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1. Lipid levels and risk of acute pancreatitis using bidirectional Mendelian randomization

Author: Biqi Wang, Jacqueline S. Dron, Yuxuan Wang, Seung Hoan Choi, Jennifer E. Huffman, Kelly Cho, Peter W. F. Wilson, Pradeep Natarajan, and Gina M. Peloso
Subjects: Lipids, Acute pancreatitis, Mendelian randomization, Medicine, Science
Abstract: Abstract Previous studies found lipid levels, especially triglycerides (TG), are associated with acute pancreatitis, but their causalities and bi-directions were not fully examined. We determined whether abnormal levels of TG, high-density lipoprotein cholesterol (HDL-C), and low-density lipoprotein cholesterol (LDL-C) are precursors and/or consequences of acute pancreatitis using bidirectional two-sample Mendelian randomization (MR) with two non-overlapping genome-wide association study (GWAS) summary statistics for lipid levels and acute pancreatitis. We found phenotypic associations that both higher TG levels and lower HDL-C levels contributed to increased risk of acute pancreatitis. Our GWAS meta-analysis of acute pancreatitis identified seven independent signals. Genetically predicted TG was positively associated with acute pancreatitis when using the variants specifically associated with TG using univariable MR [Odds ratio (OR), 95% CI 2.02, 1.22–3.31], but the reversed direction from acute pancreatitis to TG was not observed (mean difference = 0.003, SE = 0.002, P-value = 0.138). However, a bidirectional relationship of HDL-C and acute pancreatitis was observed: A 1-SD increment of genetically predicted HDL-C was associated with lower risk of acute pancreatitis (OR, 95% CI 0.84, 0.76–0.92) and genetically predisposed individuals with acute pancreatitis have, on average, 0.005 SD lower HDL-C (mean difference = − 0.005, SE = 0.002, P-value = 0.004). Our MR analysis confirms the evidence of TG as a risk factor of acute pancreatitis but not a consequence. A potential bidirectional relationship of HDL-C and acute pancreatitis occurs and raises the prospect of HDL-C modulation in the acute pancreatitis prevention and treatment.
Published: 2024
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2. Epigenome-wide DNA methylation association study of circulating IgE levels identifies novel targets for asthmaResearch in context

Author: Kathryn Recto, Priyadarshini Kachroo, Tianxiao Huan, David Van Den Berg, Gha Young Lee, Helena Bui, Dong Heon Lee, Jessica Gereige, Chen Yao, Shih-Jen Hwang, Roby Joehanes, Scott T. Weiss, George T. O’Connor, Daniel Levy, Dawn L. DeMeo, Namiko Abe, Gonçalo Abecasis, Francois Aguet, Christine Albert, Laura Almasy, Alvaro Alonso, Seth Ament, Peter Anderson, Pramod Anugu, Deborah Applebaum-Bowden, Kristin Ardlie, Dan Arking, Donna K. Arnett, Allison Ashley-Koch, Stella Aslibekyan, Tim Assimes, Paul Auer, Dimitrios Avramopoulos, Najib Ayas, Adithya Balasubramanian, John Barnard, Kathleen Barnes, R. Graham Barr, Emily Barron-Casella, Lucas Barwick, Terri Beaty, Gerald Beck, Diane Becker, Lewis Becker, Rebecca Beer, Amber Beitelshees, Emelia Benjamin, Takis Benos, Marcos Bezerra, Larry Bielak, Joshua Bis, Thomas Blackwell, John Blangero, Nathan Blue, Eric Boerwinkle, Donald W. Bowden, Russell Bowler, Jennifer Brody, Ulrich Broeckel, Jai Broome, Deborah Brown, Karen Bunting, Esteban Burchard, Carlos Bustamante, Erin Buth, Brian Cade, Jonathan Cardwell, Vincent Carey, Julie Carrier, April P. Carson, Cara Carty, Richard Casaburi, Juan P. Casas Romero, James Casella, Peter Castaldi, Mark Chaffin, Christy Chang, Yi-Cheng Chang, Daniel Chasman, Sameer Chavan, Bo-Juen Chen, Wei-Min Chen, Yii-Der Ida Chen, Michael Cho, Seung Hoan Choi, Lee-Ming Chuang, Mina Chung, Ren-Hua Chung, Clary Clish, Suzy Comhair, Matthew Conomos, Elaine Cornell, Adolfo Correa, Carolyn Crandall, James Crapo, L. Adrienne Cupples, Joanne Curran, Jeffrey Curtis, Brian Custer, Coleen Damcott, Dawood Darbar, Sean David, Colleen Davis, Michelle Daya, Mariza de Andrade, Lisa de las Fuentes, Paul de Vries, Michael DeBaun, Ranjan Deka, Dawn DeMeo, Scott Devine, Huyen Dinh, Harsha Doddapaneni, Qing Duan, Shannon Dugan-Perez, Ravi Duggirala, Jon Peter Durda, Susan K. Dutcher, Charles Eaton, Lynette Ekunwe, Adel El Boueiz, Patrick Ellinor, Leslie Emery, Serpil Erzurum, Charles Farber, Jesse Farek, Tasha Fingerlin, Matthew Flickinger, Myriam Fornage, Nora Franceschini, Chris Frazar, Mao Fu, Stephanie M. Fullerton, Lucinda Fulton, Stacey Gabriel, Weiniu Gan, Shanshan Gao, Yan Gao, Margery Gass, Heather Geiger, Bruce Gelb, Mark Geraci, Soren Germer, Robert Gerszten, Auyon Ghosh, Richard Gibbs, Chris Gignoux, Mark Gladwin, David Glahn, Stephanie Gogarten, Da-Wei Gong, Harald Goring, Sharon Graw, Kathryn J. Gray, Daniel Grine, Colin Gross, C. Charles Gu, Yue Guan, Xiuqing Guo, Namrata Gupta, Jeff Haessler, Michael Hall, Yi Han, Patrick Hanly, Daniel Harris, Nicola L. Hawley, Jiang He, Ben Heavner, Susan Heckbert, Ryan Hernandez, David Herrington, Craig Hersh, Bertha Hidalgo, James Hixson, Brian Hobbs, John Hokanson, Elliott Hong, Karin Hoth, Chao (Agnes) Hsiung, Jianhong Hu, Yi-Jen Hung, Haley Huston, Chii Min Hwu, Marguerite Ryan Irvin, Rebecca Jackson, Deepti Jain, Cashell Jaquish, Jill Johnsen, Andrew Johnson, Craig Johnson, Rich Johnston, Kimberly Jones, Hyun Min Kang, Robert Kaplan, Sharon Kardia, Shannon Kelly, Eimear Kenny, Michael Kessler, Alyna Khan, Ziad Khan, Wonji Kim, John Kimoff, Greg Kinney, Barbara Konkle, Charles Kooperberg, Holly Kramer, Christoph Lange, Ethan Lange, Leslie Lange, Cathy Laurie, Cecelia Laurie, Meryl LeBoff, Jiwon Lee, Sandra Lee, Wen-Jane Lee, Jonathon LeFaive, David Levine, Joshua Lewis, Xiaohui Li, Yun Li, Henry Lin, Honghuang Lin, Xihong Lin, Simin Liu, Yongmei Liu, Yu Liu, Ruth J.F. Loos, Steven Lubitz, Kathryn Lunetta, James Luo, Ulysses Magalang, Michael Mahaney, Barry Make, Ani Manichaikul, Alisa Manning, JoAnn Manson, Lisa Martin, Melissa Marton, Susan Mathai, Rasika Mathias, Susanne May, Patrick McArdle, Merry-Lynn McDonald, Sean McFarland, Stephen McGarvey, Daniel McGoldrick, Caitlin McHugh, Becky McNeil, Hao Mei, James Meigs, Vipin Menon, Luisa Mestroni, Ginger Metcalf, Deborah A. Meyers, Emmanuel Mignot, Julie Mikulla, Nancy Min, Mollie Minear, Ryan L. Minster, Braxton D. Mitchell, Matt Moll, Zeineen Momin, May E. Montasser, Courtney Montgomery, Donna Muzny, Josyf C. Mychaleckyj, Girish Nadkarni, Rakhi Naik, Take Naseri, Pradeep Natarajan, Sergei Nekhai, Sarah C. Nelson, Bonnie Neltner, Caitlin Nessner, Deborah Nickerson, Osuji Nkechinyere, Kari North, Jeff O'Connell, Tim O'Connor, Heather Ochs-Balcom, Geoffrey Okwuonu, Allan Pack, David T. Paik, Nicholette Palmer, James Pankow, George Papanicolaou, Cora Parker, Gina Peloso, Juan Manuel Peralta, Marco Perez, James Perry, Ulrike Peters, Patricia Peyser, Lawrence S. Phillips, Jacob Pleiness, Toni Pollin, Wendy Post, Julia Powers Becker, Meher Preethi Boorgula, Michael Preuss, Bruce Psaty, Pankaj Qasba, Dandi Qiao, Zhaohui Qin, Nicholas Rafaels, Laura Raffield, Mahitha Rajendran, Vasan S. Ramachandran, D.C. Rao, Laura Rasmussen-Torvik, Aakrosh Ratan, Susan Redline, Robert Reed, Catherine Reeves, Elizabeth Regan, Alex Reiner, Muagututi‘a Sefuiva Reupena, Ken Rice, Stephen Rich, Rebecca Robillard, Nicolas Robine, Dan Roden, Carolina Roselli, Jerome Rotter, Ingo Ruczinski, Alexi Runnels, Pamela Russell, Sarah Ruuska, Kathleen Ryan, Ester Cerdeira Sabino, Danish Saleheen, Shabnam Salimi, Sejal Salvi, Steven Salzberg, Kevin Sandow, Vijay G. Sankaran, Jireh Santibanez, Karen Schwander, David Schwartz, Frank Sciurba, Christine Seidman, Jonathan Seidman, Frédéric Sériès, Vivien Sheehan, Stephanie L. Sherman, Amol Shetty, Aniket Shetty, Wayne Hui-Heng Sheu, M. Benjamin Shoemaker, Brian Silver, Edwin Silverman, Robert Skomro, Albert Vernon Smith, Jennifer Smith, Josh Smith, Nicholas Smith, Tanja Smith, Sylvia Smoller, Beverly Snively, Michael Snyder, Tamar Sofer, Nona Sotoodehnia, Adrienne M. Stilp, Garrett Storm, Elizabeth Streeten, Jessica Lasky Su, Yun Ju Sung, Jody Sylvia, Adam Szpiro, Daniel Taliun, Hua Tang, Margaret Taub, Kent Taylor, Matthew Taylor, Simeon Taylor, Marilyn Telen, Timothy A. Thornton, Machiko Threlkeld, Lesley Tinker, David Tirschwell, Sarah Tishkoff, Hemant Tiwari, Catherine Tong, Russell Tracy, Michael Tsai, Dhananjay Vaidya, Peter VandeHaar, Scott Vrieze, Tarik Walker, Robert Wallace, Avram Walts, Fei Fei Wang, Heming Wang, Jiongming Wang, Karol Watson, Jennifer Watt, Daniel E. Weeks, Joshua Weinstock, Bruce Weir, Lu-Chen Weng, Jennifer Wessel, Cristen Willer, Kayleen Williams, L. Keoki Williams, Scott Williams, Carla Wilson, James Wilson, Lara Winterkorn, Quenna Wong, Baojun Wu, Joseph Wu, Huichun Xu, Lisa Yanek, Ivana Yang, Ketian Yu, Seyedeh Maryam Zekavat, Yingze Zhang, Snow Xueyan Zhao, Wei Zhao, Xiaofeng Zhu, Elad Ziv, Michael Zody, and Sebastian Zoellner
Subjects: EWAS, DNA methylation, IgE, Asthma, RNA-Sequencing, Mendelian randomization, Medicine, Medicine (General), R5-920
Abstract: Summary: Background: Identifying novel epigenetic signatures associated with serum immunoglobulin E (IgE) may improve our understanding of molecular mechanisms underlying asthma and IgE-mediated diseases. Methods: We performed an epigenome-wide association study using whole blood from Framingham Heart Study (FHS; n = 3,471, 46% females) participants and validated results using the Childhood Asthma Management Program (CAMP; n = 674, 39% females) and the Genetic Epidemiology of Asthma in Costa Rica Study (CRA; n = 787, 41% females). Using the closest gene to each IgE-associated CpG, we highlighted biologically plausible pathways underlying IgE regulation and analyzed the transcription patterns linked to IgE-associated CpGs (expression quantitative trait methylation loci; eQTMs). Using prior UK Biobank summary data from genome-wide association studies of asthma and allergy, we performed Mendelian randomization (MR) for causal inference testing using the IgE-associated CpGs from FHS with methylation quantitative trait loci (mQTLs) as instrumental variables. Findings: We identified 490 statistically significant differentially methylated CpGs associated with IgE in FHS, of which 193 (39.3%) replicated in CAMP and CRA (FDR < 0.05). Gene ontology analysis revealed enrichment in pathways related to transcription factor binding, asthma, and other immunological processes. eQTM analysis identified 124 cis-eQTMs for 106 expressed genes (FDR < 0.05). MR in combination with drug-target analysis revealed CTSB and USP20 as putatively causal regulators of IgE levels (Bonferroni adjusted P
Published: 2023
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3. Associations of NINJ2 sequence variants with incident ischemic stroke in the Cohorts for Heart and Aging in Genomic Epidemiology (CHARGE) consortium.

Author: Joshua C Bis, Anita DeStefano, Xiaoming Liu, Jennifer A Brody, Seung Hoan Choi, Benjamin F J Verhaaren, Stéphanie Debette, M Arfan Ikram, Eyal Shahar, Kenneth R Butler, Rebecca F Gottesman, Donna Muzny, Christie L Kovar, Bruce M Psaty, Albert Hofman, Thomas Lumley, Mayetri Gupta, Philip A Wolf, Cornelia van Duijn, Richard A Gibbs, Thomas H Mosley, W T Longstreth, Eric Boerwinkle, Sudha Seshadri, and Myriam Fornage
Subjects: Medicine, Science
Abstract: BACKGROUND:Stroke, the leading neurologic cause of death and disability, has a substantial genetic component. We previously conducted a genome-wide association study (GWAS) in four prospective studies from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortium and demonstrated that sequence variants near the NINJ2 gene are associated with incident ischemic stroke. Here, we sought to fine-map functional variants in the region and evaluate the contribution of rare variants to ischemic stroke risk. METHODS AND RESULTS:We sequenced 196 kb around NINJ2 on chromosome 12p13 among 3,986 European ancestry participants, including 475 ischemic stroke cases, from the Atherosclerosis Risk in Communities Study, Cardiovascular Health Study, and Framingham Heart Study. Meta-analyses of single-variant tests for 425 common variants (minor allele frequency [MAF] ≥ 1%) confirmed the original GWAS results and identified an independent intronic variant, rs34166160 (MAF = 0.012), most significantly associated with incident ischemic stroke (HR = 1.80, p = 0.0003). Aggregating 278 putatively-functional variants with MAF≤ 1% using count statistics, we observed a nominally statistically significant association, with the burden of rare NINJ2 variants contributing to decreased ischemic stroke incidence (HR = 0.81; p = 0.026). CONCLUSION:Common and rare variants in the NINJ2 region were nominally associated with incident ischemic stroke among a subset of CHARGE participants. Allelic heterogeneity at this locus, caused by multiple rare, low frequency, and common variants with disparate effects on risk, may explain the difficulties in replicating the original GWAS results. Additional studies that take into account the complex allelic architecture at this locus are needed to confirm these findings.
Published: 2014
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4. Whole Genome Sequence Analysis of the Plasma Proteome in Black Adults Provides Novel Insights Into Cardiovascular Disease

Author: Daniel H. Katz, Usman A. Tahir, Alexander G. Bick, Akhil Pampana, Debby Ngo, Mark D. Benson, Zhi Yu, Jeremy M. Robbins, Zsu-Zsu Chen, Daniel E. Cruz, Shuliang Deng, Laurie Farrell, Sumita Sinha, Alec A. Schmaier, Dongxiao Shen, Yan Gao, Michael E. Hall, Adolfo Correa, Russell P. Tracy, Peter Durda, Kent D. Taylor, Yongmei Liu, W. Craig Johnson, Xiuqing Guo, Jie Yao, Yii-Der Ida Chen, Ani W. Manichaikul, Deepti Jain, Claude Bouchard, Mark A. Sarzynski, Stephen S. Rich, Jerome I. Rotter, Thomas J. Wang, James G. Wilson, Pradeep Natarajan, Robert E. Gerszten, Namiko Abe, Gonçalo Abecasis, Francois Aguet, Christine Albert, Laura Almasy, Alvaro Alonso, Seth Ament, Peter Anderson, Pramod Anugu, Deborah Applebaum-Bowden, Kristin Ardlie, Dan Arking, Donna K. Arnett, Allison Ashley-Koch, Stella Aslibekyan, Tim Assimes, Paul Auer, Dimitrios Avramopoulos, Najib Ayas, Adithya Balasubramanian, John Barnard, Kathleen Barnes, R. Graham Barr, Emily Barron-Casella, Lucas Barwick, Terri Beaty, Gerald Beck, Diane Becker, Lewis Becker, Rebecca Beer, Amber Beitelshees, Emelia Benjamin, Takis Benos, Marcos Bezerra, Larry Bielak, Joshua Bis, Thomas Blackwell, John Blangero, Eric Boerwinkle, Donald W. Bowden, Russell Bowler, Jennifer Brody, Ulrich Broeckel, Jai Broome, Deborah Brown, Karen Bunting, Esteban Burchard, Carlos Bustamante, Erin Buth, Brian Cade, Jonathan Cardwell, Vincent Carey, Julie Carrier, April Carson, Cara Carty, Richard Casaburi, Juan P. Casas Romero, James Casella, Peter Castaldi, Mark Chaffin, Christy Chang, Yi-Cheng Chang, Daniel Chasman, Sameer Chavan, Bo-Juen Chen, Wei-Min Chen, Michael Cho, Seung Hoan Choi, Lee-Ming Chuang, Mina Chung, Ren-Hua Chung, Clary Clish, Suzy Comhair, Matthew Conomos, Elaine Cornell, Carolyn Crandall, James Crapo, L. Adrienne Cupples, Joanne Curran, Jeffrey Curtis, Brian Custer, Coleen Damcott, Dawood Darbar, Sean David, Colleen Davis, Michelle Daya, Mariza de Andrade, Lisa de las Fuentes, Paul de Vries, Michael DeBaun, Ranjan Deka, Dawn DeMeo, Scott Devine, Huyen Dinh, Harsha Doddapaneni, Qing Duan, Shannon Dugan-Perez, Ravi Duggirala, Jon Peter Durda, Susan K. Dutcher, Charles Eaton, Lynette Ekunwe, Adel El Boueiz, Patrick Ellinor, Leslie Emery, Serpil Erzurum, Charles Farber, Jesse Farek, Tasha Fingerlin, Matthew Flickinger, Myriam Fornage, Nora Franceschini, Chris Frazar, Mao Fu, Stephanie M. Fullerton, Lucinda Fulton, Stacey Gabriel, Weiniu Gan, Shanshan Gao, Margery Gass, Heather Geiger, Bruce Gelb, Mark Geraci, Soren Germer, Robert Gerszten, Auyon Ghosh, Richard Gibbs, Chris Gignoux, Mark Gladwin, David Glahn, Stephanie Gogarten, Da-Wei Gong, Harald Goring, Sharon Graw, Kathryn J. Gray, Daniel Grine, Colin Gross, C. Charles Gu, Yue Guan, Namrata Gupta, David M. Haas, Jeff Haessler, Michael Hall, Yi Han, Patrick Hanly, Daniel Harris, Nicola L. Hawley, Jiang He, Ben Heavner, Susan Heckbert, Ryan Hernandez, David Herrington, Craig Hersh, Bertha Hidalgo, James Hixson, Brian Hobbs, John Hokanson, Elliott Hong, Karin Hoth, Chao (Agnes) Hsiung, Jianhong Hu, Yi-Jen Hung, Haley Huston, Chii Min Hwu, Marguerite Ryan Irvin, Rebecca Jackson, Cashell Jaquish, Jill Johnsen, Andrew Johnson, Craig Johnson, Rich Johnston, Kimberly Jones, Hyun Min Kang, Robert Kaplan, Sharon Kardia, Shannon Kelly, Eimear Kenny, Michael Kessler, Alyna Khan, Ziad Khan, Wonji Kim, John Kimoff, Greg Kinney, Barbara Konkle, Charles Kooperberg, Holly Kramer, Christoph Lange, Ethan Lange, Leslie Lange, Cathy Laurie, Cecelia Laurie, Meryl LeBoff, Jiwon Lee, Sandra Lee, Wen-Jane Lee, Jonathon LeFaive, David Levine, Dan Levy, Joshua Lewis, Xiaohui Li, Yun Li, Henry Lin, Honghuang Lin, Xihong Lin, Simin Liu, Yu Liu, Ruth J.F. Loos, Steven Lubitz, Kathryn Lunetta, James Luo, Ulysses Magalang, Michael Mahaney, Barry Make, Ani Manichaikul, Alisa Manning, JoAnn Manson, Lisa Martin, Melissa Marton, Susan Mathai, Rasika Mathias, Susanne May, Patrick McArdle, Merry-Lynn McDonald, Sean McFarland, Stephen McGarvey, Daniel McGoldrick, Caitlin McHugh, Becky McNeil, Hao Mei, James Meigs, Vipin Menon, Luisa Mestroni, Ginger Metcalf, Deborah A. Meyers, Emmanuel Mignot, Julie Mikulla, Nancy Min, Mollie Minear, Ryan L. Minster, Braxton D. Mitchell, Matt Moll, Zeineen Momin, May E. Montasser, Courtney Montgomery, Donna Muzny, Josyf C. Mychaleckyj, Girish Nadkarni, Rakhi Naik, Take Naseri, Sergei Nekhai, Sarah C. Nelson, Bonnie Neltner, Caitlin Nessner, Deborah Nickerson, Osuji Nkechinyere, Kari North, Jeff O’Connell, Tim O’Connor, Heather Ochs-Balcom, Geoffrey Okwuonu, Allan Pack, David T. Paik, Nicholette Palmer, James Pankow, George Papanicolaou, Cora Parker, Gina Peloso, Juan Manuel Peralta, Marco Perez, James Perry, Ulrike Peters, Patricia Peyser, Lawrence S. Phillips, Jacob Pleiness, Toni Pollin, Wendy Post, Julia Powers Becker, Meher Preethi Boorgula, Michael Preuss, Bruce Psaty, Pankaj Qasba, Dandi Qiao, Zhaohui Qin, Nicholas Rafaels, Laura Raffield, Mahitha Rajendran, Vasan S. Ramachandran, D.C. Rao, Laura Rasmussen-Torvik, Aakrosh Ratan, Susan Redline, Robert Reed, Catherine Reeves, Elizabeth Regan, Alex Reiner, Muagututi’a Sefuiva Reupena, Ken Rice, Stephen Rich, Rebecca Robillard, Nicolas Robine, Dan Roden, Carolina Roselli, Jerome Rotter, Ingo Ruczinski, Alexi Runnels, Pamela Russell, Sarah Ruuska, Kathleen Ryan, Ester Cerdeira Sabino, Danish Saleheen, Shabnam Salimi, Sejal Salvi, Steven Salzberg, Kevin Sandow, Vijay G. Sankaran, Jireh Santibanez, Karen Schwander, David Schwartz, Frank Sciurba, Christine Seidman, Jonathan Seidman, Frédéric Sériès, Vivien Sheehan, Stephanie L. Sherman, Amol Shetty, Aniket Shetty, Wayne Hui-Heng Sheu, M. Benjamin Shoemaker, Brian Silver, Edwin Silverman, Robert Skomro, Albert Vernon Smith, Jennifer Smith, Josh Smith, Nicholas Smith, Tanja Smith, Sylvia Smoller, Beverly Snively, Michael Snyder, Tamar Sofer, Nona Sotoodehnia, Adrienne M. Stilp, Garrett Storm, Elizabeth Streeten, Jessica Lasky Su, Yun Ju Sung, Jody Sylvia, Adam Szpiro, Daniel Taliun, Hua Tang, Margaret Taub, Matthew Taylor, Simeon Taylor, Marilyn Telen, Timothy A. Thornton, Machiko Threlkeld, Lesley Tinker, David Tirschwell, Sarah Tishkoff, Hemant Tiwari, Catherine Tong, Russell Tracy, Michael Tsai, Dhananjay Vaidya, David Van Den Berg, Peter VandeHaar, Scott Vrieze, Tarik Walker, Robert Wallace, Avram Walts, Fei Fei Wang, Heming Wang, Jiongming Wang, Karol Watson, Jennifer Watt, Daniel E. Weeks, Joshua Weinstock, Bruce Weir, Scott T. Weiss, Lu-Chen Weng, Jennifer Wessel, Cristen Willer, Kayleen Williams, L. Keoki Williams, Carla Wilson, James Wilson, Lara Winterkorn, Quenna Wong, Joseph Wu, Huichun Xu, Lisa Yanek, Ivana Yang, Ketian Yu, Seyedeh Maryam Zekavat, Yingze Zhang, Snow Xueyan Zhao, Wei Zhao, Xiaofeng Zhu, Michael Zody, and Sebastian Zoellner
Subjects: Adult, Male, Proteomics, Aging, Whole genome sequence analysis, Proteome, Clinical Sciences, Black People, Disease, Computational biology, race and ethnicity, Cardiorespiratory Medicine and Haematology, Cardiovascular, Article, proteomics, cardiovascular disease, Physiology (medical), Genetics, 2.1 Biological and endogenous factors, Humans, Medicine, Aetiology, Lung, Heart Disease - Coronary Heart Disease, and Blood Institute TOPMed (Trans-Omics for Precision Medicine) Consortium†, business.industry, Prevention, Human Genome, National Heart, Genomics, Blood proteins, Genetic architecture, Heart Disease, Good Health and Well Being, Cardiovascular System & Hematology, Cardiovascular Diseases, Public Health and Health Services, Female, Cardiology and Cardiovascular Medicine, business, Biotechnology, Genome-Wide Association Study
Abstract: Background: Plasma proteins are critical mediators of cardiovascular processes and are the targets of many drugs. Previous efforts to characterize the genetic architecture of the plasma proteome have been limited by a focus on individuals of European descent and leveraged genotyping arrays and imputation. Here we describe whole genome sequence analysis of the plasma proteome in individuals with greater African ancestry, increasing our power to identify novel genetic determinants. Methods: Proteomic profiling of 1301 proteins was performed in 1852 Black adults from the Jackson Heart Study using aptamer-based proteomics (SomaScan). Whole genome sequencing association analysis was ascertained for all variants with minor allele count ≥5. Results were validated using an alternative, antibody-based, proteomic platform (Olink) as well as replicated in the Multi-Ethnic Study of Atherosclerosis and the HERITAGE Family Study (Health, Risk Factors, Exercise Training and Genetics). Results: We identify 569 genetic associations between 479 proteins and 438 unique genetic regions at a Bonferroni-adjusted significance level of 3.8×10 -11 . These associations include 114 novel locus-protein relationships and an additional 217 novel sentinel variant-protein relationships. Novel cardiovascular findings include new protein associations at the APOE gene locus including ZAP70 (sentinel single nucleotide polymorphism [SNP] rs7412-T, β=0.61±0.05, P =3.27×10 -30 ) and MMP-3 (β=-0.60±0.05, P =1.67×10 -32 ), as well as a completely novel pleiotropic locus at the HPX gene, associated with 9 proteins. Further, the associations suggest new mechanisms of genetically mediated cardiovascular disease linked to African ancestry; we identify a novel association between variants linked to APOL1-associated chronic kidney and heart disease and the protein CKAP2 (rs73885319-G, β=0.34±0.04, P =1.34×10 -17 ) as well as an association between ATTR amyloidosis and RBP4 levels in community-dwelling individuals without heart failure. Conclusions: Taken together, these results provide evidence for the functional importance of variants in non-European populations, and suggest new biological mechanisms for ancestry-specific determinants of lipids, coagulation, and myocardial function.
Published: 2022

5. Monogenic and Polygenic Contributions to Atrial Fibrillation Risk

Author: Mark Chaffin, Sean J. Jurgens, Lu-Chen Weng, Steven A. Lubitz, Amit Khera, Seung Hoan Choi, Christina J.-Y. Lee, James P. Pirruccello, Kathryn L. Lunetta, Carolina Roselli, Amelia W. Hall, and Patrick T. Ellinor
Subjects: Male, Multifactorial Inheritance, Physiology, Population, Penetrance, Polymorphism, Single Nucleotide, Article, Loss of Function Mutation, Databases, Genetic, Atrial Fibrillation, Humans, Medicine, Connectin, Exome, Genetic Predisposition to Disease, education, Aged, Biological Specimen Banks, Genetic association, Genetics, education.field_of_study, business.industry, Atrial fibrillation, Middle Aged, medicine.disease, Biobank, Female, Cardiology and Cardiovascular Medicine, business, Genome-Wide Association Study
Abstract: Rationale: Genome-wide association studies have identified over 100 genetic loci for atrial fibrillation (AF); recent work described an association between loss-of-function (LOF) variants in TTN and early-onset AF. Objective: We sought to determine the contribution of rare and common genetic variation to AF risk in the general population. Methods: The UK Biobank is a population-based study of 500 000 individuals including a subset with genome-wide genotyping and exome sequencing. In this case-control study, we included AF cases and controls of genetically determined white-European ancestry; analyses were performed using a logistic mixed-effects model adjusting for age, sex, the first 4 principal components of ancestry, empirical relationships, and case-control imbalance. An exome-wide, gene-based burden analysis was performed to examine the relationship between AF and rare, high-confidence LOF variants in genes with ≥10 LOF carriers. A polygenic risk score for AF was estimated using the LDpred algorithm. We then compared the contribution of AF polygenic risk score and LOF variants to AF risk. Results: The study included 1546 AF cases and 41 593 controls. In an analysis of 9099 genes with sufficient LOF variant carriers, a significant association between AF and rare LOF variants was observed in a single gene, TTN (odds ratio, 2.71, P =2.50×10 −8 ). The association with AF was more significant (odds ratio, 6.15, P =3.26×10 −14 ) when restricting to LOF variants located in exons highly expressed in cardiac tissue ( TTN LOF ). Overall, 0.44% of individuals carried TTN LOF variants, of whom 14% had AF. Among individuals in the highest 0.44% of the AF polygenic risk score only 9.3% had AF. In contrast, the AF polygenic risk score explained 4.7% of the variance in AF susceptibility, while TTN LOF variants only accounted for 0.2%. Conclusions: Both monogenic and polygenic factors contribute to AF risk in the general population. While rare TTN LOF variants confer a substantial AF penetrance, the additive effect of many common variants explains a larger proportion of genetic susceptibility to AF.
Published: 2020

6. Genetic Determinants of Electrocardiographic P-Wave Duration and Relation to Atrial Fibrillation

Author: Michiel L. Bots, Annette Peters, Jennifer A. Brody, Pim van der Harst, Niek Verweij, Torben Hansen, Lu-Chen Weng, Marco V Perez, Honghuang Lin, Nona Sotoodehnia, Katharina Schramm, Dennis O. Mook-Kanamori, Marcus Dörr, Susan R. Heckbert, Henry J. Lin, Jie Yao, Paul L. Huang, Melanie Waldenberger, Bruno H. Stricker, Cornelia M. van Duijn, Jelena Kornej, Kent D. Taylor, Stephan B. Felix, Julia Ramirez, Xiuqing Guo, Peter van der Meer, Patrick T. Ellinor, Emelia J. Benjamin, Amelia W. Hall, Martina Müller-Nurasyid, Steven A. Lubitz, Alexander Teumer, Ilonca Vaartjes, Niels Grarup, Kathryn L. Lunetta, Marten E. van den Berg, Aaron Isaacs, Uwe Völker, Bruce M. Psaty, Jan A. Kors, Alvaro Alonso, Seung Hoan Choi, Rudolf A. de Boer, Allan Linneberg, Sandosh Padmanabhan, Helen R. Warren, Jerome I. Rotter, Nathan A. Bihlmeyer, Man Li, Jeffrey Haessler, Charles Kooperberg, Moritz F. Sinner, Sean J. Jurgens, Folkert W. Asselbergs, Dan E. Arking, Ruifang Li-Gao, Jessica van Setten, Patricia B. Munroe, Jørgen K. Kanters, Stefan Kääb, Fysiologie, RS: FHML MaCSBio, RS: Carim - B01 Blood proteins & engineering, Erasmus MC other, Medical Informatics, Internal Medicine, Epidemiology, and Cardiology
Subjects: 0301 basic medicine, PROTEIN, population, 030204 cardiovascular system & hematology, Cardiovascular, Electrocardiography, 0302 clinical medicine, MYH6, Atrial Fibrillation, 2.1 Biological and endogenous factors, Connectin, atrial fibrillation, Aetiology, Exome, MYOSIN HEAVY-CHAIN, RISK, education.field_of_study, NAV1.8 Voltage-Gated Sodium Channel/genetics, Connectin/genetics, Atrial fibrillation, General Medicine, ASSOCIATION, Heart Disease, Duration (music), Cardiology, EXPRESSION, medicine.medical_specialty, HMGA2, Population, INDEXES, Quantitative Trait Loci, Transcription Factors/genetics, Electrophysiology, Genetic, Genome-wide Association Studies, Article, NAV1.8 Voltage-Gated Sodium Channel, 03 medical and health sciences, Myosin Heavy Chains/genetics, Clinical Research, Internal medicine, Cardiac conduction, Cardiac Myosins/genetics, P wave duration, medicine, Genetics, Humans, education, RECURRENCE, Homeodomain Proteins, Myosin Heavy Chains, business.industry, Human Genome, Genetic Variation, medicine.disease, electrophysiology, Atrial Fibrillation/ethnology, 030104 developmental biology, genome-wide association studies, Homeodomain Proteins/genetics, genetic, business, Cardiac Myosins, exome, Transcription Factors, Genome-Wide Association Study
Abstract: Background: The P-wave duration (PWD) is an electrocardiographic measurement that represents cardiac conduction in the atria. Shortened or prolonged PWD is associated with atrial fibrillation (AF). We used exome-chip data to examine the associations between common and rare variants with PWD. Methods: Fifteen studies comprising 64 440 individuals (56 943 European, 5681 African, 1186 Hispanic, 630 Asian) and ≈230 000 variants were used to examine associations with maximum PWD across the 12-lead ECG. Meta-analyses summarized association results for common variants; gene-based burden and sequence kernel association tests examined low-frequency variant-PWD associations. Additionally, we examined the associations between PWD loci and AF using previous AF genome-wide association studies. Results: We identified 21 common and low-frequency genetic loci (14 novel) associated with maximum PWD, including several AF loci ( TTN , CAND2 , SCN10A , PITX2 , CAV1 , SYNPO2L , SOX5 , TBX5, MYH6, RPL3L ). The top variants at known sarcomere genes ( TTN, MYH6 ) were associated with longer PWD and increased AF risk. However, top variants at other loci (eg, PITX2 and SCN10A ) were associated with longer PWD but lower AF risk. Conclusions: Our results highlight multiple novel genetic loci associated with PWD, and underscore the shared mechanisms of atrial conduction and AF. Prolonged PWD may be an endophenotype for several different genetic mechanisms of AF.
Published: 2020

7. Whole Genome Sequencing Identifies CRISPLD2 as a Lung Function Gene in Children With Asthma

Author: Priyadarshini Kachroo, Julian Hecker, Bo L. Chawes, Tarunveer S. Ahluwalia, Michael H. Cho, Dandi Qiao, Rachel S. Kelly, Su H. Chu, Yamini V. Virkud, Mengna Huang, Kathleen C. Barnes, Esteban G. Burchard, Celeste Eng, Donglei Hu, Juan C. Celedón, Michelle Daya, Albert M. Levin, Hongsheng Gui, L. Keoki Williams, Erick Forno, Angel C.Y. Mak, Lydiana Avila, Manuel E. Soto-Quiros, Michelle M. Cloutier, Edna Acosta-Pérez, Glorisa Canino, Klaus Bønnelykke, Hans Bisgaard, Benjamin A. Raby, Christoph Lange, Scott T. Weiss, Jessica A. Lasky-Su, Namiko Abe, Goncalo Abecasis, Christine Albert, Nicholette (Nichole) Palmer Allred, Laura Almasy, Alvaro Alonso, Seth Ament, Peter Anderson, Pramod Anugu, Deborah Applebaum-Bowden, Dan Arking, Donna K. Arnett, Allison Ashley-Koch, Stella Aslibekyan, Tim Assimes, Paul Auer, Dimitrios Avramopoulos, John Barnard, Kathleen Barnes, R. Graham Barr, Emily Barron-Casella, Terri Beaty, Diane Becker, Lewis Becker, Rebecca Beer, Ferdouse Begum, Amber Beitelshees, Emelia Benjamin, Marcos Bezerra, Larry Bielak, Joshua Bis, Thomas Blackwell, John Blangero, Eric Boerwinkle, Ingrid Borecki, Russell Bowler, Jennifer Brody, Ulrich Broeckel, Jai Broome, Karen Bunting, Esteban Burchard, Jonathan Cardwell, Cara Carty, Richard Casaburi, James Casella, Mark Chaffin, Christy Chang, Daniel Chasman, Sameer Chavan, Bo-Juen Chen, Wei-Min Chen, Yii-Der Ida Chen, Seung Hoan Choi, Lee-Ming Chuang, Mina Chung, Elaine Cornell, Adolfo Correa, Carolyn Crandall, James Crapo, L. Adrienne Cupples, Joanne Curran, Jeffrey Curtis, Brian Custer, Coleen Damcott, Dawood Darbar, Sayantan Das, Sean David, Colleen Davis, Mariza de Andrade, Michael DeBaun, Ranjan Deka, Dawn DeMeo, Scott Devine, Ron Do, Qing Duan, Ravi Duggirala, Peter Durda, Susan Dutcher, Charles Eaton, Lynette Ekunwe, Patrick Ellinor, Leslie Emery, Charles Farber, Leanna Farnam, Tasha Fingerlin, Matthew Flickinger, Myriam Fornage, Nora Franceschini, Mao Fu, Stephanie M. Fullerton, Lucinda Fulton, Stacey Gabriel, Weiniu Gan, Yan Gao, Margery Gass, Bruce Gelb, Xiaoqi (Priscilla) Geng, Soren Germer, Chris Gignoux, Mark Gladwin, David Glahn, Stephanie Gogarten, Da-Wei Gong, Harald Goring, C. Charles Gu, Yue Guan, Xiuqing Guo, Jeff Haessler, Michael Hall, Daniel Harris, Nicola Hawley, Jiang He, Ben Heavner, Susan Heckbert, Ryan Hernandez, David Herrington, Craig Hersh, Bertha Hidalgo, James Hixson, John Hokanson, Kramer Holly, Elliott Hong, Karin Hoth, Chao (Agnes) Hsiung, Haley Huston, Chii Min Hwu, Marguerite Ryan Irvin, Rebecca Jackson, Deepti Jain, Cashell Jaquish, Min A. Jhun, Jill Johnsen, Andrew Johnson, Craig Johnson, Rich Johnston, Kimberly Jones, Hyun Min Kang, Robert Kaplan, Sharon Kardia, Sekar Kathiresan, Laura Kaufman, Shannon Kelly, Eimear Kenny, Michael Kessler, Alyna Khan, Greg Kinney, Barbara Konkle, Charles Kooperberg, Stephanie Krauter, Ethan Lange, Leslie Lange, Cathy Laurie, Cecelia Laurie, Meryl LeBoff, Seunggeun Shawn Lee, Wen-Jane Lee, Jonathon LeFaive, David Levine, Dan Levy, Joshua Lewis, Yun Li, Honghuang Lin, Keng Han Lin, Simin Liu, Yongmei Liu, Ruth Loos, Steven Lubitz, Kathryn Lunetta, James Luo, Michael Mahaney, Barry Make, Ani Manichaikul, JoAnn Manson, Lauren Margolin, Lisa Martin, Susan Mathai, Rasika Mathias, Patrick McArdle, Merry-Lynn McDonald, Sean McFarland, Stephen McGarvey, Hao Mei, Deborah A. Meyers, Julie Mikulla, Nancy Min, Mollie Minear, Ryan L. Minster, Braxton Mitchell, May E. Montasser, Solomon Musani, Stanford Mwasongwe, Josyf C. Mychaleckyj, Girish Nadkarni, Rakhi Naik, Pradeep Natarajan, Sergei Nekhai, Deborah Nickerson, Kari North, Jeff O'Connell, Tim O'Connor, Heather Ochs-Balcom, James Pankow, George Papanicolaou, Margaret Parker, Afshin Parsa, Sara Penchev, Juan Manuel Peralta, Marco Perez, James Perry, Ulrike Peters, Patricia Peyser, Lawrence S. Phillips, Sam Phillips, Toni Pollin, Wendy Post, Julia Powers Becker, Meher Preethi Boorgula, Michael Preuss, Dmitry Prokopenko, Bruce Psaty, Pankaj Qasba, Zhaohui Qin, Nicholas Rafaels, Laura Raffield, Vasan Ramachandran, D.C. Rao, Laura Rasmussen-Torvik, Aakrosh Ratan, Susan Redline, Robert Reed, Elizabeth Regan, Alex Reiner, Ken Rice, Stephen Rich, Dan Roden, Carolina Roselli, Jerome Rotter, Ingo Ruczinski, Pamela Russell, Sarah Ruuska, Kathleen Ryan, Phuwanat Sakornsakolpat, Shabnam Salimi, Steven Salzberg, Kevin Sandow, Vijay Sankaran, Christopher Scheller, Ellen Schmidt, Karen Schwander, David Schwartz, Frank Sciurba, Christine Seidman, Jonathan Seidman, Vivien Sheehan, Amol Shetty, Aniket Shetty, Wayne Hui-Heng Sheu, M. Benjamin Shoemaker, Brian Silver, Edwin Silverman, Jennifer Smith, Josh Smith, Nicholas Smith, Tanja Smith, Sylvia Smoller, Beverly Snively, Tamar Sofer, Nona Sotoodehnia, Adrienne Stilp, Elizabeth Streeten, Yun Ju Sung, Jessica Su-Lasky, Jody Sylvia, Adam Szpiro, Carole Sztalryd, Daniel Taliun, Hua Tang, Margaret Taub, Kent Taylor, Simeon Taylor, Marilyn Telen, Timothy A. Thornton, Lesley Tinker, David Tirschwell, Hemant Tiwari, Russell Tracy, Michael Tsai, Dhananjay Vaidya, Peter VandeHaar, Scott Vrieze, Tarik Walker, Robert Wallace, Avram Walts, Emily Wan, Fei Fei Wang, Karol Watson, Daniel E. Weeks, Bruce Weir, Scott Weiss, Lu-Chen Weng, Cristen Willer, Kayleen Williams, Carla Wilson, James Wilson, Quenna Wong, Huichun Xu, Lisa Yanek, Ivana Yang, Rongze Yang, Norann Zaghloul, Maryam Zekavat, Yingze Zhang, Snow Xueyan Zhao, Wei Zhao, Xiuwen Zheng, Degui Zhi, Xiang Zhou, Michael Zody, and Sebastian Zoellner
Subjects: Adult, Costa Rica, Male, Pulmonary and Respiratory Medicine, Adolescent, Vital Capacity, Single-nucleotide polymorphism, Pedigree chart, Critical Care and Intensive Care Medicine, Young Adult, 03 medical and health sciences, FEV1/FVC ratio, 0302 clinical medicine, Polymorphism (computer science), Forced Expiratory Volume, Humans, Medicine, SNP, 030212 general & internal medicine, Child, Asthma, Whole Genome Sequencing, business.industry, Middle Aged, respiratory system, medicine.disease, respiratory tract diseases, Minor allele frequency, 030228 respiratory system, Genetic epidemiology, Child, Preschool, Interferon Regulatory Factors, Immunology, Respiratory Physiological Phenomena, Female, Cardiology and Cardiovascular Medicine, business, Cell Adhesion Molecules
Abstract: BACKGROUND: Asthma is a common respiratory disorder with a highly heterogeneous nature that remains poorly understood. The objective was to use whole genome sequencing (WGS) data to identify regions of common genetic variation contributing to lung function in individuals with a diagnosis of asthma. METHODS: WGS data were generated for 1,053 individuals from trios and extended pedigrees participating in the family-based Genetic Epidemiology of Asthma in Costa Rica study. Asthma affection status was defined through a physician’s diagnosis of asthma, and most participants with asthma also had airway hyperresponsiveness (AHR) to methacholine. Family-based association tests for single variants were performed to assess the associations with lung function phenotypes. RESULTS: A genome-wide significant association was identified between baseline FEV(1)/FVC ratio and a single-nucleotide polymorphism in the top hit cysteine-rich secretory protein LCCL domain-containing 2 (CRISPLD2) (rs12051168; P = 3.6 × 10(−8) in the unadjusted model) that retained suggestive significance in the covariate-adjusted model (P = 5.6 × 10(−6)). Rs12051168 was also nominally associated with other related phenotypes: baseline FEV(1) (P = 3.3 × 10(−3)), postbronchodilator (PB) FEV(1) (7.3 × 10(−3)), and PB FEV(1)/FVC ratio (P = 2.7 × 10(−3)). The identified baseline FEV(1)/FVC ratio and rs12051168 association was meta-analyzed and replicated in three independent cohorts in which most participants with asthma also had confirmed AHR (combined weighted z-score P = .015) but not in cohorts without information about AHR. CONCLUSIONS: These findings suggest that using specific asthma characteristics, such as AHR, can help identify more genetically homogeneous asthma subgroups with genotype-phenotype associations that may not be observed in all children with asthma. CRISPLD2 also may be important for baseline lung function in individuals with asthma who also may have AHR.
Published: 2019

8. Genetics of Myocardial Interstitial Fibrosis in the Human Heart and Association with Disease

Author: Carolina Roselli, S. A. Lubitz, James P. Pirruccello, Seung Hoan Choi, Shaan Khurshid, Valerie N. Morrill, Patrick T. Ellinor, Samuel Friedman, Paolo Di Achille, Puneet Batra, Marcus D. R. Klarqvist, J. W. Cunningham, Kenney Ng, Lu-Chen Weng, Victor Nauffal, Anthony A. Philippakis, and M. Nekoui
Subjects: medicine.medical_specialty, business.industry, Cardiomyopathy, Atrial fibrillation, Systemic inflammation, medicine.disease, Sudden cardiac death, medicine.anatomical_structure, Heart failure, Internal medicine, medicine, Cardiology, Glucose homeostasis, Myocardial fibrosis, Interventricular septum, medicine.symptom, business
Abstract: Myocardial interstitial fibrosis is a common thread in multiple cardiovascular diseases including heart failure, atrial fibrillation, conduction disease and sudden cardiac death. To investigate the biologic pathways that underlie interstitial fibrosis in the human heart, we developed a machine learning model to measure myocardial T1 time, a marker of myocardial interstitial fibrosis, in 42,654 UK Biobank participants. Greater T1 time was associated with impaired glucose metabolism, systemic inflammation, renal disease, aortic stenosis, cardiomyopathy, heart failure, atrial fibrillation and conduction disease. In genome-wide association analysis, we identified 12 independent loci associated with native myocardial T1 time with evidence of high genetic correlation between the interventricular septum and left ventricle free wall (r2g = 0.82). The identified loci implicated genes involved in glucose homeostasis (SLC2A12), iron homeostasis (HFE, TMPRSS6), tissue repair (ADAMTSL1, VEGFC), oxidative stress (SOD2), cardiac hypertrophy (MYH7B) and calcium signaling (CAMK2D). Transcriptome-wide association studies highlighted the role of expression of ADAMTSL1 and SLC2A12 in human cardiac tissue in modulating myocardial tissue characteristics and interstitial fibrosis. Harnessing machine learning to perform large-scale phenotyping of interstitial fibrosis in the human heart, our results yield novel insights into biologically relevant pathways for myocardial fibrosis and prioritize investigation of pathways for the development of anti-fibrotic therapies.
Published: 2021

9. Using Machine Learning to Elucidate the Spatial and Genetic Complexity of the Ascending Aorta

Author: Joyce C. Ho, Victor Nauffal, Puneet Batra, Samuel Friedman, Kenney Ng, S. A. Lubitz, Patrick T. Ellinor, Seung Hoan Choi, Mark E. Lindsay, Anthony A. Philippakis, Paolo Di Achille, Mahan Nekoui, and James P. Pirruccello
Subjects: Genetic complexity, Prioritization, medicine.medical_specialty, Aorta, business.industry, Sinotubular Junction, medicine.disease, Thoracic aortic aneurysm, Stenosis, Internal medicine, medicine.artery, Ascending aorta, cardiovascular system, medicine, Cardiology, Ventricular outflow tract, business
Abstract: BackgroundThe left ventricular outflow tract (LVOT) and ascending aorta are spatially complex, with distinct pathologies and embryologic origins. Prior work examined genetics of thoracic aortic diameter in a single plane. We sought to elucidate the genetic basis for the diameter of the LVOT, the aortic root, and the ascending aorta.MethodsWe used deep learning to analyze 2.3 million cardiac magnetic resonance images from 43,317 UK Biobank participants. We computed the diameters of the LVOT, the aortic root, and at six locations in the ascending aorta. For each diameter, we conducted a genome-wide association study and generated a polygenic score. Finally, we investigated associations between these polygenic scores and disease incidence.Results79 loci were significantly associated with at least one diameter. Of these, 35 were novel, and a majority were associated with one or two diameters. A polygenic score of aortic diameter approximately 13mm from the sinotubular junction most strongly predicted thoracic aortic aneurysm in UK Biobank participants (n=427,016; HR=1.42 per standard deviation; CI=1.34-1.50, P=6.67×10−21). A polygenic score predicting a smaller aortic root was predictive of aortic stenosis (n=426,502; HR=1.08 per standard deviation; CI=1.03-1.12, P=5×10−6).ConclusionsWe detected distinct common genetic loci underpinning the diameters of the LVOT, the aortic root, and at several segments in the ascending aorta. We spatially defined a region of aorta whose genetics may be most relevant to predicting thoracic aortic aneurysm. We further described a genetic signature that may predispose to aortic stenosis. Understanding the genetic contributions to the diameter of the proximal aorta may enable identification of individuals at risk for life-threatening aortic disease and facilitate prioritization of therapeutic targets.
Published: 2021

10. The Genetic Determinants of Aortic Distension

Author: Seung Hoan Choi, Mahan Nekoui, Dejan Juric, Samuel Friedman, James P. Pirruccello, Anthony A. Philippakis, Sean J. Jurgens, Mark E. Lindsay, James R. Stone, Mark Chaffin, Patrick T. Ellinor, Puneet Batra, Kenney Ng, and Elizabeth L. Chou
Subjects: medicine.medical_specialty, Aorta, Cardiac cycle, medicine.diagnostic_test, Vascular disease, business.industry, Diastole, Genome-wide association study, Distension, medicine.disease, Cardiac magnetic resonance imaging, Internal medicine, medicine.artery, cardiovascular system, medicine, Cardiology, Systole, business
Abstract: As the largest conduit vessel, the aorta is responsible for the conversion of phasic systolic inflow from ventricular ejection into more continuous blood delivery to peripheral arteries. Distension during systole and recoil during diastole conserves ventricular energy and is enabled by the specialized composition of the aortic extracellular matrix. Aortic distensibility decreases with age and prematurely in vascular disease. To discover genetic determinants of aortic distensibility we trained a deep learning model to quantify aortic size throughout the cardiac cycle and calculate aortic distensibility and aortic strain in 42,342 participants in the UK Biobank with available cardiac magnetic resonance imaging. In up to 40,028 participants with genetic data, common variant analysis identified 12 and 26 loci for ascending and 11 and 21 loci for descending aortic distensibility and strain, respectively. Of the newly identified loci, 22 were specific to strain or distensibility and were not identified in a thoracic aortic diameter GWAS within the same samples. Loci associated with both aortic diameter and aortic strain or distensibility demonstrated a consistent, inverse directionality. Transcriptome-wide analyses, rare-variant burden tests, and analyses of gene expression in single nucleus RNA sequencing of human aorta were performed to prioritize genes at individual loci. Loci highlighted multiple genes involved in elastogenesis, matrix degradation, and extracellular polysaccharide generation. Characterization of the genetic determinants of aortic function may provide novel targets for medical intervention in aortic disease.
Published: 2021

11. Endophenotype Effect Sizes Provide Evidence Supporting Variant Pathogenicity in Monogenic Disease Susceptibility Genes

Author: Christian T. Ruff, Heidi L. Rehm, Wendy S. Post, Charles Kooperberg, Nicholas A Marston, Eric Boerwinkle, Peter F. Schnatz, Susan R. Heckbert, Kenneth Rice, Christopher M. Haggerty, Ruth J. F. Loos, Jennifer L. Halford, James P. Pirruccello, Stephanie L. Harris, Braxton D. Mitchell, Christina Austin-Tse, Shaan Khurshid, Victor Nauffal, Namrata Gupta, Susan Redline, Amelia W. Hall, Brandon K. Fornwalt, Nona Sotoodehnia, Elsayed Z. Soliman, Adolfo Correa, Marc S. Sabatine, Alanna C. Morrison, Sean J. Jurgens, Charles C. Hong, Lu-Chen Weng, Stephen S. Rich, Bruce M. Psaty, Steven A. Lubitz, Sophia Gunn, Seung Hoan Choi, Kathryn L. Lunetta, Jennifer A. Brody, Valerie N. Morrill, Eugene K. Wong, Jerome I. Rotter, Patrick T. Ellinor, Emelia J. Benjamin, Henry J. Lin, and Giorgio E. M. Melloni
Subjects: Genetics, education.field_of_study, business.industry, Long QT syndrome, Population, Familial hypercholesterolemia, medicine.disease, Pathogenicity, QT interval, Monogenic disease, Endophenotype, Diabetes mellitus, medicine, education, business
Abstract: Accurate and efficient classification of variant pathogenicity is critical for research and clinical care. Using data from three large studies, we demonstrate that population-based associations between rare variants and quantitative endophenotypes for three monogenic diseases (low-density-lipoprotein cholesterol for familial hypercholesterolemia, electrocardiographic QTc interval for long QT syndrome, and glycosylated hemoglobin for maturity-onset diabetes of the young) are proxies for variant pathogenicity. Effect sizes were associated with pathogenic ClinVar assertions (P
Published: 2021

12. Inherited basis of visceral, abdominal subcutaneous and gluteofemoral fat depots

Author: Anthony A. Philippakis, Marcus D. R. Klarqvist, Joseph Shin, Seung Hoan Choi, Melina Claussnitzer, Amit Khera, Sean J. Jurgens, Kenney Ng, Puneet Batra, Patrick T. Ellinor, Hesam Dashti, Nathaniel Diamant, Minxian Wang, and Saaket Agrawal
Subjects: education.field_of_study, Population, Physiology, Heritability, Biology, medicine.disease, Familial partial lipodystrophy, LMNA, Insulin resistance, medicine, Trait, education, Body mass index, Metabolic profile
Abstract: For any given level of overall adiposity – as commonly quantified by body mass index (BMI) within clinical practice – individuals vary considerably in fat distribution. We and others have noted that increased visceral fat (VAT) is associated with increased cardiometabolic risk, while gluteofemoral fat (GFAT) may be protective. Familial partial lipodystrophy (FPLD) – often caused by rare variants in the LMNA gene – represents an extreme example of this paradigm, leading to a severe shift to visceral fat with subsequent insulin resistance and adverse metabolic profile. By contrast, the inherited basis of body fat distribution in the broader population is not fully understood. Here, we studied up to 38,965 UK Biobank participants with VAT, abdominal subcutaneous (ASAT), and GFAT volumes precisely quantified using abdominal MRI. Because genetic associations with these raw depot volumes were largely driven by variants known to affect BMI, we next studied six phenotypes of local adiposity: VAT adjusted for BMI (VATadjBMI), ASATadjBMI, GFATadjBMI, VAT/ASAT, VAT/GFAT, and ASAT/GFAT. We identify 178 unique loci associated with at least one adiposity trait, including 29 newly-identified loci. Rare variant association studies extend prior evidence of association for PDE3B as an important modulator of fat distribution. Sex-specific analyses of local adiposity traits noted overall higher estimated heritability in females, increased effect sizes for identified loci, and 25 female-specific associations. Individuals in the extreme tails of fat distribution phenotypes were highly enriched for predisposing common variants, as quantified using polygenic scores. Taking GFATadjBMI as an example, individuals with extreme values were 3.8-fold (95%CI 2.8 to 5.2) more likely to have a polygenic score within the top 5% of the distribution. These results – using more precise and BMI-independent measures of local adiposity – confirm fat distribution as a highly heritable trait with important implications for cardiometabolic health outcomes.
Published: 2021

13. Titin Truncating Variants in Adults Without Known Congestive Heart Failure

Author: Patrick T. Ellinor, Carolyn Y. Ho, Amit Khera, Kenney Ng, Mark Chaffin, Steven A. Lubitz, Anthony A. Philippakis, Krishna G. Aragam, Seung Hoan Choi, Sekar Kathiresan, James P. Pirruccello, and Alexander G. Bick
Subjects: Adult, Male, 030204 cardiovascular system & hematology, Bioinformatics, Article, DNA sequencing, 03 medical and health sciences, 0302 clinical medicine, medicine, Humans, Connectin, 030212 general & internal medicine, Gene, Aged, Heart Failure, biology, business.industry, Genetic Variation, Atrial fibrillation, Dilated cardiomyopathy, Middle Aged, medicine.disease, Heart failure, Asymptomatic Diseases, biology.protein, Female, Titin, Cardiology and Cardiovascular Medicine, business
Abstract: Truncating variants in the gene encoding titin (TTNtv) are the most commonly identified pathogenic variants in cross-sectional studies of patients with dilated cardiomyopathy or atrial fibrillation ([1][1],[2][2]). In principle, gene sequencing to identify individuals who harbor a TTNtv prior to
Published: 2020

14. Loss-of-function genomic variants highlight potential therapeutic targets for cardiovascular disease

Author: Whitney E. Hornsby, Patricia A. Peyser, Albert V. Smith, Anita Pandit, Allison E. Ashley-Koch, Brooke N. Wolford, Morten S. Olesen, Michael Boehnke, Steven A. Lubitz, Lars G. Fritsche, Charles Kooperberg, Wayne Huey-Herng Sheu, Rasika A. Mathias, Sarah E. Graham, Ketian Yu, Yii Der Chen, Scott T. Weiss, Juan M. Peralta, David Schlessinger, Austen Grooms, Seyed Mehdi Nouraie, Xingnan Li, Ying Zhao, Russell P. Tracy, Chad M. Brummett, Sachin Kheterpal, Kent D. Taylor, Jill M. Johnsen, Jerome I. Rotter, Kristian Hveem, Pia R. Lundegaard, Vivek Rai, Victor R. Gordeuk, Anne Heidi Skogholt, Stella Aslibekyan, Alexander P. Reiner, Sebastian Schoenherr, Adolfo Correa, Matthew Zawistowski, Lewis C. Becker, Lukas Forer, Michelle Daya, Jonathon LeFaive, Mari Løset, Ben Michael Brumpton, Bertha Hidalgo, Marguerite R. Irvin, Seunggeun Lee, Ren-Hua Chung, Maiken Elvestad Gabrielsen, Francesco Cucca, William Overton, Gregory J.M. Zajac, Luis Villacorta, Stephen S. Rich, Sayantan Das, Karen Schwander, Yingze Zhang, Thomas W. Blackwell, Ida Surakka, Pradeep Natarajan, Solomon K. Musani, Tanmoy Roychowdhury, Kathleen C. Barnes, Donna K. Arnett, Jonas B. Nielsen, Vivien A. Sheehan, Akua Acheampong, Oddgeir L. Holmen, He Zhang, Carlo Sidore, Lisa R. Yanek, Oren Rom, Jessica Lasky-Su, Nicholette D. Palmer, Seung Hoan Choi, Amanda Schaefer, Yuhao Liu, Sarah A Gagliano Taliun, John Blangero, Daniel Taliun, Y. Eugene Chen, Deborah A. Meyers, L. Adrienne Cupples, Courtney G. Montgomery, Sekar Kathiresan, James G. Wilson, Marilyn J. Telen, Ramachandran S. Vasan, Jin Chen, Nicholas Rafaels, Bjørn Olav Åsvold, Lawrence F. Bielak, Hyun Min Kang, Christian Fuchsberger, Barbara A. Konkle, Sebastian Zöllner, Wei Zhou, Rebecca D. Jackson, Patrick T. Ellinor, Gonçalo R. Abecasis, Jifeng Zhang, Eugene R. Bleecker, Xiuqing Guo, Jennifer A. Smith, Cristen J. Willer, and Joanne E. Curran
Subjects: 0301 basic medicine, LOCI, EXOME, General Physics and Astronomy, Genome-wide association study, Disease, 030204 cardiovascular system & hematology, Bioinformatics, Genome-wide association studies, chemistry.chemical_compound, THALASSEMIA, 0302 clinical medicine, Loss of Function Mutation, WIDE ASSOCIATION, Medicine, Molecular Targeted Therapy, Phenomics, Biological Specimen Banks, Multidisciplinary, Fatty liver, Lipids, Cardiovascular diseases, Liver, Gene Targeting, Science, METABOLISM, Article, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Humans, Gene Silencing, Adverse effect, Genome, Human, business.industry, Cholesterol, PATHWAYS, General Chemistry, medicine.disease, United Kingdom, Computational biology and bioinformatics, MODEL, 030104 developmental biology, Receptors, LDL, chemistry, LDL receptor, Liver function, business, Dyslipidemia, GENERATION, Genome-Wide Association Study
Abstract: Pharmaceutical drugs targeting dyslipidemia and cardiovascular disease (CVD) may increase the risk of fatty liver disease and other metabolic disorders. To identify potential novel CVD drug targets without these adverse effects, we perform genome-wide analyses of participants in the HUNT Study in Norway (n = 69,479) to search for protein-altering variants with beneficial impact on quantitative blood traits related to cardiovascular disease, but without detrimental impact on liver function. We identify 76 (11 previously unreported) presumed causal protein-altering variants associated with one or more CVD- or liver-related blood traits. Nine of the variants are predicted to result in loss-of-function of the protein. This includes ZNF529:p.K405X, which is associated with decreased low-density-lipoprotein (LDL) cholesterol (P = 1.3 × 10−8) without being associated with liver enzymes or non-fasting blood glucose. Silencing of ZNF529 in human hepatoma cells results in upregulation of LDL receptor and increased LDL uptake in the cells. This suggests that inhibition of ZNF529 or its gene product should be prioritized as a novel candidate drug target for treating dyslipidemia and associated CVD., Drugs targeting cardiovascular disease (CVD) can have negative consequences for liver function. Here, the authors combine genome wide analyses on 69,479 individuals to identify loss-of-function variants with beneficial effects on CVD-related traits without negative impacts on liver function.
Published: 2020

15. B-YIA1-02 MONOGENIC AND POLYGENIC CONTRIBUTIONS TO QTC PROLONGATION IN THE POPULATION

Author: Charles Kooperberg, Adolfo Correa, Christina Austin-Tse, Seung Hoan Choi, Victor Nauffal, Elsayed Z. Soliman, Lu-Chen Weng, Emelia J. Benjamin, Ruth J. F. Loos, Nona Sotoodehnia, Brandon K. Fornwalt, Patrick T. Ellinor, Eric Boerwinkle, Wendy S. Post, Bruce M. Psaty, Christopher M. Haggerty, Steven A. Lubitz, Henry Lin, Susan Redline, Amelia W. Hall, Jerome I. Rotter, Valerie N. Morrill, Susan R. Heckbert, Braxton D. Mitchell, Sean S. Jurgens, Alanna C. Morrison, Kathryn L. Lunetta, Heidi L. Rehm, and Jenifer Halford
Subjects: QTC PROLONGATION, medicine.medical_specialty, education.field_of_study, business.industry, Physiology (medical), Internal medicine, Population, Cardiology, Medicine, Cardiology and Cardiovascular Medicine, business, education
Published: 2021

16. Abstract 15005: Associations Between Alcohol Intake and Genetic Predisposition With Atrial Fibrillation Risk in a National Biobank

Author: Shaan Khurshid, Ludovic Trinquart, Sean J. Jurgens, Emelia J. Benjamin, Seung Hoan Choi, Patrick T. Ellinor, Lu-Chen Weng, Jennifer L. Halford, Steven A. Lubitz, and Valerie N. Morrill
Subjects: medicine.medical_specialty, business.industry, Physiology (medical), Internal medicine, Genetic predisposition, Medicine, Alcohol intake, Atrial fibrillation, Cardiology and Cardiovascular Medicine, business, medicine.disease, Biobank
Abstract: Introduction: Excess alcohol intake and inherited predisposition may increase risk of atrial fibrillation (AF). We sought to characterize the association between alcohol intake and incident AF and determine whether the effect of alcohol is modified by inherited predisposition to AF. Methods: We analyzed UK Biobank participants without prevalent AF and with complete alcohol consumption, genomic, and clinical data collected between 2006-2010. Exposures included alcohol consumption (stratified by an acceptable range of ≤98 grams/week for women or ≤196 grams/week for men and analyzed as a continuous variable) and an AF polygenic risk score (PRS). Cox proportional hazard models were adjusted for established AF risk factors. The cumulative incidence of AF was assessed at 5 years. Results: Among 376,776 participants (47.5% male, mean age 56.9 years), 6,293 developed AF during a median of 6.9 years of follow-up. Alcohol consumption was associated with AF (hazard ratio [HR] 1.10; 95% CI 1.05-1.16 for intake above an acceptable range; HR 1.04 per 100 grams/week; 95% CI 1.02-1.06). An AF PRS was associated with AF (HR 1.38 per standard deviation [SD]; 95% CI 1.35-1.41). In models including both alcohol intake and the AF PRS, each remained associated with AF. The 5-year cumulative incidence of AF for individuals with alcohol intake above an acceptable range and in the highest decile of polygenic risk was 2.33% (95% CI 2.07-2.59), compared to 0.69% (95% CI 0.58-0.80) for those with alcohol intake within acceptable range and in the lowest decile of polygenic risk. Conclusions: Alcohol consumption is associated with risk of incident AF across a range of polygenic predisposition to AF. Preventive counseling regarding alcohol intake may reduce the risk of AF regardless of the degree of risk conferred by inherited predisposition.
Published: 2020

17. Abstract 13588: Cardiovascular Outcomes in Patients With Established Atherosclerosis and LDLR Loss of Function: Results From the FOURIER Trial

Author: Nicholas A Marston, Seung Hoan Choi, Marc S. Sabatine, Anthony C Keech, Christian T. Ruff, Huei Wang, Patrick T. Ellinor, Frederick K. Kamanu, Robert P. Giugliano, Giorgio E. M. Melloni, Steven A. Lubitz, James P. Pirruccello, Peter S. Sever, Armando Lira Pineda, and Anthony A. Philippakis
Subjects: Ldl receptor gene, business.industry, Gene mutation, medicine.disease, Bioinformatics, Physiology (medical), LDL receptor, Hyperlipidemia, medicine, In patient, Cardiology and Cardiovascular Medicine, business, Cardiovascular outcomes, Loss function
Abstract: Introduction: Patients with loss of function (LoF) mutations of the LDL receptor gene (LDLR) have lifelong elevations in LDL-C. We investigated their risk of cardiovascular (CV) events compared with patients with intact LDLR function. Methods: We performed a prospective genetic cohort analysis from the FOURIER trial including all 14,297 patients who consented for genetic testing, passed QC, and were of European ancestry. All patients had established ASCVD and were on moderate or high intensity statin therapy. Whole exome sequencing was performed and LoF mutations in LDLR were identified using LOFTEE, a tool for detecting protein-truncating variants. Polygenic risk for CAD was also calculated for each patient using a previously validated 27-SNP genetic risk score, with high and low risk defined as above and below the median. The primary endpoint was a composite of CV death, myocardial infarction, stroke, unstable angina, or coronary revascularization. Results: There were 111 (0.8%) patients identified with an LDLR LoF mutation, representing an approximately 4-fold enrichment compared to the general population. These patients had mean baseline LDL-C levels 62 mg/dl higher than those without an identified LDLR LoF mutation (160 vs. 98 mg/dl, pFigure, a ). When polygenic risk for CAD was combined with LDLR mutation status there was a significant gradient of risk identified (p-trend=0.001). Patients without a monogenic LDLR mutation or high polygenic risk had a 2.5-year KM event rate of 8.6%; those with either one had a 10.0-12.9% event rate; those with both had a 17.1% event rate ( Figure, b ). Conclusion: ASCVD patients with LDLR LoF mutations have persistently elevated LDL-C and increased CV risk despite intensive statin therapy. The combination of a monogenic LDLR mutation with high polygenic risk for CAD appears additive in this secondary prevention cohort.
Published: 2020

18. Rare Non-coding Variation Identified by Large Scale Whole Genome Sequencing Reveals Unexplained Heritability of Type 2 Diabetes

Author: Heming Wang, Lu-Chen Weng, Ryan W. Kim, May E. Montasser, Stephen T. McGarvey, Anubha Mahajan, Robert Sladek, Marcio Almeida, Dan M. Roden, Deepti Jain, Barry I. Freedman, Jeffrey R. O'Connell, Donna K. Arnett, Alanna C. Morrison, Susan R. Heckbert, Nicholette D. Palmer, Jie Yao, Jorge Ferrer, Timothy D. Majarian, Wei Zhao, JoAnn E. Manson, Mark I. McCarthy, Sharon L.R. Kardia, James A. Perry, Nicholas L. Smith, Alain G. Bertoni, James G. Wilson, Mark O. Goodarzi, Leslie A. Lange, Donald W. Bowden, L. Adrienne Cupples, Laura J. Rasmussen-Torvik, Yii-Der Ida Chen, Jennifer A. Smith, James S. Floyd, Sílvia Bonàs-Guarch, Zachary T. Yoneda, Rita R. Kalyani, Won Jung Choi, Ramachandran S. Vasan, Eric Boerwinkle, Ching-Ti Liu, Stephen C. J. Parker, Susan Redline, Paul S. de Vries, Huichun Xu, Daniel DiCorpo, Adolfo Correa, James S. Pankow, Stephen S. Rich, Heather M. Highland, Ravindranath Duggirala, Elizabeth Selvin, Kent D. Taylor, Dawood Darbar, Tanika N. Kelly, Bruce M. Psaty, Simin Liu, Xianyong Yin, Michael H. Cho, Abigail S. Baldridge, Alexander P. Reiner, Patricia A. Peyser, Seung Hoan Choi, Brian E. Cade, Chloé Sarnowski, Aladdin H. Shadyab, Gregory L Kinney, Daniel E. Weeks, Braxton D. Mitchell, Alisa K. Manning, Douglas Loesch, Steven A. Lubitz, Josée Dupuis, Ryan Irvin, Samantha Lent, Sridharan Raghavan, Bertha Hidalgo, Arushi Varshney, Ricardo D’Oliveira Albanus, Xiuqing Guo, Jennifer Wessel, Rasika A. Mathias, Jennifer A. Brody, Aaron Leong, John Blangero, James B. Meigs, Chung-Shiuan Chen, Lawrence F. Bielak, Lisa R. Yanek, Stella Aslibekyan, Rami Nassir, Karine A. Viaud-Martinez, Natalie R Hasbani, Irene Miguel-Escalada, Alvaro Alonso, Charles Kooperberg, Juan M. Peralta, Jose C. Florez, M. Benjamin Shoemaker, Seonwook Lee, Peitao Wu, Jerome I. Rotter, Jiang He, Patrick T. Ellinor, Mindy D. Szeto, and Joanne E. Curran
Subjects: Whole genome sequencing, Genetics, Minor allele frequency, medicine, Type 2 diabetes, Biology, Heritability, medicine.disease, Scale (music)
Abstract: Type 2 diabetes is increasing in all ancestry groups1. Part of its genetic basis may reside among the rare (minor allele frequency 2. We analyzed high-coverage (mean depth 38.2x) whole genome sequencing from 9,639 individuals with T2D and 34,994 controls in the NHLBI’s Trans-Omics for Precision Medicine (TOPMed) program2 to show that rare, non-coding variants that are poorly captured by genotyping arrays or imputation panels contribute h2=53% (P=4.2×10−5) to the genetic component of risk in the largest (European) ancestry subset. We coupled sequence variation with islet epigenomic signatures3 to annotate and group rare variants with respect to gene expression4, chromatin state5 and three-dimensional chromatin architecture6, and show that pancreatic islet regulatory elements contribute to T2D genetic risk (h2=8%, P=2.4×10−3). We used islet annotation to create a non-coding framework for rare variant aggregation testing. This approach identified five loci containing rare alleles in islet regulatory elements that suggest novel biological mechanisms readily linked to hypotheses about variant-to-function. Large scale whole genome sequence analysis reveals the substantial contribution of rare, non-coding variation to the genetic architecture of T2D and highlights the value of tissue-specific regulatory annotation for variant-to-function discovery.
Published: 2020

19. Associations Between Alcohol Intake and Genetic Predisposition With Atrial Fibrillation Risk in a National Biobank

Author: Jennifer L. Halford, Seung Hoan Choi, Valerie N. Morrill, Lu-Chen Weng, Shaan Khurshid, Steven A. Lubitz, Patrick T. Ellinor, Emelia J. Benjamin, Sean J. Jurgens, and Ludovic Trinquart
Subjects: Male, medicine.medical_specialty, Alcohol Drinking, 030204 cardiovascular system & hematology, Article, Inherited Predisposition, 03 medical and health sciences, 0302 clinical medicine, Risk Factors, Primary prevention, Internal medicine, Atrial Fibrillation, Genetic predisposition, Medicine, Humans, Genetic Predisposition to Disease, 030212 general & internal medicine, Risk factor, Gene–environment interaction, Genetic Association Studies, Biological Specimen Banks, business.industry, Incidence, Atrial fibrillation, General Medicine, Middle Aged, medicine.disease, Biobank, Alcohol intake, Female, business
Abstract: Background: Excess alcohol intake and inherited predisposition may increase risk of atrial fibrillation (AF). We assessed the association between alcohol intake, polygenic predisposition to AF, and incident AF in the UK Biobank, a prospective cohort study. Methods: In 376 776 UK Biobank participants enrolled between 2006 and 2010, we tested alcohol consumption (stratified by the Centers of Disease Control and Prevention acceptable range of ≤98 g/wk for women or ≤196 g/wk for men; and as a continuous variable) and an AF polygenic risk score for association with incident AF. Results: Among participants (47.5% male, mean age 56.9 years), 6293 developed AF during a median of 6.9 years of follow-up. Alcohol consumption was associated with AF (hazard ratio, 1.10 [95% CI, 1.05–1.16] for intake above an acceptable range; hazard ratio, 1.04 per 100 g/wk [95% CI, 1.02–1.06]). An AF polygenic risk score was associated with AF (hazard ratio, 1.38 per SD [95% CI, 1.35–1.41]). In models including both alcohol and the AF polygenic risk score, each remained associated with AF. The 5-year cumulative risk of AF for individuals with alcohol intake above an acceptable range and in the highest decile of polygenic risk was 2.33% (95% CI, 2.07–2.59), compared with 0.69% (95% CI, 0.58–0.80) for those with alcohol intake within an acceptable range and in the lowest decile of polygenic risk. Conclusions: Alcohol consumption is associated with increased risk of AF across a range of polygenic predisposition to AF and adds to inherited and clinical predisposition to increase AF susceptibility. Preventive efforts focused on minimizing alcohol intake may be broadly applicable.
Published: 2020

20. Transcriptional and Cellular Diversity of the Human Heart

Author: Kristin G. Ardlie, Nathan R. Tucker, Kenneth B. Margulies, Carolina Roselli, Seung Hoan Choi, Victoria A. Parsons, Christian Stegmann, Caroline N. Herndon, Amelia W. Hall, Patrick T. Ellinor, Stephen J. Fleming, Amer-Denis Akkad, Alessandro Arduini, Mehrtash Babadi, Kenneth Bedi, Irinna Papangeli, François Aguet, and Mark Chaffin
Subjects: Transcription, Genetic, Cell, 030204 cardiovascular system & hematology, Genome, Transcriptome, 0302 clinical medicine, cardiovascular disease, Gene expression, Adipocytes, Medicine, Homeostasis, Myocytes, Cardiac, RNA-Seq, 0303 health sciences, Sex Characteristics, HERITABILITY, Heart, ASSOCIATION, Microfluidic Analytical Techniques, Middle Aged, STEP, medicine.anatomical_structure, Single-Cell Analysis, Cardiology and Cardiovascular Medicine, EXPRESSION, Adult, Cell type, Heart Diseases, Heart Ventricles, Myocytes, Smooth Muscle, Computational biology, Biology, Article, 03 medical and health sciences, Physiology (medical), Humans, Heart Atria, Gene, Genetic association, 030304 developmental biology, Aged, IDENTIFICATION, business.industry, Macrophages, Myocardium, RNA, Human heart, Endothelial Cells, Cardiovascular Agents, Fibroblasts, Lymphocyte Subsets, Gene Ontology, Single cell sequencing, business, Pericytes, 030217 neurology & neurosurgery, Function (biology)
Abstract: Background: The human heart requires a complex ensemble of specialized cell types to perform its essential function. A greater knowledge of the intricate cellular milieu of the heart is critical to increase our understanding of cardiac homeostasis and pathology. As recent advances in low-input RNA sequencing have allowed definitions of cellular transcriptomes at single-cell resolution at scale, we have applied these approaches to assess the cellular and transcriptional diversity of the nonfailing human heart. Methods: Microfluidic encapsulation and barcoding was used to perform single nuclear RNA sequencing with samples from 7 human donors, selected for their absence of overt cardiac disease. Individual nuclear transcriptomes were then clustered based on transcriptional profiles of highly variable genes. These clusters were used as the basis for between-chamber and between-sex differential gene expression analyses and intersection with genetic and pharmacologic data. Results: We sequenced the transcriptomes of 287 269 single cardiac nuclei, revealing 9 major cell types and 20 subclusters of cell types within the human heart. Cellular subclasses include 2 distinct groups of resident macrophages, 4 endothelial subtypes, and 2 fibroblast subsets. Comparisons of cellular transcriptomes by cardiac chamber or sex reveal diversity not only in cardiomyocyte transcriptional programs but also in subtypes involved in extracellular matrix remodeling and vascularization. Using genetic association data, we identified strong enrichment for the role of cell subtypes in cardiac traits and diseases. Intersection of our data set with genes on cardiac clinical testing panels and the druggable genome reveals striking patterns of cellular specificity. Conclusions: Using large-scale single nuclei RNA sequencing, we defined the transcriptional and cellular diversity in the normal human heart. Our identification of discrete cell subtypes and differentially expressed genes within the heart will ultimately facilitate the development of new therapeutics for cardiovascular diseases.
Published: 2020

21. Deep learning enables genetic analysis of the human thoracic aorta

Author: Rajat M. Gupta, Anthony A. Philippakis, Stephen J. Fleming, Shaan Khurshid, Seung Hoan Choi, Samuel Friedman, Honghuang Lin, Mark Chaffin, Mark E. Lindsay, Udo Hoffmann, Amer-Denis Akkad, Patrick T. Ellinor, Carolina Roselli, Ramachandran S. Vasan, Steven A. Lubitz, Dejan Juric, Christian Stegmann, Lu-Chen Weng, Jennifer E. Ho, Emelia J. Benjamin, Mahan Nekoui, Alessandro Arduini, James P. Pirruccello, Shamsudheen K. Vellarikkal, Elizabeth L. Chou, Alexander G. Bick, James R. Stone, Nathan R. Tucker, Amelia W. Hall, and Puneet Batra
Subjects: Adult, Male, medicine.medical_specialty, PATHOGENESIS, Quantitative Trait Loci, Aorta, Thoracic, DETERMINANTS, Dissection (medical), VARIANTS, Quantitative trait locus, Biology, Thoracic aortic aneurysm, Sudden death, DISEASE, ANEURYSM, Aortic aneurysm, Aneurysm, Deep Learning, Internal medicine, medicine.artery, Genetics, medicine, Image Processing, Computer-Assisted, Thoracic aorta, Humans, COMPUTED-TOMOGRAPHY, GENOME-WIDE ASSOCIATION, Aged, Aorta, business.industry, DIAMETER, Hazard ratio, Middle Aged, medicine.disease, Magnetic Resonance Imaging, REFERENCE VALUES, Aortic Aneurysm, CARDIAC STRUCTURE, Biological Variation, Population, Descending aorta, cardiovascular system, Cardiology, Female, business, Transcriptome, Genome-Wide Association Study
Abstract: The aorta is the largest blood vessel in the body, and enlargement or aneurysm of the aorta can predispose to dissection, an important cause of sudden death. While rare syndromes have been identified that predispose to aortic aneurysm, the common genetic basis for the size of the aorta remains largely unknown. By leveraging a deep learning architecture that was originally developed to recognize natural images, we trained a model to evaluate the dimensions of the ascending and descending thoracic aorta in cardiac magnetic resonance imaging. After manual annotation of just 116 samples, we applied this model to 3,840,140 images from the UK Biobank. We then conducted a genome-wide association study in 33,420 individuals, revealing 68 loci associated with ascending and 35 with descending thoracic aortic diameter, of which 10 loci overlapped. Integration of common variation with transcriptome-wide analyses, rare-variant burden tests, and single nucleus RNA sequencing prioritized SVIL, a gene highly expressed in vascular smooth muscle, that was significantly associated with the diameter of the ascending and descending aorta. A polygenic score for ascending aortic diameter was associated with a diagnosis of thoracic aortic aneurysm in the remaining 391,251 UK Biobank participants who did not undergo imaging (HR = 1.44 per standard deviation; P = 3.7·10−12). Defining the genetic basis of the diameter of the aorta may enable the identification of asymptomatic individuals at risk for aneurysm or dissection and facilitate the prioritization of potential therapeutic targets for the prevention or treatment of aortic aneurysm. Finally, our results illustrate the potential for rapidly defining novel quantitative traits derived from a deep learning model, an approach that can be more broadly applied to biomedical imaging data.
Published: 2020

22. Initial Precipitants and Recurrence of Atrial Fibrillation

Author: Olivia L. Hulme, Shaan Khurshid, Lu-Chen Weng, Ludovic Trinquart, Jeffrey M. Ashburner, Emelia J. Benjamin, Daniel E. Singer, Patrick T. Ellinor, Seung Hoan Choi, Steven J. Atlas, Steven A. Lubitz, Allan J. Walkey, Elizabeth Y. Wang, and David D. McManus
Subjects: Adult, Male, medicine.medical_specialty, Risk Assessment, Article, Recurrence, Risk Factors, Physiology (medical), Internal medicine, Atrial Fibrillation, medicine, Humans, Prospective Studies, Risk factor, Stroke, Aged, Aged, 80 and over, Heart Failure, business.industry, Incidence, Atrial fibrillation, Middle Aged, medicine.disease, United States, Survival Rate, Heart failure, Cardiology, Female, Cardiology and Cardiovascular Medicine, business, Algorithms, Follow-Up Studies
Abstract: Background: Atrial fibrillation (AF) may occur after an acute precipitant and subsequently resolve. Management guidelines for AF in these settings are unclear as the risk of recurrent AF and related morbidity is poorly understood. We examined the relations between acute precipitants of AF and long-term recurrence of AF in a clinical setting. Methods: From a multi-institutional longitudinal electronic medical record database, we identified patients with newly diagnosed AF between 2000 and 2014. We developed algorithms to identify acute AF precipitants (surgery, sepsis, pneumonia, pneumothorax, respiratory failure, myocardial infarction, thyrotoxicosis, alcohol, pericarditis, pulmonary embolism, and myocarditis). We assessed risks of AF recurrence in individuals with and without a precipitant and the relations between AF recurrence and heart failure, stroke, and mortality. Results: Among 10 723 patients with newly diagnosed AF (67.9±9.9 years, 41% women), 19% had an acute AF precipitant, the most common of which were cardiac surgery (22%), pneumonia (20%), and noncardiothoracic surgery (15%). The cumulative incidence of AF recurrence at 5 years was 41% among individuals with a precipitant compared with 52% in those without a precipitant (adjusted hazard ratio [HR], 0.75 [95% CI, 0.69–0.81]; P P P P Conclusions: AF after an acute precipitant frequently recurs, although the risk of recurrence is lower than among individuals without an acute precipitant. Recurrence is associated with substantial long-term morbidity and mortality. Future studies should address surveillance and management after newly diagnosed AF in the setting of an acute precipitant.
Published: 2020

23. Genomic and drug target evaluation of 90 cardiovascular proteins in 30,931 individuals

Author: Tom Palmer, Lars Lind, George Davey Smith, Ting Qi, Michael W. Nagle, Paul W. Franks, Bram P. Prins, Julie Lee, Jingyuan Fu, Niclas Eriksson, Peter K. Joshi, Chris Haley, Ljubica Perisic Matic, Jeremy D. Gale, Mika Ala-Korpela, Michael V. Holmes, Urmo Võsa, Adam S. Butterworth, Eric B. Fauman, Anette Kalnapenkis, Reedik Mägi, Åsa Johansson, James F. Wilson, Mikael Landén, Gunnar Engström, Johan Ärnlöv, Anders Hamsten, Ozren Polasek, Andres Ingason, Andrew J. Schork, Agneta Siegbahn, Lasse Folkersen, Qin Wang, Andrew P. Morris, Johan Sundström, Daria V. Zhernakova, Olle Melander, Erik Ingelsson, Federico De Masi, Lude Franke, James E. Peters, Alexandra Zhernakova, Seung Hoan Choi, Rasmus Wernersson, Thibaud Boutin, Karl Michaëlsson, Stefan Gustafsson, Bianca E. Suur, Karen Page, Yang Wu, Caroline Hayward, Marketa Sjögren, Cecilia M. Lindgren, Stefan Enroth, Tõnu Esko, Amira Quazi, John Danesh, Anders Mälarstig, Daniel Hvidberg Hansen, Åsa K Hedman, Jan Nilsson, Ulf Gyllensten, Vilmantas Giedraitis, J. Gustav Smith, Martin Magnusson, Marju Orho-Melander, Steven A. Lubitz, Erin Macdonald-Dunlop, Thomas Werge, Praveen Surendran, Yan Chen, Céline Fernandez, Weidong Zhang, Lars Wallentin, Andrew D. Bretherick, Jian Yang, Peter M. Nilsson, Jesper R. Gådin, Annique Claringbould, Sölve Elmståhl, Sarah E Bergen, Harm-Jan Westra, Erik Pålsson, Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), Translational Immunology Groningen (TRIGR), Center for Liver, Digestive and Metabolic Diseases (CLDM), Stem Cell Aging Leukemia and Lymphoma (SALL), United Kingdom Research and Innovation, Folkersen, Lasse [0000-0003-0708-9530], Hansen, Daniel Hvidberg [0000-0003-3285-605X], Wu, Yang [0000-0002-0128-7280], Eriksson, Niclas [0000-0002-2152-4343], Bretherick, Andrew D [0000-0001-9258-3140], Enroth, Stefan [0000-0002-5056-9137], Lee, Julie [0000-0001-6090-6718], Ala-Korpela, Mika [0000-0001-5905-1206], Claringbould, Annique [0000-0002-9201-6557], Davey Smith, George [0000-0002-1407-8314], Fauman, Eric [0000-0002-9739-0249], Fernandez, Celine [0000-0003-1290-4982], Franke, Lude [0000-0002-5159-8802], Franks, Paul W [0000-0002-0520-7604], Giedraitis, Vilmantas [0000-0003-3423-2021], Haley, Chris [0000-0002-9811-0210], Johansson, Åsa [0000-0002-2915-4498], Lubitz, Steven [0000-0002-9599-4866], Palmer, Tom [0000-0003-4655-4511], Macdonald-Dunlop, Erin [0000-0001-6569-6086], Magnusson, Martin [0000-0003-1710-5936], Michaelsson, Karl [0000-0003-2815-1217], Nagle, Michael W [0000-0002-4677-7582], Nilsson, Peter M [0000-0002-5652-8459], Nilsson, Jan [0000-0002-9752-7479], Prins, Bram [0000-0001-5774-034X], Sundström, Johan [0000-0003-2247-8454], Werge, Thomas [0000-0003-1829-0766], Westra, Harm-Jan [0000-0001-7038-567X], Fu, Jingyuan [0000-0001-5578-1236], Esko, Tõnu [0000-0003-1982-6569], Hayward, Caroline [0000-0002-9405-9550], Landen, Mikael [0000-0002-4496-6451], Butterworth, Adam S [0000-0002-6915-9015], Holmes, Michael V [0000-0001-6617-0879], Ingelsson, Erik [0000-0003-2256-6972], Mälarstig, Anders [0000-0003-2608-1358], Apollo - University of Cambridge Repository, and 30387078 - Magnusson, P. Martin
Subjects: Proteomics, Proteome, Endocrinology, Diabetes and Metabolism, Asthma, ATP Binding Cassette Transporter 1, Cardiovascular System, Chromosome Mapping, Drug Delivery Systems, Gene Knockdown Techniques, Genome-Wide Association Study, Genomics, Humans, Inflammatory Bowel Diseases, Interleukin-1 Receptor-Like 1 Protein, Intracellular Signaling Peptides and Proteins, Linkage Disequilibrium, Mendelian Randomization Analysis, Protein-Serine-Threonine Kinases, Quantitative Trait Loci, Receptors, CCR2, Receptors, CCR5, Genome-wide association study, 030204 cardiovascular system & hematology, Chemokine receptor, 0302 clinical medicine, RECEPTOR ANTAGONIST, GWAS, Cardiac and Cardiovascular Systems, 0303 health sciences, Molecular medicine, 3. Good health, Medical genetics, Medical Genetics, Life Sciences & Biomedicine, medicine.medical_specialty, Computational biology, Biology, Protein Serine-Threonine Kinases, Article, 03 medical and health sciences, Endocrinology & Metabolism, Physiology (medical), Mendelian randomization, Internal Medicine, medicine, 030304 developmental biology, Science & Technology, Cell Biology, GENE, ANTIBODY
Abstract: Circulating proteins are vital in human health and disease and are frequently used as biomarkers for clinical decision-making or as targets for pharmacological intervention. Here, we map and replicate protein quantitative trait loci (pQTL) for 90 cardiovascular proteins in over 30,000 individuals, resulting in 451 pQTLs for 85 proteins. For each protein, we further perform pathway mapping to obtain trans-pQTL gene and regulatory designations. We substantiate these regulatory findings with orthogonal evidence for trans-pQTLs using mouse knockdown experiments (ABCA1 and TRIB1) and clinical trial results (chemokine receptors CCR2 and CCR5), with consistent regulation. Finally, we evaluate known drug targets, and suggest new target candidates or repositioning opportunities using Mendelian randomization. This identifies 11 proteins with causal evidence of involvement in human disease that have not previously been targeted, including EGF, IL-16, PAPPA, SPON1, F3, ADM, CASP-8, CHI3L1, CXCL16, GDF15 and MMP-12. Taken together, these findings demonstrate the utility of large-scale mapping of the genetics of the proteome and provide a resource for future precision studies of circulating proteins in human health.
Published: 2020
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24. Multi-ancestry GWAS of the electrocardiographic PR interval identifies 202 loci underlying cardiac conduction

Author: Dennis O. Mook-Kanamori, Yalda Jamshidi, Peter K. Joshi, Seung Hoan Choi, Henry J. Lin, Rebecca D. Jackson, Alison D. Murray, May E. Montasser, Veikko Salomaa, Charles Kooperberg, Moritz F. Sinner, Gianfranco Sinagra, Luisa Foco, James G. Wilson, Johan Sundström, Kathleen A. Ryan, Eric A. Whitsel, Bruno H. Stricker, Sandosh Padmanabhan, Christopher Newton-Cheh, Ozren Polasek, Unnur Thorsteinsdottir, Niek Verweij, Pier D. Lambiase, Nathan R. Tucker, Stefan Kääb, Jun Ding, Stefan Weiss, Daniel F. Gudbjartsson, David Conen, Lars Lind, Ivana Kolcic, Lu-Chen Weng, J. Wouter Jukema, Kirill V. Tarasov, Xiuqing Guo, Stella Trompet, Patricia B. Munroe, Albert V. Smith, Elsayed Z. Soliman, Andrew Tinker, Antti Jula, J. Gustav Smith, Alexander P. Reiner, Sébastien Thériault, Kathryn L. Lunetta, Vilmundur Gudnason, Mika Kähönen, Massimo Mangino, Raymond Noordam, Joshua C. Bis, Alan R. Shuldiner, Tim D. Spector, Borbala Mifsud, Stefan van Duijvenboden, Jeffrey R. O'Connell, Emelia J. Benjamin, M. Benjamin Shoemaker, Stephan B. Felix, Peter W. Macfarlane, Lorenz Risch, Uwe Völker, Stephanie M. Gogarten, Maria Fernanda Lima-Costa, Julia Ramirez, Morten S. Olesen, Konstantin Strauch, Annette Peters, Aaron Isaacs, Steven A. Lubitz, Eric Boerwinkle, Carolina Roselli, James H. Cartwright, Nathalia M. Araujo, Ruth J. F. Loos, Diane Fatkin, Harry Campbell, Blair H. Smith, Thomas Meitinger, André G. Uitterlinden, Paul L. Huang, Tamara B. Harris, Kathleen F. Kerr, David J. Porteous, Martina Müller-Nurasyid, Francesco Cucca, Michiel Rienstra, Davíð O. Arnar, Amanda A. Seyerle, Caroline Hayward, M. Abdullah Said, Catriona L. K. Barnes, Kent D. Taylor, Nona Sotoodehnia, Nina Mononen, Dan M. Roden, Jonathan Marten, Terho Lehtimäki, Dan E. Arking, Anna F. Dominiczak, Jan A. Kors, Olli T. Raitakari, Igor Rudan, Yordi J. van de Vegte, Christopher P. Nelson, Erik Ingelsson, Ulrike Peters, Girish N. Nadkarni, Eduardo Tarazona-Santos, Edward G. Lakatta, Nina Hutri-Kähönen, Bruce M. Psaty, Patrick T. Ellinor, Christian Fuchsberger, Katharina Schramm, Amelia W. Hall, M. Yldau van der Ende, Alvaro Alonso, James F. Wilson, Sheila Ulivi, Rosa B. Thorolfsdottir, Stefanie Aeschbacher, Mary L. Biggs, Marten E. van den Berg, Nilesh J. Samani, Thibaud Boutin, Vilmantas Giedraitis, Honghuang Lin, Kjell Nikus, Helen R. Warren, Arie C. Maan, James J. Cranley, Adolfo Correa, Martin Gögele, Ian Ford, Katri Sääksjärvi, Georg Ehret, Michele Orini, Susan R. Heckbert, Cecilia M. Lindgren, Jie Yao, Maria Pina Concas, Pim van der Harst, Ioanna Ntalla, Jeffrey Haessler, Jerome I. Rotter, Pashupati P. Mishra, Michael J. Cutler, Erwin P. Bottinger, Cornelia M. van Duijn, Jennifer A. Brody, Paolo Gasparini, Lenore J. Launer, Andrew P. Morris, Renée de Mutsert, Aki S. Havulinna, James P. Cook, Hilma Holm, Patrick Sulem, Alessandro De Grandi, Cristian Pattaro, Gardar Sveinbjornsson, Antonio Luiz Pinho Ribeiro, Mark J. Caulfield, Gudmar Thorleifsson, Marcus Dörr, Muhammad B. Riaz, Peter P. Pramstaller, Yong Qian, Anubha Mahajan, Cathy C. Laurie, Kenneth Rice, Mark Chaffin, Kari Stefansson, Andrew A. Hicks, Solmaz Assa, Hao Mei, Leo-Pekka Lyytikäinen, Fabiola Del Greco M, Renan P. Souza, Michael Preuss, Adrienne M. Stilp, Barry London, Melanie Waldenberger, Christy L. Avery, Daniel Levy, Michael R. Barnes, Medical Informatics, Epidemiology, Internal Medicine, Weng, Lu-Chen [0000-0003-1475-4930], Hall, Amelia Weber [0000-0002-7915-0313], Tucker, Nathan R [0000-0002-5071-4218], Chaffin, Mark D [0000-0002-1234-5562], Roselli, Carolina [0000-0001-5267-6756], Barnes, Michael R [0000-0001-9097-7381], Mifsud, Borbala [0000-0003-3429-3094], Hayward, Caroline [0000-0002-9405-9550], Concas, Maria Pina [0000-0003-3598-2537], Boutin, Thibaud [0000-0003-4754-1675], Kolcic, Ivana [0000-0001-7918-6052], Rudan, Igor [0000-0001-6993-6884], Souza, Renan P [0000-0002-9479-4432], Giedraitis, Vilmantas [0000-0003-3423-2021], Ingelsson, Erik [0000-0003-2256-6972], Mahajan, Anubha [0000-0001-5585-3420], Morris, Andrew P [0000-0002-6805-6014], Hicks, Andrew A [0000-0001-6320-0411], Sundström, Johan [0000-0003-2247-8454], Nelson, Christopher P [0000-0001-8025-2897], Riaz, Muhammad B [0000-0002-5512-1745], Sinagra, Gianfranco [0000-0003-2700-8478], Mishra, Pashupati P [0000-0001-5177-3431], Caulfield, Mark J [0000-0001-9295-3594], Dominiczak, Anna [0000-0003-4913-3608], Risch, Lorenz [0000-0003-2692-6699], Joshi, Peter K [0000-0002-6361-5059], Wilson, James F [0000-0001-5751-9178], Isaacs, Aaron [0000-0001-5037-4834], van Duijn, Cornelia M [0000-0002-2374-9204], Gudnason, Vilmundur [0000-0001-5696-0084], Smith, Albert V [0000-0003-1942-5845], Loos, Ruth JF [0000-0002-8532-5087], Preuss, Michael H [0000-0001-5266-8465], Correa, Adolfo [0000-0002-9501-600X], Müller-Nurasyid, Martina [0000-0003-3793-5910], Waldenberger, Melanie [0000-0003-0583-5093], Mangino, Massimo [0000-0002-2167-7470], Rienstra, Michiel [0000-0002-2581-070X], van der Harst, Pim [0000-0002-2713-686X], Verweij, Niek [0000-0002-4303-7685], Fatkin, Diane [0000-0002-9010-9856], Brody, Jennifer A [0000-0001-8509-148X], Rice, Kenneth [0000-0002-3071-7278], Pattaro, Cristian [0000-0002-4119-0109], Wouter Jukema, J [0000-0002-3246-8359], Weiss, Stefan [0000-0002-3553-4315], Havulinna, Aki S [0000-0002-4787-8959], Sääksjärvi, Katri [0000-0002-5061-4911], Salomaa, Veikko [0000-0001-7563-5324], Rotter, Jerome I [0000-0001-7191-1723], Taylor, Kent D [0000-0002-2756-4370], Lakatta, Edward G [0000-0002-4772-0035], Lin, Honghuang [0000-0003-3043-3942], Lunetta, Kathryn L [0000-0002-9268-810X], Murray, Alison D [0000-0003-4915-4847], Porteous, David J [0000-0003-1249-6106], Smith, Blair H [0000-0002-5362-9430], Uitterlinden, André [0000-0002-7276-3387], Peters, Ulrike [0000-0001-5666-9318], Alonso, Alvaro [0000-0002-2225-8323], Ehret, Georg B [0000-0002-5730-0675], Soliman, Elsayed Z [0000-0001-5632-8150], Gogarten, Stephanie M [0000-0002-7231-9745], Kerr, Kathleen F [0000-0002-6438-9583], Abdullah Said, M [0000-0003-2920-7745], Orini, Michele [0000-0001-5773-0344], Ramirez, Julia [0000-0003-4130-5866], Van Duijvenboden, Stefan [0000-0001-8897-558X], Gudbjartsson, Daniel F [0000-0002-5222-9857], Sulem, Patrick [0000-0001-7123-6123], Thorolfsdottir, Rosa B [0000-0001-7475-0398], Benjamin, Emelia J [0000-0003-4076-2336], Stefansson, Kari [0000-0003-1676-864X], Ellinor, Patrick T [0000-0002-2067-0533], Jamshidi, Yalda [0000-0003-0151-6482], Lubitz, Steven A [0000-0002-9599-4866], Munroe, Patricia B [0000-0002-4176-2947], Apollo - University of Cambridge Repository, Medicum, Institute for Molecular Medicine Finland, Complex Disease Genetics, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Cardiovascular Centre (CVC), Ntalla, I., Weng, L. -C., Cartwright, J. H., Hall, A. W., Sveinbjornsson, G., Tucker, N. R., Choi, S. H., Chaffin, M. D., Roselli, C., Barnes, M. R., Mifsud, B., Warren, H. R., Hayward, C., Marten, J., Cranley, J. J., Concas, M. P., Gasparini, P., Boutin, T., Kolcic, I., Polasek, O., Rudan, I., Araujo, N. M., Lima-Costa, M. F., Ribeiro, A. L. P., Souza, R. P., Tarazona-Santos, E., Giedraitis, V., Ingelsson, E., Mahajan, A., Morris, A. P., Del Greco M, F., Foco, L., Gogele, M., Hicks, A. A., Cook, J. P., Lind, L., Lindgren, C. M., Sundstrom, J., Nelson, C. P., Riaz, M. B., Samani, N. J., Sinagra, G., Ulivi, S., Kahonen, M., Mishra, P. P., Mononen, N., Nikus, K., Caulfield, M. J., Dominiczak, A., Padmanabhan, S., Montasser, M. E., O'Connell, J. R., Ryan, K., Shuldiner, A. R., Aeschbacher, S., Conen, D., Risch, L., Theriault, S., Hutri-Kahonen, N., Lehtimaki, T., Lyytikainen, L. -P., Raitakari, O. T., Barnes, C. L. K., Campbell, H., Joshi, P. K., Wilson, J. F., Isaacs, A., Kors, J. A., van Duijn, C. M., Huang, P. L., Gudnason, V., Harris, T. B., Launer, L. J., Smith, A. V., Bottinger, E. P., Loos, R. J. F., Nadkarni, G. N., Preuss, M. H., Correa, A., Mei, H., Wilson, J., Meitinger, T., Muller-Nurasyid, M., Peters, A., Waldenberger, M., Mangino, M., Spector, T. D., Rienstra, M., van de Vegte, Y. J., van der Harst, P., Verweij, N., Kaab, S., Schramm, K., Sinner, M. F., Strauch, K., Cutler, M. J., Fatkin, D., London, B., Olesen, M., Roden, D. M., Benjamin Shoemaker, M., Gustav Smith, J., Biggs, M. L., Bis, J. C., Brody, J. A., Psaty, B. M., Rice, K., Sotoodehnia, N., De Grandi, A., Fuchsberger, C., Pattaro, C., Pramstaller, P. P., Ford, I., Wouter Jukema, J., Macfarlane, P. W., Trompet, S., Dorr, M., Felix, S. B., Volker, U., Weiss, S., Havulinna, A. S., Jula, A., Saaksjarvi, K., Salomaa, V., Guo, X., Heckbert, S. R., Lin, H. J., Rotter, J. I., Taylor, K. D., Yao, J., de Mutsert, R., Maan, A. C., Mook-Kanamori, D. O., Noordam, R., Cucca, F., Ding, J., Lakatta, E. G., Qian, Y., Tarasov, K. V., Levy, D., Lin, H., Newton-Cheh, C. H., Lunetta, K. L., Murray, A. D., Porteous, D. J., Smith, B. H., Stricker, B. H., Uitterlinden, A., van den Berg, M. E., Haessler, J., Jackson, R. D., Kooperberg, C., Peters, U., Reiner, A. P., Whitsel, E. A., Alonso, A., Arking, D. E., Boerwinkle, E., Ehret, G. B., Soliman, E. Z., Avery, C. L., Gogarten, S. M., Kerr, K. F., Laurie, C. C., Seyerle, A. A., Stilp, A., Assa, S., Abdullah Said, M., Yldau van der Ende, M., Lambiase, P. D., Orini, M., Ramirez, J., Van Duijvenboden, S., Arnar, D. O., Gudbjartsson, D. F., Holm, H., Sulem, P., Thorleifsson, G., Thorolfsdottir, R. B., Thorsteinsdottir, U., Benjamin, E. J., Tinker, A., Stefansson, K., Ellinor, P. T., Jamshidi, Y., Lubitz, S. A., Munroe, P. B., Fysiologie, RS: FHML MaCSBio, RS: Carim - B01 Blood proteins & engineering, Læknadeild (HÍ), Faculty of Medicine (UI), Heilbrigðisvísindasvið (HÍ), School of Health Sciences (UI), Verkfræði- og náttúruvísindasvið (HÍ), School of Engineering and Natural Sciences (UI), Háskóli Íslands, and University of Iceland
Subjects: 0301 basic medicine, Male, Multifactorial Inheritance, General Physics and Astronomy, Gene Expression, Genome-wide association study, 030204 cardiovascular system & hematology, Arrhythmias, Genome-wide association studies, CALCINEURIN, Electrocardiography, 0302 clinical medicine, Cardiovascular Disease, Multi-ancestry GWAS, ELEMENTS, Medicine, Cardiac and Cardiovascular Systems, Blóðrásarsjúkdómar, lcsh:Science, RISK, DECREASE, education.field_of_study, Multidisciplinary, Kardiologi, medicine.diagnostic_test, 1184 Genetics, developmental biology, physiology, Atrial fibrillation, 3142 Public health care science, environmental and occupational health, 3. Good health, Endophenotype, Arrhythmias, Cardiac, Cardiovascular Diseases, Endophenotypes, Female, Genetic Loci, Genetic Predisposition to Disease, Genetic Variation, Genome-Wide Association Study, Humans, Quantitative Trait Loci, cardiovascular system, Cardiology, medicine.symptom, Erfðarannsóknir, Cardiac, Medical Genetics, Human, Bradycardia, medicine.medical_specialty, Science, GENOME-WIDE ASSOCIATION, ATRIAL-FIBRILLATION, MUTATIONS, DURATION, CARDIOMYOPATHY, BRADYCARDIA, Population, Article, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Internal medicine, Cardiac conduction, PR interval, education, Medicinsk genetik, business.industry, Cardiovascular genetics, General Chemistry, Arfgengi, medicine.disease, 030104 developmental biology, lcsh:Q, business
Abstract: Publisher's version (útgefin grein), The electrocardiographic PR interval reflects atrioventricular conduction, and is associated with conduction abnormalities, pacemaker implantation, atrial fibrillation (AF), and cardiovascular mortality. Here we report a multi-ancestry (N = 293,051) genome-wide association meta-analysis for the PR interval, discovering 202 loci of which 141 have not previously been reported. Variants at identified loci increase the percentage of heritability explained, from 33.5% to 62.6%. We observe enrichment for cardiac muscle developmental/contractile and cytoskeletal genes, highlighting key regulation processes for atrioventricular conduction. Additionally, 8 loci not previously reported harbor genes underlying inherited arrhythmic syndromes and/or cardiomyopathies suggesting a role for these genes in cardiovascular pathology in the general population. We show that polygenic predisposition to PR interval duration is an endophenotype for cardiovascular disease, including distal conduction disease, AF, and atrioventricular pre-excitation. These findings advance our understanding of the polygenic basis of cardiac conduction, and the genetic relationship between PR interval duration and cardiovascular disease., We provide all investigator and study-specific acknowledgements in Supplementary Note 1, and funding sources in Supplementary Note 2.
Published: 2020

25. Genetic Predisposition, Clinical Risk Factor Burden, and Lifetime Risk of Atrial Fibrillation

Author: Seung Hoan Choi, Lu-Chen Weng, Patrick T. Ellinor, Ludovic Trinquart, Kathryn L. Lunetta, Honghuang Lin, Biqi Wang, Olivia L. Hulme, David D. McManus, Sarah R. Preis, Emelia J. Benjamin, Laila Staerk, Steven A. Lubitz, and Martin G. Larson
Subjects: Adult, Male, Community-Based Participatory Research, medicine.medical_specialty, Myocardial Infarction, 030204 cardiovascular system & hematology, Polymorphism, Single Nucleotide, Article, Cohort Studies, 03 medical and health sciences, 0302 clinical medicine, Risk Factors, Physiology (medical), Atrial Fibrillation, Epidemiology, medicine, Genetic predisposition, Humans, Genetic Predisposition to Disease, Longitudinal Studies, 030212 general & internal medicine, Risk factor, Intensive care medicine, Antihypertensive Agents, business.industry, Atrial fibrillation, Middle Aged, medicine.disease, United States, Hypertension, Risk stratification, Female, Lifetime risk, Polygenic risk score, Medical emergency, Cardiology and Cardiovascular Medicine, business, Clinical risk factor, Follow-Up Studies
Abstract: Background: The long-term probability of developing atrial fibrillation (AF) considering genetic predisposition and clinical risk factor burden is unknown. Methods: We estimated the lifetime risk of AF in individuals from the community-based Framingham Heart Study. Polygenic risk for AF was derived using a score of ≈1000 AF-associated single-nucleotide polymorphisms. Clinical risk factor burden was calculated for each individual using a validated risk score for incident AF comprised of height, weight, systolic and diastolic blood pressure, current smoking status, antihypertensive medication use, diabetes mellitus, history of myocardial infarction, and history of heart failure. We estimated the lifetime risk of AF within tertiles of polygenic and clinical risk. Results: Among 4606 participants without AF at 55 years of age, 580 developed incident AF (median follow-up, 9.4 years; 25th–75th percentile, 4.4–14.3 years). The lifetime risk of AF >55 years of age was 37.1% and was substantially influenced by both polygenic and clinical risk factor burden. Among individuals free of AF at 55 years of age, those in low-polygenic and clinical risk tertiles had a lifetime risk of AF of 22.3% (95% confidence interval, 15.4−9.1), whereas those in high-risk tertiles had a risk of 48.2% (95% confidence interval, 41.3−55.1). A lower clinical risk factor burden was associated with later AF onset after adjusting for genetic predisposition ( P Conclusions: In our community-based cohort, the lifetime risk of AF was 37%. Estimation of polygenic AF risk is feasible and together with clinical risk factor burden explains a substantial gradient in long-term AF risk.
Published: 2018

26. Prevalence and clinical importance of titin truncating variants in adults without known congestive heart failure

Author: Anthony A. Philippakis, James P. Pirruccello, Samuel Friedman, Alexander G. Bick, Seung Hoan Choi, Sekar Kathiresan, Mark Chaffin, Amit Khera, Steven A. Lubitz, Krishna G. Aragam, Kenney Ng, Patrick T. Ellinor, and Carolyn Y. Ho
Subjects: 0303 health sciences, medicine.medical_specialty, Ejection fraction, medicine.diagnostic_test, business.industry, Hazard ratio, Dilated cardiomyopathy, 030204 cardiovascular system & hematology, medicine.disease, Asymptomatic, 3. Good health, 03 medical and health sciences, 0302 clinical medicine, Cardiac magnetic resonance imaging, Relative risk, Internal medicine, Heart failure, medicine, Cardiology, medicine.symptom, business, Prospective cohort study, 030304 developmental biology
Abstract: BackgroundCross-sectional studies of various forms of dilated cardiomyopathy have noted a truncating mutation in the gene encoding titin (‘TTNtv’) in 7-30% of patients, but the clinical importance of identifying a TTNtv in an asymptomatic adult is largely unknown. In contrast to cross-sectional studies, prospective cohort studies allow for unbiased estimates of the disease risks associated with a genotype exposure.ObjectivesTo determine the prevalence of cardiac imaging abnormalities and risk of incident disease among middle-aged TTNtv carriers without known congestive heart failure.MethodsWe analyze exome sequencing data of 45,747 participants of the UK Biobank without known congestive heart failure to identify TTNtv carriers. Among 10,552 with cardiac magnetic resonance imaging (MRI), we determine the relationship between TTNtv carrier status and left ventricular ejection fraction. In this prospective cohort, we quantify the absolute and relative risks of incident disease in TTNtv carriers versus noncarriers.ResultsAmong 45,747 middle-aged participants without known congestive heart failure, 196 (0.43%) harbored a TTNtv. The average ejection fraction was 61% in TTNtv carriers versus 65% in noncarriers (P = 1.8 × 10−8), with a 9.3-fold increase (95% CI 3.9 – 22.2) in odds of subnormal ejection fraction (P = 5.7 × 10−5). Over a median follow-up of 6.9 years, a composite endpoint of incident dilated cardiomyopathy, congestive heart failure, or all-cause mortality was observed in 6.6% of TTNtv carriers versus 2.9% of non-carriers (adjusted hazard ratio 2.5; 95% CI 1.4 – 4.3; p = 1.1 × 10−3).ConclusionsApproximately 1 in 230 middle-aged adults without known congestive heart failure harbored a TTNtv. These carriers had a substantially increased relative risk—but modest absolute risk—of having a subnormal ejection fraction or manifesting clinical disease during prospective follow-up.Condensed AbstractCross-sectional studies of dilated cardiomyopathy have noted a truncating mutation in the gene encoding titin (‘TTNtv’) in up to 30% of patients—but the clinical importance of TTNtv in asymptomatic adults is largely unknown. Here, we observe a TTNtv in 0.43% of 45,747 middle-aged adults. Average ejection fraction was 61% in TTNtv carriers versus 65% in non-carriers (p
Published: 2019
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27. Multi-ancestry GWAS of the electrocardiographic PR interval identifies 210 loci underlying cardiac conduction

Author: Lorenz Risch, Igor Rudan, Hilma Holm, Christopher P. Nelson, Jan A. Kors, Stefanie Aeschbacher, Stefan Kääb, Peter W. Macfarlane, Lars Lind, Amanda A. Seyerle, Ozren Polasek, Daniel F. Gudbjartsson, Xiuqing Guo, Nilesh J. Samani, Bruce M. Psaty, Rosa B. Thorolfsdottir, Elsayed Z. Soliman, Yong Qian, Mary L. Biggs, Antti Jula, Vilmundur Gudnason, Paul L. Huang, Tamara B. Harris, Gianfranco Sinagra, Luisa Foco, Anubha Mahajan, Mika Kähönen, Lu-Chen Weng, Borbala Mifsud, Stefan van Duijvenboden, Terho Lehtimäki, Jennifer A. Brody, Paolo Gasparini, Kathleen A. Ryan, Marten E. van den Berg, James J. Cranley, Eric Boerwinkle, Cathy C. Laurie, Annette Peters, Joshua C. Bis, Raymond Noordam, Andrew P. Morris, Johan Sundström, Lenore J. Launer, Stefan Weiss, Rebecca D. Jackson, Alison D. Murray, Jeffrey R. O'Connell, Aki S. Havulinna, Dennis O. Mook-Kanamori, Sheila Ulivi, Renée de Mutsert, Eric A. Whitsel, Adrienne M. Stilp, James P. Cook, Nona Sotoodehnia, Antonio Luiz Pinho Ribeiro, Seung Hoan Choi, Mark J. Caulfield, Sébastien Thériault, Henry J. Lin, Dan M. Roden, J. Wouter Jukema, James F. Wilson, Veikko Salomaa, Honghuang Lin, Andrew A. Hicks, Christy L. Avery, Nina Mononen, Dan E. Arking, Ruth J. F. Loos, Yalda Jamshidi, André G. Uitterlinden, Nina Hutri-Kähönen, Andrew Tinker, Gudmar Thorleifsson, Daniel Levy, Martina Müller-Nurasyid, Alexander P. Reiner, Bruno H. Stricker, Caroline Hayward, Yordi J. van de Vegte, Ioanna Ntalla, Tim D. Spector, Niek Verweij, Michael R. Barnes, Martin Gögele, Nathan R. Tucker, Arie C. Maan, Eduardo Tarazona-Santos, Katri Sääksjärvi, Maria Pina Concas, Pim van der Harst, Georg Ehret, Cecilia M. Lindgren, David Conen, Cornelia M. van Duijn, Muhammad B. Riaz, Leo-Pekka Lyytikäinen, Amelia W. Hall, Peter P. Pramstaller, Maria Fernanda Lima-Costa, Vilmantas Giedraitis, Emelia J. Benjamin, M. Fabiola Del Greco, Thomas Meitinger, Erwin P. Bottinger, Francesco Cucca, Aaron Isaacs, Carolina Roselli, James H. Cartwright, Massimo Mangino, Adolfo Correa, Patrick Sulem, Thibaud Boutin, Michiel Rienstra, Stephan B. Felix, Julia Ramirez, Kathleen F. Kerr, Jonathan Marten, David J. Porteous, Kent D. Taylor, Patrick T. Ellinor, Michele Orini, Susan R. Heckbert, Olli T. Raitakari, Girish N. Nadkarni, Edward G. Lakatta, Anna F. Dominiczak, Jie Yao, Erik Ingelsson, Christopher Newton-Cheh, Katharina Schramm, Jerome I. Rotter, Michael J. Cutler, Pashupati P. Mishra, Diane Fatkin, Marcus Dörr, Ulrike Peters, Solmaz Assa, Christian Fuchsberger, M. Abdullah Said, Catriona L. K. Barnes, Peter K. Joshi, M. Yldau van der Ende, Alvaro Alonso, James G. Wilson, Jun Ding, Kathryn L. Lunetta, Kjell Nikus, Helen R. Warren, Charles Kooperberg, Moritz F. Sinner, Sandosh Padmanabhan, Patricia B. Munroe, Jeffrey Haessler, Albert V. Smith, Alan R. Shuldiner, Morten S. Olesen, Konstantin Strauch, Steven A. Lubitz, J. Gustav Smith, Renan P. Souza, Michael Preuss, Kirill V. Tarasov, M. Benjamin Shoemaker, Barry London, Melanie Waldenberger, Cristian Pattaro, David O. Arnar, Gardar Sveinbjornsson, Alessandro De Grandi, Ian Ford, Kenneth Rice, Mark Chaffin, Kari Stefansson, Hao Mei, Uwe Völker, Blair H. Smith, Nathalia M. Araujo, Harry Campbell, Pier D. Lambiase, Stephanie M. Gogarten, May E. Montasser, Unnur Thorsteinsdottir, Ivana Kolcic, and Stella Trompet
Subjects: 0303 health sciences, medicine.medical_specialty, education.field_of_study, business.industry, Population, Cardiomyopathy, Atrial fibrillation, Genome-wide association study, Disease, 030204 cardiovascular system & hematology, medicine.disease, 3. Good health, 03 medical and health sciences, 0302 clinical medicine, Internal medicine, Endophenotype, Cardiac conduction, medicine, Cardiology, PR interval, business, education, 030304 developmental biology
Abstract: The electrocardiographic PR interval reflects atrioventricular conduction, and is associated with conduction abnormalities, pacemaker implantation, atrial fibrillation (AF), and cardiovascular mortality1,2. We performed multi-ancestry (N=293,051) and European only (N=271,570) genome-wide association (GWAS) meta-analyses for the PR interval, discovering 210 loci of which 149 are novel. Variants at all loci nearly doubled the percentage of heritability explained, from 33.5% to 62.6%. We observed enrichment for genes involved in cardiac muscle development/contraction and the cytoskeleton highlighting key regulation processes for atrioventricular conduction. Additionally, 19 novel loci harbour genes underlying inherited monogenic heart diseases suggesting the role of these genes in cardiovascular pathology in the general population. We showed that polygenic predisposition to PR interval duration is an endophenotype for cardiovascular disease risk, including distal conduction disease, AF, atrioventricular pre-excitation, non-ischemic cardiomyopathy, and coronary heart disease. These findings advance our understanding of the polygenic basis of cardiac conduction, and the genetic relationship between PR interval duration and cardiovascular disease.
Published: 2019

28. Loss-of-function genomic variants with impact on liver-related blood traits highlight potential therapeutic targets for cardiovascular disease

Author: Gregory J.M. Zajac, Jerome I. Rotter, Rasika A. Mathias, Vivek Rai, David Schlessinger, Tanmoy Roychowdhury, Yuhao Liu, Kathleen C. Barnes, Maiken Elvestad Gabrielsen, John Blangero, Russell P. Tracy, Xiuqing Guo, Albert V. Smith, Mari Løset, Luis Villacorta, Anita Pandit, Xingnan Li, Kent D. Taylor, Anne Heidi Skogholt, Seunggeun Lee, Brooke N. Wolford, Allison E. Ashley-Koch, Scott T. Weiss, Yingze Zhang, Akua Acheampong, Seung Hoan Choi, Steven A. Lubitz, Ketian Yu, Ren-Hua Chung, Jill M. Johnsen, Seyed Mehdi Nouraie, Lars G. Fritsche, Lisa R. Yanek, Yii Der Chen, Austen Grooms, Jessica Lasky-Su, Ida Surakka, Pradeep Natarajan, Michael Boehnke, Lukas Forer, Victor R. Gordeuk, Hyun Min Kang, Whitney E. Hornsby, Stella Aslibekyan, Wayne Huey-Herng Sheu, Ben Michael Brumpton, Sarah A Gagliano Taliun, Patrick T. Ellinor, Francesco Cucca, Karen Schwander, Patricia A. Peyser, Lewis C. Becker, Rebecca D. Jackson, Joanne E. Curran, Jonathon LeFaive, Sebastian Schoenherr, Marguerite R. Irvin, Sarah E. Graham, Eugene R. Bleecker, Solomon K. Musani, Michelle Daya, Alexander P. Reiner, Adolfo Correa, William Overton, Vivien A. Sheehan, Oddgeir L. Holmen, Cristen J. Willer, Bertha A. Hildalgo, Christian Fuchsberger, Chad M. Brummett, Sachin Kheterpal, Matthew Zawistowski, Kristian Hveem, Sekar Kathiresan, James G. Wilson, Marilyn J. Telen, Ramachandran S. Vasan, Bjørn Olav Åsvold, Donna K. Arnett, Sebastian Zöllner, Wei Zhou, Nicholette D. Palmer, Gonçalo R. Abecasis, Jennifer A. Smith, L. Adrienne Cupples, Nicholas M. Rafaels, Lawrence F. Bielak, Barbara A. Konkle, Charles Kooperberg, C Sidore, Juan M. Peralta, Jifeng Zhang, Daniel Taliun, Deborah A. Meyers, Stephen S. Rich, Sayantan Das, Jonas B. Nielsen, Thomas W. Blackwell, Oren Rom, Amanda Schaefer, Y. Eugene Chen, and Courtney G. Montgomery
Subjects: 2. Zero hunger, 0303 health sciences, education.field_of_study, business.industry, Population, Fatty liver, Blood lipids, Genome-wide association study, Disease, 030204 cardiovascular system & hematology, Bioinformatics, medicine.disease, 3. Good health, 03 medical and health sciences, Liver disease, 0302 clinical medicine, Diabetes mellitus, Medicine, Liver function, business, education, 030304 developmental biology
Abstract: SUMMARYCardiovascular diseases (CVD), and in particular cerebrovascular and ischemic heart diseases, are leading causes of death globally.1Lowering circulating lipids is an important treatment strategy to reduce risk.2,3However, some pharmaceutical mechanisms of reducing CVD may increase risk of fatty liver disease or other metabolic disorders.4,5,6To identify potential novel therapeutic targets, which may reduce risk of CVD without increasing risk of metabolic disease, we focused on the simultaneous evaluation of quantitative traits related to liver function and CVD. Using a combination of low-coverage (5×) whole-genome sequencing and targeted genotyping, deep genotype imputation based on the TOPMed reference panel7, and genome-wide association study (GWAS) meta-analysis, we analyzed 12 liver-related blood traits (including liver enzymes, blood lipids, and markers of iron metabolism) in up to 203,476 people from three population-based cohorts of different ancestries. We identified 88 likely causal protein-altering variants that were associated with one or more liver-related blood traits. We identified several loss-of-function (LoF) variants reducing low-density lipoprotein cholesterol (LDL-C) or risk of CVD without increased risk of liver disease or diabetes, including variants in known lipid genes (e.g.APOB,LPL). A novel LoF variant,ZNF529:p.K405X, was associated with decreased levels of LDL-C (P=1.3×10−8) but demonstrated no association with liver enzymes or non-fasting blood glucose levels. Silencing ofZNF529in human hepatocytes resulted in upregulation of LDL receptor (LDLR) and increased LDL-C uptake in the cells, suggesting that inhibition ofZNF529or its gene product could be used for treating hypercholesterolemia and hence reduce the risk of CVD. Taken together, we demonstrate that simultaneous consideration of multiple phenotypes and a focus on rare protein-altering variants may identify promising therapeutic targets.
Published: 2019

29. Serum magnesium and calcium levels in relation to ischemic stroke Mendelian randomization study

Author: Susanna C. Larsson, Matthew Traylor, Stephen Burgess, Giorgio B. Boncoraglio, Christina Jern, Karl Michaëlsson, Hugh S. Markus, Rainer Malik, Ganesh Chauhan, Muralidharan Sargurupremraj, Yukinori Okada, Aniket Mishra, Loes Rutten-Jacobs, Anne-Katrin Giese, Sander W van der Laan, Solveig Gretarsdottir, Christopher D Anderson, Michael Chong, Hieab HH Adams, Tetsuro Ago, Peter Almgren, Philippe Amouyel, Hakan Ay, raci M Bartz, Oscar R Benavente, Steve Bevan, Giorgio B Boncoraglio, Robert D Brown, Adam S Butterworth, Caty Carrera, Cara L Carty, Daniel I Chasman, Wei-Min Chen, John W Cole, Adolfo Correa, Ioana Cotlarciuc, Carlos Cruchaga, John Danesh, Paul IW de Bakker, Anita L DeStefano, Marcel den Hoed, Qing Duan, Stefan T Engelter, Guido J Falcone, Rebecca F Gottesman, Raji P Grewal, Vilmundur Gudnason, Stefan Gustafsson, Jeffrey Haessler, Tamara B Harris, Ahamad Hassan, Aki S Havulinna, Susan R Heckbert, Elizabeth G Holliday, George Howard, Fang-Chi Hsu, Hyacinth I Hyacinth, M Arfan Ikram, Erik Ingelsson, Marguerite R Irvin, Xueqiu Jian, Jordi Jiménez-Conde, Julie A Johnson, J Wouter Jukema, Masahiro Kanai, Keith L Keene, Brett M Kissela, Dawn O Kleindorfer, Charles Kooperberg, Michiaki Kubo, Leslie A Lange, Carl D Langefeld, Claudia Langenberg, Lenore J Launer, Jin-Moo Lee, Robin Lemmens, Didier Leys, Cathryn M Lewis, Wei-Yu Lin, Arne G Lindgren, Erik Lorentzen, Patrik K Magnusson, Jane Maguire, Ani Manichaikul, Patrick F McArdle, James F Meschia, Braxton D Mitchell, Thomas H Mosley, Michael A Nalls, Toshiharu Ninomiya, Martin J O'Donnell, Bruce M Psaty, Sara L Pulit, Kristiina Rannikmäe, Alexander P Reiner, Kathryn M Rexrode, Kenneth Rice, Stephen S Rich, Paul M Ridker, Natalia S Rost, Peter M Rothwell, Jerome I Rotter, Tatjana Rundek, Ralph L Sacco, Saori Sakaue, Michele M Sale, Veikko Salomaa, Bishwa R Sapkota, Reinhold Schmidt, Carsten O Schmidt, Ulf Schminke, Pankaj Sharma, Agnieszka Slowik, Cathie LM Sudlow, Christian Tanislav, Turgut Tatlisumak, Kent D Taylor, Vincent NS Thijs, Gudmar Thorleifsson, Unnur Thorsteinsdottir, Steffen Tiedt, Stella Trompet, Christophe Tzourio, Cornelia M van Duijn, Matthew Walters, Nicholas J Wareham, Sylvia Wassertheil-Smoller, James G Wilson, Kerri L Wiggins, Qiong Yang, Salim Yusuf, Najaf Amin, Hugo S Aparicio, Donna K Arnett, John Attia, Alexa S Beiser, Claudine Berr, Julie E Buring, Mariana Bustamante, Valeria Caso, Yu-Ching Cheng, Seung Hoan Choi, Ayesha Chowhan, Natalia Cullell, Jean-François Dartigues, Hossein Delavaran, Pilar Delgado, Marcus Dörr, Gunnar Engström, Ian Ford, Wander S Gurpreet, Anders Hamsten, Laura Heitsch, Atsushi Hozawa, Laura Ibanez, Andreea Ilinca, Martin Ingelsson, Motoki Iwasaki, Rebecca D Jackson, Katarina Jood, Pekka Jousilahti, Sara Kaffashian, Lalit Kalra, Masahiro Kamouchi, Takanari Kitazono, Olafur Kjartansson, Manja Kloss, Peter J Koudstaal, Jerzy Krupinski, Daniel L Labovitz, Cathy C Laurie, Christopher R Levi, Linxin Li, Lars Lind, Cecilia M Lindgren, Vasileios Lioutas, Yong Mei Liu, Oscar L Lopez, Hirata Makoto, Nicolas Martinez-Majander, Koichi Matsuda, Naoko Minegishi, Joan Montaner, Andrew P Morris, Elena Muiño, Martina Müller-Nurasyid, Bo Norrving, Soichi Ogishima, Eugenio A Parati, Leema Reddy Peddareddygari, Nancy L Pedersen, Joanna Pera, Markus Perola, Alessandro Pezzini, Silvana Pileggi, Raquel Rabionet, Iolanda Riba-Llena, Marta Ribasés, Jose R Romero, Jaume Roquer, Anthony G Rudd, Antti-Pekka Sarin, Ralhan Sarju, Chloe Sarnowski, Makoto Sasaki, Claudia L Satizabal, Mamoru Satoh, Naveed Sattar, Norie Sawada, Gerli Sibolt, Ásgeir Sigurdsson, Albert Smith, Kenji Sobue, Carolina Soriano-Tárraga, Tara Stanne, O Colin Stine, David J Stott, Konstantin Strauch, Takako Takai, Hideo Tanaka, Kozo Tanno, Alexander Teumer, Liisa Tomppo, Nuria P Torres-Aguila, Emmanuel Touze, Shoichiro Tsugane, Andre G Uitterlinden, Einar M Valdimarsson, Sven J van der Lee, Henry Völzke, Kenji Wakai, David Weir, Stephen R Williams, Charles DA Wolfe, Quenna Wong, Huichun Xu, Taiki Yamaji, Dharambir K Sanghera, Olle Melander, Daniel Strbian, Israel Fernandez-Cadenas, W T Longstreth, Arndt Rolfs, Jun Hata, Daniel Woo, Jonathan Rosand, Guillaume Pare, Jemma C Hopewell, Danish Saleheen, Kari Stefansson, Bradford B Worrall, Steven J Kittner, Sudha Seshadri, Myriam Fornage, Hugh S Markus, Joanna MM Howson, Yoichiro Kamatani, Stephanie Debette, Martin Dichgans, Berr, Claudine, Unit of Cardiovascular and Nutritional Epidemiology [Stockholm, Sweden], Karolinska Institutet [Stockholm]-Institute of Environmental Medicine [Stockholm, Sweden], Stroke Research Group [London, UK] (Department of Brain Repair and Rehabilitation), University of London - UCL [London, UK], MRC Biostatistics Unit [Cambridge, UK], University of Cambridge [UK] (CAM), Department of Public Health and Primary Care [Cambridge, UK] (Institute of Public Health), Fondazione IRCCS Istituto Neurologico 'Carlo Besta', Section of Clinical Immunology [Uppsala, Sweden] (Department of Immunology, Genetics and Pathology), Uppsala University, Department of Surgical Sciences [Uppsala, Sweden], This work was supported by the Swedish Research Council for Health, Working Life and Welfare (Forte) and the Swedish Research Council. Hugh Markus is supported by an NIHR Senior Investigator award. His and Matthew Traylor’s work is supported by infrastructural support from the Cambridge University Hospitals Trust NIHR Biomedical Research Centre., MEGASTROKE project of the International Stroke Genetics Consortium : Malik R, Chauhan G, Traylor M, Sargurupremraj M, Okada Y, Mishra A, Rutten-Jacobs L, Giese AK, van der Laan SW, Gretarsdottir S, Anderson CD, Chong M, Adams HH, Ago T, Almgren P, Amouyel P, Ay H, Bartz RM, Benavente OR, Bevan S, Boncoraglio GB, Brown RD Jr, Butterworth AS, Carrera C, Carty CL, Chasman DI, Chen WM, Cole JW, Correa A, Cotlarciuc I, Cruchaga C, Danesh J, de Bakker PI, DeStefano AL, Hoed MD, Duan Q, Engelter ST, Falcone GJ, Gottesman RF, Grewal RP, Gudnason V, Gustafsson S, Haessler J, Harris TB, Hassan A, Havulinna AS, Heckbert SR, Holliday EG, Howard G, Hsu FC, Hyacinth HI, Ikram MA, Ingelsson E, Irvin MR, Jian X, Jiménez-Conde J, Johnson JA, Jukema JW, Kanai M, Keene KL, Kissela BM, Kleindorfer DO, Kooperberg C, Kubo M, Lange LA, Langefeld CD, Langenberg C, Launer LJ, Lee JM, Lemmens R, Leys D, Lewis CM, Lin WY, Lindgren AG, Lorentzen E, Magnusson PK, Maguire J, Manichaikul A, McArdle PF, Meschia JF, Mitchell BD, Mosley TH, Nalls MA, Ninomiya T, O'Donnell MJ, Psaty BM, Pulit SL, Rannikmäe K, Reiner AP, Rexrode KM, Rice K, Rich SS, Ridker PM, Rost NS, Rothwell PM, Rotter JI, Rundek T, Sacco RL, Sakaue S, Sale MM, Salomaa V, Sapkota BR, Schmidt R, Schmidt CO, Schminke U, Sharma P, Slowik A, Sudlow CL, Tanislav C, Tatlisumak T, Taylor KD, Thijs VN, Thorleifsson G, Thorsteinsdottir U, Tiedt S, Trompet S, Tzourio C, van Duijn CM, Walters M, Wareham NJ, Wassertheil-Smoller S, Wilson JG, Wiggins KL, Yang Q, Yusuf S, Amin N, Aparicio HS, Arnett DK, Attia J, Beiser AS, Berr C, Buring JE, Bustamante M, Caso V, Cheng YC, Choi SH, Chowhan A, Cullell N, Dartigues JF, Delavaran H, Delgado P, Dörr M, Engström G, Ford I, Gurpreet WS, Hamsten A, Heitsch L, Hozawa A, Ibanez L, Ilinca A, Ingelsson M, Iwasaki M, Jackson RD, Jood K, Jousilahti P, Kaffashian S, Kalra L, Kamouchi M, Kitazono T, Kjartansson O, Kloss M, Koudstaal PJ, Krupinski J, Labovitz DL, Laurie CC, Levi CR, Li L, Lind L, Lindgren CM, Lioutas V, Liu YM, Lopez OL, Makoto H, Martinez-Majander N, Matsuda K, Minegishi N, Montaner J, Morris AP, Muiño E, Müller-Nurasyid M, Norrving B, Ogishima S, Parati EA, Peddareddygari LR, Pedersen NL, Pera J, Perola M, Pezzini A, Pileggi S, Rabionet R, Riba-Llena I, Ribasés M, Romero JR, Roquer J, Rudd AG, Sarin AP, Sarju R, Sarnowski C, Sasaki M, Satizabal CL, Satoh M, Sattar N, Sawada N, Sibolt G, Sigurdsson Á, Smith A, Sobue K, Soriano-Tárraga C, Stanne T, Stine OC, Stott DJ, Strauch K, Takai T, Tanaka H, Tanno K, Teumer A, Tomppo L, Torres-Aguila NP, Touze E, Tsugane S, Uitterlinden AG, Valdimarsson EM, van der Lee SJ, Völzke H, Wakai K, Weir D, Williams SR, Wolfe CD, Wong Q, Xu H, Yamaji T, Sanghera DK, Melander O, Jern C, Strbian D, Fernandez-Cadenas I, Longstreth WT Jr, Rolfs A, Hata J, Woo D, Rosand J, Pare G, Hopewell JC, Saleheen D, Stefansson K, Worrall BB, Kittner SJ, Seshadri S, Fornage M, Markus HS, Howson JM, Kamatani Y, Debette S, Dichgans M., Larsson, Susanna C [0000-0003-0118-0341], Apollo - University of Cambridge Repository, and Neurology
Subjects: medicine.medical_specialty, Neurology, Heredity, Neurologi, [SDV]Life Sciences [q-bio], chemistry.chemical_element, Calcium, Polymorphism, Single Nucleotide, Gastroenterology, Article, Brain Ischemia, Brain ischemia, 03 medical and health sciences, 0302 clinical medicine, Human genetics, Internal medicine, Mendelian randomization, Medicine, Humans, Magnesium, 030212 general & internal medicine, Stroke, Herència (Biologia), Genètica humana, business.industry, Neurosciences, Mendelian Randomization Analysis, Odds ratio, medicine.disease, Confidence interval, 3. Good health, [SDV] Life Sciences [q-bio], Intracranial Embolism, chemistry, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Neurology (clinical), business, 030217 neurology & neurosurgery, Neurovetenskaper
Abstract: Comment inThe yin and yang of magnesium and calcium: New genetic insights for stroke? [Neurology. 2019]; International audience; Objective To determine whether serum magnesium and calcium concentrations are causally associated with ischemic stroke or any of its subtypes using the mendelian randomization approach. Methods Analyses were conducted using summary statistics data for 13 single-nucleotide polymorphisms robustly associated with serum magnesium (n = 6) or serum calcium (n = 7) concentrations. The corresponding data for ischemic stroke were obtained from the MEGASTROKE consortium (34,217 cases and 404,630 noncases). Results In standard mendelian randomization analysis, the odds ratios for each 0.1 mmol/L (about 1 SD) increase in genetically predicted serum magnesium concentrations were 0.78 (95% confidence interval [CI] 0.69-0.89; p = 1.3 × 10 −4) for all ischemic stroke, 0.63 (95% CI 0.50-0.80; p = 1.6 × 10 −4) for cardioembolic stroke, and 0.60 (95% CI 0.44-0.82; p = 0.001) for large artery stroke; there was no association with small vessel stroke (odds ratio 0.90, 95% CI 0.67-1.20; p = 0.46). Only the association with cardioembolic stroke was robust in sensitivity analyses. There was no association of genetically predicted serum calcium concentrations with all ischemic stroke (per 0.5 mg/dL [about 1 SD] increase in serum calcium: odds ratio 1.03, 95% CI 0.88-1.21) or with any subtype. Conclusions This study found that genetically higher serum magnesium concentrations are associated with a reduced risk of cardioembolic stroke but found no significant association of genetically higher serum calcium concentrations with any ischemic stroke subtype.
Published: 2019

30. Identification of additional risk loci for stroke and small vessel disease

Author: Matthew Traylor, Vilmundur Gudnason, Kerri L. Wiggins, Christophe Tzourio, Reinhold E. Schmidt, Hugo J. Aparicio, Tamara B. Harris, Audrey Y. Chu, Oscar R. Benavente, Anton J. M. de Craen, Nancy L. Pedersen, Lars Lannfelt, Didier Leys, Erkki Vartiainen, Myriam Fornage, Marileen L.P. Portegies, Nicholas L. Smith, Daniel Woo, Martin Dichgans, John W. Cole, Christina Jern, Christopher R Levi, Kenneth Rice, André G. Uitterlinden, Rebecca F. Gottesman, M. Arfan Ikram, Ralph L. Sacco, Cornelia M. van Duijn, Samuli Ripatti, Anita L. DeStefano, Donna K. Arnett, Curtis R. French, Tobias Kurth, Tomi Pastinen, Raji P. Grewal, Susan R. Heckbert, Jordi Jimenez-Conde, Jemma C. Hopewell, Cecilia M. Lindgren, Azadeh Reyahi, Michèle M. Sale, Marcello Ricardo Paulista Markus, Albert Hofman, Seung Hoan Choi, Peter J. Koudstaal, Veikko Salomaa, Robert Clarke, Arne Lindgren, B. Gwen Windham, Farid Radmanesh, Peter M. Rothwell, Carsten Oliver Schmidt, Xueqiu Jian, David S. Knopman, Yongmei Liu, Joan Montaner, Jean-François Dartigues, Paul M. Ridker, Julie A. Johnson, Stefan Gustafsson, Jerome I. Rotter, Manja Kloss, Tatjana Rundek, David J. Stott, Ganesh Chauhan, Ordan J. Lehmann, Ali Moussavi Nik, Marcel den Hoed, Alessandro Pezzini, Jin-Moo Lee, Hans J. Grabe, Sylvia Wassertheil-Smoller, Anders Hamsten, Thomas H. Mosley, Muralidharan Sargurupremraj, Lenore J. Launer, Kathryn M. Rexrode, Quenna Wong, Jonathan Rosand, David A. Bennett, Philip L. De Jager, James F. Meschia, Alexa S. Beiser, J. Wouter Jukema, Traci M. Bartz, Mike A. Nalls, Cathie Sudlow, Erik Ingelsson, Yoichiro Kamatani, Ulf Schminke, Joris Deelen, Stéphanie Debette, Andrew P. Morris, Aki S. Havulinna, Sudha Seshadri, Bradford B. Worrall, Stephen S. Rich, Lars Lindgren, Hieab H.H. Adams, Ani Manichaikul, Jean-Sébastien Vidal, Bruce M. Psaty, Julie E. Buring, Jean Dallongeville, Oscar L. Lopez, Corey R. Arnold, Olle Melander, Olafur Kjartansson, Alexander Teumer, Sarah J. Childs, William T. Longstreth, Charles C. White, Stefan T. Engelter, Daniel I. Chasman, Norrina B. Allen, Rainer Malik, Vincent Thijs, Stella Trompet, Joshua C. Bis, Ian Ford, Peter Carlsson, Céline Bellenguez, Sara L. Pulit, Pankaj Sharma, Patrik K. E. Magnusson, Flora Xue, Giorgio B. Boncoraglio, Mark Lathrop, Melissa E. Garcia, Andrew D. Johnson, Steve Bevan, Albert V. Smith, Claudia L. Satizabal, Agnieszka Slowik, Michael Griswold, Claudine Berr, and Hugh S. Markus
Subjects: Adult, Male, 0301 basic medicine, Adolescent, Population, Genome-wide association study, Biology, Bioinformatics, Article, Brain ischemia, Mice, Young Adult, 03 medical and health sciences, 0302 clinical medicine, SDG 3 - Good Health and Well-being, medicine, Animals, Humans, Child, education, Allele frequency, Stroke, Aged, Aged, 80 and over, education.field_of_study, Cerebral infarction, Forkhead Transcription Factors, Odds ratio, Middle Aged, 16. Peace & justice, medicine.disease, R1, 3. Good health, Minor allele frequency, 030104 developmental biology, Genetic Loci, Cerebral Small Vessel Diseases, Child, Preschool, Female, Neurology (clinical), 030217 neurology & neurosurgery, Genome-Wide Association Study
Abstract: Background Genetic determinants of stroke, the leading neurological cause of death and disability, are poorly understood and have seldom been explored in the general population. Our aim was to identify additional loci for stroke by doing a meta-analysis of genome-wide association studies. Methods For the discovery sample, we did a genome-wide analysis of common genetic variants associated with incident stroke risk in 18 population-based cohorts comprising 84â€ˆ961 participants, of whom 4348 had stroke. Stroke diagnosis was ascertained and validated by the study investigators. Mean age at stroke ranged from 45Â·8 years to 76Â·4 years, and data collection in the studies took place between 1948 and 2013. We did validation analyses for variants yielding a significant association (at pâˆ’6) with all-stroke, ischaemic stroke, cardioembolic ischaemic stroke, or non-cardioembolic ischaemic stroke in the largest available cross-sectional studies (70â€ˆ804 participants, of whom 19â€ˆ816 had stroke). Summary-level results of discovery and follow-up stages were combined using inverse-variance weighted fixed-effects meta-analysis, and in-silico lookups were done in stroke subtypes. For genome-wide significant findings (at pâˆ’8), we explored associations with additional cerebrovascular phenotypes and did functional experiments using conditional (inducible) deletion of the probable causal gene in mice. We also studied the expression of orthologs of this probable causal gene and its effects on cerebral vasculature in zebrafish mutants. Findings We replicated seven of eight known loci associated with risk for ischaemic stroke, and identified a novel locus at chromosome 6p25 (rs12204590, near FOXF2) associated with risk of all-stroke (odds ratio [OR] 1Â·08, 95% CI 1Â·05â€“1Â·12, p=1Â·48â€ˆÃ—â€ˆ10âˆ’8; minor allele frequency 21%). The rs12204590 stroke risk allele was also associated with increased MRI-defined burden of white matter hyperintensityâ€”a marker of cerebral small vessel diseaseâ€”in stroke-free adults (n=21â€ˆ079; p=0Â·0025). Consistently, young patients (aged 2â€“32 years) with segmental deletions of FOXF2 showed an extensive burden of white matter hyperintensity. Deletion of Foxf2 in adult mice resulted in cerebral infarction, reactive gliosis, and microhaemorrhage. The orthologs of FOXF2 in zebrafish (foxf2b and foxf2a) are expressed in brain pericytes and mutant foxf2bâˆ’/âˆ’ cerebral vessels show decreased smooth muscle cell and pericyte coverage. Interpretation We identified common variants near FOXF2 that are associated with increased stroke susceptibility. Epidemiological and experimental data suggest that FOXF2 mediates this association, potentially via differentiation defects of cerebral vascular mural cells. Further expression studies in appropriate human tissues, and further functional experiments with long follow-up periods are needed to fully understand the underlying mechanisms. Funding NIH, NINDS, NHMRC, CIHR, European national research institutions, Fondation Leducq.
Published: 2016

31. Phenotypic Refinement of Heart Failure in a National Biobank Facilitates Genetic Discovery

Author: Barry London, Christopher Newton-Cheh, Sekar Kathiresan, Seung Hoan Choi, Dan M. Roden, Mary E. Haas, J. Gustav Smith, Quinn S. Wells, Lu-Chen Weng, Steven A. Lubitz, Patrick T. Ellinor, Rebecca T. Levinson, M. Benjamin Shoemaker, Mark Chaffin, Krishna G. Aragam, Gregory McDermott, and Mark E. Lindsay
Subjects: 0303 health sciences, medicine.medical_specialty, business.industry, Cardiomyopathy, Genome-wide association study, 030204 cardiovascular system & hematology, medicine.disease, Heritable disorder, Bioinformatics, Biobank, Phenotype, Article, 03 medical and health sciences, 0302 clinical medicine, Nonischemic cardiomyopathy, Physiology (medical), Heart failure, medicine, Medical genetics, Cardiology and Cardiovascular Medicine, business, 030304 developmental biology
Abstract: Background: Heart failure (HF) is a morbid and heritable disorder for which the biological mechanisms are incompletely understood. We therefore examined genetic associations with HF in a large national biobank, and assessed whether refined phenotypic classification would facilitate genetic discovery. Methods: We defined all-cause HF among 488 010 participants from the UK Biobank and performed a genome-wide association analysis. We refined the HF phenotype by classifying individuals with left ventricular dysfunction and without coronary artery disease as having nonischemic cardiomyopathy (NICM), and repeated a genetic association analysis. We then pursued replication of lead HF and NICM variants in independent cohorts, and performed adjusted association analyses to assess whether identified genetic associations were mediated through clinical HF risk factors. In addition, we tested rare, loss-of-function mutations in 24 known dilated cardiomyopathy genes for association with HF and NICM. Finally, we examined associations between lead variants and left ventricular structure and function among individuals without HF using cardiac magnetic resonance imaging (n=4158) and echocardiographic data (n=30 201). Results: We identified 7382 participants with all-cause HF in the UK Biobank. Genome-wide association analysis of all-cause HF identified several suggestive loci ( P –6 ), the majority linked to upstream HF risk factors, ie, coronary artery disease ( CDKN2B-AS1 and MAP3K7CL ) and atrial fibrillation ( PITX2 ). Refining the HF phenotype yielded a subset of 2038 NICM cases. In contrast to all-cause HF, genetic analysis of NICM revealed suggestive loci that have been implicated in dilated cardiomyopathy ( BAG3 , CLCNKA-ZBTB17 ). Dilated cardiomyopathy signals arising from our NICM analysis replicated in independent cohorts, persisted after HF risk factor adjustment, and were associated with indices of left ventricular dysfunction in individuals without clinical HF. In addition, analyses of loss-of-function variants implicated BAG3 as a disease susceptibility gene for NICM (loss-of-function variant carrier frequency=0.01%; odds ratio,12.03; P =3.62×10 –5 ). Conclusions: We found several distinct genetic mechanisms of all-cause HF in a national biobank that reflect well-known HF risk factors. Phenotypic refinement to a NICM subtype appeared to facilitate the discovery of genetic signals that act independently of clinical HF risk factors and that are associated with subclinical left ventricular dysfunction.
Published: 2018

32. Frequency of Cardiac Rhythm Abnormalities in a Half Million Adults

Author: Ludovic Trinquart, Shaan Khurshid, Patrick T. Ellinor, Emelia J. Benjamin, Elizabeth Y. Wang, Steven A. Lubitz, Seung Hoan Choi, and Lu-Chen Weng
Subjects: Male, Bradycardia, medicine.medical_specialty, Action Potentials, Comorbidity, 030204 cardiovascular system & hematology, Risk Assessment, Article, 03 medical and health sciences, 0302 clinical medicine, Heart Conduction System, Heart Rate, Risk Factors, Interquartile range, Physiology (medical), Internal medicine, Atrial Fibrillation, Prevalence, Humans, Medicine, Prospective Studies, 030212 general & internal medicine, Prospective cohort study, Life Style, Aged, business.industry, Incidence, Hazard ratio, Age Factors, Arrhythmias, Cardiac, Atrial fibrillation, Middle Aged, medicine.disease, United Kingdom, Confidence interval, Heart failure, Cardiology, Female, Electrical conduction system of the heart, medicine.symptom, Cardiology and Cardiovascular Medicine, business
Abstract: Background: The frequency of cardiac rhythm abnormalities and their risk factors in community-dwelling adults are not well characterized. Methods: We determined the frequency of rhythm abnormalities in the UK Biobank, a national prospective cohort. We tested associations between risk factors and incident rhythm abnormalities using multivariable proportional hazards regression. Results: Of 502 627 adults (median age, 58 years [interquartile range, 13]; 54.4% women), 2.35% had a baseline rhythm abnormality. The prevalence increased with age with 4.84% of individuals aged 65 to 73 years affected. During 3 368 332 person-years of follow-up, 15 906 new rhythm abnormalities were detected (4.72 per 1000 person-years; 95% confidence interval [CI]: 4.65–4.80). Atrial fibrillation (3.11 per 1000 person-years; 95% CI: 3.05–3.17), bradyarrhythmias (0.89 per 1000 person-years; 95% CI: 0.86–0.92), and conduction system diseases (1.06 per 1000 person-years; 95% CI: 1.02–1.09) were more common than supraventricular (0.51 per 1000 person-years; 95% CI: 0.48–0.53) and ventricular arrhythmias (0.57 per 1000 person-years; 95% CI: 0.55–0.60). Older age (hazard ratio [HR]: 2.35 per 10-year increase; 95% CI: 2.29–2.41; P P P P P Conclusions: The frequency of rhythm abnormalities in middle-aged to older community-dwelling adults is substantial. Atrial fibrillation, bradyarrhythmias, and conduction system diseases account for most rhythm conditions.
Published: 2018

33. P1‐149: THE ALZHEIMER'S DISEASE SEQUENCING PROJECT (ADSP) DATA UPDATE 2018

Author: Jason Waligorski, John J. Farrell, Eric Boerwinkle, Yuk Yee Leung, Laura B. Cantwell, Amanda B. Kuzma, Seung Hoan Choi, Sudha Seshadri, Elizabeth L. Appelbaum, Tatiana Foroud, Adam C. Naj, Namrata Gupta, Gerard D. Schellenberg, Kelley Faber, Otto Valladares, Joshua C. Bis, Li-San Wang, Liming Qu, Kara L. Hamilton-Nelson, Anita L. DeStefano, Yi Zhao, Donna M. Muzny, Briana Vogel, Robert S. Fulton, Dolly Reyes-Dumeyer, and William J Salerno
Subjects: Psychiatry and Mental health, Cellular and Molecular Neuroscience, Developmental Neuroscience, Epidemiology, business.industry, Health Policy, Medicine, Neurology (clinical), Computational biology, Disease, Geriatrics and Gerontology, business
Published: 2018

34. Genome-wide polygenic scores for common diseases identify individuals with risk equivalent to monogenic mutations

Author: Krishna G. Aragam, Carolina Roselli, Pradeep Natarajan, Sekar Kathiresan, Seung Hoan Choi, Mark Chaffin, Steven A. Lubitz, Mary E. Haas, Amit Khera, Patrick T. Ellinor, Eric S. Lander, Massachusetts Institute of Technology. Department of Biology, and Broad Institute of MIT and Harvard
Subjects: Adult, Male, 0301 basic medicine, Multifactorial Inheritance, Population, Type 2 diabetes, Disease, Biology, medicine.disease_cause, Bioinformatics, Polymorphism, Single Nucleotide, Inflammatory bowel disease, Coronary artery disease, 03 medical and health sciences, Breast cancer, Risk Factors, Genetics, medicine, Humans, Genetic Predisposition to Disease, education, Aged, Mutation, education.field_of_study, Middle Aged, medicine.disease, 030104 developmental biology, Female, Genome-Wide Association Study
Abstract: A key public health need is to identify individuals at high risk for a given disease to enable enhanced screening or preventive therapies. Because most common diseases have a genetic component, one important approach is to stratify individuals based on inherited DNA variation 1 . Proposed clinical applications have largely focused on finding carriers of rare monogenic mutations at several-fold increased risk. Although most disease risk is polygenic in nature 2–5 , it has not yet been possible to use polygenic predictors to identify individuals at risk comparable to monogenic mutations. Here, we develop and validate genome-wide polygenic scores for five common diseases. The approach identifies 8.0, 6.1, 3.5, 3.2, and 1.5% of the population at greater than threefold increased risk for coronary artery disease, atrial fibrillation, type 2 diabetes, inflammatory bowel disease, and breast cancer, respectively. For coronary artery disease, this prevalence is 20-fold higher than the carrier frequency of rare monogenic mutations conferring comparable risk 6 . We propose that it is time to contemplate the inclusion of polygenic risk prediction in clinical care, and discuss relevant issues.
Published: 2018

35. Multi-ethnic genome-wide association study for atrial fibrillation

Author: Marcus E. Kleber, Raji P. Grewal, Yingchang Lu, Sanghamitra Mohanty, Harry J.G.M. Crijns, Han Sun, Ilkka Seppälä, Jonathan D. Smith, Albert Hofman, Yii-Der Ida Chen, Diane Fatkin, Patrik K. E. Magnusson, Pil Sung Yang, Jari Laurikka, Saman Nazarian, Peter W. Macfarlane, Natalia S. Rost, Sekar Kathiresan, Heribert Schunkert, Sandosh Padmanabhan, Tõnu Esko, Bruno H. Stricker, Rebecca Gutmann, Alfredo José Mansur, Jonathan Rosand, Jesper Hastrup Svendsen, Alvaro Alonso, J. Gustav Smith, Benjamin Neumann, John Barnard, Christopher D. Anderson, Joanna Pera, Samir Saba, Lynne J. Hocking, Siew-Kee Low, Daniel I. Chasman, Patrick T. Ellinor, Nancy L. Pedersen, Stephan B. Felix, Vilmundur Gudnason, Kjell Nikus, Kahraman Tanriverdi, David J. Porteous, Samuel C. Dudley, Clive R. Pullinger, Tamara B. Harris, Barry London, Lorenz Risch, Ruth J. F. Loos, Rainer Malik, Isabelle C. Van Gelder, John F. Carlquist, Lena Refsgaard, Carolina Roselli, Albert Y. Sun, Man Li, Lenore J. Launer, Anders Hamsten, Svati H. Shah, Lin Y. Chen, Martina Müller-Nurasyid, Michiel Rienstra, Kent D. Taylor, Katharina Schramm, Jennifer A. Brody, Honghuang Lin, Eric Boerwinkle, Rozenn N. Lemaitre, Olle Melander, Hugh Calkins, Elsayed Z. Soliman, Moritz F. Sinner, Heather L. Bloom, Nicholas L. Smith, Nada Esa, John W. Cole, Maartje N. Niemeijer, David R. Van Wagoner, Anubha Mahajan, Roopinder K. Sandhu, Henry J. Lin, Jordi Jimenez-Conde, Ian Ford, Eue Keun Choi, Stacey Knight, Scott M. Damrauer, Markku Eskola, Claudia Schurman, Stuart A. Scott, Sara L. Pulit, Raymond Noordam, Mika Kähönen, Jay A. Montgomery, Agnieszka Slowik, Esra Gucuk Ipek, Joylene E. Siland, Lingyao Zeng, Andrew P. Morris, Oscar H. Franco, Bas L.J.H. Kietselaer, Adnan Kastrati, Dan E. Arking, José Eduardo Krieger, J. Wouter Jukema, Stefan Gustafsson, Nathan R. Tucker, Zachary T. Yoneda, Daniel Woo, Winfried März, Lauren Margolin, Uwe Völker, Stefan Kääb, Marju Orho-Melander, Lars Lind, Yoichiro Kamatani, Maris Teder-Laving, Paul M. Ridker, Bradford B. Worrall, Jaemin Shim, Bob Weijs, Ingrid E. Christophersen, Kenneth B. Margulies, James P. Cook, Graciela Delgado, Andrea Natale, Stefan Weiss, Gustav Ahlberg, Jie Huang, Guillaume Paré, M. Benjamin Shoemaker, Marcus Dörr, Arnljot Tveit, Elton A. M. P. Dudink, Thomas P. Cappola, Bruce M. Psaty, Alaa Shalaby, Gregory M. Marcus, Sébastien Thériault, Niek Verweij, Traci M. Bartz, Thorsten Kessler, Michael Morley, Xiuqing Guo, Alexandre C. Pereira, Efthymia Vlachopoulou, Albert V. Smith, Andrea R. V. R. Horimoto, David Conen, Erik Ingelsson, Jie Yao, Raul Weiss, David D. McManus, Michiaki Kubo, Lu-Chen Weng, Michael A. Rosenberg, Nona Sotoodehnia, Jennifer E. Huffman, Hui Nam Pak, Dan M. Roden, Peter Weeke, Joshua C. Bis, Archie Campbell, Marta Ribasés, Renee Johnson, Renate B. Schnabel, Christian M. Shaffer, Krishna G. Aragam, Seung Hoan Choi, André G. Uitterlinden, Morten S. Olesen, Toshihiro Tanaka, Daniel J. Rader, Mina K. Chung, Stella Trompet, Steven A. Lubitz, Martin Dichgans, Peter Almgren, Christine M. Albert, Blair H. Smith, Petra Katschnig-Winter, Joshua C. Denny, Christopher Newton-Cheh, Paulus Kirchhof, Namrata Gupta, Emelia J. Benjamin, Stefanie Aeschbacher, Marja-Liisa Lokki, Jorge A. Wong, Quinn S. Wells, Jussi Hernesniemi, Cecilia M. Lindgren, Mark Chaffin, Kaoru Ito, Jerome I. Rotter, Michael J. Cutler, Kerri L. Wiggins, Maryam Kavousi, Nathan A. Bihlmeyer, Bastiaan Geelhoed, Susan R. Heckbert, Caroline Hayward, Alexander Teumer, Paul L. Huang, Terho Lehtimäki, Juha Sinisalo, John P. Kane, Kirsten Leineweber, Tanja Zeller, Hong Euy Lim, Kathryn L. Lunetta, Brian R. Daniels, Heidi Oellers, Biqi Wang, Pim van der Harst, Peter M. Nilsson, Dawood Darbar, Erwin B. Bottinger, Leo-Pekka Lyytikäinen, Epidemiology, Internal Medicine, RS: Carim - H01 Clinical atrial fibrillation, Cardiologie, MUMC+: MA Cardiologie (3), RS: CARIM - R2.01 - Clinical atrial fibrillation, RS: CARIM - R3.11 - Imaging, MUMC+: MA Med Staf Spec Cardiologie (9), MUMC+: MA Med Staf Artsass Cardiologie (9), Cardiovascular Centre (CVC), and MUMC+: MA Cardiologie (9)
Subjects: 0301 basic medicine, medicine.medical_specialty, Identification, Annotation, Quantitative Trait Loci, Genome-wide association study, 030204 cardiovascular system & hematology, Quantitative trait locus, Biology, methods [Genome-Wide Association Study], Gene, genetics [Ethnic Groups], Article, DISEASE, 03 medical and health sciences, COMPONENTS-ANALYSIS, 0302 clinical medicine, ddc:570, Atrial Fibrillation, Cardiac conduction, Ethnicity, Genetics, medicine, Humans, Genetic Predisposition to Disease, genetics [Atrial Fibrillation], Genetic association, Imputation, ethnology [Atrial Fibrillation], Loci, Case-control study, Variants, METANÁLISE, Polymorphic ventricular-tachycardia, 030104 developmental biology, GWAS CATALOG, Susceptibility, Case-Control Studies, Expression quantitative trait loci, genetics [Ethnicity], Medical genetics, Transcriptome, Imputation (genetics), Mutations, Genome-Wide Association Study
Abstract: Atrial fibrillation (AF) affects more than 33 million individuals worldwide 1 and has a complex heritability 2 . We conducted the largest meta-analysis of genome-wide association studies (GWAS) for AF to date, consisting of more than half a million individuals, including 65,446 with AF. In total, we identified 97 loci significantly associated with AF, including 67 that were novel in a combined-ancestry analysis, and 3 that were novel in a European-specific analysis. We sought to identify AF-associated genes at the GWAS loci by performing RNA-sequencing and expression quantitative trait locus analyses in 101 left atrial samples, the most relevant tissue for AF. We also performed transcriptome-wide analyses that identified 57 AF-associated genes, 42 of which overlap with GWAS loci. The identified loci implicate genes enriched within cardiac developmental, electrophysiological, contractile and structural pathways. These results extend our understanding of the biological pathways underlying AF and may facilitate the development of therapeutics for AF.
Published: 2018

36. Heritability of Atrial Fibrillation

Author: Lu-Chen Weng, Emelia J. Benjamin, J. Gustav Smith, Derek Klarin, Kathryn L. Lunetta, Seung Hoan Choi, Patrick T. Ellinor, Steven A. Lubitz, Mark Chaffin, Carolina Roselli, Sekar Kathiresan, Josée Dupuis, Po-Ru Loh, Christopher Newton-Cheh, and Olivia L. Hulme
Subjects: Male, 0301 basic medicine, medicine.medical_specialty, Population, Genome-wide association study, 030204 cardiovascular system & hematology, Biology, Polymorphism, Single Nucleotide, Linkage Disequilibrium, White People, Article, 03 medical and health sciences, 0302 clinical medicine, Gene Frequency, Risk Factors, Internal medicine, Atrial Fibrillation, Genetic variation, Genetics, medicine, Humans, Genetic Predisposition to Disease, education, Allele frequency, Genetics (clinical), Aged, education.field_of_study, Middle Aged, Heritability, Explained variation, United Kingdom, Confidence interval, Minor allele frequency, 030104 developmental biology, Female, Cardiology and Cardiovascular Medicine, Genome-Wide Association Study
Abstract: Background— Previous reports have implicated multiple genetic loci associated with AF, but the contributions of genome-wide variation to AF susceptibility have not been quantified. Methods and Results— We assessed the contribution of genome-wide single-nucleotide polymorphism variation to AF risk (single-nucleotide polymorphism heritability, h 2 g ) using data from 120 286 unrelated individuals of European ancestry (2987 with AF) in the population-based UK Biobank. We ascertained AF based on self-report, medical record billing codes, procedure codes, and death records. We estimated h 2 g using a variance components method with variants having a minor allele frequency ≥1%. We evaluated h 2 g in age, sex, and genomic strata of interest. The h 2 g for AF was 22.1% (95% confidence interval, 15.6%–28.5%) and was similar for early- versus older-onset AF (≤65 versus >65 years of age), as well as for men and women. The proportion of AF variance explained by genetic variation was mainly accounted for by common (minor allele frequency, ≥5%) variants (20.4%; 95% confidence interval, 15.1%–25.6%). Only 6.4% (95% confidence interval, 5.1%–7.7%) of AF variance was attributed to variation within known AF susceptibility, cardiac arrhythmia, and cardiomyopathy gene regions. Conclusions— Genetic variation contributes substantially to AF risk. The risk for AF conferred by genomic variation is similar to that observed for several other cardiovascular diseases. Established AF loci only explain a moderate proportion of disease risk, suggesting that further genetic discovery, with an emphasis on common variation, is warranted to understand the causal genetic basis of AF.
Published: 2017

37. Convergent genetic and expression data implicate immunity in Alzheimer's disease

Author: John R. Gilbert, Simon Lovestone, Diana Zelenika, Walter A. Kukull, Peter Passmore, Chiao-Feng Lin, Nathalie Fievet, Brian W. Kunkle, Dominique Campion, Philip L. De Jager, Adam C. Naj, Kara L. Hamilton-Nelson, Lina Keller, Jean-Charles Lambert, Denise Harold, Paul K. Crane, John Powell, Kathryn L. Lunetta, Paolo Caffarra, Lei Yu, Anthony Bayer, Tricia A. Thornton-Wells, Christiane Reitz, Eric B. Larson, Florentino Sanchez Garcia, Lindsay A. Farrer, Charlene Thomas, Ekaterina Rogaeva, Victoria Alavarez, Alfredo Ramirez, Pascale Barberger-Gateau, Dan Rujescu, Paul Hollingworth, Margaret A. Pericak-Vance, Daniela Galimberti, J. Kornhuber, Alexey Vedernikov, Philippe Amouyel, Peter Holmans, Gianfranco Spalletta, Carole Dufouil, Wolfgang Maier, Patrick G. Kehoe, Florence Pasquier, Lesley Jones, Harald Hampel, Stephen Todd, Valur Emilsson, Pau Pastor, Manuel Mayhaus, Claudine Berr, Seth Love, Michelangelo Mancuso, Mikko Hiltunen, Simon Mead, Hilkka Soininen, Vincent Deramecourt, Bernadette McGuinness, Magda Tsolaki, Jean-François Dartigues, Jordi Clarimón, Marie-Thérèse Bihoreau, Laura Fratiglioni, Duane Beekly, Sabrina Pichler, Caroline Graff, Albert V. Smith, Nick C. Fox, Amy Gerrish, Karen Ritchie, Carlos Cruchaga, John Hardy, Benedetta Nacmias, Maria Candida Deniz Naranjo, Christine Van Broeckhoven, Laura B. Cantwell, Minerva M. Carrasquillo, Richard Mayeux, Karolien Bettens, Vincent Chouraki, Clive Holmes, Thomas H. Mosley, David C. Rubinsztein, Gyungah Jun, Anita L. DeStefano, Lenore J. Launer, Alexander Richards, Jerome I. Rotter, Lars Lannfelt, Annette L. Fitzpatrick, Fanggeng Zou, Joseph D. Buxbaum, Cristina Razquin, Mercè Boada, Najaf Amin, Palmi V. Jonsson, Martin Dichgans, Thomas J. Montine, Yoichiro Kamatani, Debby W. Tsuang, Alexis Brice, Hakon Hakonarson, John Collinge, Albert Hofman, Eden R. Martin, Oscar L. Lopez, Olivier Hanon, Melanie L. Dunstan, Kevin Morgan, Nicola Jones, Cornelia M. van Duijn, Valentina Escott-Price, Vilmundur Gudnason, Susanne Moebus, Peter St George-Hyslop, Michael Conlon O'Donovan, Michael Gill, Tim Becker, Markus M. Nöthen, Sandro Sorbi, Céline Bellenguez, Mike A. Nalls, Martin Ingelsson, Otto Valladares, Kristel Sleegers, Sudha Seshadri, Gerard D. Schellenberg, María J. Bullido, Patrizia Mecocci, Eric Boerwinkle, Michael John Owen, Helena Schmidt, Kristelle Brown, Julie Williams, Renée F.A.G. de Bruijn, Jonathan L. Haines, Mark Lathrop, Maria Del Zompo, Denis A. Evans, Rebecca Sims, Badri N. Vardarajan, John S. K. Kauwe, Luc Letteneur, Agustín Ruiz, David Craig, Steven G. Younkin, Bruce M. Psaty, Ignacio Mateo, Tatiana Foroud, David Wallon, P. Bosco, Alberti Lleò, Amanda J. Myers, Alberto Pilotto, Petra Proitsi, Reinhold Schmidt, Matthew J. Huentelman, David A. Bennett, Onofre Combarros, Kelley Faber, Gudny Eiriksdottir, M. Arfan Ikram, Lluís Tárraga, Francesco Panza, Carla A. Ibrahim-Verbaas, Joshua C. Bis, Li-San Wang, Matthias Riemenschneider, Gary W. Beecham, Alison Goate, Seung Hoan Choi, John Gallacher, Robert Clarke, Didier Hannequin, Deborah Blacker, Frank Jessen, Christophe Tzourio, Tamara B. Harris, Benjamin Grenier-Boley, Paola Bossù, Janet A. Johnston, M. Ilyas Kamboh, Giancarlo Russo, Timothy Stone, Carol Brayne, Eliecer Coto, French National Foundation on Alzheimer’s Disease and Related Disorders, Institut Pasteur, National Institutes of Health (US), Centre National de Genotypage (France), Fédération pour la Recherche sur le Cerveau (France), Erasmus University Rotterdam, Medical Research Council (UK), International Genomics of Alzheimer's Disease Consortium (IGAP), Neurology, and Epidemiology
Subjects: Pathway analysis, Epidemiology, ALIGATOR, Alzheimer's disease, Cholesterol metabolism, Dementia, Endocytosis, Immune response, Neurodegeneration, Ubiquitination, Weighted gene co-expression network analysis, Medizin, Genome-wide association study, genetics [Alzheimer Disease], Gene expression, Genetics, education.field_of_study, Health Policy, Brain, Single Nucleotide, 3. Good health, Psychiatry and Mental Health, Algorithms, Alzheimer Disease, Genome-Wide Association Study, Humans, Polymorphism, Single Nucleotide, Genetic Predisposition to Disease, Developmental Neuroscience, Neurology (clinical), Geriatrics and Gerontology, Cellular and Molecular Neuroscience, Alzheimer’s disease, metabolism [Alzheimer Disease], Population, Genomics, Biology, Aligator, Article, Biological pathway, SDG 3 - Good Health and Well-being, medicine, ddc:610, Polymorphism, education, medicine.disease, Protein ubiquitination, metabolism [Brain], Human medicine
Abstract: © 2015, Elsevier Inc. All rights reserved. Background: Late-onset Alzheimer's disease (AD) is heritable with 20 genes showing genome-wide association in the International Genomics of Alzheimer's Project (IGAP). To identify the biology underlying the disease, we extended these genetic data in a pathway analysis. Methods: The ALIGATOR and GSEA algorithms were used in the IGAP data to identify associated functional pathways and correlated gene expression networks in human brain. Results: ALIGATOR identified an excess of curated biological pathways showing enrichment of association. Enriched areas of biology included the immune response (P = 3.27 × 10-12 after multiple testing correction for pathways), regulation of endocytosis (P = 1.31 × 10-11), cholesterol transport (P = 2.96 × 10-9), and proteasome-ubiquitin activity (P = 1.34 × 10-6). Correlated gene expression analysis identified four significant network modules, all related to the immune response (corrected P =.002-.05). Conclusions: The immune response, regulation of endocytosis, cholesterol transport, and protein ubiquitination represent prime targets for AD therapeutics., Medical Research Council, Alzheimer’s Research UK, and theWelsh Assembly Government. ADGC and CHARGE were supported by the National Institutes of Health, National Institute on Aging (NIH-NIA). CHARGE was also supported by Erasmus Medical Center and Erasmus University. IGAP was funded by the French National Foundation on Alzheimer’s Disease and Related Disorders, the Centre National de Genotypage and the Institut Pasteur de Lille, Inserm, FRC (Fondation pour la Recherche sur le Cerveau), and Rotary. This work has been developed and supported by the LABEX (Laboratory of Excellence Program Investment for the Future) DISTALZ grant (Development of Innovative Strategies for a Transdisciplinary approach to ALZheimer’s disease).
Published: 2015

38. Rare coding variants in PLCG2, ABI3, and TREM2 implicate microglial-mediated innate immunity in Alzheimer's disease

Author: John Hardy, Nick C. Fox, Lena Lilius, Christine Van Broeckhoven, Mindy J. Katz, Carlos Cruchaga, Joshua W. Miller, Carol Brayne, Letizia Concari, Christopher Shaw, Minerva M. Carrasquillo, Richard Mayeux, Anne Boland, Charles DeCarli, Helena C. Chui, Laura B. Cantwell, Yoland Aladro Benito, Chuang Kuo Wu, Elaine R. Peskind, Andrew McDavid, M. Ilyas Kamboh, Amanda Smith, Pascual Sánchez-Juan, Jean-François Deleuze, Jayanadra J. Himali, Thomas H. Mosley, Thomas J. Montine, Chuanhai Cao, Andreas J. Forstner, Thomas G. Beach, Robert Barber, Miquel Aguilar, Liming Qu, Jerome I. Rotter, Matthew J. Huentelman, Christiane Reitz, Christopher J. O'Donnell, Steven G. Younkin, Bradley T. Hyman, Bruce L. Miller, Rachelle S. Doody, Eric B. Larson, Ronald L. Hamilton, Todd E. Golde, Steven E. Arnold, Melissa E. Garcia, Rachel Raybould, Lena Kilander, Mark A. Sager, Kevin Morgan, Kathryn L. Lunetta, William Perry, Joseph D. Buxbaum, Craig S. Atwood, Thomas D. Bird, Michael Conlon O'Donovan, Robert Olaso, Juan Fortea, Susanne Moebus, Lisa L. Barnes, Rachel Marshall, Huntington Potter, Mercè Boada, Shahzad Ahmad, Paolo Caffarra, Daniel C. Marson, Jonathan L. Haines, Perrie M. Adams, John M Olichney, Lars Lannfelt, Stefanie Heilmann-Heimbach, Markus M. Nöthen, Shubhabrata Mukherjee, John Malamon, Xue Wang, Christopher S. Carlson, Karen Ritchie, Roger N. Rosenberg, Paul K. Crane, Alexa S. Beiser, Céline Bellenguez, Robert C. Green, Maria Urbano, Petra Proitsi, John Powell, Elisa Majounie, Ammar Al-Chalabi, Hakon Hakonarson, Yogen Patel, Martin Scherer, Julie Williams, Richard B. Lipton, Vincent Dermecourt, Adam L. Boxer, Gerard D. Schellenberg, David G. Clark, Anita L. DeStefano, Joel H. Kramer, Victoria Alvarez, Nandini Badarinarayan, Oscar L. Lopez, Chris Corcoran, Ubaldo Bonuccelli, Donald R. Royall, James Bowen, Monica Diez Fairen, Tricia A. Thornton-Wells, Nilufer Ertekin-Taner, Florence Pasquier, Martin Ingelsson, Yi Zhao, John R. Gilbert, Valentina Escott-Price, Amanda B. Kuzma, Fabienne Garzia, Reinhard Heun, Otto Valladares, Andrew J. Saykin, Sara Ortega-Cubero, Liana G. Apostolova, Henry L. Paulson, John K Kauwe, Imelda Barber, Carolina Ceballos Diaz, Douglas Galasko, M. Arfan Ikram, Lluís Tárraga, Carlo Caltagirone, Joan S. Reisch, Wolfgang Maier, Bruno Vellas, Rebecca Sims, Angela Hodges, Matthew P. Frosch, Isabel Henández, Annakaisa Haapasalo, Thor Aspelund, Håkan Thonberg, Aimee Pierce, Roger L. Albin, Wayne W. Poon, Rebecca Sussams, Amy Braddel, Ranjan Duara, Albert V. Smith, Kirk C. Wilhelmsen, Gianfranco Spalletta, Simon Lovestone, Peter Passmore, Ana Frank-García, Cynthia M. Carlsson, Jade Chapman, Nathan D. Price, Philip L. De Jager, John M. Ringman, Seung Hoan Choi, Nicola Denning, Michael John Owen, Clinton T. Baldwin, Amalia C. Bruni, Denis A. Evans, Rudolph E. Tanzi, Dominique Campion, Laura Fratiglioni, Alberto Lleó, Per Hoffmann, Carole Dufouil, Charlotte Forsell, Alun Meggy, Charlene Thomas, Robert S. Stern, James B. Leverenz, Tatiana Foroud, William W. Seeley, James J. Lah, Brian A. Lawlor, Kenneth B. Fallon, Matthias Riemenschneider, Ryan M. Huebinger, Regina M. Carney, Clinton B. Wright, Didier Hannequin, Deborah Blacker, Anne Kinhult-Ståhlbom, Ekaterina Rogaeva, Andrew P. Lieberman, Bernardino Ghetti, Linda J. Van Eldik, Bernadette McGuinness, Thomas Fairchild, Margaret A. Pericak-Vance, Ashok Raj, Reinhold Schmidt, Ronald C. Petersen, Harald Hampel, María J. Bullido, Steven L. Carroll, Maria Candida Deniz Naranjo, Kathleen A. Welsh-Bohmer, Myriam Fornage, Joseph F. Quinn, Caroline Graff, Claudia L. Satizabal, Patrice L. Whitehead, David Wallon, Christopher Medway, Lindsay A. Farrer, Vilmundur Gudnason, Peter St George-Hyslop, Pau Pastor, Frank Jessen, Erin L. Abner, Johanna Jakobsdottir, Hieab H.H. Adams, Roberta Cecchetti, Walter A. Kukull, Thomas S. Wingo, Michelle K. Lupton, Valur Emilsson, Susan M. McCurry, Simon Mead, Hilkka Soininen, Sandra Weintraub, Amy Gerrish, Lindy E. Harrell, Lina Keller, Jean-Charles Lambert, Denise Harold, Stephen Todd, Wei Gu, Maura Gallo, Najaf Amin, Lenore J. Launer, Eleonora Sacchinelli, Mikko Hiltunen, Cécile Dulary, Eliecer Coto, Xueqiu Jian, Nathalie Fievet, Patrizia Mecocci, Sarah Taylor, Eric Boerwinkle, Maria Serpente, Ronald G. Munger, Ina Giegling, Carlo Masullo, Aoibhinn Lynch, Eliezer Masliah, Anne M. Koivisto, Chang En Yu, Qiong Yang, Benedetta Nacmias, Wayne C. McCormick, Kristelle Brown, Alessio Squassina, Deborah C. Mash, Brian W. Kunkle, Makrina Daniilidou, Alison Goate, David Carrell, Kara L. Hamilton-Nelson, Sandra Barral, Vincent Chouraki, Kristel Sleegers, Frank J. Wolters, Joseph E. Parisi, Iwona Kłoszewska, Ronald C. Kim, Sonia Moreno-Grau, Marina Arcaro, Carmen Muñoz Fernadez, Vernon S. Pankratz, Duane Beekly, Sabrina Pichler, Gislain Septier, Delphine Bacq, Amanda J. Myers, Adam C. Naj, Frank Martiniuk, Sudha Seshadri, Badri N. Vardarajan, Joshua A. Sonnen, M.-Marsel Mesulam, Howard J. Rosen, James T. Becker, Chiara Fenoglio, Ge Li, Alberto Pilotto, Mary Sano, Olivier Hanon, Honghuang Lin, Jean Paul G. Vonsattel, W. T. Longstreth, Daniela Galimberti, David C. Rubinsztein, RoseMarie Brundin, Vilmantas Giedraitis, Christine M. Hulette, Peter Holmans, Martin Dichgans, Maria Vronskaya, Céline Derbois, Michelangelo Mancuso, Constantine G. Lyketsos, Christophe Tzourio, Jacques Epelbaum, Raffaele Maletta, Mariet Allen, Hong-Dong Li, James R. Burke, Rik Vandenberghe, David G. Mann, Bruce M. Psaty, Lawrence S. Honig, Beth A. Dombroski, Erik D. Roberson, Cornelia M. van Duijn, Benjamin Grenier-Boley, Seppo Helisalmi, Jean-François Dartigues, Russell H. Swerdlow, Paola Bossù, Ashley R. Winslow, Elio Scarpini, Lesley Jones, Sebastien Engelborghs, John Q. Trojanowski, Jeffrey Kaye, Jenny Lord, Chiara Cupidi, Janet A. Johnston, Dan Rujescu, Feroze Golamaully, Anne Braae, Rafael Blesa, L. Adrienne Cupples, Dennis W. Dickson, Gail P. Jarvik, David W. Fardo, David H. Cribbs, Michael Gill, Jose Bras, Allan I. Levey, Jennifer Williamson, Rhodri Thomas, John C. Morris, Lei Yu, Debby W. Tsuang, Annette M. Hartmann, John H. Growdon, John Collinge, Claudine Berr, Fernando Rivadeneira, Oliver Peters, Albert Hofman, Frank M. LaFerla, Vivianna M. Van Deerlin, James Uphill, David A. Bennett, Onofre Combarros, Gudny Eiriksdottir, Jeremy D. Burgess, Melanie L. Dunstan, Elizabeth Crocco, Keeley J. Brookes, Robert R. Graham, Lon S. Schneider, Eden R. Martin, Matt Hill, Neill R. Graff-Radford, Joseph T. Hughes, Vincenzo Solfrizzi, Taniesha Morgan, Antonio Ciaramella, Bruno Dubois, Juan C. Troncoso, Paolo Bosco, Jordi Clarimón, Daniel H. Geschwind, Virginia Boccardi, Barry Reisberg, Timothy W. Behrens, Annette L. Fitzpatrick, Salvatore Spina, Alexis Brice, Eileen H. Bigio, Marla Gearing, Jeffrey M. Burns, Carol A. Miller, Marilyn S. Albert, Sven J. van der Lee, Sandro Sorbi, C. Dirk Keene, Daniel Levy, Antonio Daniele, Eric M. Reiman, Paramita Chakrabarty, Oscar Sotolongo-Grau, Helena Schmidt, Francesco Panza, Murray A. Raskind, Rita Guerreiro, Gyungah Jun, Anna Karydas, Markus Leber, Harry V. Vinters, Cory C. Funk, Charles C. White, Jill R. Murrell, Sid E. O'Bryant, Nigel J. Cairns, Josée Dupuis, Ann C. McKee, Julie A. Schneider, Megan L. Grove, Malcolm B. Dick, Bradley F. Boeve, Jennifer A. Brody, Sanjay Asthana, Agustín Ruiz, Stefan Herms, Yuning Chen, David Craig, Neil W. Kowall, Maria Donata Orfei, JoAnn T. Tschanz, Florentino Sanchez Garcia, Manuel Mayhaus, Alfredo Ramirez, James Turton, André G. Uitterlinden, Davide Seripa, Lee-Way Jin, Kelley Faber, Maria C. Norton, Shuo Li, Steven H. Ferris, Steffi G. Riedel-Heller, Joshua C. Bis, Li-San Wang, Johannes Kornhuber, Peter Paul De Deyn, Martin R. Farlow, Randall L. Woltjer, Gary W. Beecham, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Erasmus University Medical Center [Rotterdam] (Erasmus MC), Hospital of the University of Pennsylvania (HUP), Perelman School of Medicine, University of Pennsylvania [Philadelphia]-University of Pennsylvania [Philadelphia], Facteurs de Risque et Déterminants Moléculaires des Maladies liées au Vieillissement - U 1167 (RID-AGE), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Icelandic Heart Association [Kopavogur, Iceland] (IHA), John P. Hussman Institute for Human Genomics [Miami, FL, USA], University of Miami [Coral Gables], Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Department of Medicine, University of Washington [Seattle], Dr. John T. Macdonald Foundation [Miami, FL, USA] (Department of Human Genetics), Epidémiologie des maladies chroniques : impact des interactions gène environnement sur la santé des populations, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille, Droit et Santé, Department of Genomics [Bonn, Germany] (Institute of Human Genetics), University of Bonn-Institute of Human Genetics [Bonn, Germany], Department of Molecular Genetics, Institut Català de Neurociències Aplicades [Barcelona, Spain], Well Advanced Solutions, Centre National de Génotypage (CNG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Translational Centre for Regenerative Medicine (TRM), Department of Cell Therapy, Universität Leipzig [Leipzig]-Universität Leipzig [Leipzig], The University of Texas Health Science Center at Houston (UTHealth), Columbia University [New York], University of Eastern Finland, Life & Brain Center - Department of Genomics, Rheinische Friedrich-Wilhelms-Universität Bonn, Génétique, Reproduction et Développement (GReD), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Santé et de la Recherche Médicale (INSERM), John P. Hussman Institute for Human Genomics, Neurobiologie de la Croissance et de la Senescence, Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Emmy Noether Project (SFB 833), Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Boston University [Boston] (BU), Department of Genomics, Institute for Systems Biology [Seattle, WA, USA], Universitätsklinikum Bonn (UKB), Centre of Excellence for Robotic Vision [Canberra], Australian Research Council [Canberra] (ARC), Neuroscience and Mental Health Research Institute [Cardiff, UK] (School of Medicine), Boston University School of Medicine (BUSM), Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, University of Pennsylvania [Philadelphia], Section of Neuroscience and Clinical Pharmacology, University of Cagliari, Department of Epidemiology and Biostatistics, ERASMUS, Hospital Universitario Doctor Negrín [Las Palmas de Gran Canaria, Spain], Department of Neurodegenerative Diseases, University of Mississippi Medical Center (UMMC), Pathology and Laboratory Medicine [Philadelphia, PA, USA] (Penn Neurodegeneration Genomics Center), UNIROUEN - UFR Santé (UNIROUEN UFR Santé), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU), Génétique du cancer et des maladies neuropsychiatriques (GMFC), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Bioinformatics, GlaxoSmithKline, Aging Research Center [Karolinska Institutet] (ARC ), Stockholm University-Karolinska Institutet [Stockholm], University of Nottingham, UK (UON), University of Texas Health Science Center, Department of Neurobiology, Caring Sciences and Society (NVS), University of Bari Aldo Moro (UNIBA), Ageing Group, Centre for Public Health, Queen's University [Belfast] (QUB), Mayo Clinic [Jacksonville], Maurice Wohl Clinical Neuroscience Institut, King‘s College London, Istituto di Ricovero e Cura a Carattere Scientifico, Ospedale Casa Sollievo della Sofferenza [San Giovanni Rotondo] (IRCCS), Università degli Studi di Perugia (UNIPG), Framingham Heart Study, Boston University [Boston] (BU)-National Heart, Lung, and Blood Institute [Bethesda] (NHLBI), CHU Rouen, Normandie Université (NU), Universidad Autonoma de Madrid (UAM), Centro de Investigacion Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III [Madrid] (ISC), National Heart, Lung, and Blood Institute [Bethesda] (NHLBI), University of Florida [Gainesville] (UF), University of Parma = Università degli studi di Parma [Parme, Italie], Center for Cognitive Disorders AUSL [Parma, Italy], School of Public Health [Boston], Uppsala University, Institut de la Mémoire et de la Maladie d'Alzheimer [Paris] (IM2A), Université Pierre et Marie Curie - Paris 6 (UPMC), National Institute on Aging [Bethesda, USA] (NIA), National Institutes of Health [Bethesda] (NIH), Xi'an Jiaotong University (Xjtu), Department of Public health and Caring Sciences, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden, Institute of Gerontology and Geriatrics, Troubles cognitifs dégénératifs et vasculaires - U 1171 (TCDV), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Geriatric Medicine and Metabolic Diseases, Departments of Nuclear Medicine, University Medical Centre Hamburg-Eppendorf [Hamburg, Germany], University of Texas Southwestern Medical Center [Dallas], University of Cologne, Laboratoire d'Etudes et de Recherche en Informatique d'Angers (LERIA), Université d'Angers (UA), Johns Hopkins University (JHU), Universität Leipzig [Leipzig], University of Iceland [Reykjavik], Metacohorts Consortium, Harvard School of Public Health, Catholic University of Rome, Medical University Graz, Baylor College of Medicine (BCM), Baylor University, University of North Texas Health Science Center [Fort Worth], Santa Lucia Foundation (IRCCS), Nextel S.A. [Bilbao], Massachusetts General Hospital [Boston], Department of Pathology and Laboratory Medicine and Indiana Alzheimer disease Center, Indiana University School of Medicine, Indiana University System-Indiana University System, Joint Institute for the Study of the Atmosphere and Ocean (JISAO), Beijing University of Technology, University of Pittsburgh (PITT), Pennsylvania Commonwealth System of Higher Education (PCSHE), Saul B. Korey Department of Neurology, Albert Einstein College of Medicine [New York]-Yeshiva University, Utah State University (USU), Fundació per la Recerca Biomèdica i Social Mútua Terrassa [Barcelona, Spain], Hospital Universitario Mutua de Terrassa, Département de neurologie [Montpellier], Université Montpellier 1 (UM1)-Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Hôpital Gui de Chauliac [Montpellier]-Université de Montpellier (UM), Department of neurology, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland, Department of neurology, University of Eastern Finland-University Hospital of Kuopio-University of Eastern Finland-University Hospital of Kuopio, Medical University of Łódź (MUL), University of Leicester, MRC Prion Unit, Fondazione IRCCS Ca' Granda - Ospedale Maggiore Policlinico, University of Milan, Fondazione Istituto di Ricerca e Cura Carattere Scientifico [Rome], Università degli Studi di Roma Tor Vergata [Roma], Saarland University Hospital, Universitat Autònoma de Barcelona (UAB), Regional Neurogenetic Centre [Lamezia Terme, Italy] (CRN - ASP Catanzaro), Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Institute for Medical Informatics, Biometry and Epidemiology, University Hospital of Essen, Universidade do Porto, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Experimental and Clinical Pharmacology, St. James Hospital and Trinity College [Dublin, Ireland], School of Medicine [Dublin], Trinity College Dublin, University of Sheffield [Sheffield], Lancaster University, University of Michigan [Ann Arbor], University of Michigan System, David Geffen School of Medicine [Los Angeles], University of California [Los Angeles] (UCLA), University of California-University of California, University of Wisconsin-Madison, Rush Alzheimer Disease Center [Chicago, IL, États-Unis], Rush University Medical Center [Chicago], Institute for Advanced Biosciences / Institut pour l'Avancée des Biosciences (Grenoble) (IAB), Centre Hospitalier Universitaire [Grenoble] (CHU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Etablissement français du sang - Auvergne-Rhône-Alpes (EFS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), School of Engineering [Cardiff], Department of Psychiatry [Pittsburgh], University of Pittsburgh School of Medicine, Pennsylvania Commonwealth System of Higher Education (PCSHE)-Pennsylvania Commonwealth System of Higher Education (PCSHE), Northwestern University Feinberg School of Medicine, Mayo Clinic [Rochester], Swedish Medical Center [Seattle, WA, USA], University of California [San Francisco] (UCSF), University of California, Duke University [Durham], University of Kansas Medical Center [Lawrence], Laboratory of Molecular Neuropsychiatry, Icahn School of Medicine at Mount Sinai [New York] (MSSM), Washington University in Saint Louis (WUSTL), University of South Florida [Tampa] (USF), Fred Hutchinson Cancer Research Center [Seattle] (FHCRC), Medical University of South Carolina [Charleston] (MUSC), University of Southern California (USC), Los Alamos National Laboratory (LANL), Centre de biologie du développement (CBD), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Neurology Department, University of California, Davis (UCDavis-Neuro), University of California [Davis] (UC Davis), University of California [Irvine] (UCI), Mount Sinai Medical Center, Indiana State University, University of Alabama at Birmingham [ Birmingham] (UAB), University of Kentucky, New York University [New York] (NYU), NYU System (NYU), Department of Medical and Molecular Genetics, Department of Epidemiology and biostatistics, VU University Medical Center [Amsterdam], Emory University [Atlanta, GA], Department of Neurology, University of California-University of California-David Geffen School of Medicine [Los Angeles], Brigham & Women’s Hospital [Boston] (BWH), Harvard Medical School [Boston] (HMS), Department of Medical Genetics, HMNC Brain Health, Alzheimer Disease Research Laboratory, Harvard Medical School [Boston] (HMS)-Massachusetts General Hospital [Boston], Oregon Health and Science University [Portland] (OHSU), Cleveland Clinic, Laboratoire d'Informatique, Systèmes, Traitement de l'Information et de la Connaissance (LISTIC), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Department of Psychiatry, School of Medicine-Johns Hopkins University and Johns Hopkins Bayview Medical Center, Douglas Mental Health University Institute [Montréal], McGill University = Université McGill [Montréal, Canada], Department of neurosciences, University of California [San Diego] (UC San Diego), Department of Physics and Astronomy [Fort Worth], Texas Christian University (TCU), Department of Computer Science [University of California, Davis], Indiana University System, Institute for Aging and Alzheimer’s Disease Research [Fort Worth] (IAADR), Department of Laboratory Medicine and Pathology, Mayo Clinic, Institute for Memory Impairments and Neurological Disorders [Irvine], University of Colorado Anschutz [Aurora], Tanz Center Research in Neurodegenerative Diseases [Toronto], University of Toronto, Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], Keck School of Medicine [Los Angeles], Indiana University [South Bend], Massachusetts General Hospital, Novartis Institutes for Biomedical Research [Cambridge, MA, USA], Departments of Pathology and Laboratory Medicine (Neuropathology) and Neurology, UCLA Medical Center-David Geffen School of Medicine [Los Angeles], University of California-University of California-University of California [Los Angeles] (UCLA), University of North Carolina [Chapel Hill] (UNC), University of North Carolina System (UNC), Institut de Génomique d'Evry (IG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, University of Antwerp (UA), Institute Born-Bunge, Karolinska Institutet [Stockholm], Karolinska University Hospital [Stockholm], University of Kuopio, Centre Mémoire de Ressources et de Recherche [Lille-Bailleul] (CMRR), Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Hôpital Roger Salengro [Lille], Laboratoire d'Analyse Génomique, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Inserm-U1167, Dpt Gériatrie [CHU Broca], AP-HP - Hôpital Cochin Broca Hôtel Dieu [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Neuroépidémiologie, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut du Cerveau et de la Moëlle Epinière = Brain and Spine Institute (ICM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Neuropsychiatrie : recherche épidémiologique et clinique (PSNREC), Université Montpellier 1 (UM1)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Alzheimer Precision Medicine [CHU Pitié-Salpétriêre] (GRC 21 AMP), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Department of Epidemiology, University of Washington, School of Medicine [Los Angeles], Albert Einstein College of Medicine [New York], IdiPAZ - Instituto de Investigación La Paz [Madrid, Spain], Instituto de Física Teórica UAM/CSIC (IFT), Universidad Autonoma de Madrid (UAM)-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Department of Internal Medicine, University of Central Asturias [Oviedo, Spain], Human Genome Sequencing Center, Baylor College of Medicine, Baylor University-Baylor University, Department of Epidemiology, Erasmus Medical Centre, Translational Genomics Research Institute [Phoenix, AZ, USA], University of Arizona, Banner Alzheimer's Institute [Phoenix, AZ, États-Unis], University of Texas Health Science Center at San Antonio [San Antonio], Mount Sinai School of Medicine, Department of Psychiatry-Icahn School of Medicine at Mount Sinai [New York] (MSSM), Department. of Neurological Sciences, University of Milan, IRCCS Ospedale Maggiore Policlinico, Centre for Research in Neurodegenerative Diseases, VA Puget Sound Health Care System/GRECC [Seattle, WA, USA], University of Pisa - Università di Pisa, Pfizer Worldwide Research and Development [Cambridge, MA, USA], Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt), Texas Tech University Health Sciences Center, Texas Tech University [Lubbock] (TTU), Saarland University [Saarbrücken], University of Bonn, Department of Public Health and Primary Care, University of Cambridge [UK] (CAM), Cambridge Institute for Medical Research (CIMR), Department of Molecular Neurosciences, Institute of Neurology, UCL, Institute of Psychiatry, Institute of psychiatry, University of British Columbia (UBC), the Clinical Neuroscience Research Group, University of Manchester [Manchester]-Greater Manchester Neurosciences Centre, Aristotle University of Thessaloniki, Memory and Dementia Centre, 3rd Department of Neurology, G. Pa, University of Barcelona, University of Southampton, Department of Psychiatry [Oxford] (POWIC), University of Oxford [Oxford]-The Warneford Hospital, School of Psychology [Cardiff University], Department of Medical Sciences, UCL, Institute of Neurology [London], Washington University School of Medicine, Netherlands Genomics Initiative, Netherlands Consortium for Healthy Aging [Leiden, Netherlands] (NCHA), School of Medecine, Center for Translational and Computational Neuroimmunology [New York, NY, États-Unis] (CTCN), Department of Neurology [New York, NY, États-Unis], Columbia University Medical Center (CUMC), Columbia University [New York]-Columbia University [New York]-Columbia University Medical Center (CUMC), Columbia University [New York]-Columbia University [New York], School of Life Sciences, Department of Neuroscience, Mayo Clinic Jacksonville, Icelandic Heart Association, Heart Preventive Clinic and Research Institute, Klinik für Psychiatrie, Martin-Luther-University Halle-Wittenberg, Epidémiologie et Biostatistique [Bordeaux], Université Bordeaux Segalen - Bordeaux 2-Institut de Santé Publique, d'Épidémiologie et de Développement (ISPED)-Institut National de la Santé et de la Recherche Médicale (INSERM), The Center for Applied Genomics, Children’s Hospital of Philadelphia (CHOP ), Clínica Universidad de Navarra [Pamplona], Neurodegenerative Brain Diseases Group, VIB, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University-Medical Research Council, Brigham Young University (BYU), Institut de Santé Publique, d'Epidémiologie et de Développement (ISPED), Université Bordeaux Segalen - Bordeaux 2, The Gertrude H Sergivesky Center, Columbia University College of Physicians and Surgeons, Genetic Epidemiology Unit, Section of Clinical and Molecular Neurogenetics, Universität zu Lübeck [Lübeck], University of Pennsylvania - Department of Pathology & Laboratory Medecine, Framingham Heart Study [Framingham, MA, USA], ANR-10-IAHU-0006,IHU-A-ICM,Institut de Neurosciences Translationnelles de Paris(2010), European Project: 29845,LSH-ACC-MENTOR, University of Pennsylvania-University of Pennsylvania, Universität Bonn = University of Bonn-Institute of Human Genetics [Bonn, Germany], Universität Leipzig-Universität Leipzig, Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), University of Pennsylvania, Università degli studi di Bari Aldo Moro = University of Bari Aldo Moro (UNIBA), Università degli Studi di Perugia = University of Perugia (UNIPG), Universidad Autónoma de Madrid (UAM), Università degli studi di Parma = University of Parma (UNIPR), Institut de la Mémoire et de la Maladie d'Alzheimer [CHU Pitié-Salpétriêre] (IM2A), Université Pierre et Marie Curie - Paris 6 (UPMC)-CHU Pitié-Salpêtrière [AP-HP], Troubles cognitifs dégénératifs et vasculaires - U 1171 - EA 1046 (TCDV), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille, Droit et Santé-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Universität Leipzig, Università cattolica del Sacro Cuore = Catholic University of the Sacred Heart [Roma] (Unicatt), Yeshiva University- Albert Einstein College of Medicine [New York], Université Montpellier 1 (UM1)-Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Hôpital Gui de Chauliac [CHU Montpellier], Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Université de Montpellier (UM), Università degli Studi di Milano = University of Milan (UNIMI), Saarland University Hospital (UKS), Università degli Studi di Firenze = University of Florence (UniFI), Universidade do Porto = University of Porto, University of California (UC)-University of California (UC), University of California [San Francisco] (UC San Francisco), University of California (UC), University of Kansas Medical Center [Kansas City, KS, USA], Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), University of California [Irvine] (UC Irvine), University of Kentucky (UK), University of California (UC)-University of California (UC)-David Geffen School of Medicine [Los Angeles], Department of Computer Science [Univ California Davis] (CS - UC Davis), University of California (UC)-University of California (UC)-University of California [Los Angeles] (UCLA), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Groupe de recherche clinique Alzheimer Precision Medicine (GRC 21 - APM), Sorbonne Université (SU), Universidad Autónoma de Madrid (UAM)-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), University of Texas Health Science Center at San Antonio [San Antonio, Tx, USA], Universität Bonn = University of Bonn, University of Oxford-The Warneford Hospital, Medical Research Council-Cardiff University, Universität zu Lübeck = University of Lübeck [Lübeck], Epidemiology, Neurology, Gastroenterology & Hepatology, Internal Medicine, Facteurs de Risque et Déterminants Moléculaires des Maladies liées au Vieillissement (Inserm U1167 - RID-AGE - Institut Pasteur), Génétique, Reproduction et Développement - Clermont Auvergne (GReD), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne (UCA)-Centre National de la Recherche Scientifique (CNRS), Eberhard Karls Universität Tübingen, IRCCS 'Casa Sollievo della Sofferenza', Centro de Investigación Biomédica en Red para Enfermedades Neurodegenerativas (Ciberned), University of Florida [Gainesville], University of Parma, Troubles cognitifs dégénératifs et vasculaires (U1171), Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-INSERM, Yeshiva University- Albert Einstein College of Medicine, Institut d’Électronique, de Microélectronique et de Nanotechnologie (IEMN) - UMR 8520 (IEMN), Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Université Polytechnique Hauts-de-France (UPHF)-Ecole Centrale de Lille-Université Polytechnique Hauts-de-France (UPHF)-Institut supérieur de l'électronique et du numérique (ISEN), Autonomous University of Barcelona (UAB), Università degli Studi di Firenze [Firenze], Universidade do Porto [Porto], Centre Hospitalier Universitaire [Grenoble] (CHU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Etablissement français du sang - Auvergne-Rhône-Alpes (EFS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Washington University in St Louis, University of South Florida (USF), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, McGill University, Charité - Universitätsmedizin Berlin / Charite - University Medicine Berlin, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [APHP]-Centre National de la Recherche Scientifique (CNRS), Neuropsychiatrie : recherche épidémiologique et clinique, Alzheimer Precision Medicine GRC n°21 (APM), CHU Pitié-Salpêtrière [APHP], Albert Einstein College of Medicine, Universidad Autonoma de Madrid (UAM)-Consejo Superior de Investigaciones Científicas [Spain] (CSIC), Università Cattolica del S. Cuore - Catholic University of the Sacred Hearth, University of Florence (UNIFI), CIBER de Enfermedades Neurodegenerativas (CIBERNED), Universität zu Lübeck [Lübeck] - University of Lübeck [Lübeck], [ANR-10-IAIHU-06],« Investissements d'avenir » ,Agence nationale de la recherche (ANR), Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Centre Hospitalier Universitaire [Grenoble] (CHU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Etablissement français du sang - Auvergne-Rhône-Alpes (EFS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-CHU Pitié-Salpêtrière [AP-HP], Icahn School of Medicine at Mount Sinai [New York] (MSSM)-Department of Psychiatry, van der Lee, Sven J [0000-0003-1606-8643], Naj, Adam C [0000-0002-9621-2942], Badarinarayan, Nandini [0000-0002-6944-748X], Chouraki, Vincent [0000-0002-4698-1794], Graham, Robert R [0000-0001-7151-4277], Hoffmann, Per [0000-0002-6573-983X], Smith, Albert V [0000-0003-1942-5845], Satizabal, Claudia L [0000-0002-1115-4430], Brody, Jennifer A [0000-0001-8509-148X], Wolters, Frank J [0000-0003-2226-4050], Lupton, Michelle K [0000-0002-7274-7299], Lin, Honghuang [0000-0003-3043-3942], Adams, Hieab H [0000-0003-3687-2508], Giedraitis, Vilmantas [0000-0003-3423-2021], Pasquier, Florence [0000-0001-9880-9788], Chen, Yuning [0000-0002-7358-7055], Bossù, Paola [0000-0002-1432-0078], Ghetti, Bernardino [0000-0002-1842-8019], Yang, Qiong [0000-0002-3658-1375], Aspelund, Thor [0000-0002-7998-5433], Bullido, María J [0000-0002-6477-1117], Rivadeneira, Fernando [0000-0001-9435-9441], Rubinsztein, David C [0000-0001-5002-5263], Al-Chalabi, Ammar [0000-0002-4924-7712], Tsolaki, Magda [0000-0002-2072-8010], De Jager, Philip L [0000-0002-8057-2505], Dickson, Dennis W [0000-0001-7189-7917], Van Broeckhoven, Christine [0000-0003-0183-7665], Ikram, M Arfan [0000-0003-0372-8585], Amouyel, Philippe [0000-0001-9088-234X], Lambert, Jean-Charles [0000-0003-0829-7817], Apollo - University of Cambridge Repository, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), Alzheimer Precision Medicine [CHU Pitié-Salpétriêre] (GRC 21 APM), Berr, Claudine, Institut de Neurosciences Translationnelles de Paris - - IHU-A-ICM2010 - ANR-10-IAHU-0006 - IAHU - VALID, and Mentoring of LifeSciHealth-Multipliers in the Accession Candidate Countries - LSH-ACC-MENTOR - 29845 - OLD
Subjects: 0301 basic medicine, Linkage disequilibrium, [SDV]Life Sciences [q-bio], Medizin, Sequence Homology, Genome-wide association study, genetics [Alzheimer Disease], metabolism [Microglia], Linkage Disequilibrium, 0302 clinical medicine, genetics [Protein Interaction Maps], genetics [Membrane Glycoproteins], Gene Frequency, Immunologic, genetics [Adaptor Proteins, Signal Transducing], Receptors, genetics [Exome], Odds Ratio, Innate, genetics [Receptors, Immunologic], Exome, Protein Interaction Maps, genetics [Genetic Predisposition to Disease], Receptors, Immunologic, ABI3 protein, human, Genetics, Adaptor Proteins, Signal Transducing, Alzheimer Disease, Amino Acid Sequence, Case-Control Studies, Gene Expression Profiling, Genetic Predisposition to Disease, Genotype, Humans, Immunity, Innate, Membrane Glycoproteins, Microglia, Phospholipase C gamma, Sequence Homology, Amino Acid, Polymorphism, Single Nucleotide, Adaptor Proteins, Single Nucleotide, 3. Good health, [SDV] Life Sciences [q-bio], Amino Acid, Settore MED/26 - NEUROLOGIA, genetics [Phospholipase C gamma], [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], Alzheimer's disease, Common disease-common variant, Biology, Article, 03 medical and health sciences, ddc:570, medicine, Journal Article, [SDV.NEU] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], Polymorphism, Allele frequency, TREM2 protein, human, TREM2, Case-control study, Signal Transducing, Immunity, medicine.disease, R1, Minor allele frequency, genetics [Immunity, Innate], 030104 developmental biology, Human medicine, 030217 neurology & neurosurgery
Abstract: International audience; We identified rare coding variants associated with Alzheimer's disease in a three-stage case-control study of 85,133 subjects. In stage 1, we genotyped 34,174 samples using a whole-exome microarray. In stage 2, we tested associated variants (P < 1 × 10-4) in 35,962 independent samples using de novo genotyping and imputed genotypes. In stage 3, we used an additional 14,997 samples to test the most significant stage 2 associations (P < 5 × 10-8) using imputed genotypes. We observed three new genome-wide significant nonsynonymous variants associated with Alzheimer's disease: a protective variant in PLCG2 (rs72824905: p.Pro522Arg, P = 5.38 × 10-10, odds ratio (OR) = 0.68, minor allele frequency (MAF)cases = 0.0059, MAFcontrols = 0.0093), a risk variant in ABI3 (rs616338: p.Ser209Phe, P = 4.56 × 10-10, OR = 1.43, MAFcases = 0.011, MAFcontrols = 0.008), and a new genome-wide significant variant in TREM2 (rs143332484: p.Arg62His, P = 1.55 × 10-14, OR = 1.67, MAFcases = 0.0143, MAFcontrols = 0.0089), a known susceptibility gene for Alzheimer's disease. These protein-altering changes are in genes highly expressed in microglia and highlight an immune-related protein-protein interaction network enriched for previously identified risk genes in Alzheimer's disease. These genetic findings provide additional evidence that the microglia-mediated innate immune response contributes directly to the development of Alzheimer's disease.
Published: 2017

39. [P3–090]: THE ALZHEIMER's DISEASE SEQUENCING PROJECT (ADSP) DATA UPDATE 2017

Author: Rebecca Cweibel, Elizabeth L. Appelbaum, John J. Farrell, Robert S. Fulton, Otto Valladares, Sudha Seshadri, Eric Boerwinkle, Laura B. Cantwell, Tatiana Foroud, Adam C. Naj, Seung Hoan Choi, Namrata Gupta, Liming Qu, Jason Waligorski, Mike Feolo, Gerard D. Schellenberg, Kara L. Hamilton-Nelson, Yuk Yee Leung, Amanda B. Kuzma, Anita L. DeStefano, Han-Jen Lin, Adam Stine, Dolly Reyes-Dumeyer, William J Salerno, Donna M. Muzny, Joshua C. Bis, Li-San Wang, and Kelley Faber
Subjects: Psychiatry and Mental health, Cellular and Molecular Neuroscience, Developmental Neuroscience, Epidemiology, business.industry, Health Policy, Medicine, Neurology (clinical), Computational biology, Disease, Geriatrics and Gerontology, business
Published: 2017

40. Large-scale analyses of common and rare variants identify 12 new loci associated with atrial fibrillation

Author: Joshua C. Bis, Daniel I. Chasman, Archie Campbell, J. Wouter Jukema, Yoichiro Kamatani, Joylene E. Siland, Siegfried Perz, Jie Huang, Jorge A. Wong, Jared W. Magnani, Stefan Weiss, Caroline Hayward, Christopher D. Anderson, Carolina Roselli, Alexander P. Reiner, Maartje N. Niemeijer, Efthymia Vlachopoulou, David R. Van Wagoner, Elsayed Z. Soliman, Lenore J. Launer, Claudia Schurmann, Jeffrey Haessler, Joshua C. Denny, Qiong Yang, Mika Kähönen, Henry J. Lin, Lu-Chen Weng, Molong Li, Paul L. Huang, Terho Lehtimäki, Bruno H. Stricker, Lewin Eisele, Christopher Newton-Cheh, Marcus E. Kleber, Alexander Teumer, Rainer Malik, Juha Sinisalo, Siew-Kee Low, Xiaoyan Yin, Stéphanie Debette, Jennifer A. Brody, Marco V Perez, Derek Klarin, Farid Radmanesh, Ian Ford, Dan M. Roden, Paul M. Ridker, Jan Heeringa, Jonathan Rosand, Andrew P. Morris, Winfried März, Stefan Gustafsson, Xiuqing Guo, Nathan R. Tucker, Dawood Darbar, Daniel J. Rader, Martin Dichgans, Stefan Kääb, Lars Lind, Patrick T. Ellinor, Nancy L. Pedersen, Stefanie Aeschbacher, Erwin B. Bottinger, Leo-Pekka Lyytikäinen, Peter Lichtner, Marcus Dörr, Svati H. Shah, Lin Y. Chen, Alvaro Alonso, Marja-Liisa Lokki, Albert V. Smith, Guillaume Paré, Ruth J. F. Loos, Christine M. Albert, Markku Eskola, Jonathan D. Smith, Kjell Nikus, Martina Müller-Nurasyid, Yanick Hagemeijer, Lorenz Risch, Nona Sotoodehnia, Jussi Hernesniemi, Albert Y. Sun, Man Li, Jemma C. Hopewell, Olle Melander, Albert Hofman, Annette Peters, Pim van der Harst, Michiel Rienstra, Ilkka Seppälä, Kent D. Taylor, Charles Kooperberg, Moritz F. Sinner, Jerome I. Rotter, Stuart A. Scott, Toshihiro Tanaka, Steven A. Lubitz, Uwe Völker, Marju Orho-Melander, Patrik K. E. Magnusson, Jari Laurikka, M. Benjamin Shoemaker, Niek Verweij, J. Gustav Smith, José Eduardo Krieger, Sébastien Thériault, Andrea R. V. R. Horimoto, Natalia S. Rost, André G. Uitterlinden, Oscar H. Franco, David Conen, Cecilia M. Lindgren, Sekar Kathiresan, Michiaki Kubo, Marina Arendt, Graciela Delgado, Anders Hamsten, Rajat Deo, Lars Lannfelt, Sebastian Clauss, Sandosh Padmanabhan, Emelia J. Benjamin, Roopinder K. Sandhu, Bruce M. Psaty, Peter Weeke, Mark Chaffin, Traci M. Bartz, Erik Ingelsson, Alfredo José Mansur, Nathan A. Bihlmeyer, Christian M. Shaffer, Lynne J. Hocking, Stella Trompet, Melanie Waldenberger, Honghuang Lin, Stephan B. Felix, David J. Porteous, Vilmundur Gudnason, Eric Boerwinkle, Dan E. Arking, Alexandre C. Pereira, Bastiaan Geelhoed, Susan R. Heckbert, Jie Yao, Bradford B. Worrall, Ingrid E. Christophersen, Jennifer Kriebel, Peter Almgren, Blair H. Smith, Jennifer E. Huffman, Seung Hoan Choi, Mina K. Chung, Karl-Heinz Jöckel, Yingchang Lu, Yii-Der Ida Chen, Peter W. Macfarlane, John Barnard, Tamara B. Harris, Kathryn L. Lunetta, Stefanie Heilmann-Heimbach, Ganesh Chauhan, Epidemiology, Internal Medicine, and Cardiovascular Centre (CVC)
Subjects: 0301 basic medicine, Quantitative Trait Loci, Medizin, genetics [White People], SNP, Genome-wide association study, 030204 cardiovascular system & hematology, Biology, SUSCEPTIBILITY, Bioinformatics, GENOMAS, ANNOTATION, White People, 03 medical and health sciences, 0302 clinical medicine, ddc:570, Genetic variation, Atrial Fibrillation, Genetics, medicine, Journal Article, TOOL, Humans, Genetic Predisposition to Disease, genetics [Atrial Fibrillation], GENOME-WIDE ASSOCIATION, Stroke, METAANALYSIS, Genetic association, RISK, genetics [Black or African American], GENETIC-VARIATION, Atrial fibrillation, medicine.disease, R1, 3. Good health, Black or African American, genetics [European Continental Ancestry Group], 030104 developmental biology, Genetic Loci, Heart failure, Meta-analysis, VISUALIZATION, genetics [African Americans], BURDEN, Genome-Wide Association Study
Abstract: Atrial fibrillation affects more than 33 million people worldwide and increases the risk of stroke, heart failure, and death(1,2). Fourteen genetic loci have been associated with atrial fibrillation in European and Asian ancestry groups(3-7). To further define the genetic basis of atrial fibrillation, we performed large-scale, trans-ancestry meta-analyses of common and rare variant association studies. The genome-wide association studies (GWAS) included 17,931 individuals with atrial fibrillation and 115,142 referents; the exome-wide association studies (ExWAS) and rare variant association studies (RVAS) involved 22,346 cases and 132,086 referents. We identified 12 new genetic loci that exceeded genome-wide significance, implicating genes involved in cardiac electrical and structural remodeling. Our results nearly double the number of known genetic loci for atrial fibrillation, provide insights into the molecular basis of atrial fibrillation, and may facilitate the identification of new potential targets for drug discovery(8).
Published: 2017

41. Association Between Titin Loss-of-Function Variants and Early-Onset Atrial Fibrillation

Author: Patrick T. Ellinor, Seung Hoan Choi, Christine M. Albert, Mina K. Chung, Lu-Chen Weng, Daniel I. Chasman, Stephanie M. Gogarten, David R. Van Wagoner, Eric Boerwinkle, Stacey Gabriel, Emelia J. Benjamin, Brandon K. Fornwalt, Dan E. Arking, Susan R. Heckbert, Dawood Darbar, Cashell E. Jaquish, John Barnard, Frederick E. Dewey, David J. Carey, Christian M. Shaffer, Michael F. Murray, Nicholas L. Smith, Christopher M. Haggerty, Esteban G. Burchard, Kathryn L. Lunetta, Nathan R. Tucker, Dan M. Roden, Gonçalo R. Abecasis, Nona Sotoodehnia, Sekar Kathiresan, Namrata Gupta, Mark Chaffin, Ramachandran S. Vasan, Honghuang Lin, Edwin K. Silverman, Diane T. Smelser, M. Benjamin Shoemaker, Jonathan D. Smith, Aris Baras, Alvaro Alonso, Cecelia A. Laurie, Zachary T. Yoneda, Steven A. Lubitz, George J. Papanicolaou, Thomas W. Blackwell, Bruce M. Psaty, Lauren Margolin, Carolina Roselli, Marisa A. Shea, and Susan Redline
Subjects: Adult, Male, Quality Control, 0301 basic medicine, Heterozygote, medicine.medical_specialty, Population, Genome-wide association study, 030204 cardiovascular system & hematology, Article, 03 medical and health sciences, 0302 clinical medicine, Loss of Function Mutation, Internal medicine, Atrial Fibrillation, medicine, Humans, Connectin, Genetic Predisposition to Disease, Age of Onset, education, Genetic association, education.field_of_study, business.industry, Case-control study, Atrial fibrillation, General Medicine, Odds ratio, Middle Aged, medicine.disease, 030104 developmental biology, Case-Control Studies, Female, Age of onset, business, Genome-Wide Association Study, Cohort study
Abstract: Importance Atrial fibrillation (AF) is the most common arrhythmia affecting 1% of the population. Young individuals with AF have a strong genetic association with the disease, but the mechanisms remain incompletely understood. Objective To perform large-scale whole-genome sequencing to identify genetic variants related to AF. Design, setting, and participants The National Heart, Lung, and Blood Institute's Trans-Omics for Precision Medicine Program includes longitudinal and cohort studies that underwent high-depth whole-genome sequencing between 2014 and 2017 in 18 526 individuals from the United States, Mexico, Puerto Rico, Costa Rica, Barbados, and Samoa. This case-control study included 2781 patients with early-onset AF from 9 studies and identified 4959 controls of European ancestry from the remaining participants. Results were replicated in the UK Biobank (346 546 participants) and the MyCode Study (42 782 participants). Exposures Loss-of-function (LOF) variants in genes at AF loci and common genetic variation across the whole genome. Main outcomes and measures Early-onset AF (defined as AF onset in persons Results Among 2781 participants with early-onset AF (the case group), 72.1% were men, and the mean (SD) age of AF onset was 48.7 (10.2) years. Participants underwent whole-genome sequencing at a mean depth of 37.8 fold and mean genome coverage of 99.1%. At least 1 LOF variant in TTN, the gene encoding the sarcomeric protein titin, was present in 2.1% of case participants compared with 1.1% in control participants (odds ratio [OR], 1.76 [95% CI, 1.04-2.97]). The proportion of individuals with early-onset AF who carried a LOF variant in TTN increased with an earlier age of AF onset (P value for trend, 4.92 × 10-4), and 6.5% of individuals with AF onset prior to age 30 carried a TTN LOF variant (OR, 5.94 [95% CI, 2.64-13.35]; P = 1.65 × 10-5). The association between TTN LOF variants and AF was replicated in an independent study of 1582 patients with early-onset AF (cases) and 41 200 control participants (OR, 2.16 [95% CI, 1.19-3.92]; P = .01). Conclusions and relevance In a case-control study, there was a statistically significant association between an LOF variant in the TTN gene and early-onset AF, with the variant present in a small percentage of participants with early-onset AF (the case group). Further research is necessary to understand whether this is a causal relationship.
Published: 2018

42. O1‐09‐04: Identification of Whole Exome Sequencing Variants Associated with Late‐Onset Alzheimer's Disease in the Cohorts for Heart and Aging Research in Genomic Epidemiology (Charge) Consortium

Author: Sudha Seshadri, Sven J. van der Lee, Thomas H. Mosley, Myriam Fornage, Eric Boerwinkle, M. Arfan Ikram, L. Adrienne Cupples, Seung Hoan Choi, Bruce M. Psaty, Cornelia M. van Duijn, Anita L. DeStefano, Annette L. Fitzpatrick, Shahzad Ahmad, Oscar L. Lopez, Xueqiu Jian, Josée Dupuis, Yuning Chen, and Joshua C. Bis
Subjects: Genetics, medicine.medical_specialty, Epidemiology, Health Policy, Late onset, Disease, Biology, Psychiatry and Mental health, Cellular and Molecular Neuroscience, Developmental Neuroscience, medicine, Identification (biology), Neurology (clinical), Geriatrics and Gerontology, Exome sequencing
Published: 2016

43. Evaluation of a Genetic Risk Score to Improve Risk Prediction for Alzheimer's Disease

Author: Annette L. Fitzpatrick, P. Amouyel, Richard Mayeux, Johanna Jakobsdottir, Hieab H.H. Adams, Anita L. DeStefano, Badri N. Vardarajan, Chouraki, de Jager Pl, David A. Bennett, Jean-François Dartigues, Shubhabrata Mukherjee, Seung Hoan Choi, M. A. Ikram, Christiane Reitz, Eric B. Larson, Oscar L. Lopez, Fleur Maury, Jean-Charles Lambert, Sudha Seshadri, Lei Yu, van der Lee Sj, Albert Hofman, van Duijn C, J. C. Bis, Gudnason, L. J. Launer, A.G. Uitterlinden, Carla A. Ibrahim-Verbaas, Paul K. Crane, Céline Bellenguez, Claudine Berr, Epidemiology, Internal Medicine, and Neurology
Subjects: 0301 basic medicine, Male, medicine.medical_specialty, Apolipoprotein E4, Genome-wide association study, Neuropsychological Tests, Polymorphism, Single Nucleotide, Risk Assessment, Article, Cohort Studies, 03 medical and health sciences, 0302 clinical medicine, Alzheimer Disease, Predictive Value of Tests, Risk Factors, Internal medicine, Statistics, medicine, Humans, Genetic Predisposition to Disease, Genetic Testing, Genetic testing, Aged, Proportional Hazards Models, Aged, 80 and over, Psychiatric Status Rating Scales, Framingham Risk Score, medicine.diagnostic_test, business.industry, Proportional hazards model, General Neuroscience, Hazard ratio, General Medicine, Psychiatry and Mental health, Clinical Psychology, 030104 developmental biology, Meta-analysis, Educational Status, Female, Geriatrics and Gerontology, business, Risk assessment, 030217 neurology & neurosurgery, Cohort study, Genome-Wide Association Study
Abstract: Effective prevention of Alzheimer's disease (AD) requires the development of risk prediction tools permitting preclinical intervention. We constructed a genetic risk score (GRS) comprising common genetic variants associated with AD, evaluated its association with incident AD and assessed its capacity to improve risk prediction over traditional models based on age, sex, education, and APOE epsilon 4. In eight prospective cohorts included in the International Genomics of Alzheimer's Project (IGAP), we derived weighted sum of risk alleles from the 19 top SNPs reported by the IGAPGWAS in participants aged 65 and older without prevalent dementia. Hazard ratios (HR) of incident AD were estimated in Cox models. Improvement in risk prediction was measured by the difference in C-index (Delta-C), the integrated discrimination improvement (IDI) and continuous net reclassification improvement (NRI>0). Overall, 19,687 participants at risk were included, of whom 2,782 developed AD. The GRS was associated with a 17% increase in AD risk (pooled HR=1.17; 95% CI = [1.13-1.21] per standard deviation increase in GRS; p-value = 2.86x10(-16)). This association was stronger among persons with at least one APOE epsilon 4 allele (HRGRS = 1.24; 95% CI = [1.15-1.34]) than in others (HRGRS = 1.13; 95% CI = [1.08-1.18]; p(interaction) = 3.45x10(-2)). Risk prediction after seven years of follow-up showed a small improvement when adding the GRS to age, sex, APOE epsilon 4, and education (Delta-Cindex = 0.0043 [0.0019-0.0067]). Similar patterns were observed for IDI and NRI>0. In conclusion, a risk score incorporating common genetic variation outside the APOE epsilon 4 locus improved AD risk prediction and may facilitate risk stratification for prevention trials.
Published: 2016

44. Rare Functional Variant in TM2D3 is Associated with Late-Onset Alzheimer's Disease

Author: Johanna Jakobsdottir, Sven J van der Lee, Joshua C Bis, Vincent Chouraki, David Li-Kroeger, Shinya Yamamoto, Megan L Grove, Adam Naj, Maria Vronskaya, Jose L Salazar, Anita L DeStefano, Jennifer A Brody, Albert V Smith, Najaf Amin, Rebecca Sims, Carla A Ibrahim-Verbaas, Seung-Hoan Choi, Claudia L Satizabal, Oscar L Lopez, Alexa Beiser, M Arfan Ikram, Melissa E Garcia, Caroline Hayward, Tibor V Varga, Samuli Ripatti, Paul W Franks, Göran Hallmans, Olov Rolandsson, Jan-Håkon Jansson, David J Porteous, Veikko Salomaa, Gudny Eiriksdottir, Kenneth M Rice, Hugo J Bellen, Daniel Levy, Andre G Uitterlinden, Valur Emilsson, Jerome I Rotter, Thor Aspelund, Cohorts for Heart and Aging Research in Genomic Epidemiology consortium, Alzheimer’s Disease Genetic Consortium, Genetic and Environmental Risk in Alzheimer’s Disease consortium, Christopher J O'Donnell, Annette L Fitzpatrick, Lenore J Launer, Albert Hofman, Li-San Wang, Julie Williams, Gerard D Schellenberg, Eric Boerwinkle, Bruce M Psaty, Sudha Seshadri, Joshua M Shulman, Vilmundur Gudnason, Cornelia M van Duijn, Epidemiology, Neurology, Radiology & Nuclear Medicine, Internal Medicine, VU University medical center, Clinicum, Institute for Molecular Medicine Finland, Samuli Olli Ripatti / Principal Investigator, Department of Public Health, Biostatistics Helsinki, Complex Disease Genetics, and Haines, Jonathan L
Subjects: Male, Apolipoprotein E, Genetic and Environmental Risk in Alzheimer’s Disease consortium, Aging, PROTEIN, Social Sciences, Genome-wide association study, Tropomyosin, Alzheimer's Disease, Cell Signaling, Sociology, Age of Onset, Aetiology, MUTATION, Notch Signaling, Drosophila Melanogaster, Intracellular Signaling Peptides and Proteins, COMMON VARIANTS, Genomics, Phenotypes, Drosophila melanogaster, Neurology, medicine.medical_specialty, Notch, European Continental Ancestry Group, White People, APOLIPOPROTEIN-E, Presenilin, 03 medical and health sciences, Apolipoproteins E, SDG 3 - Good Health and Well-being, Clinical Research, Alzheimer Disease, Genetics, Humans, Rare functional variant, GENOME-WIDE ASSOCIATION, Molecular Biology, Alleles, Ecology, Evolution, Behavior and Systematics, Aged, Embryos, Organisms, Correction, Biology and Life Sciences, Odds ratio, Invertebrates, 030104 developmental biology, Endocrinology, Genetic Loci, Mutation, Dementia, Developmental Biology, 0301 basic medicine, Embryology, Cancer Research, Iceland, Neurodegenerative, QH426-470, Amyloid beta-Protein Precursor, Alzheimer’s Disease Genetic Consortium, Consortia, Receptors, Invertebrate Genomics, Medicine and Health Sciences, Drosophila Proteins, 2.1 Biological and endogenous factors, Exome, DROSOPHILA-MELANOGASTER DEVELOPMENT, Genetics (clinical), Receptors, Notch, Neurodegenerative Diseases, Animal Models, Insects, Phenotype, Neurological, Female, Drosophila, Neurovetenskaper, Research Article, Signal Transduction, Arthropoda, UNITED-STATES, Late onset, Biology, Research and Analysis Methods, IDENTIFIES VARIANTS, Model Organisms, Internal medicine, Mental Health and Psychiatry, Acquired Cognitive Impairment, medicine, Animals, Allele, HAPLOTYPE RECONSTRUCTION, Human Genome, Neurosciences, Membrane Proteins, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), Cell Biology, Cohorts for Heart and Aging Research in Genomic Epidemiology consortium, Brain Disorders, Animal Genomics, RC0321, 3111 Biomedicine, Age of onset, Genome-Wide Association Study
Abstract: We performed an exome-wide association analysis in 1393 late-onset Alzheimer’s disease (LOAD) cases and 8141 controls from the CHARGE consortium. We found that a rare variant (P155L) in TM2D3 was enriched in Icelanders (~0.5% versus, Author Summary Alzheimer’s disease (AD) is the most common cause of dementia in the older adult population. There is substantial evidence for an important genetic contribution to AD risk. While prior work has comprehensively evaluated the contribution of common genetic variants in large population-based cohorts, the role of rare variants remains to be defined. Here, we have used a newer genotyping array to characterize less common variants, including those likely to impact the function of encoded proteins, in a combined cohort of 1393 AD cases and 8141 control subjects without AD. Our results implicate a novel, amino acid-changing variant, P155L, in the TM2D3 gene. This variant was discovered to be more common in the Icelandic population, where it was significantly associated with both increased risk and earlier age of onset of AD. Lastly, in order to examine the potential functional impact of the implicated variant, we performed additional studies in the fruit fly. Our results suggest that P155L causes a loss-of-function in TM2D3, in the context of Notch-Presenilin signal transduction. In sum, we identify a novel, rare TM2D3 variant in association with AD risk and highlight functional connections with AD-relevant biology.
Published: 2016

45. PLD3-variants in population studies

Author: Rutger W W Brouwer, Wiesje M. van der Flier, Seung Hoan Choi, Megan L. Grove, Edwin Oole, Sudha Seshadri, Tsz Hang Wong, Cornelia M. van Duijn, Thor Aspelund, Christopher J. O'Donnell, M. Arfan Ikram, Gudny Eirkisdottir, Jeroen van Rooij, Melissa E. Garcia, Johanna Jakobsdottir, Sven J. van der Lee, Anita L. DeStefano, Henne Holstege, Alexa S. Beiser, Wilfred F. J. van IJcken, Daniel Levy, Vilmundur Gudnason, Albert V. Smith, Mirjam C G N van den Hout, Albert Hofman, André G. Uitterlinden, John C. van Swieten, Yolande A.L. Pijnenburg, Bruce M. Psaty, Eric Boerwinkle, Najaf Amin, Lenore J. Launer, Joshua C. Bis, Valur Emilsson, Vincent Chouraki, Jerome I. Rotter, Philip Scheltens, Eva Louwersheimer, Human genetics, Neurology, NCA - neurodegeneration, Epidemiology, Internal Medicine, and Cell biology
Subjects: Genetics, Oncology, medicine.medical_specialty, education.field_of_study, Multidisciplinary, Confounding, Population, Odds ratio, Biology, Confidence interval, Article, Internal medicine, Genetic variation, Multiple comparisons problem, Cohort, medicine, education, Genetic association
Abstract: Cruchaga et al.1 report that rare genetic variants in PLD3(phospholipase D3) are associated with increased Alzheimer’s disease(AD) risk. They showed that PLD3 is involved in amyloid-β precursor protein (APP) processing and overexpressed in brain tissue from AD patients. However, even the key variant PLD3-Val232Met, did not pass genome wide significance. This observation raises the question if the genetic association of PLD3 with AD replicates. We associated PLD3-Val232Met with AD in 3 large population-based studies and 3 case-control studies. In total, we meta-analyzed results from 1914 AD cases and 8021 controls of European descent. Additionally we searched for other coding PLD3-variants in sequence data of 1067 AD cases and 1553 controls. Carrier frequencies of PLD3-Val232Met in controls ranged from 0.34-1.42%, consistent with 0-1.17% reported by Cruchaga et al.1 (Table 1). Likewise, the frequencies of PLD3-Val232Met in cases ranged from 0.66-2.19% compared to 0.7-2.6%.1 We note that the range of carrier frequencies overlaps between cases and controls, such that in some population based cohorts, the carrier frequency in controls (e.g., 1.28% in FHS) is higher than that of cases in other cohorts (e.g., 0.68% in AGES). Within each cohort frequencies of PLD3-Val232Met were higher in cases than controls (Table 1), but in none of the populations the case carrier frequency for PLD3-Val232Met was significantly increased. However, pooled analyses showed a 1.94 fold increased risk of AD of carriers compared to non-carriers (Odds Ratio [OR] 1.94, adjusted for age and sex, 95% confidence interval=1.05 to 3.57) that was marginally significant (p-value = 0.03)(Table 1). Of note, the crude ORs often differed considerably from the age and sex adjusted estimates. With the exception of ADNI, the ORs were higher after adjustment for age and sex, suggesting that many a-symptomatic carriers were relatively young compared to cases and age needs to be controlled for in the analyses as a putative confounder. Table 1 Association of PLD3-Val232Met with Alzheimer’s disease We further associated other coding variants in PLD3 with AD and performed a gene-based test using sequence data from two studies encompassing 1067 AD cases and 1553 controls. We meta-analyzed results of whole genome sequence data of the ADNI study, 499 AD cases and 293 controls, with results of a combined cohort of 568 Dutch AD cases and 1260 Dutch controls. We observed 21 rare polymorphic coding variants and 1 splice site variant. Of the 20 observed PLD3-variants detected by Cruchaga et al.1, we observed 9 (S63G, P76A, V232M, N284S, C300Y, A442A, G452E, D447G and R488C). Five variants showed the same direction of effect as seen by Cruchaga et al.1. PLD3-A442A was one of the variants that showed a same direction of effect(Odds Ratio [OR] 1.24, 95% confidence interval = 0.74 to 2.06, p-value = 0.41). After correcting the p-value for multiple testing, none of the variants observed in our study conferred a significant increase in AD risk. Gene-based analysis also did not show significant association of PLD3-variants with AD risk (SKAT-O p-value = 0.61 and burden test OR 1.27 95% confidence interval [CI] =0.85 to 1.9, p-value = 0.24). In conclusion, the carrier frequencies of PLD3-Val232Met in our data set are consistent with those reported by Cruchaga et al.1 and we showed a nominally significant association of PLD3-Val232Met with AD. This is in contrast to findings presented in companion papers by Heilmann et al., Lambert et al. and Hooli et al. However, in contrast to Cruchaga et al.1 we found no significant association of other PLD3-variants with AD in the single variant or gene based analyses. Therefore, in our analyses PLD3 does not yet meet the criteria proposed by MacArthur et al.2 to be implicated in AD. Hence, our data do not strongly support an important contribution of rare PLD3-variants in the etiology of AD. The most notable findings in our study are the need to control for age as a confounder in rare variant analyses and the high variability of the frequency of PLD3-Val232Met across populations. The latter finding highlights the need for careful matching of cases and controls for ethnic background when investigating rare variants.
Published: 2015

46. Polygenic Overlap Between C-Reactive Protein, Plasma Lipids, and Alzheimer Disease

Author: Stacy Steinberg, Vilmundur Gudnason, Anita L. DeStefano, Rahul S. Desikan, Dominic Holland, Ole A. Andreassen, Daniel I. Chasman, Lindsay A. Farrer, John Hardy, Yunpeng Wang, Richard Mayeux, Bruce M. Psaty, Tormod Fladby, Bradley T. Hyman, Ingun Ulstein, Arvid Rongve, Lenore J. Launer, Abbas Dehghan, Sudha Seshadri, Joshua C. Bis, Michael Conlon O'Donovan, Linda R. White, Julie Williams, Jonathan L. Haines, Gerard D. Schellenberg, Jon Snaedal, Srdjan Djurovic, Kari Stefansson, Rebecca Sims, Seung Hoan Choi, David S. Karow, Chi-Hua Chen, Margaret A. Pericak-Vance, Cornelia M. van Duijn, Dag Aarsland, James B. Brewer, Hreinn Stefansson, Sven J. van der Lee, Andrew J. Schork, Aree Witoelar, Christopher P. Hess, Linda K. McEvoy, M. Arfan Ikram, Anders M. Dale, Paul M. Ridker, Wesley K. Thompson, Sigrid Botne Sando, Gastroenterology & Hepatology, and Epidemiology
Subjects: Male, Multifactorial Inheritance, Blood lipids, Genome-wide association study, Peroxisomal Bifunctional Enzyme, Polymorphism, Single Nucleotide, Article, lipids, Alzheimer Disease, Risk Factors, Physiology (medical), medicine, Humans, Genetic association, Aged, Dyslipidemias, Genetics, Aged, 80 and over, Inflammation, biology, C-reactive protein, Brain, Odds ratio, medicine.disease, Lipids, Chromosome 4, C-Reactive Protein, Phenotype, biology.protein, Female, Alzheimer's disease, Sulfotransferases, Cardiology and Cardiovascular Medicine, Dyslipidemia, Biomarkers, Genome-Wide Association Study
Abstract: Background— Epidemiological findings suggest a relationship between Alzheimer disease (AD), inflammation, and dyslipidemia, although the nature of this relationship is not well understood. We investigated whether this phenotypic association arises from a shared genetic basis. Methods and Results— Using summary statistics ( P values and odds ratios) from genome-wide association studies of >200 000 individuals, we investigated overlap in single-nucleotide polymorphisms associated with clinically diagnosed AD and C-reactive protein (CRP), triglycerides, and high- and low-density lipoprotein levels. We found up to 50-fold enrichment of AD single-nucleotide polymorphisms for different levels of association with C-reactive protein, low-density lipoprotein, high-density lipoprotein, and triglyceride single-nucleotide polymorphisms using a false discovery rate threshold HS3ST1 ; odds ratio=1.07; 95% confidence interval=1.05–1.11; P =2.86×10 −8 ) and chromosome 10 (rs7920721; closest gene, ECHDC3 ; odds ratio=1.07; 95% confidence interval=1.04–1.11; P =3.38×10 −8 ). We also found that gene expression of HS3ST1 and ECHDC3 was altered in AD brains compared with control brains. Conclusions— We demonstrate genetic overlap between AD, C-reactive protein, and plasma lipids. By conditioning on the genetic association with the cardiovascular phenotypes, we identify novel AD susceptibility loci, including 2 genome-wide significant variants conferring increased risk for AD.
Published: 2015

47. Genetic overlap between Alzheimer's disease and Parkinson's disease at the MAPT locus

Author: Julie Williams, Jonathan L. Haines, Sudha Seshadri, Anne H. Smith, Aree Witoelar, Linda K. McEvoy, Srdjan Djurovic, Chi-Hua Chen, Kari Stefansson, Alexis Brice, Nicholas W. Wood, M. A. Ikram, Bradley T. Hyman, Joshua C. Bis, Jon Snaedal, Michael Conlon O'Donovan, Ole A. Andreassen, Andrew J. Schork, Rahul S. Desikan, Thompson Wk, Seung Hoan Choi, Gerard D. Schellenberg, Annette L. Fitzpatrick, Maria Martinez, Dag Aarsland, James B. Brewer, C M van Duijn, Lindsay A. Farrer, Yunpeng Wang, AB Singleton, T. Gasser, Dominic Holland, Manu Sharma, Anders M. Dale, Michael John Owen, John Hardy, Richard Mayeux, Hreinn Stefansson, Lenore J. Launer, Ingun Ulstein, Anita L. DeStefano, Denise Harold, Tormod Fladby, Margaret A. Pericak-Vance, Peter Heutink, Gastroenterology & Hepatology, Internal Medicine, Radiology & Nuclear Medicine, Erasmus MC other, and Epidemiology
Subjects: Male, Aging, Parkinson's disease, Genome-wide association study, genetics [Alzheimer Disease], Neurodegenerative, Alzheimer's Disease, Medical and Health Sciences, 0302 clinical medicine, pathology [Brain], genetics [Parkinson Disease], ADNI, 80 and over, 2.1 Biological and endogenous factors, Alzheimer's Disease including Alzheimer's Disease Related Dementias, Aetiology, Genetics, Psychiatry, Aged, 80 and over, 0303 health sciences, Parkinson's Disease, Neurodegeneration, Brain, Parkinson Disease, Genetic Pleiotropy, Single Nucleotide, Biological Sciences, Middle Aged, Chromosome 17 (human), Psychiatry and Mental health, Neurological, ADGC, Female, Psychology, Human, Single-nucleotide polymorphism, Locus (genetics), MAPT protein, human, tau Proteins, and over, Polymorphism, Single Nucleotide, Article, Chromosomes, 03 medical and health sciences, Cellular and Molecular Neuroscience, Apolipoproteins E, Alzheimer Disease, medicine, Acquired Cognitive Impairment, CHARGE and IPDGC Investigators, Humans, GERAD, ddc:610, Allele, Polymorphism, Molecular Biology, Alleles, 030304 developmental biology, Genetic association, Aged, Pair 17, Prevention, Human Genome, Psychology and Cognitive Sciences, Neurosciences, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), medicine.disease, Brain Disorders, genetics [tau Proteins], Genetic Loci, genetics [Apolipoproteins E], Dementia, 030217 neurology & neurosurgery, Chromosomes, Human, Pair 17, Genome-Wide Association Study
Abstract: © 2015 Macmillan Publishers Limited We investigated the genetic overlap between Alzheimer’s disease (AD) and Parkinson’s disease (PD). Using summary statistics (P-values) from large recent genome-wide association studies (GWAS) (total n=89 904 individuals), we sought to identify single nucleotide polymorphisms (SNPs) associating with both AD and PD. We found and replicated association of both AD and PD with the A allele of rs393152 within the extended MAPT region on chromosome 17 (meta analysis P-value across five independent AD cohorts=1.65 × 10-7). In independent datasets, we found a dose-dependent effect of the A allele of rs393152 on intra-cerebral MAPT transcript levels and volume loss within the entorhinal cortex and hippocampus. Our findings identify the tau-associated MAPT locus as a site of genetic overlap between AD and PD, and extending prior work, we show that the MAPT region increases risk of Alzheimer’s neurodegeneration.Molecular Psychiatry advance online publication, 17 February 2015; doi:10.1038/mp.2015.6.
Published: 2015

48. The Alzheimer's Disease Sequencing Project: Study design and sample selection

Author: Myriam Fornage, Stacey Gabriel, Seung Hoan Choi, Anita L. DeStefano, Lindsay A. Farrer, Eden R. Martin, William S. Bush, Sudha Seshadri, A. Goate, Tatiana Foroud, Bruce M. Psaty, Gerard D. Schellenberg, Margaret A. Pericak-Vance, Joshua C. Bis, Eric Boerwinkle, Richard Mayeux, Daniel C. Koboldt, Ellen M. Wijsman, David E. Larson, C M van Duijn, Gary W. Beecham, Adam C. Naj, William J Salerno, Jonathan L. Haines, and Epidemiology
Subjects: 0301 basic medicine, Gerontology, medicine.medical_specialty, Disease, 03 medical and health sciences, Rotterdam Study, 0302 clinical medicine, Framingham Heart Study, Epidemiology, Medicine, Dementia, Clinical/Scientific Notes, Genetics (clinical), business.industry, Public health, medicine.disease, 3. Good health, 030104 developmental biology, Genetic epidemiology, Neurology (clinical), Alzheimer's disease, business, 030217 neurology & neurosurgery
Abstract: Late-onset Alzheimer disease (LOAD) is the leading cause of dementia worldwide, with substantial economic and public health implications.1 LOAD is a neurodegenerative disease characterized by progressive dementia typically manifesting in the seventh to ninth decades. Neuropathological changes precede clinical symptoms by 10–20 years, resulting in clinically asymptomatic individuals carrying neuropathologic features of LOAD.2 Much of the heritability of LOAD remains unexplained, despite LOAD having a high heritability (60%–80%) and despite the identification of the APOE locus, a major genetic determinant for LOAD.3 Genetic analyses have identified more than 25 other variants associated with smaller individual effects on disease risk.4 Acknowledgment: The Alzheimer's Disease Sequencing Project (ADSP) comprises 2 Alzheimer's Disease (AD) genetics consortia and 3 National Human Genome Research Institute (NHGRI)-funded Large Scale Sequencing and Analysis Centers (LSAC). The 2 AD genetics consortia are the Alzheimer's Disease Genetics Consortium (ADGC) funded by the NIA (U01 AG032984), and the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) funded by the NIA (R01 AG033193), the National Heart, Lung, and Blood Institute (NHLBI), other NIH institutes, and other foreign governmental and nongovernmental organizations. The Discovery Phase analysis of sequence data is supported through UF1AG047133 (to G. Schellenberg, L.A. Farrer, M.A. Pericak-Vance, R. Mayeux, and J.L. Haines); U01AG049505 to S. Seshadri; U01AG049506 to E. Boerwinkle; U01AG049507 to E. Wijsman; and U01AG049508 to A. Goate. Data generation and harmonization in the Follow-up Phases is supported by U54AG052427 (to G. Schellenberg and Wang). The ADGC cohorts include Adult Changes in Thought (ACT), the Alzheimer's Disease Centers (ADC), the Chicago Health and Aging Project (CHAP), the Memory and Aging Project (MAP), Mayo Clinic (MAYO), Mayo Parkinson's Disease controls, the University of Miami, the Multi-Institutional Research in Alzheimer's Genetic Epidemiology Study (MIRAGE), the National Cell Repository for Alzheimer's Disease (NCRAD), the National Institute on Aging Late Onset Alzheimer's Disease Family Study (NIA-LOAD), the Religious Orders Study (ROS), the Texas Alzheimer's Research and Care Consortium (TARC), Vanderbilt University/Case Western Reserve University (VAN/CWRU), the Washington Heights-Inwood Columbia Aging Project (WHICAP) and the Washington University Sequencing Project (WUSP), the Columbia University Hispanic–Estudio Familiar de Influencia Genetica de Alzheimer (EFIGA), the University of Toronto (UT), and Genetic Differences (GD). The CHARGE cohorts with funding provided by 5RC2HL102419 and HL105756, include the following: the Atherosclerosis Risk in Communities (ARIC) Study which is conducted as a collaborative study supported by NHLBI contracts (HHSN268201100005C, HHSN268201100006C, HHSN268201100007C, HHSN268201100008C, HHSN268201100009C, HHSN268201100010C, HHSN268201100011C, and HHSN268201100012C), the Austrian Stroke Prevention Study (ASPS), the Cardiovascular Health Study (CHS), the Erasmus Rucphen Family Study (ERF), the Framingham Heart Study (FHS), and the Rotterdam Study (RS). The 3 LSACs are the Human Genome Sequencing Center at the Baylor College of Medicine (U54 HG003273), the Broad Institute Genome Center (U54HG003067), and the Washington University Genome Institute (U54HG003079). Biological samples and associated phenotypic data used in primary data analyses were stored at Study Investigators institutions and at the National Cell Repository for Alzheimer's Disease (NCRAD, U24AG021886) at Indiana University funded by the NIA. Associated Phenotypic Data used in primary and secondary data analyses were provided by Study Investigators, the NIA-funded Alzheimer's Disease Centers (ADCs), and the National Alzheimer's Coordinating Center (NACC, U01AG016976) and the National Institute on Aging Genetics of Alzheimer's Disease Data Storage Site (NIAGADS, U24AG041689) at the University of Pennsylvania, funded by the NIA and at the Database for Genotypes and Phenotypes (dbGaP) funded by the NIH. This research was supported in part by the Intramural Research Program of the NIH and the National Library of Medicine. Contributors to the Genetic Analysis Data included Study Investigators on projects that were individually funded by the NIA and other NIH institutes, and by private U.S. organizations, or foreign governmental or nongovernmental organizations.
Published: 2017

49. F4‐04‐03: DO THE VARIANTS IDENTIFIED IN IGAP IMPROVE RISK PREDICTION OF ALZHEIMER'S DISEASE?

Author: Vincent Antoine Chouraki, Anita DeStefano, Céline Bellenguez, Christiane Reitz, Cornelia Duijn, David Bennett, Fleur Maury, null International Genomics of Alzheimer's Project (IGAP), Jean‐Charles Lambert, Johanna Jakobsdottir, Joshua C. Bis, Lenore Launer, Paul Crane, Richard Mayeux, Seung Hoan Choi, and Sudha Seshadri
Subjects: Psychiatry and Mental health, Cellular and Molecular Neuroscience, Developmental Neuroscience, Epidemiology, business.industry, Health Policy, Medicine, Neurology (clinical), Disease, Geriatrics and Gerontology, Bioinformatics, business
Published: 2014

50. Rare genetic variant analysis on blood pressure in related samples

Author: Chen Lu, Seán Lacey, Han Chen, Jacqueline N. Milton, Josée Dupuis, Honghuang Lin, Catherine Allard, Jaeyoung Hong, and Seung Hoan Choi
Subjects: 0303 health sciences, Candidate gene, business.industry, 0402 animal and dairy science, 04 agricultural and veterinary sciences, General Medicine, Computational biology, Heritability, Bioinformatics, 040201 dairy & animal science, Genetic analysis, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Proceedings, Blood pressure, Sample size determination, Medicine, business, Gene, 030304 developmental biology, Type I and type II errors, Genetic association
Abstract: The genetic variants associated with blood pressure identified so far explain only a small proportion of the total heritability of this trait. With recent advances in sequencing technology and statistical methodology, it becomes feasible to study the association between blood pressure and rare genetic variants. Using real baseline phenotype data and imputed dosage data from Genetic Analysis Workshop 18, we performed a candidate gene association analysis. We focused on 8 genes shown to be associated with either systolic or diastolic blood pressure to identify the association with both common and rare genetic variants, and then did a genome-wide rare-variant analysis on blood pressure. We performed association analysis for rare coding and splicing variants within each gene region and all rare variants in each sliding window, using either burden tests or sequence kernel association tests accounting for familial correlation. With a sample size of only 747, we failed to find any novel associated genetic loci. Consequently, we performed analyses on simulated data, with knowledge of the underlying simulating model, to evaluate the type I error rate and power for the methods used in real data analysis.
Published: 2014

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