Reinout W. Wiers, John J. Foxe, Edythe D. London, Murat Yücel, Tristram A. Lett, Dick J. Veltman, Andreas Heinz, Lianne Schmaal, Hugh Garavan, Janna Cousijn, Ruth J. van Holst, Ozlem Korucuoglu, Zsuzsika Sjoerds, Reza Momenan, Paul M. Thompson, Amsterdam Neuroscience - Mood, Anxiety, Psychosis, Stress & Sleep, Anatomy and neurosciences, Psychiatry, Amsterdam Neuroscience - Brain Imaging, Amsterdam Neuroscience - Compulsivity, Impulsivity & Attention, Ontwikkelingspsychologie (Psychologie, FMG), Adult Psychiatry, ANS - Brain Imaging, ANS - Compulsivity, Impulsivity & Attention, and APH - Mental Health
Subjects: Computer science, alcohol dependence, 02 engineering and technology, Alcohol use disorder, Logistic regression, Machine Learning, Alcohol Use and Health, 0302 clinical medicine, 0202 electrical engineering, electronic engineering, information engineering, genetic algorithm, Multicenter Studies as Topic, Research Articles, Cerebral Cortex, Radiological and Ultrasound Technology, 05 social sciences, Putamen, Substance Abuse, Experimental Psychology, Magnetic Resonance Imaging, Regression, Alcoholism, machine learning, Neurology, Neurological, 020201 artificial intelligence & image processing, Cognitive Sciences, addiction, Anatomy, Research Article, Feature selection, Neuroimaging, multi‐site, 050105 experimental psychology, Cross-validation, 03 medical and health sciences, multi-site, Genetic algorithm, medicine, Humans, Generalizability theory, 0501 psychology and cognitive sciences, Radiology, Nuclear Medicine and imaging, structural MRI, Receiver operating characteristic, business.industry, Alcohol dependence, Neurosciences, Reproducibility of Results, Pattern recognition, prediction, medicine.disease, Brain Disorders, Exploratory data analysis, Test set, Neurology (clinical), Artificial intelligence, business, 170 000 Motivational & Cognitive Control, Developmental Psychopathology, 030217 neurology & neurosurgery
Abstract: To identify neuroimaging biomarkers of alcohol dependence (AD) from structural magnetic resonance imaging, it may be useful to develop classification models that are explicitly generalizable to unseen sites and populations. This problem was explored in a mega‐analysis of previously published datasets from 2,034 AD and comparison participants spanning 27 sites curated by the ENIGMA Addiction Working Group. Data were grouped into a training set used for internal validation including 1,652 participants (692 AD, 24 sites), and a test set used for external validation with 382 participants (146 AD, 3 sites). An exploratory data analysis was first conducted, followed by an evolutionary search based feature selection to site generalizable and high performing subsets of brain measurements. Exploratory data analysis revealed that inclusion of case‐ and control‐only sites led to the inadvertent learning of site‐effects. Cross validation methods that do not properly account for site can drastically overestimate results. Evolutionary‐based feature selection leveraging leave‐one‐site‐out cross‐validation, to combat unintentional learning, identified cortical thickness in the left superior frontal gyrus and right lateral orbitofrontal cortex, cortical surface area in the right transverse temporal gyrus, and left putamen volume as final features. Ridge regression restricted to these features yielded a test‐set area under the receiver operating characteristic curve of 0.768. These findings evaluate strategies for handling multi‐site data with varied underlying class distributions and identify potential biomarkers for individuals with current AD., To identify neuroimaging biomarkers of alcohol dependence (AD) from structural magnetic resonance imaging, we developed classifiers on data collected from multiple sites. Exploratory data analysis revealed that inclusion of case‐ and control‐only sites led to the inadvertent learning of site‐effects. Evolutionary‐based feature selection leveraging leave‐one‐site‐out cross‐validation, to combat unintentional learning, yielded a test‐set area under the receiver operating characteristic curve of 0.768.
Published: 2022
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22. Clinical Characterization of Copy Number Variants Associated With Neurodevelopmental Disorders in a Large-scale Multiancestry Biobank

Author: Rebecca Birnbaum, Behrang Mahjani, Ruth J. F. Loos, and Andrew J. Sharp
Subjects: Male, Psychiatry and Mental health, Depressive Disorder, Major, Sleep Apnea, Obstructive, DNA Copy Number Variations, Autism Spectrum Disorder, Neurodevelopmental Disorders, Humans, Female, Obesity, Renal Insufficiency, Biological Specimen Banks, Original Investigation
Abstract: IMPORTANCE: Past studies identified rare copy number variants (CNVs) as risk factors for neurodevelopmental disorders (NDDs), including autism spectrum disorder and schizophrenia. However, the clinical characterization of NDD CNVs is understudied in population cohorts unselected for neuropsychiatric disorders and in cohorts of diverse ancestry. OBJECTIVE: To identify individuals harboring NDD CNVs in a multiancestry biobank and to query their enrichment for select neuropsychiatric disorders as well as association with multiple medical disorders. DESIGN, SETTINGS, AND PARTICIPANTS: In a series of phenotypic enrichment and association analyses, NDD CNVs were clinically characterized among 24 877 participants in the BioMe biobank, an electronic health record–linked biobank derived from the Mount Sinai Health System, New York, New York. Participants were recruited into the biobank since September 2007 across diverse ancestry and medical and neuropsychiatric specialties. For the current analyses, electronic health record data were analyzed from May 2004 through May 2019. MAIN OUTCOMES AND MEASURES: NDD CNVs were identified using a consensus of 2 CNV calling algorithms, based on whole-exome sequencing and genotype array data, followed by novel in-silico clinical assessments. RESULTS: Of 24 877 participants, 14 586 (58.7%) were female; self-reported ancestry categories included 5965 (24.0%) who were of African ancestry, 7892 (31.7%) who were of European ancestry, and 8536 (34.3%) who were of Hispanic ancestry; and the mean (SD) age was 50.5 (17.3) years. Among 24 877 individuals, the prevalence of 64 NDD CNVs was 2.5% (n = 627), with prevalence varying by locus, corroborating the presence of some relatively highly prevalent NDD CNVs (eg, 15q11.2 deletion/duplication). An aggregate set of NDD CNVs were enriched for congenital disorders (odds ratio, 2.0; 95% CI, 1.1-3.5; P = .01) and major depressive disorder (odds ratio, 1.5; 95% CI, 1.1-2.0; P = .01). In a meta-analysis of medical diagnoses (n = 195 hierarchically clustered diagnostic codes), NDD CNVs were significantly associated with several medical outcomes, including essential hypertension (z score = 3.6; P = 2.8 × 10(−4)), kidney failure (z score = 3.3; P = 1.1 × 10(−3)), and obstructive sleep apnea (z score = 3.4; P = 8.1 × 10(−4)) and, in another analysis, morbid obesity (z score = 3.8; P = 1.3 × 10(−4)). Further, NDD CNVs were associated with increased body mass index in a multiancestry analysis (β = 0.19; 95% CI, 0.10-0.31; P = .003). For 36 common serum tests, there was no association with NDD CNVs. CONCLUSIONS AND RELEVANCE: Clinical features of individuals harboring NDD CNVs were elucidated in a large-scale, multiancestry biobank, identifying enrichments for congenital disorders and major depressive disorder as well as associations with several medical outcomes, including hypertension, kidney failure, and obesity and obesity-related phenotypes, specifically obstructive sleep apnea and increased body mass index. The association between NDD CNVs and obesity outcomes indicate further potential pleiotropy of NDD CNVs beyond neurodevelopmental outcomes previously reported. Future clinical genetic investigations may lead to insights of at-risk individuals and therapeutic strategies targeting specific genetic variants. The importance of diverse inclusion within biobanks and considering the effect of rare genetic variants in a multiancestry context is evident.
Published: 2023

23. Multi-ethnic GWAS and fine-mapping of glycaemic traits identify novel loci in the PAGE Study

Author: Carolina G. Downie, Sofia F. Dimos, Stephanie A. Bien, Yao Hu, Burcu F. Darst, Linda M. Polfus, Yujie Wang, Genevieve L. Wojcik, Ran Tao, Laura M. Raffield, Nicole D. Armstrong, Hannah G. Polikowsky, Jennifer E. Below, Adolfo Correa, Marguerite R. Irvin, Laura J. F. Rasmussen-Torvik, Christopher S. Carlson, Lawrence S. Phillips, Simin Liu, James S. Pankow, Stephen S. Rich, Jerome I. Rotter, Steven Buyske, Tara C. Matise, Kari E. North, Christy L. Avery, Christopher A. Haiman, Ruth J. F. Loos, Charles Kooperberg, Mariaelisa Graff, and Heather M. Highland
Subjects: Blood Glucose, Genome-wide association study, HbA1c, Endocrinology, Diabetes and Metabolism, Clinical Sciences, Polymorphism, Single Nucleotide, Article, Paediatrics and Reproductive Medicine, Endocrinology & Metabolism, Diabetes Mellitus, Genetics, Internal Medicine, Insulin, Humans, HbA(1c), Polymorphism, Metabolic and endocrine, Transethnic population, Glycaemic traits, Prevention, Fine-mapping, Human Genome, Diabetes, Single Nucleotide, Genomics, Glucose, Diabetes Mellitus, Type 2, Public Health and Health Services, Type 2, Genome-Wide Association Study
Abstract: Aims/hypothesis: Type 2 diabetes is a growing global public health challenge. Investigating quantitative traits, including fasting glucose, fasting insulin and HbA1c, that serve as early markers of type 2 diabetes progression may lead to a deeper understanding of the genetic aetiology of type 2 diabetes development. Previous genome-wide association studies (GWAS) have identified over 500 loci associated with type 2 diabetes, glycaemic traits and insulin-related traits. However, most of these findings were based only on populations of European ancestry. To address this research gap, we examined the genetic basis of fasting glucose, fasting insulin and HbA1c in participants of the diverse Population Architecture using Genomics and Epidemiology (PAGE) Study. Methods: We conducted a GWAS of fasting glucose (n = 52,267), fasting insulin (n = 48,395) and HbA1c (n = 23,357) in participants without diabetes from the diverse PAGE Study (23% self-reported African American, 46% Hispanic/Latino, 40% European, 4% Asian, 3% Native Hawaiian, 0.8% Native American), performing transethnic and population-specific GWAS meta-analyses, followed by fine-mapping to identify and characterise novel loci and independent secondary signals in known loci. Results: Four novel associations were identified (p < 5 × 10−9), including three loci associated with fasting insulin, and a novel, low-frequency African American-specific locus associated with fasting glucose. Additionally, seven secondary signals were identified, including novel independent secondary signals for fasting glucose at the known GCK locus and for fasting insulin at the known PPP1R3B locus in transethnic meta-analysis. Conclusions/interpretation: Our findings provide new insights into the genetic architecture of glycaemic traits and highlight the continued importance of conducting genetic studies in diverse populations. Data availability: Full summary statistics from each of the population-specific and transethnic results are available at NHGRI-EBI GWAS catalog (https://www.ebi.ac.uk/gwas/downloads/summary-statistics).
Published: 2021
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24. Disparity in peripheral and renal B-cell depletion with rituximab in systemic lupus erythematosus: an opportunity for obinutuzumab?

Author: Geraldine Cambridge, David A. Isenberg, Loren Kell, Samuel J Taylor, Maria J. Leandro, Kavina Shah, Ruth J Pepper, Venkat Reddy, Mark S. Cragg, Scott R. Henderson, and Christian Klein
Subjects: Antibodies, Monoclonal, Humanized, CD19, chemistry.chemical_compound, Rheumatology, immune system diseases, Obinutuzumab, hemic and lymphatic diseases, medicine, Humans, Lupus Erythematosus, Systemic, Pharmacology (medical), B-cell activating factor, B cell, Whole blood, CD20, B-Lymphocytes, biology, business.industry, Antigens, CD20, medicine.disease, medicine.anatomical_structure, chemistry, Rheumatoid arthritis, Immunology, biology.protein, Rituximab, business, medicine.drug
Abstract: Objectives To investigate key factors that may contribute to the variability of rituximab-mediated peripheral and renal B cell depletion (BCD) in SLE. Methods We analysed: (i) CD19+ B cell counts in patients with SLE before and 1, 2, 3 and 6 months after treatment with rituximab, comparing them with RA patients; (ii) the presence of B cells in renal biopsies after rituximab therapy; (iii) whether the duration of BCD correlated with patient demographics and B cell expression of CD20 and FcγRIIb; and (iv) the effect of B cell activation factor (BAFF) on the efficiency of rituximab and obinutuzumab at inducing BCD in whole blood assays, in vitro. Results In SLE (n = 71), the duration of BCD was shorter compared with RA (n = 27). B cells were detectable in renal biopsy samples (n = 6) after treatment with rituximab in all patients with poor response while peripheral blood B cells remained low or undetectable in the same patients. There were no significant relationships between peripheral BCD and patient age, disease duration, serum C3 levels or the level of expression of B cell surface proteins CD20 and FcγRIIb. Obinutuzumab was more efficient than rituximab at inducing BCD in whole blood assays, regardless of excess BAFF. Conclusions BCD in SLE is less efficient than in RA. Renal B cell presence following rituximab treatment was associated with poor outcomes. No significant relationships between any measured B cell related, clinical or laboratory parameters and the efficiency of BCD by rituximab was found. Obinutuzumab was superior to rituximab at inducing BCD.
Published: 2021
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25. Educational attainment of same-sex and opposite-sex dizygotic twins

Author: Glen E. Duncan, Juan R. Ordoñana, Aline Jelenkovic, Esther Rebato, Amie E. Hwang, Wendy Cozen, Zengchang Pang, Weilong Li, Matthew Hotopf, Sisira Siribaddana, Leonie Helen Bogl, Dedra Buchwald, Robert F. Krueger, Brooke M. Huibregtse, Dorret I. Boomsma, Karri Silventoinen, Catherine Derom, Meike Bartels, Lucía Colodro-Conde, Ruth J. F. Loos, Catharina E. M. van Beijsterveldt, Athula Sumathipala, Jessica Tyler, Sarah E. Medland, Nicholas G. Martin, Fruhling Rijsdijk, Robert Vlietinck, Shandell Pahlen, Tracy L. Nelson, Kauko Heikkilä, Richard J. Rose, Anna K. Dahl Aslan, Thorkild I. A. Sørensen, Virgilia Toccaceli, Patrik K. E. Magnusson, Judy L. Silberg, John L. Hopper, Thomas M. Mack, Emanuela Medda, Grant W. Montgomery, Antti Latvala, Juan F. Sánchez-Romera, Qihua Tan, Dongfeng Zhang, Gonneke Willemsen, Matt McGue, Nancy L. Pedersen, Keith E. Whitfield, Jaakko Kaprio, Eero Vuoksimaa, Lorenza Nisticò, Christian Kandler, Hermine H. Maes, Robin P. Corley, Biological Psychology, APH - Health Behaviors & Chronic Diseases, APH - Mental Health, APH - Personalized Medicine, APH - Methodology, Helsinki Inequality Initiative (INEQ), Demography, Population Research Unit (PRU), Center for Population, Health and Society, Sociology, Department of Social Research (2010-2017), Institute for Molecular Medicine Finland, Clinicum, Department of Physiology, Department of Public Health, Cognitive and Brain Aging, Faculty Common Matters (Faculty of Medicine), Institute of Criminology and Legal Policy, Faculty Common Matters (Faculty of Education), and Technology Centre
Subjects: Male, Twins, Dizygotic twins, Education, Cohort Studies, 03 medical and health sciences, Behavioral Neuroscience, 0302 clinical medicine, Endocrinology, 5. Gender equality, Sex differences in education, RA0421, Twins, Dizygotic, Humans, Medicine, Testosterone, 10. No inequality, Birth Year, Medicinsk genetik, 030304 developmental biology, Sex Characteristics, 0303 health sciences, Psykologi (exklusive tillämpad psykologi), Endocrine and Autonomic Systems, business.industry, Public Health, Global Health, Social Medicine and Epidemiology, Testosterone (patch), Twin study, Testosterone exposure, Confidence interval, Educational attainment, Psychology (excluding Applied Psychology), Folkhälsovetenskap, global hälsa, socialmedicin och epidemiologi, 5141 Sociology, Cohort, Educational Status, 1182 Biochemistry, cell and molecular biology, Female, business, Medical Genetics, RA, Twin testosterone transfer hypothesis, SDG 4 - Quality Education, 030217 neurology & neurosurgery, Demography
Abstract: Comparing twins from same- and opposite-sex pairs can provide information on potential sex differences in a variety of outcomes, including socioeconomic-related outcomes such as educational attainment. It has been suggested that this design can be applied to examine the putative role of intrauterine exposure to testosterone for educational attainment, but the evidence is still disputed. Thus, we established an international database of twin data from 11 countries with 88,290 individual dizygotic twins born over 100 years and tested for differences between twins from same- and opposite-sex dizygotic pairs in educational attainment. Effect sizes with 95% confidence intervals (CI) were estimated by linear regression models after adjusting for birth year and twin study cohort. In contrast to the hypothesis, no difference was found in women (β = −0.05 educational years, 95% CI −0.11, 0.02). However, men with a same-sex co-twin were slightly more educated than men having an opposite-sex co-twin (β = 0.14 educational years, 95% CI 0.07, 0.21). No consistent differences in effect sizes were found between individual twin study cohorts representing Europe, the USA, and Australia or over the cohorts born during the 20th century, during which period the sex differences in education reversed favoring women in the latest birth cohorts. Further, no interaction was found with maternal or paternal education. Our results contradict the hypothesis that there would be differences in the intrauterine testosterone levels between same-sex and opposite-sex female twins affecting education. Our findings in men may point to social dynamics within same-sex twin pairs that may benefit men in their educational careers. CC BY 4.0Correspondence Address: Silventoinen, K.; University of Helsinki, P.O. Box 18, Finland; email: karri.silventoinen@helsinki.fi© 2021 The Authors
Published: 2021
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26. Phthalate and novel plasticizer concentrations in food items from U.S. fast food chains: a preliminary analysis

Author: Alice Yau, Brianna N VanNoy, Gary Adamkiewicz, Ruth J. Geller, Nathan L. McCray, Lariah Edwards, and Ami R. Zota
Subjects: Epidemiology, Phthalic Acids, Public Health, Environmental and Occupational Health, Phthalate, Plasticizer, Food Contamination, Toxicology, Pollution, Dibutyl Phthalate, Food handling, Preliminary analysis, chemistry.chemical_compound, Food chain, chemistry, Plasticizers, Diethylhexyl Phthalate, Fast Foods, Humans, Food science, Gas chromatography–mass spectrometry, Food contaminant, Dioctyl terephthalate
Abstract: Background Fast food consumption is associated with biomarkers of ortho-phthalates exposures. However, the chemical content of fast food is unknown; certain ortho-phthalates (i.e., di-n-butyl phthalate (DnBP) and di(2-ethylhexyl) phthalate (DEHP)) have been phased out and replaced with other plasticizers (e.g., dioctyl terephthalate (DEHT)). Objective We conducted a preliminary study to examine ortho-phthalate and replacement plasticizer concentrations in foods and food handling gloves from U.S. fast food restaurants. Methods We obtained hamburgers, fries, chicken nuggets, chicken burritos, cheese pizza (n = 64 food samples) and gloves (n = 3) from restaurants and analyzed them for 11 chemicals using gas chromatography mass spectrometry. Results We found DEHT at the highest concentrations in both foods (n = 19; median = 2510 µg/kg; max = 12,400 µg/kg) and gloves (n = 3; range: 28–37% by weight). We detected DnBP and DEHP in 81% and 70% of food samples, respectively. Median DEHT concentrations were significantly higher in burritos than hamburgers (6000 µg/kg vs. 2200 µg/kg; p Significance To our knowledge, these are the first measurements of DEHT in food. Our preliminary findings suggest that ortho-phthalates remain ubiquitous and replacement plasticizers may be abundant in fast food meals. Impact statement A selection of popular fast food items sampled in this study contain detectable levels of replacement plasticizers and concerning ortho-phthalates. In addition, food handling gloves contain replacement plasticizers, which may be a source of food contamination. These results, if confirmed, may inform individual and regulatory exposure reduction strategies.
Published: 2021
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27. Clinical characteristics and risk factors of preventable hospital readmissions within 30 days

Author: Najla El Morabet, Meike H. van der Ree, Hilde J. S. ten Horn, Elien B. Uitvlugt, Carl E. H. Siegert, Dirk W. Schölvinck, Nicky van der Heijde, Laura F. Taverne, Philou C. W. Noordman, Ruth J. Stoffels, Fatma Karapinar-Çarkit, Maurice A. A. J. van den Bosch, Pim B. J. E. Hulshof, Elsemieke A. I. M. Meurs, and Josien van Es
Subjects: Male, medicine.medical_specialty, Science, Specialty, Patient Readmission, Risk Assessment, Article, Neoplasms, Health care, medicine, Humans, Prospective Studies, Aged, Quality of Health Care, Retrospective Studies, Multidisciplinary, business.industry, Single type, After discharge, Middle Aged, Patient Discharge, Hospitalization, Cross-Sectional Studies, Risk factors, Emergency medicine, Medicine, Female, business
Abstract: Knowledge regarding preventable hospital readmissions is scarce. Our aim was to compare the clinical characteristics of potentially preventable readmissions (PPRs) with non-PPRs. Additionally, we aimed to identify risk factors for PPRs. Our study included readmissions within 30 days after discharge from 1 of 7 hospital departments. Preventability was assessed by multidisciplinary meetings. Characteristics of the readmissions were collected and 23 risk factors were analyzed. Of the 1120 readmissions, 125 (11%) were PPRs. PPRs occurred equally among different departments (p = 0.21). 29.6% of PPRs were readmitted by a practitioner of a different medical specialty than the initial admission (IA) specialist. The PPR group had more readmissions within 7 days (PPR 54% vs. non-PPR 44%, p = 0.03). The median LOS was 1 day longer for PPRs (p = 0.16). Factors associated with PPR were higher age (p = 0.004), higher socio-economic status (p = 0.049), fewer prior hospital admissions (p = 0.004), and no outpatient visit prior to readmission (p = 0.025). This study found that PPRs can occur at any department in the hospital. There is not a single type of patient that can easily be pinpointed to be at risk of a PPR, probably due to the multifactorial nature of PPRs.
Published: 2021

28. Whole-genome sequencing in diverse subjects identifies genetic correlates of leukocyte traits: The NHLBI TOPMed program

Author: Nicholas L. Smith, James A. Perry, Cecelia A. Laurie, Nancy J. Cox, Gonçalo R. Abecasis, Jerome I. Rotter, Laura Almasy, Zhe Wang, Michelle Daya, Yun Li, Eric Jorgenson, Adolfo Correa, Jai G. Broome, Nancy Min, Lisa R. Yanek, Alanna C. Morrison, Lynette Ekunwe, Debby Ngo, Victor E. Ortega, Klaudia Walter, John Blangero, Laura M. Raffield, Corey Cox, Terri H. Beaty, Deborah A. Meyers, Hua Tang, Marsha M. Wheeler, Kari E. North, Xue Zhong, Yann Ilboudo, Andrew D. Johnson, Caitlin P. McHugh, Jeffrey R. O'Connell, Ming-Huei Chen, Russell P. Tracy, Ramachandran S. Vasan, Nathan Pankratz, Joshua P. Lewis, Dawn L. DeMeo, Linda M. Polfus, Leslie A. Lange, Nancy L. Heard-Costa, Robert C. Kaplan, Meher Preethi Boorgula, Robert E. Gerszten, Albert V. Smith, Paul L. Auer, Sameer Chavan, Jennifer A. Brody, Charles Kooperberg, Michael Preuss, David C. Glahn, Rasika A. Mathias, Paul S. de Vries, Jonathon Rosen, Anna V. Mikhaylova, Joe Zein, Eric Boerwinkle, Nathalie Chami, Kathleen C. Barnes, Joanne E. Curran, Edwin K. Silverman, Matthew P. Conomos, Stephen S. Rich, Nicole Soranzo, Heather M. Highland, Michael H. Cho, Donald M. Lloyd-Jones, Myriam Fornage, Guillaume Lettre, Tyne W Miller-Fleming, Kathleen A. Ryan, Thomas W. Blackwell, Bruce M. Psaty, Lewis C. Becker, Nauder Faraday, Hélène Choquet, Alexander P. Reiner, Adam S. Butterworth, Kousik Kundu, Deepti Jain, Timothy A. Thornton, Brian D. Hobbs, Braxton D. Mitchell, Jee-Young Moon, Lifang Hou, Ani Manichaikul, Praveen Surendran, Suraj S. Nongmaithem, Quan Sun, Bingshan Li, Deborah A. Nickerson, and Ruth J. F. Loos
Subjects: Proteome, Quantitative Trait Loci, Genome-wide association study, Biology, Polymorphism, Single Nucleotide, Article, Dermatitis, Atopic, Pulmonary Disease, Chronic Obstructive, Leukocytes, Genetics, medicine, Humans, Genetic Predisposition to Disease, Gene, Genetics (clinical), X chromosome, Genetic association, Whole genome sequencing, Autosome, Whole Genome Sequencing, Genome, Human, Monocyte, Prognosis, Asthma, United Kingdom, United States, Phenotype, medicine.anatomical_structure, National Heart, Lung, and Blood Institute (U.S.), Biomarkers, Imputation (genetics), Genome-Wide Association Study
Abstract: Many common and rare variants associated with hematologic traits have been discovered through imputation on large-scale reference panels. However, the majority of genome-wide association studies (GWASs) have been conducted in Europeans, and determining causal variants has proved challenging. We performed a GWAS of total leukocyte, neutrophil, lymphocyte, monocyte, eosinophil, and basophil counts generated from 109,563,748 variants in the autosomes and the X chromosome in the Trans-Omics for Precision Medicine (TOPMed) program, which included data from 61,802 individuals of diverse ancestry. We discovered and replicated 7 leukocyte trait associations, including (1) the association between a chromosome X, pseudo-autosomal region (PAR), noncoding variant located between cytokine receptor genes (CSF2RA and CLRF2) and lower eosinophil count; and (2) associations between single variants found predominantly among African Americans at the S1PR3 (9q22.1) and HBB (11p15.4) loci and monocyte and lymphocyte counts, respectively. We further provide evidence indicating that the newly discovered eosinophil-lowering chromosome X PAR variant might be associated with reduced susceptibility to common allergic diseases such as atopic dermatitis and asthma. Additionally, we found a burden of very rare FLT3 (13q12.2) variants associated with monocyte counts. Together, these results emphasize the utility of whole-genome sequencing in diverse samples in identifying associations missed by European-ancestry-driven GWASs.
Published: 2021
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29. The genetic architecture of membranous nephropathy and its potential to improve non-invasive diagnosis

Author: Taner Basturk, Ali G. Gharavi, Patrick Hamilton, Nan Chen, Kai-Uwe Eckardt, Weiming Wang, Paul Brenchley, Olivia Balderes, Dong Ki Kim, Elisabet Ars, Antonio Amoroso, Mehmet Sukru Sever, Neil Ashman, Bartosz Foroncewicz, Dan Zhang, Maddalena Marasa, Francesca Lugani, Elion Hoxha, Mario Bonomini, Gang Liu, Detlef Bockenhauer, Hakki Arikan, Pietro A. Canetta, Bruno Vogt, Magdalena Durlik, Carlo Sidore, Abdulmecit Yildiz, Mehmet Koc, Magdalena Zoledziewska, Simone Sanna-Cherchi, Antonello Pani, Domenico Santoro, Francesca Zanoni, Landino Allegri, Matthias Kretzler, Ireneusz Habura, Claudia Izzi, Naomi Issler, Carmelita Marcantoni, Isabella Pisani, Monica Bodria, Hajeong Lee, Krzysztof Mucha, Ruth J. F. Loos, Lawrence H. Beck, Laura H. Mariani, Rolf A.K. Stahl, Eimear E. Kenny, Gonca E. Karahan, Pierre Ronco, Robert Kleta, Francesco Scolari, José Ballarín, Francesco Londrino, Bénédicte Stengel, Dario Roccatello, Atlas Khan, Belong Cho, Gerald B. Appel, Lili Liu, Xiaofan Hu, Savas Ozturk, Karla Mehl, Ming hui Zhao, Ruth J. Pepper, Shreeram Akilesh, Zhao Cui, Yifu Li, Anna Köttgen, Lambertus A. Kiemeney, Fatih Ozay, Jack F.M. Wetzels, Stephen H. Powis, Jun Zhang, Silvana Savoldi, Hong Ren, Matthias Wuttke, John O. Connolly, Yon Su Kim, Gianluigi Zaza, Chris Cheshire, Simona Granata, Andrew S. Bomback, Nurhan Seyahi, Donatella Spotti, Vladimir Tesar, Stephanie Dufek, Fernando C. Fervenza, Krzysztof Kiryluk, Barbara Moszczuk, Leszek Pączek, Agnieszka Perkowska-Ptasińska, Nikol Mladkova, Shelly Harris, Loreto Gesualdo, Hitoshi Suzuki, Jin Ho Park, Jana Reiterova, Julia M. Hofstra, Francesco Cucca, Li Lin, Laila Yasmin Mani, Sanjana Gupta, Ben Sprangers, Iuliana Ionita-Laza, Daniel C. Cattran, Gian Marco Ghiggeri, Sebahat Akgul, Horia Stanescu, Matthew G. Sampson, Piergiorgio Messa, Xialian Yu, Marieke J H Coenen, Hanna Debiec, Jingyuan Xie, Jing Xu, Yasar Caliskan, Raphael J. Rosen, Priya Krithivasan, Marco Galliani, Xie, Jingyuan, Liu, Lili, Mladkova, Nikol, Li, Yifu, Ren, Hong, Wang, Weiming, Cui, Zhao, Lin, Li, Hu, Xiaofan, Yu, Xialian, Xu, Jing, Liu, Gang, Caliskan, Yasar, Sidore, Carlo, Balderes, Olivia, Rosen, Raphael J., Bodria, Monica, Zanoni, Francesca, Zhang, Jun Y., Krithivasan, Priya, Mehl, Karla, Marasa, Maddalena, Khan, Atlas, Ozay, Fatih, Canetta, Pietro A., Bomback, Andrew S., Appel, Gerald B., Sanna-Cherchi, Simone, Sampson, Matthew G., Mariani, Laura H., Perkowska-Ptasinska, Agnieszka, Durlik, Magdalena, Mucha, Krzysztof, Moszczuk, Barbara, Foroncewicz, Bartosz, Paczek, Leszek, Habura, Ireneusz, Ars, Elisabet, Ballarin, Jose, Mani, Laila-Yasmin, Vogt, Bruno, Ozturk, Savas, Yildiz, Abdulmecit, Seyahi, Nurhan, Arikan, Hakki, Koc, Mehmet, Basturk, Taner, Karahan, Gonca, Akgul, Sebahat Usta, Sever, Mehmet Sukru, Zhang, Dan, Santoro, Domenico, Bonomini, Mario, Londrino, Francesco, Gesualdo, Loreto, Reiterova, Jana, Tesar, Vladimir, Izzi, Claudia, Savoldi, Silvana, Spotti, Donatella, Marcantoni, Carmelita, Messa, Piergiorgio, Galliani, Marco, Roccatello, Dario, Granata, Simona, Zaza, Gianluigi, Lugani, Francesca, Ghiggeri, GianMarco, Pisani, Isabella, Allegri, Landino, Sprangers, Ben, Park, Jin-Ho, Cho, BeLong, Kim, Yon Su, Kim, Dong Ki, Suzuki, Hitoshi, Amoroso, Antonio, Cattran, Daniel C., Fervenza, Fernando C., Pani, Antonello, Hamilton, Patrick, Harris, Shelly, Gupta, Sanjana, Cheshire, Chris, Dufek, Stephanie, Issler, Naomi, Pepper, Ruth J., Connolly, John, Powis, Stephen, Bockenhauer, Detlef, Stanescu, Horia C., Ashman, Neil, Loos, Ruth J. F., Kenny, Eimear E., Wuttke, Matthias, Eckardt, Kai-Uwe, Koettgen, Anna, Hofstra, Julia M., Coenen, Marieke J. H., Kiemeney, Lambertus A., Akilesh, Shreeram, Kretzler, Matthias, Beck, Lawrence H., Stengel, Benedicte, Debiec, Hanna, Ronco, Pierre, Wetzels, Jack F. M., Zoledziewska, Magdalena, Cucca, Francesco, Ionita-Laza, Iuliana, Lee, Hajeong, Hoxha, Elion, Stahl, Rolf A. K., Brenchley, Paul, Scolari, Francesco, Zhao, Ming-hui, Gharavi, Ali G., Kleta, Robert, Chen, Nan, Kiryluk, Krzysztof, İÜC, Cerrahpaşa Tıp Fakültesi, Dahili Tıp Bilimleri Bölümü, Bursa Uludağ Üniversitesi/Tıp Fakültesi/Dahili Tıp Bilimleri., Yıldız, Abdülmecit, and GJU-0662-2022
Subjects: diagnosis, Phospholipase A2 receptor, Genome-wide association study, Gene, Glomerulonephritis, Membranous, DISEASE, membranous nephropahty, PLA2R1 protein, human, 0302 clinical medicine, Models, Phospholipase A2, Ethnicity, GWAS, genetics, Membranous Nephropathy, lcsh:Science, Diagnostic test accuracy study, RISK ALLELES, NFKB1 protein, human, 3. Good health, HLA, Urological cancers Radboud Institute for Health Sciences [Radboudumc 15], Cohort analysis, Testing method, Human, medicine.medical_specialty, Science, Immunology, European Continental Ancestry Group, Case control study, Single-nucleotide polymorphism, Locus (genetics), Major clinical study, Human leukocyte antigen, European, Article, General Biochemistry, Genetics and Molecular Biology, White People, 03 medical and health sciences, Membranous nephropathy, Asian People, Humans, Amino Acid Sequence, Polymorphism, GENOME-WIDE ASSOCIATION, Antibody, Alleles, METAANALYSIS, Ancestry, Autoimmune disease, Receptors, Phospholipase A2, Case-control study, Molecular, medicine.disease, 030104 developmental biology, Immunoglobulin enhancer binding protein, Case-Control Studies, lcsh:Q, Renal disorders Radboud Institute for Health Sciences [Radboudumc 11], MHC, 0301 basic medicine, Models, Molecular, Enzyme linked immunosorbent assay, PLA2R1 gene, genetics, membranous nephropahty, GWAS, HLA, NF-KAPPA-B, 030232 urology & nephrology, General Physics and Astronomy, Gene locus, ACTIVATION, Glomerulonephritis, Receptors, Membranous Nephropathy, genome-wide association study (GWAS), diagnosis, Interferon regulatory factor 4, East Asian, Allele, Multidisciplinary, Genetic analysis, Membrane, Single Nucleotide, Sensitivity and specificity, Interferon regulatory factor, Interferon Regulatory Factors, Asian Continental Ancestry Group, EXPRESSION, Detection method, HLA antigen, SUSCEPTIBILITY LOCI, 610 Medicine & health, Caucasian, Membranous, Polymorphism, Single Nucleotide, Multidisciplinary sciences, Molecular model, Non invasive measurement, Internal medicine, NF-kappa B p50 Subunit, Genome-Wide Association Study, medicine, Human tissue, Membranous glomerulonephritis, Genetic risk, Multifactorial Inheritance, Summary Statistic, Single Nucleotide Polymorphism, RECEPTOR, business.industry, General Chemistry, genome-wide association study (GWAS), Single nucleotide polymorphism, Inflammatory diseases Radboud Institute for Health Sciences [Radboudumc 5], business, Controlled study, Meta analysis
Abstract: Vogt, Bruno/0000-0002-1548-6387; Dufek, Stephanie/0000-0002-6323-6673; Liu, Lili/0000-0002-2622-9669; Paczek, Leszek/0000-0003-0160-3009; Cui, Zhao/0000-0002-5837-1926; amoroso, antonio/0000-0002-9437-9407; Rosen, Raphael/0000-0003-1025-1965; Loos, Ruth/0000-0002-8532-5087; coenen, marieke/0000-0001-8796-2031; zanoni, francesca/0000-0001-9567-6713; CUCCA, Francesco/0000-0002-7414-1995; Ars, Elisabet/0000-0002-4118-4358; Hamilton, Patrick/0000-0001-6703-3745 WOS:000563559600001 PubMed ID: 32231244 Membranous Nephropathy (MN) is a rare autoimmune cause of kidney failure. Here we report a genome-wide association study (GWAS) for primary MN in 3,782 cases and 9,038 controls of East Asian and European ancestries. We discover two previously unreported loci, NFKB1 (rs230540, OR = 1.25, P = 3.4 x 10(-12)) and IRF4 (rs9405192, OR = 1.29, P = 1.4 x 10(-14)), fine-map the PLA2R1 locus (rs17831251, OR = 2.25, P = 4.7 x 10(-103)) and report ancestry-specific effects of three classical HLA alleles: DRB1*1501 in East Asians (OR = 3.81, P = 2.0 x 10(-49)), DQA1*0501 in Europeans (OR = 2.88, P = 5.7 x 10(-93)), and DRB1*0301 in both ethnicities (OR = 3.50, P = 9.2 x 10(-23) and OR = 3.39, P = 5.2 x 10(-82), respectively). GWAS loci explain 32% of disease risk in East Asians and 25% in Europeans, and correctly re-classify 20-37% of the cases in validation cohorts that are antibody-negative by the serum anti-PLA2R ELISA diagnostic test. Our findings highlight an unusual genetic architecture of MN, with four loci and their interactions accounting for nearly one-third of the disease risk. National Institute for Diabetes and Digestive Kidney Diseases (NIDDK) [RC2-DK116690, R01-DK105124, R01-DK097053, R01-DK108805]; National Institute on Minority Health and Health Disparities (NIMHD)United States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Institute on Minority Health & Health Disparities (NIMHD) [R01-MD009223]; Charles Woodson Clinical Research Fund; Nephrotic Syndrome Study Network Consortium (NEPTUNE) [U54-DK-083912]; Columbia University, Columbia Glomerular Center; Office of Rare Diseases Research, National Center for Advancing Translational Sciences (NCATS); National Institute of Diabetes, Digestive, and Kidney Diseases (NIDDK)United States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Institute of Diabetes & Digestive & Kidney Diseases (NIDDK); University of MichiganUniversity of Michigan System; NephCure Kidney International; Halpin Foundation; National Key Research and Development Program of China [2016YFC0904100]; Natural Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [81621092]; National Natural Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [81870460, 81570598]; Science and Technology Innovation Action Plan of Shanghai Science and Technology Committee [17441902200]; Shanghai Municipal Education Commission, Gaofeng, Clinical Medicine Grant [20152207]; Shanghai Jiao Tong University School of Medicine, Multi-Center Clinical Research Project [DLY201510]; International Cooperation and Exchange Projects of Shanghai Science and Technology Committee [14430721000]; Outstanding Young Scholar Award [81622009]; Shanghai Health and Family Planning Committee Hundred Talents Program [2018BR37]; Seoul National University Hospital Human Biobank, a member of the National Biobank of Korea - Ministry of Health and Welfare, Republic of Korea; MRCMedical Research Council UK (MRC) [MR/J010847/1]; Manchester Academic Health Science Centre [MAHSC 186/200]; Greater Manchester Local Clinical Research Network; Kidneys for Life Charity; David and Elaine Potter Charitable Foundation; St Peter's Trust for Kidney, Bladder and Prostate Research; Kids Kidney Research UKKidney Research UK (KRUK); Kidney Research UKKidney Research UK (KRUK); Italian Ministry of Health grantMinistry of Health, Italy [GR-2011-02350438]; Department of Excellence Grant 2018-2022 - Italian Ministry of Education for the Department of Medical Sciences of the University of Turin; Columbia University; Poznan University of Medical Sciences, Poland; German Ministry of Education and Research (BMBF)Federal Ministry of Education & Research (BMBF) [01ER0804]; KfH Foundation for Preventive Medicine; Bayer Pharma AG; German Research FoundationGerman Research Foundation (DFG) [CRC 1140, KO 3598/3-1, CRC 992]; European Research CouncilEuropean Research Council (ERC) [ERC-2012ADG_2012-0314, 322947]; 7th Framework Programme of the European Community contract [2012-305608]; National Research Agency grant MNaims [ANR-17-CE17-0012-01]; Dutch Kidney Foundation [OW08, KJPB11.021]; National Human Genome Research Institute (NHGRI)United States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Human Genome Research Institute (NHGRI); NIMHD We are grateful to all study participants across multiple nephrology centres worldwide for their contributions to this work. This work was supported by the following institutions, grants and funding agencies in the US: Columbia University, Columbia Glomerular Center, National Institute for Diabetes and Digestive Kidney Diseases (NIDDK) grants RC2-DK116690 (K.K., M.K.), R01-DK105124 (K.K.), R01-DK097053 (L.H.B., M.K.), R01-DK108805 (M.G.S.), and National Institute on Minority Health and Health Disparities (NIMHD) grant R01-MD009223 (K.K., A.G.G., A.B.). M.G.S. is additionally supported by the Charles Woodson Clinical Research Fund. The Nephrotic Syndrome Study Network Consortium (NEPTUNE), U54-DK-083912, is a part of the National Institutes of Health (NIH) Rare Disease Clinical Research Network (RDCRN), supported through a collaboration between the Office of Rare Diseases Research, National Center for Advancing Translational Sciences (NCATS) and the National Institute of Diabetes, Digestive, and Kidney Diseases (NIDDK). Additional funding and/or programmatic support for this project has also been provided by the University of Michigan, the NephCure Kidney International and the Halpin Foundation. The recruitment and analysis of the Chinese cohorts were supported by the National Key Research and Development Program of China (2016YFC0904100), Natural Science Foundation of China to the Innovation Research Group (81621092), National Natural Science Foundation of China (No. 81870460, 81570598), Science and Technology Innovation Action Plan of Shanghai Science and Technology Committee (No.17441902200), Shanghai Municipal Education Commission, Gaofeng, Clinical Medicine Grant (No.20152207), Shanghai Jiao Tong University School of Medicine, Multi-Center Clinical Research Project (No.DLY201510), International Cooperation and Exchange Projects of Shanghai Science and Technology Committee (No.14430721000), the Outstanding Young Scholar Award for Zhao Cui (No.81622009), and Shanghai Health and Family Planning Committee Hundred Talents Program for Jingyuan Xie (No.2018BR37). The recruitment of the Korean cohort was supported by the Seoul National University Hospital Human Biobank, a member of the National Biobank of Korea, financed by the Ministry of Health and Welfare, Republic of Korea. P.B. and P.H. acknowledge financial support from MRC project "Autoimmunity in Membranous Nephropathy", grant MR/J010847/1 which funded the sample collection from MN patients across the UK. P.B., P.H. and S.H. acknowledge support from Manchester Academic Health Science Centre (MAHSC 186/200), the Greater Manchester Local Clinical Research Network and Kidneys for Life Charity for supporting research in MN in Manchester. We are grateful to the MENTOR study (clinical trials no. NCT01180036), for contributing blood samples of trial participants. The UK cohort was supported in part by grants from the David and Elaine Potter Charitable Foundation (to S.H.P. and R.K.), St Peter's Trust for Kidney, Bladder and Prostate Research (to D.B., H.C.S., S.H.P. and R.K.), Kids Kidney Research UK and Kidney Research UK (to D.B. and R.K.). The Italian cohorts were supported by the Italian Ministry of Health grant GR-2011-02350438 (G.Z., S.G.) and the Department of Excellence Grant 2018-2022 funded by the Italian Ministry of Education for the Department of Medical Sciences of the University of Turin (A.A.).; The recruitment of Polish cases was sponsored by the Polish Kidney Genetics Network (POLYGENES), a collaborative effort between Columbia University and Poznan University of Medical Sciences, Poland. The full list of POLYGENES collaborators can be found in the Supplementary Materials. The GCKD (German Chronic Kidney Disease) study was funded by grants from the German Ministry of Education and Research (BMBF, No. 01ER0804) and the KfH Foundation for Preventive Medicine, with genotyping supported by Bayer Pharma AG. The list of GCKD investigators can be found in the Supplementary Materials. The work of M.W. and A.K. was funded by the CRC 1140 Initiative and by KO 3598/3-1 and CRC 992 (A.K.) of the German Research Foundation. The work of E.H. and R.A.K.S. was funded by the CRC 1192 from the German Research Foundation (Projects B1 and C1). P.R. is a recipient of European Research Council ERC-2012ADG_2012-0314 grant 322947, 7th Framework Programme of the European Community contract 2012-305608 (European Consortium for High-Throughput Research in Rare Kidney Diseases), and the National Research Agency grant MNaims (ANR-17-CE17-0012-01). The Dutch studies were supported by grants from the Dutch Kidney Foundation to JMH and JFW (Nierstichting Nederland grant OW08 and grant KJPB11.021). We would like to thank the Population Architecture Using Genomics and Epidemiology (PAGE) consortium, funded by the National Human Genome Research Institute (NHGRI) with co-funding from the NIMHD, for providing population controls for this study. For full acknowledgment of the PAGE consortium, please see Supplementary Materials. The funding sources were not involved in the study design, collection, analysis, and interpretation of data, writing of the report, or in the decision to submit the paper for publication.
Published: 2020
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30. 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, Søren Karl, 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, 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, Alizadeh, Behrooz Z., Boezen, H. Marike, Franke, Lude, Swertz, Morris, Wijmenga, Tjitske Nienke, van der Harst, Pim, Navis, Gerjan, Rots, Marianne, Wolffenbuttel, Bruce H. R., 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., Hoed, Marcel den, Epidemiology, Internal Medicine, Tampere University, Department of Clinical Chemistry, Clinical Medicine, Department of Clinical Physiology and Nuclear Medicine, Wang, Zhe, Emmerich, Andrew, Pillon, Nicolas J, Moore, Tim, Hyppönen, Elina, den Hoed, Marcel, Lifelines Cohort Study, Alizadeh, B.Z., Boezen, H.M., Franke, L., Swertz, M., Wijmenga, C., van der Harst, P., Navis, G., Rots, M., Wolffenbuttel, BHR, Wang, Zhe [0000-0002-8046-4969], Emmerich, Andrew [0000-0002-0908-9924], Pillon, Nicolas J [0000-0003-1107-9490], Moore, Tim [0000-0003-4250-3370], Ameur, Adam [0000-0001-6085-6749], Bis, Joshua C [0000-0002-3409-1110], Boehnke, Michael [0000-0002-6442-7754], Bouchard, Claude [0000-0002-0048-491X], Chasman, Daniel I [0000-0003-3357-0862], Smith, George Davey [0000-0002-1407-8314], de Geus, Eco JC [0000-0001-6022-2666], Dörr, Marcus [0000-0001-7471-475X], Ferrucci, Luigi [0000-0002-6273-1613], Fornage, Myriam [0000-0003-0677-8158], Garland, Theodore [0000-0002-7916-3552], Gyllensten, Ulf [0000-0002-6316-3355], Hansen, Torben [0000-0001-8748-3831], Horta, Bernardo L [0000-0001-9843-412X], Hyppönen, Elina [0000-0003-3670-9399], Johnson, W Craig [0000-0002-3161-3753], Kiemeney, Lambertus A [0000-0002-2368-1326], Laakso, Markku [0000-0002-3394-7749], Langenberg, Claudia [0000-0002-5017-7344], Lehtimäki, Terho [0000-0002-2555-4427], Magnusson, Patrik KE [0000-0002-7315-7899], Martin, Nicholas G [0000-0003-4069-8020], Melbye, Mads [0000-0001-8264-6785], Metspalu, Andres [0000-0002-3718-796X], Meyre, David [0000-0003-4850-7444], North, Kari E [0000-0002-8903-0366], Ohlsson, Claes [0000-0002-9633-2805], Oldehinkel, Albertine J [0000-0003-3925-3913], Orho-Melander, Marju [0000-0002-3578-2503], Pare, Guillaume [0000-0002-6795-4760], Park, Taesung [0000-0002-8294-590X], Pedersen, Oluf [0000-0002-3321-3972], Pers, Tune H [0000-0003-0207-4831], Polasek, Ozren [0000-0002-5765-1862], Prokopenko, Inga [0000-0003-1624-7457], Rotimi, Charles N [0000-0001-5759-053X], Sim, Xueling [0000-0002-1233-7642], Snieder, Harold [0000-0003-1949-2298], Sørensen, Thorkild IA [0000-0003-4821-430X], Spector, Tim D [0000-0002-9795-0365], Timpson, Nicholas J [0000-0002-7141-9189], Voortman, Trudy [0000-0003-2830-6813], Waeber, Gérard [0000-0003-4193-788X], Wareham, Nicholas J [0000-0003-1422-2993], Weir, David R [0000-0002-1661-2402], Wilson, James F [0000-0001-5751-9178], Krook, Anna [0000-0002-0891-0258], Zierath, Juleen R [0000-0001-6891-7497], Thomis, Martine AI [0000-0001-9093-2191], Loos, Ruth JF [0000-0002-8532-5087], Hoed, Marcel den [0000-0001-8081-428X], Apollo - University of Cambridge Repository, Center for Liver, Digestive and Metabolic Diseases (CLDM), Interdisciplinary Centre Psychopathology and Emotion regulation (ICPE), Life Course Epidemiology (LCE), Geriatrics, AMS - Ageing & Vitality, APH - Aging & Later Life, Biological Psychology, APH - Health Behaviors & Chronic Diseases, APH - Personalized Medicine, APH - Mental Health, APH - Methodology, and AMS - Sports
Subjects: Vascular damage Radboud Institute for Health Sciences [Radboudumc 16], 631/208/205/2138, 610 Medicine & health, heritability, Actinin/genetics, Cross-Sectional Studies, Exercise/physiology, Genome-Wide Association Study, Humans, Leisure Activities, Sedentary Behavior, apolipoprotein-e genotype, Lifelines Cohort Study, 360 Social problems & social services, 692/308/575, Genetics, Actinin, Exercise, Medicinsk genetik, exercise, APOLIPOPROTEIN-E GENOTYPE, LD SCORE REGRESSION, GENE-EXPRESSION, EXERCISE, COMPLEX, PERFORMANCE, GWAS, HERITABILITY, MORTALITY, FITNESS, 360 Soziale Probleme, Sozialdienste, 692/308/2056, article, gwas, gene-expression, mortality, 3142 Public health care science, environmental and occupational health, fitness, Urological cancers Radboud Institute for Health Sciences [Radboudumc 15], LD score regression, 3111 Biomedicine, 610 Medizin und Gesundheit, Medical Genetics, complex, performance
Abstract: Funder: Kjell och Märta Beijers Stiftelse (Kjell and Marta Beijer Foundation); doi: https://doi.org/10.13039/501100006353, Although physical activity and sedentary behavior are moderately heritable, little is known about the mechanisms that influence these traits. Combining data for up to 703,901 individuals from 51 studies in a multi-ancestry meta-analysis of genome-wide association studies yields 99 loci that associate with self-reported moderate-to-vigorous intensity physical activity during leisure time (MVPA), leisure screen time (LST) and/or sedentary behavior at work. Loci associated with LST are enriched for genes whose expression in skeletal muscle is altered by resistance training. A missense variant in ACTN3 makes the alpha-actinin-3 filaments more flexible, resulting in lower maximal force in isolated type IIA muscle fibers, and possibly protection from exercise-induced muscle damage. Finally, Mendelian randomization analyses show that beneficial effects of lower LST and higher MVPA on several risk factors and diseases are mediated or confounded by body mass index (BMI). Our results provide insights into physical activity mechanisms and its role in disease prevention.
Published: 2022
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31. Reproducibility in the absence of selective reporting : An illustration from large-scale brain asymmetry research

Author: Kong, Xiang-Zhen, Francks, Clyde, Allen, Nicholas B., Heslenfeld, Dirk, Hester, Robert, Hibar, Derrek Paul, Ho, Beng-Choon, Ho, Tiffany C., Hoekstra, Pieter J., Holst, Ruth J., Hoogman, Martine, Høvik, Marie F., Howells, Fleur M., Ames, David, Hugdahl, Kenneth, Huyser, Chaim, Ingvar, Martin, Ishikawa, Akari, James, Anthony, Jahanshad, Neda, Jernigan, Terry L., Jönsson, Erik G, Kaleda, Vasily, Kelly, Clare, Andreassen, Ole A., Kerich, Michael, Keshavan, Matcheri S., Khadka, Sabin, Kircher, Tilo, Kohls, Gregor, Konrad, Kerstin, Korucuoglu, Ozlem, Krämer, Bernd, Krug, Axel, Kuntsi, Jonna, Vasquez, Alejandro Arias, Kwon, Jun Soo, Lambregts-Rommelse, Nanda, Landén, Mikael, Lázaro, Luisa, Lebedeva, Irina, Lenroot, Rhoshel, Lesch, Klaus-Peter, Li, Qinqin, Lim, Kelvin O., Liu, Jia, Armstrong, Nicola J., Lochner, Christine, London, Edythe D., Lorenzetti, Valentina, Luciano, Michelle, Luijten, Maartje, Lundervold, Astri J., Mackey, Scott, MacMaster, Frank P., Maingault, Sophie, Malpas, Charles B., Asherson, Phil, Malt, Ulrik F., Mataix-Cols, David, Martin-Santos, Rocio, Mayer, Andrew R., McCarthy, Hazel, Medland, Sarah, Metha, Mitul, Mitchell, Philip B., Mueller, Bryon A., Maniega, Susana Muñoz, Bergo, Felipe, Mazoyer, Bernard, McDonald, Colm, McLellan, Quinn, McMahon, Katie L., McPhilemy, Genevieve, Momenan, Reza, Morales, Angelica M., Narayanaswamy, Janardhanan C., Moreira, José Carlos Vasques, Nerland, Stener, Bastin, Mark E., Nestor, Liam, Newman, Erik, Nigg, Joel T., Nordvik, Jan Egil, Novotny, Stephanie, Weiss, Eileen Oberwelland, O'Gorman, Ruth L., Oosterlaan, Jaap, Oranje, Bob, Orr, Catherine, Batalla, Albert, Overs, Bronwyn, Paloyelis, Yannis, Pauli, Paul, Paulus, Martin, Plessen, Kerstin Jessica, Polier, Georg G., Pomarol-Clotet, Edith, Portella, Maria J., Qiu, Jiang, Radua, Joaquim, Bauer, Jochen, Ramos-Quiroga, Josep Antoni, Reddy, Y. C. Janardhan, Reif, Andreas, Roberts, Gloria, Rosa, Pedro, Rubia, Katya, Sacchet, Matthew D., Sachdev, Perminder S., Salvador, Raymond, Schmaal, Lianne, Baune, Bernhard T, Schulte-Rüther, Martin, Schweren, Lizanne, Seitz, Jochen, Serpa, Mauricio Henriques, Shaw, Philip, Shumskaya, Elena, Silk, Timothy J., Simmons, Alan N., Simulionyte, Egle, Sinha, Rajita, Baur-Streubel, Ramona, Sjoerds, Zsuzsika, Smelror, Runar Elle, Soliva, Joan Carlos, Solowij, Nadia, Souza-Duran, Fabio Luisde, Sponheim, Scott R., Stein, Dan J., Stein, Elliot A., Stevens, Michael, Strike, Lachlan T., Biederman, Joseph, Sudre, Gustavo, Sui, Jing, Tamm, Leanne, Temmingh, Hendrik S., Thoma, Robert J., Tomyshev, Alexander, Tronchin, Giulia, Turner, Jessica, Uhlmann, Anne, Erp, Theo G. M., Blaine, Sara K., Heuvel, Odile A., Meer, Dennis, Eijk, Liza, Vance, Alasdair, Veer, Ilya M., Veltman, Dick J., Venkatasubramanian, Ganesan, Vilarroya, Oscar, Vives-Gilabert, Yolanda, Voineskos, Aristotle N, Boedhoe, Premika, Völzke, Henry, Vuletic, Daniella, Walitza, Susanne, Walter, Henrik, Walton, Esther, Wardlaw, Joanna M., Wen, Wei, Westlye, Lars T., Whelan, Christopher D., White, Tonya, Bøen, Erlend, Wiers, Reinout W., Wright, Margaret J., Wittfeld, Katharina, Yang, Tony T., Yasuda, Clarissa L., Yoncheva, Yuliya, Yücel, Murat, Yun, Je-Yeon, Zanetti, Marcus Vinicius, Zhen, Zonglei, Bose, Anushree, Zhu, Xing-xing, Ziegler, Georg C., Zubicaray, Greig I., Zwiers, Marcel, Project, Karolinska Schizophrenia, Glahn, David C., Crivello, Fabrice, Fisher, Simon E., Thompson, Paul M., Bralten, Janita, Farde, Lars, Flyckt, Lena, Engberg, Göran, Erhardt, Sophie, Fatouros-Bergman, Helena, Cervenka, Simon, Schwieler, Lilly, Piehl, Fredrik, Agartz, Ingrid, Collste, Karin, Brandeis, Daniel, Victorsson, Pauliina, Malmqvist, Anna, Hedberg, Mikael, Orhan, Funda, Sellgren, Carl, Brem, Silvia, Mathias, Samuel R., Brodaty, Henry, Yüksel, Dilara, Brooks, Samantha J., Buitelaar, Jan, Bürger, Christian, Bülow, Robin, Calhoun, Vince, Calvo, Anna, Canales-Rodríguez, Erick Jorge, Cannon, Dara M., Guadalupe, Tulio, Caparelli, Elisabeth C., Castellanos, Francisco X., Cendes, Fernando, Chaim-Avancini, Tiffany Moukbel, Chantiluke, Kaylita, Chen, Qun-lin, Chen, Xiayu, Cheng, Yuqi, Christakou, Anastasia, Clark, Vincent P., Abé, Christoph, Coghill, David, Connolly, Colm G., Conzelmann, Annette, Córdova-Palomera, Aldo, Cousijn, Janna, Crow, Tim, Cubillo, Ana, Dannlowski, Udo, Bruttopilo, Sara Ambrosino, Zeeuw, Patrick, Deary, Ian J., Demeter, Damion V., Di Martino, Adriana, Dickie, Erin W, Dietsche, Bruno, Doan, Nhat Trung, Doherty, Colin P., Doyle, Alysa, Durston, Sarah, Earl, Eric, Akudjedu, Theophilus N., Ehrlich, Stefan, Ekman, Carl Johan, Elvsåshagen, Torbjørn, Epstein, Jeffery N., Fair, Damien A., Faraone, Stephen V., Fernández, Guillén, Flint, Claas, Filho, Geraldo Busatto, Förster, Katharina, Aleman, Andre, Fouche, Jean-Paul, Foxe, John J., Frodl, Thomas, Fuentes-Claramonte, Paola, Fullerton, Janice M., Garavan, Hugh, Santos Garcia, Danielle, Gotlib, Ian H., Goudriaan, Anna E., Grabe, Hans Jörgen, Alhusaini, Saud, Groenewold, Nynke A., Grotegerd, Dominik, Gruber, Oliver, Gurholt, Tiril, Haavik, Jan, Hahn, Tim, Hansell, Narelle K., Harris, Mathew A., Hartman, Catharina A., Carmen Valdés Hernández, Maria, Alhusaini, Saud, Del Carmen Valdés Hernández, Maria, Heslenfeld, Dirk, Hester, Robert, Hibar, Derrek Paul, Ho, Beng-Choon, Ho, Tiffany C., Hoekstra, Pieter J., van Holst, Ruth J., Hoogman, Martine, Høvik, Marie F., Allen, Nicholas B., Howells, Fleur M., Hugdahl, Kenneth, Huyser, Chaim, Ingvar, Martin, Ishikawa, Akari, James, Anthony, Jahanshad, Neda, Jernigan, Terry L., Jönsson, Erik G., Kaleda, Vasily, Ames, David, Kelly, Clare, Kerich, Michael, Keshavan, Matcheri S., Khadka, Sabin, Kircher, Tilo, Kohls, Gregor, Konrad, Kerstin, Korucuoglu, Ozlem, Krämer, Bernd, Krug, Axel, Andreassen, Ole A., Kuntsi, Jonna, Kwon, Jun Soo, Lambregts-Rommelse, Nanda, Landén, Mikael, Lázaro, Luisa, Lebedeva, Irina, Lenroot, Rhoshel, Lesch, Klaus-Peter, Li, Qinqin, Lim, Kelvin O., Vasquez, Alejandro Arias, Liu, Jia, Lochner, Christine, London, Edythe D., Lorenzetti, Valentina, Luciano, Michelle, Luijten, Maartje, Lundervold, Astri J., Mackey, Scott, MacMaster, Frank P., Maingault, Sophie, Armstrong, Nicola J., Malpas, Charles B., Malt, Ulrik F., Mataix-Cols, David, Martin-Santos, Rocio, Mayer, Andrew R., McCarthy, Hazel, Medland, Sarah, Metha, Mitul, Mitchell, Philip B., Mueller, Bryon A., Asherson, Phil, Maniega, Susana Muñoz, Mazoyer, Bernard, McDonald, Colm, McLellan, Quinn, McMahon, Katie L., McPhilemy, Genevieve, Momenan, Reza, Morales, Angelica M., Narayanaswamy, Janardhanan C., Moreira, José Carlos Vasques, Bergo, Felipe, Nerland, Stener, Nestor, Liam, Newman, Erik, Nigg, Joel T., Nordvik, Jan Egil, Novotny, Stephanie, Weiss, Eileen Oberwelland, O'Gorman, Ruth L., Oosterlaan, Jaap, Oranje, Bob, Bastin, Mark E., Orr, Catherine, Overs, Bronwyn, Paloyelis, Yannis, Pauli, Paul, Paulus, Martin, Plessen, Kerstin Jessica, von Polier, Georg G., Pomarol-Clotet, Edith, Portella, Maria J., Qiu, Jiang, Batalla, Albert, Radua, Joaquim, Ramos-Quiroga, Josep Antoni, Reddy, Y. C. Janardhan, Reif, Andreas, Roberts, Gloria, Rosa, Pedro, Rubia, Katya, Sacchet, Matthew D., Sachdev, Perminder S., Salvador, Raymond, Bauer, Jochen, Schmaal, Lianne, Schulte-Rüther, Martin, Schweren, Lizanne, Seitz, Jochen, Serpa, Mauricio Henriques, Shaw, Philip, Shumskaya, Elena, Silk, Timothy J., Simmons, Alan N., Simulionyte, Egle, Baune, Bernhard T., Sinha, Rajita, Sjoerds, Zsuzsika, Smelror, Runar Elle, Soliva, Joan Carlos, Solowij, Nadia, Souza-Duran, Fabio Luisde, Sponheim, Scott R., Stein, Dan J., Stein, Elliot A., Stevens, Michael, Baur-Streubel, Ramona, Strike, Lachlan T., Sudre, Gustavo, Sui, Jing, Tamm, Leanne, Temmingh, Hendrik S., Thoma, Robert J., Tomyshev, Alexander, Tronchin, Giulia, Turner, Jessica, Uhlmann, Anne, Biederman, Joseph, van Erp, Theo G. M., van den Heuvel, Odile A., van der Meer, Dennis, van Eijk, Liza, Vance, Alasdair, Veer, Ilya M., Veltman, Dick J., Venkatasubramanian, Ganesan, Vilarroya, Oscar, Vives-Gilabert, Yolanda, Blaine, Sara K., Voineskos, Aristotle N., Völzke, Henry, Vuletic, Daniella, Walitza, Susanne, Walter, Henrik, Walton, Esther, Wardlaw, Joanna M., Wen, Wei, Westlye, Lars T., Whelan, Christopher D., Boedhoe, Premika, White, Tonya, Wiers, Reinout W., Wright, Margaret J., Wittfeld, Katharina, Yang, Tony T., Yasuda, Clarissa L., Yoncheva, Yuliya, Yücel, Murat, Yun, Je-Yeon, Zanetti, Marcus Vinicius, Bøen, Erlend, Zhen, Zonglei, Zhu, Xing-Xing, Ziegler, Georg C., de Zubicaray, Greig I., Zwiers, Marcel, Project, Karolinska Schizophrenia, Glahn, David C., Crivello, Fabrice, Fisher, Simon E., Thompson, Paul M., Bose, Anushree, Francks, Clyde, Farde, Lars, Flyckt, Lena, Engberg, Göran, Erhardt, Sophie, Fatouros-Bergman, Helena, Cervenka, Simon, Schwieler, Lilly, Piehl, Fredrik, Agartz, Ingrid, Bralten, Janita, Collste, Karin, Victorsson, Pauliina, Malmqvist, Anna, Hedberg, Mikael, Orhan, Funda, Sellgren, Carl, Brandeis, Daniel, Kong, Xiang-Zhen, Brem, Silvia, Brodaty, Henry, Yüksel, Dilara, Brooks, Samantha J., Buitelaar, Jan, Bürger, Christian, Bülow, Robin, Calhoun, Vince, Calvo, Anna, Canales-Rodríguez, Erick Jorge, Mathias, Samuel R., Cannon, Dara M., Caparelli, Elisabeth C., Castellanos, Francisco X., Cendes, Fernando, Chaim-Avancini, Tiffany Moukbel, Chantiluke, Kaylita, Chen, Qun-Lin, Chen, Xiayu, Cheng, Yuqi, Christakou, Anastasia, Guadalupe, Tulio, Clark, Vincent P., Coghill, David, Connolly, Colm G., Conzelmann, Annette, Córdova-Palomera, Aldo, Cousijn, Janna, Crow, Tim, Cubillo, Ana, Dannlowski, Udo, de Bruttopilo, Sara Ambrosino, Abé, Christoph, de Zeeuw, Patrick, Deary, Ian J., Demeter, Damion V., Di Martino, Adriana, Dickie, Erin W., Dietsche, Bruno, Doan, Nhat Trung, Doherty, Colin P., Doyle, Alysa, Durston, Sarah, Earl, Eric, Ehrlich, Stefan, Ekman, Carl Johan, Elvsåshagen, Torbjørn, Epstein, Jeffery N., Fair, Damien A., Faraone, Stephen V., Fernández, Guillén, Flint, Claas, Filho, Geraldo Busatto, Akudjedu, Theophilus N., Förster, Katharina, Fouche, Jean-Paul, Foxe, John J., Frodl, Thomas, Fuentes-Claramonte, Paola, Fullerton, Janice M., Garavan, Hugh, do Santos Garcia, Danielle, Gotlib, Ian H., Goudriaan, Anna E., Aleman, Andre, Grabe, Hans Jörgen, Groenewold, Nynke A., Grotegerd, Dominik, Gruber, Oliver, Gurholt, Tiril, Haavik, Jan, Hahn, Tim, Hansell, Narelle K., Harris, Mathew A., Hartman, Catharina A., Ontwikkelingspsychologie (Psychologie, FMG), Adult Psychiatry, APH - Mental Health, ANS - Compulsivity, Impulsivity & Attention, Child and Adolescent Psychiatry & Psychosocial Care, Child Psychiatry, ANS - Cellular & Molecular Mechanisms, Laboratory Genetic Metabolic Diseases, Paediatrics, General Paediatrics, ARD - Amsterdam Reproduction and Development, Paediatric Pulmonology, Graduate School, and APH - Digital Health
Subjects: P‐hacking, Datasets as Topic, Publication bias, 0302 clinical medicine, 130 000 Cognitive Neurology & Memory, Statistics, team science, Brain asymmetry, Multicenter Studies as Topic, Cervell, Research Articles, Cerebral Cortex, Radiological and Ultrasound Technology, P-hacking, 05 social sciences, Brain, Cerebral cortex, Middle Aged, Magnetic Resonance Imaging, Discoveries in science, Escorça cerebral, Neurology, Biaix de publicació, Anatomy, Psychology, Research Article, Neuroinformatics, Adult, Adolescent, Neuroimaging, Descobriments científics, 050105 experimental psychology, Statistical power, 03 medical and health sciences, Young Adult, Magnetic resonance imaging, Imatges per ressonància magnètica, multisite collaboration, Humans, 0501 psychology and cognitive sciences, Radiology, Nuclear Medicine and imaging, ddc:610, reproducibility, Aged, publication bias, Reproducibility, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], Perspective (graphical), Reproducibility of Results, Brain Cortical Thickness, Research data, Sample size determination, Dades de recerca, Neurology (clinical), Scale (map), Developmental Psychopathology, 030217 neurology & neurosurgery
Abstract: The problem of poor reproducibility of scientific findings has received much attention over recent years, in a variety of fields including psychology and neuroscience. The problem has been partly attributed to publication bias and unwanted practices such as p‐hacking. Low statistical power in individual studies is also understood to be an important factor. In a recent multisite collaborative study, we mapped brain anatomical left–right asymmetries for regional measures of surface area and cortical thickness, in 99 MRI datasets from around the world, for a total of over 17,000 participants. In the present study, we revisited these hemispheric effects from the perspective of reproducibility. Within each dataset, we considered that an effect had been reproduced when it matched the meta‐analytic effect from the 98 other datasets, in terms of effect direction and significance threshold. In this sense, the results within each dataset were viewed as coming from separate studies in an “ideal publishing environment,” that is, free from selective reporting and p hacking. We found an average reproducibility rate of 63.2% (SD = 22.9%, min = 22.2%, max = 97.0%). As expected, reproducibility was higher for larger effects and in larger datasets. Reproducibility was not obviously related to the age of participants, scanner field strength, FreeSurfer software version, cortical regional measurement reliability, or regional size. These findings constitute an empirical illustration of reproducibility in the absence of publication bias or p hacking, when assessing realistic biological effects in heterogeneous neuroscience data, and given typically‐used sample sizes., Region‐wise effect sizes and reproducibility rates of hemispheric asymmetry effects. In general, effects with higher effect sizes showed higher reproducibility, given the same conditions (e.g., sample size and data heterogeneity).
Published: 2022
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32. Whole genome sequence analysis of platelet traits in the NHLBI Trans-Omics for Precision Medicine (TOPMed) initiative

Author: Nauder Faraday, Brian D. Hobbs, Quan Sun, Michael Preuss, Ani Manichaikul, Eric Jorgenson, Ming-Huei Chen, Eric Boerwinkle, Florian Thibord, Arunoday Bhan, Alanna C. Morrison, Ramachandran S. Vasan, Nathan Pankratz, Charles Kooperberg, Deborah A. Nickerson, Joshua P. Lewis, Hélène Choquet, Jee-Young Moon, Jeffrey R. O'Connell, Marsha M. Wheeler, Albert V. Smith, Russell P. Tracy, Nathalie Chami, Ruth J. F. Loos, Alexander P. Reiner, Nicholas L. Smith, Gonçalo R. Abecasis, Laura M. Raffield, Amarise Little, Nancy L. Heard-Costa, Andrew D. Johnson, David C. Glahn, Rasika A. Mathias, Adam S. Butterworth, John Blangero, Joanne E. Curran, Timothy A. Thornton, Laura Almasy, Jerome I. Rotter, Nancy Min, Lisa R. Yanek, Donald M. Lloyd-Jones, Zhe Wang, Matthew P. Conomos, Myriam Fornage, Hua Tang, Lewis C. Becker, Lynette Ekunwe, Cecelia A. Laurie, Adolfo Correa, Jai G. Broome, Terri H. Beaty, Jennifer A. Brody, Caitlin P. McHugh, Yao Hu, Braxton D. Mitchell, Lifang Hou, Yun Li, Kathleen A. Ryan, Paul L. Auer, Stephen S. Rich, Kari E. North, Thomas W. Blackwell, Bruce M. Psaty, Deepti Jain, Paul S Vries, Praveen Surendran, Butterworth, Adam [0000-0002-6915-9015], and Apollo - University of Cambridge Repository
Subjects: Blood Platelets, Platelet disorder, Population, Genome-wide association study, Biology, Quantitative trait locus, Polymorphism, Single Nucleotide, Medical and Health Sciences, Genome, 03 medical and health sciences, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, 0302 clinical medicine, Clinical Research, and Blood Institute (U.S.), Genetics, Humans, 2.1 Biological and endogenous factors, Polymorphism, Precision Medicine, Aetiology, Mean platelet volume, education, Hemostatic function, Lung, Molecular Biology, Genetics (clinical), 030304 developmental biology, Blood Platelet Disorders, Genetics & Heredity, 0303 health sciences, education.field_of_study, Human Genome, Single Nucleotide, National Heart, Hematology, General Medicine, Biological Sciences, United States, 3. Good health, Phenotype, Good Health and Well Being, 030220 oncology & carcinogenesis, General Article, National Heart, Lung, and Blood Institute (U.S.), Genome-Wide Association Study, Biotechnology
Abstract: Platelets play a key role in thrombosis and hemostasis. Platelet count (PLT) and mean platelet volume (MPV) are highly heritable quantitative traits, with hundreds of genetic signals previously identified, mostly in European ancestry populations. We here utilize whole genome sequencing (WGS) from NHLBI’s Trans-Omics for Precision Medicine initiative (TOPMed) in a large multi-ethnic sample to further explore common and rare variation contributing to PLT (n = 61 200) and MPV (n = 23 485). We identified and replicated secondary signals at MPL (rs532784633) and PECAM1 (rs73345162), both more common in African ancestry populations. We also observed rare variation in Mendelian platelet-related disorder genes influencing variation in platelet traits in TOPMed cohorts (not enriched for blood disorders). For example, association of GP9 with lower PLT and higher MPV was partly driven by a pathogenic Bernard-Soulier syndrome variant (rs5030764, p.Asn61Ser), and the signals at TUBB1 and CD36 were partly driven by loss of function variants not annotated as pathogenic in ClinVar (rs199948010 and rs571975065). However, residual signal remained for these gene-based signals after adjusting for lead variants, suggesting that additional variants in Mendelian genes with impacts in general population cohorts remain to be identified. Gene-based signals were also identified at several genome-wide association study identified loci for genes not annotated for Mendelian platelet disorders (PTPRH, TET2, CHEK2), with somatic variation driving the result at TET2. These results highlight the value of WGS in populations of diverse genetic ancestry to identify novel regulatory and coding signals, even for well-studied traits like platelet traits.
Published: 2021
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33. Endoscopic Resection and Mucosal Reconstitution With Epidermal Grafting: A Pilot Study in Idiopathic Subglottic Stenosis

Author: Robert R. Lorenz, Alexander T. Hillel, Ioan A. Lina, Ruth J. Davis, Kevin M. Motz, Alexander Gelbard, and Guri Sandhu
Subjects: Adult, medicine.medical_specialty, Subglottic stenosis, Pilot Projects, Constriction, Pathologic, Article, Cricoid Cartilage, Pulmonary Disease, Chronic Obstructive, 03 medical and health sciences, 0302 clinical medicine, medicine, Humans, Endoscopic resection, 030223 otorhinolaryngology, Retrospective Studies, Epidermal grafting, business.industry, Laryngostenosis, medicine.disease, Surgery, Treatment Outcome, Otorhinolaryngology, 030220 oncology & carcinogenesis, business, Laryngotracheal stenosis
Abstract: OBJECTIVE. To describe technical aspects and surgical outcomes of endoscopic resection and mucosal reconstitution with epidermal grafting (ie, the Maddern procedure) in the treatment of idiopathic subglottic stenosis. STUDY DESIGN. Medical record abstraction. SETTING. Johns Hopkins Hospital. METHODS. Retrospective series of 9 adults with idiopathic subglottic stenosis who underwent the Maddern procedure by a single surgeon over a 5-year period. Prespecified outcomes included (1) perioperative outcomes (Clavien-Dindo grade 4/5 complications, need for staged tracheostomy, hospital length of stay), (2) postoperative outcomes (peak expiratory flow rate [PEFR], need for subsequent airway surgery, tracheostomy at follow-up), and (3) patient-reported quality-of-life outcomes (Clinical COPD Questionnaire, Voice Handicap Index–10, Eating Assessment Tool–10, and 12-Item Short Form Version 2). Wilcoxon matched-pairs signed rank test and Kaplan-Meier analysis were performed. RESULTS. There were no Clavien-Dindo grade 4/5 complications; 2 patients required unplanned staged tracheostomy; and the median length of stay was 3 days. Following endoscopic resection and stent removal, a median of 2 laser resurfacing procedures were required. Two patients developed recurrent stenosis requiring cricotracheal resection (CTR). There were significant improvements in PEFR, Clinical COPD Questionnaire, and Voice Handicap Index–10, without significant difference in Eating Assessment Tool–10. The 12-Item Short Form Version 2 approximated the population norm. Kaplan-Meier analysis demonstrated significant improvement in time to surgery after the final laser resurfacing. CONCLUSION. The Maddern procedure has a low complication rate and offers durable physiologic improvement in PEFR, limiting need for additional procedures. Risks included need for CTR salvage, temporary tracheostomy, phlegm accumulation, and laryngospasm. It is a surgical option for patients with short dilation intervals who prefer to avoid the risks of CTR.
Published: 2021
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34. MR Imaging of Human Brain Mechanics In Vivo: New Measurements to Facilitate the Development of Computational Models of Brain Injury

Author: Ruth J. Okamoto, Andrew K. Knutsen, K.T. Ramesh, Aaron Carass, Philip V. Bayly, Curtis L. Johnson, Ahmed Alshareef, Kshitiz Upadhyay, John A. Butman, Jerry L. Prince, and Dzung L. Pham
Subjects: Computational model, Computer science, Traumatic brain injury, business.industry, Biomedical Engineering, Brain, Experimental data, Human brain, medicine.disease, Machine learning, computer.software_genre, Magnetic Resonance Imaging, Models, Biological, Mr imaging, Biomechanical Phenomena, Brain anatomy, medicine.anatomical_structure, Brain Injuries, medicine, Animals, Humans, Artificial intelligence, business, computer
Abstract: Computational models of the brain and its biomechanical response to skull accelerations are important tools for understanding and predicting traumatic brain injuries (TBIs). However, most models have been developed using experimental data collected on animal models and cadaveric specimens, both of which differ from the living human brain. Here we describe efforts to noninvasively measure the biomechanical response of the human brain with MRI—at non-injurious strain levels—and generate data that can be used to develop, calibrate, and evaluate computational brain biomechanics models. Specifically, this paper reports on a project supported by the National Institute of Neurological Disorders and Stroke to comprehensively image brain anatomy and geometry, mechanical properties, and brain deformations that arise from impulsive and harmonic skull loadings. The outcome of this work will be a publicly available dataset ( http://www.nitrc.org/projects/bbir ) that includes measurements on both males and females across an age range from adolescence to older adulthood. This article describes the rationale and approach for this study, the data available, and how these data may be used to develop new computational models and augment existing approaches; it will serve as a reference to researchers interested in using these data.
Published: 2021
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35. Quantifying the phenome-wide disease burden of obesity using electronic health records and genomics

Author: Jamie R. Robinson, Robert J. Carroll, Lisa Bastarache, Qingxia Chen, James Pirruccello, Zongyang Mou, Wei‐Qi Wei, John Connolly, Frank Mentch, Paul K. Crane, Scott J. Hebbring, David R. Crosslin, Adam S. Gordon, Elisabeth A. Rosenthal, Ian B. Stanaway, M. Geoffrey Hayes, Wei Wei, Lynn Petukhova, Bahram Namjou‐Khales, Ge Zhang, Mayya S. Safarova, Nephi A. Walton, Christopher Still, Erwin P. Bottinger, Ruth J. F. Loos, Shawn N. Murphy, Gretchen P. Jackson, Naji Abumrad, Iftikhar J. Kullo, Gail P. Jarvik, Eric B. Larson, Chunhua Weng, Dan Roden, Amit V. Khera, and Joshua C. Denny
Subjects: Nutrition and Dietetics, Endocrinology, Diabetes and Metabolism, Medicine (miscellaneous), Genomics, Polymorphism, Single Nucleotide, Endocrinology, Phenotype, Diabetes Mellitus, Type 2, Cost of Illness, Humans, Electronic Health Records, Genetic Predisposition to Disease, Obesity, Phenomics, Genome-Wide Association Study
Abstract: High BMI is associated with many comorbidities and mortality. This study aimed to elucidate the overall clinical risk of obesity using a genome- and phenome-wide approach.This study performed a phenome-wide association study of BMI using a clinical cohort of 736,726 adults. This was followed by genetic association studies using two separate cohorts: one consisting of 65,174 adults in the Electronic Medical Records and Genomics (eMERGE) Network and another with 405,432 participants in the UK Biobank.Class 3 obesity was associated with 433 phenotypes, representing 59.3% of all billing codes in individuals with severe obesity. A genome-wide polygenic risk score for BMI, accounting for 7.5% of variance in BMI, was associated with 296 clinical diseases, including strong associations with type 2 diabetes, sleep apnea, hypertension, and chronic liver disease. In all three cohorts, 199 phenotypes were associated with class 3 obesity and polygenic risk for obesity, including novel associations such as increased risk of renal failure, venous insufficiency, and gastroesophageal reflux.This combined genomic and phenomic systematic approach demonstrated that obesity has a strong genetic predisposition and is associated with a considerable burden of disease across all disease classes.
Published: 2022

36. Investigating the causal nature of the relationship of subcortical brain volume with smoking and alcohol use

Author: Emma Logtenberg, Maartje Luijten, Damiaan Denys, Abdel Abdellaoui, Martin F. Overbeek, Ruth J. van Holst, Jacqueline M. Vink, Joëlle A. Pasman, Jorien L. Treur, Sarah E. Medland, Karin J. H. Verweij, Adult Psychiatry, Amsterdam Reproduction & Development, APH - Mental Health, Amsterdam Neuroscience - Compulsivity, Impulsivity & Attention, ANS - Compulsivity, Impulsivity & Attention, and ANS - Complex Trait Genetics
Subjects: Substance-Related Disorders, alcohol dependence, medicine.medical_treatment, Caudate nucleus, Physiology, Affect (psychology), Nicotine, 03 medical and health sciences, 0302 clinical medicine, Mendelian randomization, medicine, Humans, Mendelian randomisation, 030304 developmental biology, 0303 health sciences, business.industry, Putamen, Smoking, subcortical brain volume, Alcohol dependence, Confounding, Brain, alcohol use, Alcoholism, Psychiatry and Mental health, Causal inference, Brain size, Smoking cessation, business, Developmental Psychopathology, 030217 neurology & neurosurgery, Genome-Wide Association Study, Clinical psychology, medicine.drug
Abstract: BackgroundStructural variation in subcortical brain regions has been linked to substance use, including the most commonly used substances nicotine and alcohol. Pre-existing differences in subcortical brain volume may affect smoking and alcohol use, but there is also evidence that smoking and alcohol use can lead to structural changes.AimsWe assess the causal nature of the complex relationship of subcortical brain volume with smoking and alcohol use, using bi-directional Mendelian randomisation.MethodMendelian randomisation uses genetic variants predictive of a certain ‘exposure’ as instrumental variables to test causal effects on an ‘outcome’. Because of random assortment at meiosis, genetic variants should not be associated with confounders, allowing less biased causal inference. We used summary-level data of genome-wide association studies of subcortical brain volumes (nucleus accumbens, amygdala, caudate, hippocampus, pallidum, putamen and thalamus; n = 50 290) and smoking and alcohol use (smoking initiation, n = 848 460; cigarettes per day, n = 216 590; smoking cessation, n = 378 249; alcoholic drinks per week, n = 630 154; alcohol dependence, n = 46 568). The main analysis, inverse-variance weighted regression, was verified by a wide range of sensitivity methods.ResultsThere was strong evidence that liability to alcohol dependence decreased amygdala and hippocampal volume, and smoking more cigarettes per day decreased hippocampal volume. From subcortical brain volumes to substance use, there was no or weak evidence for causal effects.ConclusionsOur findings suggest that heavy alcohol use and smoking can causally reduce subcortical brain volume. This adds to accumulating evidence that alcohol and smoking affect the brain, and likely mental health, warranting more recognition in public health efforts.
Published: 2021
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37. Multi-ethnic genome-wide association analyses of white blood cell and platelet traits in the Population Architecture using Genomics and Epidemiology (PAGE) study

Author: Laura M. Raffield, Michael Preuss, Danyu Lin, Charles Kooperberg, Alexander P. Reiner, Antoine R Baldassari, Colleen M. Sitlani, Christy L. Avery, Laura M. Huckins, Ruth J. F. Loos, Katherine K. Nishimura, Lihong Qi, Yao Hu, Abdou Mousas, Mariaelisa Graff, Bharat Thyagarajan, Yun Li, Ran Tao, Guillaume Lettre, Quan Sun, Heather M. Highland, Jeffrey Haessler, Myriam Fornage, Kari E. North, Ulrike Peters, Chani J. Hodonsky, Weihong Tang, Zhe Wang, Paul L. Auer, Steve Buyske, Ming-Huei Chen, Stephanie A. Bien, Lucia A. Hindorff, and Genevieve L. Wojcik
Subjects: Platelets, medicine.medical_specialty, Population, Ethnic group, Genome-wide association study, Genomics, Multi-ethnic, Biology, QH426-470, Polymorphism, Single Nucleotide, 03 medical and health sciences, White blood cell, Epidemiology, medicine, Leukocytes, Genetics, Humans, GWAS, Genetic Predisposition to Disease, education, Gene, 030304 developmental biology, Genetic association, 0303 health sciences, education.field_of_study, 030305 genetics & heredity, Correction, medicine.anatomical_structure, Phenotype, White blood cells, TP248.13-248.65, Research Article, Genome-Wide Association Study, Biotechnology
Abstract: Background Circulating white blood cell and platelet traits are clinically linked to various disease outcomes and differ across individuals and ancestry groups. Genetic factors play an important role in determining these traits and many loci have been identified. However, most of these findings were identified in populations of European ancestry (EA), with African Americans (AA), Hispanics/Latinos (HL), and other races/ethnicities being severely underrepresented. Results We performed ancestry-combined and ancestry-specific genome-wide association studies (GWAS) for white blood cell and platelet traits in the ancestrally diverse Population Architecture using Genomics and Epidemiology (PAGE) Study, including 16,201 AA, 21,347 HL, and 27,236 EA participants. We identified six novel findings at suggestive significance (P < 5E-8), which need confirmation, and independent signals at six previously established regions at genome-wide significance (P < 2E-9). We confirmed multiple previously reported genome-wide significant variants in the single variant association analysis and multiple genes using PrediXcan. Evaluation of loci reported from a Euro-centric GWAS indicated attenuation of effect estimates in AA and HL compared to EA populations. Conclusions Our results highlighted the potential to identify ancestry-specific and ancestry-agnostic variants in participants with diverse backgrounds and advocate for continued efforts in improving inclusion of racially/ethnically diverse populations in genetic association studies for complex traits.
Published: 2021

38. The unique immune microenvironment of liver metastases: Challenges and opportunities

Author: Ruth J. Muschel, Aaron Ciner, Pnina Brodt, and Keaton Jones
Subjects: 0301 basic medicine, Cancer Research, Colorectal cancer, Context (language use), Disease, Immune tolerance, 03 medical and health sciences, 0302 clinical medicine, Immune system, Immunity, Tumor Microenvironment, medicine, Animals, Humans, business.industry, Liver Neoplasms, medicine.disease, Acquired immune system, 3. Good health, 030104 developmental biology, 13. Climate action, 030220 oncology & carcinogenesis, Cancer cell, Cancer research, Colorectal Neoplasms, business
Abstract: Liver metastases from gastrointestinal and non-gastrointestinal malignancies remain a major cause of cancer-related mortality and a major clinical challenge. The liver has unique properties that facilitate metastatic expansion, including a complex immune system that evolved to dampen immunity to neoantigens entering the liver from the gut, through the portal circulation. In this review, we describe the unique microenvironment encountered by cancer cells in the liver, focusing on elements of the innate and adaptive immune response that can act as a double-edge sword, contributing to the elimination of cancer cells on the one hand and promoting their survival and growth, on the other. We discuss this microenvironment in a clinical context, particularly for colorectal carcinoma, and highlight how a better understanding of the role of the microenvironment has spurred an intense effort to develop novel and innovative strategies for targeting liver metastatic disease, some of which are currently being tested in the clinic.
Published: 2021
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39. The effect of non-invasive brain stimulation on executive functioning in healthy controls: A systematic review and meta-analysis

Author: Ysbrand D. van der Werf, Anna E. Goudriaan, Renée S. Schluter, Ruth J. van Holst, Nina S. de Boer, and Joost G. Daams
Subjects: Cognitive Neuroscience, medicine.medical_treatment, Prefrontal Cortex, Stimulation, Stop signal, Transcranial Direct Current Stimulation, behavioral disciplines and activities, Transcranial electrical current stimulation, Task (project management), Executive Function, 03 medical and health sciences, Behavioral Neuroscience, Cognition, 0302 clinical medicine, Humans, Medicine, 0501 psychology and cognitive sciences, Onderzoek in PTR, Initiation, 050102 behavioral science & comparative psychology, Non-invasive brain stimulation, Inhibition, Transcranial direct-current stimulation, business.industry, Working memory, Research in PTR, 05 social sciences, Flexibility (personality), Center for Cognition, Culture and Language (CCCL), Transcranial magnetic stimulation, Healthy individuals, Meta-analysis, Planning, Neuropsychology and Physiological Psychology, Brain stimulation, Flexibility, business, Executive functioning, Neuroscience, 170 000 Motivational & Cognitive Control, 030217 neurology & neurosurgery, psychological phenomena and processes
Abstract: In recent years, there has been a heightened interest in the effect of non-invasive brain stimulation on executive functioning. However, there is no comprehensive overview of its effects on different executive functioning domains in healthy individuals. Here, we assessed the state of the field by conducting a systematic review and meta-analysis on the effectiveness of non-invasive brain stimulation (i.e. repetitive transcranial magnetic stimulation and transcranial direct current stimulation) over prefrontal regions on tasks assessing working memory, inhibition, flexibility, planning and initiation performance. Our search yielded 63 studies (n = 1537), and the effectiveness of excitatory and inhibitory non-invasive brain stimulation were assessed per executive functioning task. Our analyses showed that excitatory non-invasive brain stimulation had a small but positive effect on Stop Signal Task and Go/No-Go Task performance, and that inhibitory stimulation had a small negative effect on Flanker Task performance. Non-invasive brain stimulation did not affect performance on working memory and flexibility tasks, and effects on planning tasks were inconclusive.
Published: 2021
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40. Serum gamma-glutamyl transferase, a marker of alcohol intake, is associated with telomere length and cardiometabolic risk in young adulthood

Author: Esmée M. Bijnens, Dries S. Martens, Steven Weyers, Evert Thiery, Catherine Derom, Tim S. Nawrot, Ruth J. F. Loos, Department of Environmental Sciences, and RS-Research Program Learning and Innovation for Resilient Social-Ecological Systems (LIRSS)
Subjects: Male, Molecular biology, Buccal swab, Physiology, chemistry.chemical_compound, 0302 clinical medicine, Medicine and Health Sciences, Medicine, Young adult, OXIDATIVE STRESS, POPULATION, METABOLIC SYNDROME, Metabolic Syndrome, 0303 health sciences, Multidisciplinary, gamma-Glutamyltransferase, Telomere, 3. Good health, Multidisciplinary Sciences, 030220 oncology & carcinogenesis, Science & Technology - Other Topics, Biomarker (medicine), Population study, Female, GLUTAMYLTRANSFERASE, Adult, Waist, Adolescent, Alcohol Drinking, Science, Article, 03 medical and health sciences, Young Adult, DIETARY, Humans, EXPOSURE, METAANALYSIS, 030304 developmental biology, Science & Technology, business.industry, Cholesterol, CONSUMPTION, Zygosity, LIFE, Blood pressure, chemistry, Risk factors, CIGARETTE-SMOKING, business, Biomarkers
Abstract: Studies based on self-reported alcohol consumption and telomere length show inconsistent results. Therefore, we studied the association between gamma-glutamyl transferase (GGT), a widely used biomarker of alcohol intake, and telomere length. The possible health relevance in young adulthood was explored by investigating cardiometabolic risk factors. Mixed modelling was performed to examine GGT and alcohol consumption in association with telomere length in buccal cells of 211 adults between 18 and 30 years old of the East Flanders Prospective Twin Survey. In addition, we investigated the association between GGT and cardiometabolic risk factors; waist circumference, systolic blood pressure, fasting glucose, HDL cholesterol, and triglycerides. Although we did not observe an association between self-reported alcohol consumption and telomere length, our results show that a doubling in serum GGT is associated with 7.80% (95% CI - 13.9 to - 1.2%; p=0.02) shorter buccal telomeres, independently from sex, chronological age, educational level, zygosity and chorionicity, waist-to-hip ratio and smoking. The association between GGT was significant for all five cardiometabolic risk factors, while adjusting for age. We show that GGT, a widely used biomarker of alcohol consumption, is associated with telomere length and with risk factors of cardiometabolic syndrome, despite the young age of this study population. This investigation is supported by the EU research council “project ENVIRONAGE” (ERC-2012-StG 310890), and the Flemish Scientifc Fund (FWO, G073315N). Dr. Bijnens holds a fellow-ship from the Marguerite-Marie Delacroix foundation. Dr. Martens is a postdoctoral fellow of the FWO (12X9620N). Since its start, the East Flanders Prospective Twin Survey has been partly supported by grants from the Fund of Scientifc Research Flanders and Twins, a non-proft Association for Scientifc Research in Multiple Births (Belgium).
Published: 2021
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41. Genetic pleiotropy of ERCC6 loss‐of‐function and deleterious missense variants links retinal dystrophy, arrhythmia, and immunodeficiency in diverse ancestries

Author: Hong-Hee Won, Shantanu Bafna, Louis R. Pasquale, Girish N. Nadkarni, Ghislain Rocheleau, Ha My T. Vy, Kumardeep Chaudhary, Ruth J. F. Loos, Judy H. Cho, Iain S. Forrest, Ron Do, and Soyeon Kim
Subjects: Retinal Disorder, Disease, Biology, Article, 03 medical and health sciences, Pleiotropy, Retinal Dystrophies, Exome Sequencing, Genetics, medicine, Genetic Pleiotropy, Humans, Missense mutation, Exome, Poly-ADP-Ribose Binding Proteins, Genetics (clinical), Exome sequencing, Immunodeficiency, Loss function, 030304 developmental biology, 0303 health sciences, 030305 genetics & heredity, DNA Helicases, Arrhythmias, Cardiac, medicine.disease, DNA Repair Enzymes
Abstract: Biobanks with exomes linked to electronic health records (EHRs) enable the study of genetic pleiotropy between rare variants and seemingly disparate diseases. We performed robust clinical phenotyping of rare, putatively deleterious variants (loss-of-function [LoF] and deleterious missense variants) in ERCC6, a gene implicated in inherited retinal disease. We analyzed 213,084 exomes, along with a targeted set of retinal, cardiac, and immune phenotypes from two large-scale EHR-linked biobanks. In the primary analysis, a burden of deleterious variants in ERCC6 was strongly associated with 1) retinal disorders; 2) cardiac and electrocardiogram perturbations; and 3) immunodeficiency and decreased immunoglobulin levels. Meta-analysis of results from the BioMe Biobank and UK Biobank showed significant association of deleterious ERCC6 burden with retinal dystrophy (OR=2.6, 95% CI 1.5-4.6; P=8.7 x 10-4 ), atypical atrial flutter (OR=3.5, 95% CI 1.9-6.5; P=6.2 x 10-5 ), arrhythmia (OR=1.5, 95% CI 1.2-2.0; P=2.7 x 10-3 ), and lymphocyte immunodeficiency (OR=3.8, 95% CI 2.1-6.8; P=5.0 x 10-6 ). Carriers of ERCC6 LoF variants who lacked a diagnosis of these conditions exhibited increased symptoms, indicating underdiagnosis. These results reveal a unique genetic link among retinal, cardiac, and immune disorders and underscore the value of EHR-linked biobanks in assessing the full clinical profile of carriers of rare variants. This article is protected by copyright. All rights reserved.
Published: 2021
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42. Whole-genome sequencing association analysis of quantitative red blood cell phenotypes: The NHLBI TOPMed program

Author: Adolfo Correa, Jai G. Broome, Chunyan Ren, Kari E. North, Nancy L. Heard-Costa, Yao Yao, Brian D. Hobbs, Mary Cushman, Leslie A. Lange, Daniel E. Bauer, Xiuwen Zheng, Braxton D. Mitchell, Yun Li, Quan Sun, Sébastian Méric de Bellefon, Terri H. Beaty, Paul S. de Vries, Ruth J. F. Loos, Adrienne M. Stilp, Albert V. Smith, Paul L. Auer, Deepti Jain, Lifang Hou, Robert C. Kaplan, Jee-Young Moon, Michael Preuss, Stephen S. Rich, Guillaume Lettre, Nicole Soranzo, Eric Boerwinkle, Kousik Kundu, Laura Almasy, Marsha M. Wheeler, Thomas W. Blackwell, Nancy Min, Nicholas L. Smith, Bruce M. Psaty, Lisa R. Yanek, Joanne E. Curran, Stacey Gabriel, Kathleen A. Ryan, Alanna C. Morrison, Lynette Ekunwe, Caitlin P. McHugh, Laura M. Raffield, Adam S. Butterworth, Deborah A. Nickerson, Ravindranath Duggirala, Gonçalo R. Abecasis, John Lane, Hélène Choquet, Andrew D. Johnson, Nauder Faraday, Russell T. Walton, Praveen Surendran, Jennifer A. Brody, Yao Hu, Alexander P. Reiner, Jerome I. Rotter, Donald M. Lloyd-Jones, Cathy C. Laurie, Zhe Wang, Hua Tang, Charles Kooperberg, Eric Jorgenson, Jeffrey R. O'Connell, Shuquan Rao, Nathalie Chami, Rasika A. Mathias, Matthew P. Conomos, Myriam Fornage, Ramachandran S. Vasan, Nathan Pankratz, Joshua P. Lewis, Lewis C. Becker, Benjamin P. Kleinstiver, Cecelia A. Laurie, Ming-Huei Chen, and John Blangero
Subjects: Adult, Male, Quality Control, 0301 basic medicine, Erythrocytes, Population, Datasets as Topic, Genome-wide association study, Biology, Quantitative trait locus, Article, 03 medical and health sciences, 0302 clinical medicine, Genetics, Humans, Indel, education, Gene, Genetics (clinical), Aged, Genetic association, Gene Editing, Whole genome sequencing, education.field_of_study, Genetic Variation, Reproducibility of Results, Correction, Middle Aged, United States, Genetic architecture, HEK293 Cells, Phenotype, 030104 developmental biology, 030220 oncology & carcinogenesis, Female, National Heart, Lung, and Blood Institute (U.S.), Chromosomes, Human, Pair 16, Genome-Wide Association Study
Abstract: Summary Whole-genome sequencing (WGS), a powerful tool for detecting novel coding and non-coding disease-causing variants, has largely been applied to clinical diagnosis of inherited disorders. Here we leveraged WGS data in up to 62,653 ethnically diverse participants from the NHLBI Trans-Omics for Precision Medicine (TOPMed) program and assessed statistical association of variants with seven red blood cell (RBC) quantitative traits. We discovered 14 single variant-RBC trait associations at 12 genomic loci, which have not been reported previously. Several of the RBC trait-variant associations (RPN1, ELL2, MIDN, HBB, HBA1, PIEZO1, and G6PD) were replicated in independent GWAS datasets imputed to the TOPMed reference panel. Most of these discovered variants are rare/low frequency, and several are observed disproportionately among non-European Ancestry (African, Hispanic/Latino, or East Asian) populations. We identified a 3 bp indel p.Lys2169del (g.88717175_88717177TCT[4]) (common only in the Ashkenazi Jewish population) of PIEZO1, a gene responsible for the Mendelian red cell disorder hereditary xerocytosis (MIM: 194380 ), associated with higher mean corpuscular hemoglobin concentration (MCHC). In stepwise conditional analysis and in gene-based rare variant aggregated association analysis, we identified several of the variants in HBB, HBA1, TMPRSS6, and G6PD that represent the carrier state for known coding, promoter, or splice site loss-of-function variants that cause inherited RBC disorders. Finally, we applied base and nuclease editing to demonstrate that the sentinel variant rs112097551 (nearest gene RPN1) acts through a cis-regulatory element that exerts long-range control of the gene RUVBL1 which is essential for hematopoiesis. Together, these results demonstrate the utility of WGS in ethnically diverse population-based samples and gene editing for expanding knowledge of the genetic architecture of quantitative hematologic traits and suggest a continuum between complex trait and Mendelian red cell disorders.
Published: 2021
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43. Voice Quality and Laryngeal Findings in Patients With Suspected Lung Cancer

Author: Barbara Messing, Ruth J. Davis, Lee M. Akst, and Neri M. Cohen
Subjects: Male, medicine.medical_specialty, Lung Neoplasms, Voice Quality, media_common.quotation_subject, Severity of Illness Index, 03 medical and health sciences, 0302 clinical medicine, Surveys and Questionnaires, Internal medicine, Prevalence, Humans, Medicine, Quality (business), In patient, Prospective Studies, Stroboscopy, 030223 otorhinolaryngology, Lung cancer, Laryngeal Neoplasms, Aged, Leukoplakia, media_common, Aged, 80 and over, business.industry, Middle Aged, Dysphonia, medicine.disease, Self Concept, Otorhinolaryngology, Case-Control Studies, 030220 oncology & carcinogenesis, Cohort, Quality of Life, Female, Surgery, business, Suspected lung cancer
Abstract: To describe laryngeal findings and voice quality in patients with suspected lung cancer, relative to voice quality and possible laryngeal pathology.Prospective cohort study.Tertiary care center.Patients with known or suspected lung cancer were approached before planned thoracic surgery, and they completed acoustic analysis, the Voice-Related Quality of Life (V-RQOL) questionnaire, and stroboscopy. The prevalence of dysphonia, V-RQOL and Cepstral Spectral Index of Dysphonia (CSID) scores, and laryngeal findings were examined and compared between patients ultimately found to have lung cancer and those without cancer.Sixty-one patients (45 cancer, 16 noncancer) were analyzed. Patients with cancer were older than those without (mean ± SD, 72.3 ± 9.94 vs 62.6 ± 9.30 years;Patients with suspected lung cancer have moderate dysphonia on acoustic measures, though self-reported impact on quality of life is low. While leukoplakia was seen in 4 patients, obvious neoplasm and occult paralysis were not seen in this cohort. Together, these findings suggest that patients with suspected lung cancer should be assessed for subjective voice dysfunction, but routine laryngeal screening may otherwise be unnecessary.
Published: 2021
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44. Genome-wide polygenic risk score for retinopathy of type 2 diabetes

Author: Ruth J. F. Loos, Ron Do, Ha My T. Vy, Aparna Saha, Louis R. Pasquale, Carla Marquez-Luna, Ghislain Rocheleau, Girish N. Nadkarni, Lili Chan, Ishan Paranjpe, Judy H. Cho, Tielman Van Vleck, Kumardeep Chaudhary, and Iain S. Forrest
Subjects: Adult, Multifactorial Inheritance, medicine.medical_specialty, Black People, 030209 endocrinology & metabolism, Type 2 diabetes, Biology, Risk Assessment, White People, Decile, 03 medical and health sciences, 0302 clinical medicine, Risk Factors, Internal medicine, Genetics, medicine, Genetic predisposition, Humans, Genetic Predisposition to Disease, Association Studies Article, Molecular Biology, Genetics (clinical), Aged, 030304 developmental biology, 0303 health sciences, Diabetic Retinopathy, Hispanic or Latino, General Medicine, Diabetic retinopathy, Odds ratio, Middle Aged, medicine.disease, Confidence interval, Diabetes Mellitus, Type 2, Polygenic risk score, Genome-Wide Association Study, Retinopathy
Abstract: Diabetic retinopathy (DR) is a common consequence in type 2 diabetes (T2D) and a leading cause of blindness in working-age adults. Yet, its genetic predisposition is largely unknown. Here, we examined the polygenic architecture underlying DR by deriving and assessing a genome-wide polygenic risk score (PRS) for DR. We evaluated the PRS in 6079 individuals with T2D of European, Hispanic, African and other ancestries from a large-scale multi-ethnic biobank. Main outcomes were PRS association with DR diagnosis, symptoms and complications, and time to diagnosis, and transferability to non-European ancestries. We observed that PRS was significantly associated with DR. A standard deviation increase in PRS was accompanied by an adjusted odds ratio (OR) of 1.12 [95% confidence interval (CI) 1.04–1.20; P = 0.001] for DR diagnosis. When stratified by ancestry, PRS was associated with the highest OR in European ancestry (OR = 1.22, 95% CI 1.02–1.41; P = 0.049), followed by African (OR = 1.15, 95% CI 1.03–1.28; P = 0.028) and Hispanic ancestries (OR = 1.10, 95% CI 1.00–1.10; P = 0.050). Individuals in the top PRS decile had a 1.8-fold elevated risk for DR versus the bottom decile (P = 0.002). Among individuals without DR diagnosis, the top PRS decile had more DR symptoms than the bottom decile (P = 0.008). The PRS was associated with retinal hemorrhage (OR = 1.44, 95% CI 1.03–2.02; P = 0.03) and earlier DR presentation (10% probability of DR by 4 years in the top PRS decile versus 8 years in the bottom decile). These results establish the significant polygenic underpinnings of DR and indicate the need for more diverse ancestries in biobanks to develop multi-ancestral PRS.
Published: 2021
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45. Metabolic consequences of obesity and type 2 diabetes: Balancing genes and environment for personalized care

Author: Ruth J. F. Loos, Sally M. Marshall, Juleen R. Zierath, and Nicolas J. Pillon
Subjects: Thermotolerance, Gerontology, Population, thermal regulation, Translational research, Type 2 diabetes, Biology, General Biochemistry, Genetics and Molecular Biology, Epigenesis, Genetic, 03 medical and health sciences, 0302 clinical medicine, Risk Factors, circadian clock, Pandemic, Prevalence, medicine, Global health, Humans, Genetic Predisposition to Disease, genetics, Obesity, Precision Medicine, education, Pandemics, 030304 developmental biology, Inflammation, 0303 health sciences, education.field_of_study, exercise, treatment, SARS-CoV-2, business.industry, COVID-19, personalized medicine, Precision medicine, medicine.disease, Circadian Rhythm, Diabetes Mellitus, Type 2, inflammation, Personalized medicine, diet, business, environment, metabolism, 030217 neurology & neurosurgery
Abstract: The prevalence of type 2 diabetes and obesity has risen dramatically for decades and is expected to rise further, secondary to the growing aging, sedentary population. The strain on global health care is projected to be colossal. This review explores the latest work and emerging ideas related to genetic and environmental factors influencing metabolism. Translational research and clinical applications, including the impact of the COVID-19 pandemic, are highlighted. Looking forward, strategies to personalize all aspects of prevention, management and care are necessary to improve health outcomes and reduce the impact of these metabolic diseases.
Published: 2021
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46. An algorithm for the sedation of patients with obstructive sleep apnea by non-anesthesiologists

Author: Robert M. Kacmarek, Ruth J. Bryan, Luca M. Bigatello, Peter F. Dunn, and Richard M. Pino
Subjects: animal structures, medicine.medical_treatment, Sedation, 030204 cardiovascular system & hematology, 03 medical and health sciences, Cpap ventilation, 0302 clinical medicine, medicine, Humans, Anesthesia, 030212 general & internal medicine, Continuous positive airway pressure, Adverse effect, health care economics and organizations, Retrospective Studies, Moderate sedation, Sleep Apnea, Obstructive, Continuous Positive Airway Pressure, business.industry, food and beverages, General Medicine, medicine.disease, respiratory tract diseases, Obstructive sleep apnea, medicine.symptom, business, Algorithm, Algorithms
Abstract: Patients with obstructive sleep apnea (OSA) are at risk for adverse events when moderate sedation is administered by nurse protocols (NAMS) under the guidance of non-anesthesiologists. An algorithm was applied for the appropriate section of patients to receive NAMS and the application of continuous positive airway pressure (CPAP).An algorithm was developed for patients with OSA who were scheduled for gastroenterology, radiology, and cardiology procedures using NAMS. Those with normal airways and without contraindications for NAMS were classified as CPAP-independent (CPAP-I; not routinely used) or CPAP-dependent (CPAP-D; always used). CPAP machines were brought in by CPAP-D patients or supplied by the hospital and set at a patient's routine setting or 10 cm HSince the inception of this protocol in 2008, 803 patients with OSA safely underwent procedures using either personal CPAP or CPAP provided by the hospital.Patients with OSA can safely have NAMS for procedures when CPAP is applied based on a protocol that considers airway evaluation, the procedure, and whether there is dependence upon CPAP.
Published: 2021
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47. Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program

Author: Nancy L. Heard-Costa, Lucas Barwick, Clary B. Clish, Celeste Eng, Joanne M. Murabito, Esteban G. Burchard, Yii-Der Ida Chen, Daniel I. Chasman, Robert C. Kaplan, James B. Meigs, Deborah A. Nickerson, Cashell E. Jaquish, Eric Boerwinkle, Jennifer A. Brody, Charles Kooperberg, Mark T. Gladwin, Sebastian Schoenherr, Keng-Han Lin, John Barnard, Ryan D. Hernandez, Andrew D. Johnson, Edwin K. Silverman, Mollie A. Minear, Michelle Daya, Barbara A. Konkle, Sharon R. Browning, Daniel E. Weeks, Wendy S. Post, Alexander P. Reiner, Kathryn L. Lunetta, Gina M. Peloso, David Van Den Berg, Dan E. Arking, Seung-been Lee, Leslie A. Lange, Cristen J. Willer, Zachary A. Szpiech, Tasha E. Fingerlin, Wayne E. Clarke, Xutong Zhao, Stephen S. Rich, Nora Franceschini, Sudha Seshadri, Chloé Sarnowski, Hyun Min Kang, Sayantan Das, Michael C. Zody, Stephanie M. Fullerton, Dean Bobo, Alanna C. Morrison, Brian Custer, Nona Sotoodehnia, Shannon Kelly, Thomas W. Blackwell, Bruce M. Psaty, Yingze Zhang, Susan R. Heckbert, Robert E. Gerszten, M. Benjamin Shoemaker, Daniel Taliun, Leslie S. Emery, André Corvelo, Michael H. Cho, Braxton D. Mitchell, Xiaoming Liu, Stella Aslibekyan, Paul L. Auer, Brandon Chalazan, Sarah C. Nelson, Seung Hoan Choi, Jeong-Sun Seo, Matthew P. Conomos, Anne-Katrin Emde, Lawrence F. Bielak, Alisa K. Manning, Allison E. Ashley-Koch, Diane Fatkin, Xiaowen Tian, Emelia J. Benjamin, D. C. Rao, Mina K. Chung, Myriam Fornage, Daniel Levy, Michael D. Kessler, Weihong Tang, Daniel J. Gottlieb, Pradeep Natarajan, Jessica Lasky-Su, Amol C. Shetty, Cathy C. Laurie, Dan M. Roden, Timothy D. O’Connor, Jedidiah Carlson, Lewis C. Becker, Achilleas N. Pitsillides, Karine A. Viaud-Martinez, Raul Torres, Adolfo Correa, Christian Fuchsberger, Deborah A. Meyers, Alvaro Alonso, Sanghamitra Mohanty, Jonathon LeFaive, Soren Germer, Julie L. Mikulla, François Aguet, Susan K. Dutcher, Sarah A Gagliano Taliun, Ani Manichaikul, Lori Garman, Xiuqing Guo, Timothy A. Thornton, David D. McManus, Albert V. Smith, Kristin G. Ardlie, Anna Köttgen, Sharon L.R. Kardia, Quenna Wong, Jill M. Johnsen, Andrea Natale, Richard A. Gibbs, Douglas P. Kiel, Ingo Ruczinski, Susan Redline, Lukas Forer, Scott I. Vrieze, May E. Montasser, Rasika A. Mathias, Jerome I. Rotter, Jacob Pleiness, Chunyu Liu, Brian L. Browning, James G. Wilson, Weiniu Gan, Christine M. Albert, Marilyn J. Telen, Courtney G. Montgomery, Steven A. Lubitz, Robert Klemmer, Ramachandran S. Vasan, Nathan Pankratz, Mariza de Andrade, Vivien A. Sheehan, Kenneth Rice, Xihong Lin, Eimear E. Kenny, Stephanie M. Gogarten, John Blangero, Donna K. Arnett, Jiang He, Pankaj Qasba, James F. Casella, Patrick T. Ellinor, Nicholette D. Palmer, R. Graham Barr, Scott T. Weiss, Joanne E. Curran, Bruce S. Weir, Kari E. North, L. Adrienne Cupples, Dawn L. DeMeo, Tanika N. Kelly, Angel C.Y. Mak, Russell P. Tracy, David A. Schwartz, Kent D. Taylor, Rebecca L. Beer, Daniel N. Harris, George J. Papanicolaou, Marguerite R. Irvin, Stephen T. McGarvey, Sebastian Zöllner, Patricia A. Peyser, Brian E. Cade, Ruth J. F. Loos, Douglas Loesch, Nicholas L. Smith, Gonçalo R. Abecasis, Jennifer A. Smith, Michael E. Hall, Lu-Chen Weng, Jeffrey R. O'Connell, Adrienne M. Stilp, Donald W. Bowden, Kathleen C. Barnes, Stacey Gabriel, Michael Boehnke, Wayne Huey-Herng Sheu, and Dawood Darbar
Subjects: Quality Control, Heterozygote, Genomics, Computational biology, Biology, Polymorphism, Single Nucleotide, Genome, Article, DNA sequencing, INDEL Mutation, Loss of Function Mutation, Genetics research, Genetic variation, Humans, Precision Medicine, Genetic association, Population Density, Multidisciplinary, Whole Genome Sequencing, Genome, Human, Genetic Variation, Rare variants, United States, Genetic architecture, Phenotype, Cytochrome P-450 CYP2D6, Haplotypes, Mutagenesis, Sample Size, Next-generation sequencing, National Heart, Lung, and Blood Institute (U.S.), Imputation (genetics), Reference genome
Abstract: The Trans-Omics for Precision Medicine (TOPMed) programme seeks to elucidate the genetic architecture and biology of heart, lung, blood and sleep disorders, with the ultimate goal of improving diagnosis, treatment and prevention of these diseases. The initial phases of the programme focused on whole-genome sequencing of individuals with rich phenotypic data and diverse backgrounds. Here we describe the TOPMed goals and design as well as the available resources and early insights obtained from the sequence data. The resources include a variant browser, a genotype imputation server, and genomic and phenotypic data that are available through dbGaP (Database of Genotypes and Phenotypes)1. In the first 53,831 TOPMed samples, we detected more than 400 million single-nucleotide and insertion or deletion variants after alignment with the reference genome. Additional previously undescribed variants were detected through assembly of unmapped reads and customized analysis in highly variable loci. Among the more than 400 million detected variants, 97% have frequencies of less than 1% and 46% are singletons that are present in only one individual (53% among unrelated individuals). These rare variants provide insights into mutational processes and recent human evolutionary history. The extensive catalogue of genetic variation in TOPMed studies provides unique opportunities for exploring the contributions of rare and noncoding sequence variants to phenotypic variation. Furthermore, combining TOPMed haplotypes with modern imputation methods improves the power and reach of genome-wide association studies to include variants down to a frequency of approximately 0.01%., The goals, resources and design of the NHLBI Trans-Omics for Precision Medicine (TOPMed) programme are described, and analyses of rare variants detected in the first 53,831 samples provide insights into mutational processes and recent human evolutionary history.
Published: 2021
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48. Implementing genomic screening in diverse populations

Author: Giovanna T. Braganza, Emily R. Soper, Ruth J. F. Loos, Noura S. Abul-Husn, Sinead Cullina, Amanda Merkelson, Judy H. Cho, Arden Moscati, Jessica E. Rodriguez, Dean Bobo, Gillian M. Belbin, Sabrina A. Suckiel, Natasha Zeid, and Eimear E. Kenny
Subjects: Adult, Male, 0301 basic medicine, medicine.medical_specialty, Adolescent, lcsh:QH426-470, Population, MEDLINE, lcsh:Medicine, Pilot Projects, Familial hypercholesterolemia, 030204 cardiovascular system & hematology, Genomic screening, Young Adult, 03 medical and health sciences, 0302 clinical medicine, Genomic Medicine, Surveys and Questionnaires, Internal medicine, Ethnicity, Genetics, medicine, Humans, Genomic medicine, Genetic Testing, education, Molecular Biology, Genetics (clinical), Aged, Aged, 80 and over, African american, education.field_of_study, business.industry, Research, lcsh:R, Age Factors, Middle Aged, medicine.disease, Biobank, Human genetics, Lynch syndrome, lcsh:Genetics, Genetics, Population, 030104 developmental biology, Molecular Medicine, Female, business
Abstract: BackgroundPopulation-based genomic screening has the predicted ability to reduce morbidity and mortality associated with medically actionable conditions. However, much research is needed to develop standards for genomic screening and to understand the perspectives of people offered this new testing modality. This is particularly true for non-European ancestry populations who are vastly underrepresented in genomic medicine research. Therefore, we implemented a pilot genomic screening program in the BioMeBiobank in New York City, where the majority of participants are of non-European ancestry.MethodsWe initiated genomic screening for well-established genes associated with hereditary breast and ovarian cancer syndrome (HBOC), Lynch syndrome (LS), and familial hypercholesterolemia (FH). We evaluated and included an additional gene (TTR) associated with hereditary transthyretin amyloidosis (hATTR), which has a common founder variant in African ancestry populations. We evaluated the characteristics of 74 participants who received results associated with these conditions. We also assessed the preferences of 7461 newly enrolled BioMeparticipants to receive genomic results.ResultsIn the pilot genomic screening program, 74 consented participants received results related to HBOC (N = 26), LS (N = 6), FH (N = 8), and hATTR (N = 34). Thirty-three of 34 (97.1%) participants who received a result related to hATTR were self-reported African American/African (AA) or Hispanic/Latinx (HL), compared to 14 of 40 (35.0%) participants who received a result related to HBOC, LS, or FH. Among the 7461 participants enrolled after the BioMeprotocol modification to allow the return of genomic results, 93.4% indicated that they would want to receive results. Younger participants, women, and HL participants were more likely to opt to receive results.ConclusionsThe addition ofTTRto a pilot genomic screening program meant that we returned results to a higher proportion of AA and HL participants, in comparison with genes traditionally included in genomic screening programs in the USA. We found that the majority of participants in a multi-ethnic biobank are interested in receiving genomic results for medically actionable conditions. These findings increase knowledge about the perspectives of diverse research participants on receiving genomic results and inform the broader implementation of genomic medicine in underrepresented patient populations.
Published: 2021

49. The genomics of childhood eating behaviours

Author: Ruth J. F. Loos, Diana L. Santos Ferreira, Nadia Micali, Bianca De Stavola, Christopher Hübel, Rachel Bryant-Waugh, Mohamed Abdulkadir, Moritz Herle, and Cynthia M. Bulik
Subjects: Multifactorial Inheritance, Longitudinal study, Anorexia Nervosa, Social Psychology, Experimental and Cognitive Psychology, Anorexia nervosa, Article, Body Mass Index, 03 medical and health sciences, Behavioral Neuroscience, 0302 clinical medicine, medicine, Humans, Genetic Predisposition to Disease, Overeating, Child, Eating behaviour, 030304 developmental biology, 0303 health sciences, Body Weight, digestive, oral, and skin physiology, Feeding Behavior, Genomics, medicine.disease, Obesity, Eating disorders, Increased risk, Psychology, Body mass index, 030217 neurology & neurosurgery, Clinical psychology
Abstract: Eating behaviours may be expressions of genetic risk for obesity and are potential antecedents of later eating disorders. However, childhood eating behaviours are heterogeneous and transient. Here we show associations between polygenic scores for body mass index (BMI-PGS) and anorexia nervosa (AN-PGS) with eating behaviour trajectories during the first 10 years of life using data from the Avon Longitudinal Study of Parents and Children (ALSPAC), n = 7,825. Results indicated that 1 s.d. increase in the BMI-PGS was associated with a 30–37% increased risk for early- and mid-childhood overeating. In contrast, 1 s.d. increase in BMI-PGS was associated with a 20% decrease in risk of persistent high levels of undereating and a 15% decrease in risk of persistent fussy eating. There was no evidence for a significant association between AN-PGS and eating behaviour trajectories. Our results support the notion that child eating behaviours share common genetic variants associated with BMI. Herle et al. provide evidence that common genetic variants associated with BMI are also associated with eating behaviour trajectories in childhood, supporting the behavioural susceptibility theory of obesity.
Published: 2021
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50. Clostridioides difficile exploits toxin-mediated inflammation to alter the host nutritional landscape and exclude competitors from the gut microbiota

Author: Colleen M. Pike, Matthew H. Foley, Stephanie A. Montgomery, Casey M. Theriot, Alissa J. Rivera, Ruth J. Parsons, Michael R. McLaren, and Joshua R. Fletcher
Subjects: Male, 0301 basic medicine, Antibiotics, General Physics and Astronomy, Gut flora, medicine.disease_cause, Mice, Sigma factor, Bacteroides, RNA-Seq, Intestinal Mucosa, Pathogen, Regulation of gene expression, Multidisciplinary, Anti-Bacterial Agents, Extracellular Matrix, RNA, Bacterial, Host-Pathogen Interactions, Female, Pathogens, medicine.symptom, medicine.drug_class, Science, Bacterial Toxins, 030106 microbiology, Sigma Factor, Inflammation, Colonisation resistance, Biology, digestive system, Article, General Biochemistry, Genetics and Molecular Biology, Bacterial genetics, Microbiology, 03 medical and health sciences, Bacterial Proteins, medicine, Animals, Humans, Colonic diseases, Toxin, Clostridioides difficile, Gene Expression Regulation, Bacterial, Nutrients, General Chemistry, Pseudomembranous colitis, biology.organism_classification, Matrix Metalloproteinases, Gastrointestinal Microbiome, Disease Models, Animal, 030104 developmental biology, Proteolysis, Clostridium Infections, Microbiome, Transcriptome
Abstract: Clostridioides difficile is a bacterial pathogen that causes a range of clinical disease from mild to moderate diarrhea, pseudomembranous colitis, and toxic megacolon. Typically, C. difficile infections (CDIs) occur after antibiotic treatment, which alters the gut microbiota, decreasing colonization resistance against C. difficile. Disease is mediated by two large toxins and the expression of their genes is induced upon nutrient depletion via the alternative sigma factor TcdR. Here, we use tcdR mutants in two strains of C. difficile and omics to investigate how toxin-induced inflammation alters C. difficile metabolism, tissue gene expression and the gut microbiota, and to determine how inflammation by the host may be beneficial to C. difficile. We show that C. difficile metabolism is significantly different in the face of inflammation, with changes in many carbohydrate and amino acid uptake and utilization pathways. Host gene expression signatures suggest that degradation of collagen and other components of the extracellular matrix by matrix metalloproteinases is a major source of peptides and amino acids that supports C. difficile growth in vivo. Lastly, the inflammation induced by C. difficile toxin activity alters the gut microbiota, excluding members from the genus Bacteroides that are able to utilize the same essential nutrients released from collagen degradation., The effects of antibiotics on the gut microbiota can lead to enhanced colonization of Clostridioides difficile (C. difficile) and toxin-mediated pathogenesis. Here, using defined toxin-mutant strains and a murine model, the authors provide insights into how toxin-induced inflammation alters C. difficile metabolism, host tissue gene expression and gut microbiota, together influencing a beneficial niche for infection.
Published: 2021

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