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Genomic basis for RNA alterations in cancer (vol 578, pg 129, 2020)

NATURE 2023年第7948期614卷 E37-E37页

作者： Calabrese, Claudia Davidson, Natalie R. Demircioglu, Deniz Fonseca, Nuno A. He, Yao Lehmann, Kjong-Van Liu, Fenglin Shiraishi, Yuichi Soulette, Cameron M. Urban, Lara Greger, Liliana Li, Siliang Liu, Dongbing Perry, Marc D. Xiang, Qian Zhang, Fan Zhang, Junjun Bailey, Peter Erkek, Serap Hoadley, Katherine A. Hou, Yong Huska, Matthew R. Kilpinen, Helena Korbel, Jan O. Marin, Maximillian G. Markowski, Julia Nandi, Tannistha Pan-Hammarstrom, Qiang Pedamallu, Chandra Sekhar Siebert, Reiner Stark, Stefan G. Su, Hong Tan, Patrick Waszak, Sebastian M. Yung, Christina Zhu, Shida Awadalla, Philip Creighton, Chad J. Meyerson, Matthew Ouellette, B. F. Francis Wu, Kui Yang, Huanming Brazma, Alvis Brooks, Angela N. Goke, Jonathan Ratsch, Gunnar Schwarz, Roland F. Stegle, Oliver Zhang, Zemin European Molecular Biology Laboratory European Bioinformatics Institute Hinxton UK European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Cambridge UK Genome Biology Unit European Molecular Biology Laboratory (EMBL) Heidelberg Germany CIBIO/InBIO - Research Center in Biodiversity and Genetic Resources Universidade do Porto Vairão Portugal Berlin Institute for Medical Systems Biology Max Delbruck Center for Molecular Medicine Berlin Germany German Cancer Consortium (DKTK) partner site Berlin Germany German Cancer Research Center (DKFZ) Heidelberg Germany Berlin Institute for Medical Systems Biology Max Delbrück Center for Molecular Medicine Berlin Germany German Cancer Consortium (DKTK) Partner site Berlin Berlin Germany European Molecular Biology Laboratory Genome Biology Unit Heidelberg Germany Division of Computational Genomics and Systems Genetics German Cancer Research Center (DKFZ) Heidelberg Germany ETH Zurich Zurich Switzerland Memorial Sloan Kettering Cancer Center New York NY USA Weill Cornell Medical College New York NY USA SIB Swiss Institute of Bioinformatics Lausanne Switzerland University Hospital Zurich Zurich Switzerland Computational Biology Center Memorial Sloan Kettering Cancer Center New York NY USA Department of Biology ETH Zurich Zürich Switzerland Department of Computer Science ETH Zurich Zurich Switzerland Korea University Seoul South Korea Computational and Systems Biology Program Memorial Sloan Kettering Cancer Center New York NY USA Department of Physiology and Biophysics Weill Cornell Medicine New York NY USA Institute for Computational Biomedicine Weill Cornell Medicine New York NY USA Controlled Department and Institution New York NY USA Englander Institute for Precision Medicine Weill Cornell Medicine New York NY USA National University of Singapore Singapore Singapore Genome Institute of Singapore Singapore Singapore Computational and Systems Biology Genome Institute of Singap

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Genetic drivers of heterogeneity in type 2 diabetes pathophysiology

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Nature 2024年第8003期627卷 347-357页

作者： Ken Suzuki Konstantinos Hatzikotoulas Lorraine Southam Henry J Taylor Xianyong Yin Kim M Lorenz Ravi Mandla Alicia Huerta-Chagoya Giorgio E M Melloni Stavroula Kanoni Nigel W Rayner Ozvan Bocher Ana Luiza Arruda Kyuto Sonehara Shinichi Namba Simon S K Lee Michael H Preuss Lauren E Petty Philip Schroeder Brett Vanderwerff Mart Kals Fiona Bragg Kuang Lin Xiuqing Guo Weihua Zhang Jie Yao Young Jin Kim Mariaelisa Graff Fumihiko Takeuchi Jana Nano Amel Lamri Masahiro Nakatochi Sanghoon Moon Robert A Scott James P Cook Jung-Jin Lee Ian Pan Daniel Taliun Esteban J Parra Jin-Fang Chai Lawrence F Bielak Yasuharu Tabara Yang Hai Gudmar Thorleifsson Niels Grarup Tamar Sofer Matthias Wuttke Chloé Sarnowski Christian Gieger Darryl Nousome Stella Trompet Soo-Heon Kwak Jirong Long Meng Sun Lin Tong Wei-Min Chen Suraj S Nongmaithem Raymond Noordam Victor J Y Lim Claudia H T Tam Yoonjung Yoonie Joo Chien-Hsiun Chen Laura M Raffield Bram Peter Prins Aude Nicolas Lisa R Yanek Guanjie Chen Jennifer A Brody Edmond Kabagambe Ping An Anny H Xiang Hyeok Sun Choi Brian E Cade Jingyi Tan K Alaine Broadaway Alice Williamson Zoha Kamali Jinrui Cui Manonanthini Thangam Linda S Adair Adebowale Adeyemo Carlos A Aguilar-Salinas Tarunveer S Ahluwalia Sonia S Anand Alain Bertoni Jette Bork-Jensen Ivan Brandslund Thomas A Buchanan Charles F Burant Adam S Butterworth Mickaël Canouil Juliana C N Chan Li-Ching Chang Miao-Li Chee Ji Chen Shyh-Huei Chen Yuan-Tsong Chen Zhengming Chen Lee-Ming Chuang Mary Cushman John Danesh Swapan K Das H Janaka de Silva George Dedoussis Latchezar Dimitrov Ayo P Doumatey Shufa Du Qing Duan Kai-Uwe Eckardt Leslie S Emery Daniel S Evans Michele K Evans Krista Fischer James S Floyd Ian Ford Oscar H Franco Timothy M Frayling Barry I Freedman Pauline Genter Hertzel C Gerstein Vilmantas Giedraitis Clicerio González-Villalpando Maria Elena González-Villalpando Penny Gordon-Larsen Myron Gross Lindsay A Guare Sophie Hackinger Liisa Hakaste Sohee Han Andrew T Hattersley Christian Herder Momoko Horikoshi Annie-Green Howard Willa Centre for Genetics and Genomics Versus Arthritis Centre for Musculoskeletal Research Division of Musculoskeletal and Dermatological Sciences University of Manchester Manchester UK. Department of Diabetes and Metabolic Diseases Graduate School of Medicine University of Tokyo Tokyo Japan. Department of Statistical Genetics Osaka University Graduate School of Medicine Suita Japan. Institute of Translational Genomics Helmholtz Zentrum München German Research Center for Environmental Health Neuherberg Germany. konstantinos.hatzikotoulas@helmholtz-munich.de. Institute of Translational Genomics Helmholtz Zentrum München German Research Center for Environmental Health Neuherberg Germany. Center for Precision Health Research National Human Genome Research Institute National Institutes of Health Bethesda MD USA. British Heart Foundation Cardiovascular Epidemiology Unit Department of Public Health and Primary Care University of Cambridge Cambridge UK. Heart and Lung Research Institute University of Cambridge Cambridge UK. Department of Epidemiology School of Public Health Nanjing Medical University Nanjing China. Department of Biostatistics and Center for Statistical Genetics University of Michigan Ann Arbor MI USA. Corporal Michael J. Crescenz VA Medical Center Philadelphia PA USA. Department of Systems Pharmacology and Translational Therapeutics University of Pennsylvania Perelman School of Medicine Philadelphia PA USA. Department of Genetics University of Pennsylvania Perelman School of Medicine Philadelphia PA USA. Programs in Metabolism and Medical and Population Genetics Broad Institute of Harvard and MIT Cambridge MA USA. Diabetes Unit and Center for Genomic Medicine Massachusetts General Hospital Boston MA USA. TIMI Study Group Division of Cardiovascular Medicine Brigham and Women's Hospital Harvard Medical School Boston MA USA. William Harvey Research Institute Barts and the London School of Medicine and Dentistry Queen Mary University of London L

Type 2 diabetes (T2D) is a heterogeneous disease that develops through diverse pathophysiological processes and molecular mechanisms that are often specific to cell type. Here, to characterize the genetic contribution to these processes across ancestry groups, we aggregate genome-wide association study data from 2,535,601 individuals (39.7% not of European ancestry), including 428,452 cases of T2D. We identify 1,289 independent association signals at genome-wide significance (P < 5 × 10) that map to 611 loci, of which 145 loci are, to our knowledge, previously unreported. We define eight non-overlapping clusters of T2D signals that are characterized by distinct profiles of cardiometabolic trait associations. These clusters are differentially enriched for cell-type-specific regions of open chromatin, including pancreatic islets, adipocytes, endothelial cells and enteroendocrine cells. We build cluster-specific partitioned polygenic scores in a further 279,552 individuals of diverse ancestry, including 30,288 cases of T2D, and test their association with T2D-related vascular outcomes. Cluster-specific partitioned polygenic scores are associated with coronary artery disease, peripheral artery disease and end-stage diabetic nephropathy across ancestry groups, highlighting the importance of obesity-related processes in the development of vascular outcomes. Our findings show the value of integrating multi-ancestry genome-wide association study data with single-cell epigenomics to disentangle the aetiological heterogeneity that drives the development and progression of T2D. This might offer a route to optimize global access to genetically informed diabetes care.

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Single-cell analysis of experience-dependent transcriptomic states in the mouse visual cortex (vol 21, pg 120, 2018)

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NATURE NEUROSCIENCE 2018年第7期21卷 1017-1017页

作者： Hrvatin, Sinisa Hochbaum, Daniel R. Nagy, M. Aurel Cicconet, Marcelo Robertson, Keiramarie Cheadle, Lucas Zilionis, Rapolas Ratner, Alex Borges-Monroy, Rebeca Klein, Allon M. Sabatini, Bernardo L. Greenberg, Michael E. Department of Neurobiology Harvard Medical School Boston MA USA Society of Fellows Harvard University Cambridge MA USA Department of Neurobiology Howard Hughes Medical Institute Harvard Medical School Boston MA USA Image and Data Analysis Core Harvard Medical School Boston MA USA Department of Systems Biology Harvard Medical School Boston MA USA Vilnius University Institute of Biotechnology Vilnius Lithuania ICCB-L Single Cell Core Harvard Medical School Boston MA USA Program for Bioinformatics and Integrative Genomics Graduate School of Arts and Science Division of Medical Sciences Harvard University Cambridge MA USA

Activity-dependent transcriptional responses shape cortical function. However, a comprehensive understanding of the diversity of these responses across the full range of cortical cell types, and how these changes contribute to neuronal plasticity and disease, is lacking. To investigate the breadth of transcriptional changes that occur across cell types in the mouse visual cortex after exposure to light, we applied high-throughput single-cell RNA sequencing. We identified significant and divergent transcriptional responses to stimulation in each of the 30 cell types characterized, thus revealing 611 stimulus-responsive genes. Excitatory pyramidal neurons exhibited inter- and intralaminar heterogeneity in the induction of stimulus-responsive genes. Non-neuronal cells showed clear transcriptional responses that may regulate experience-dependent changes in neurovascular coupling and myelination. Together, these results reveal the dynamic landscape of the stimulus-dependent transcriptional changes occurring across cell types in the visual cortex; these changes are probably critical for cortical function and may be sites of deregulation in developmental brain disorders.

关键词： Gene expression analysis Molecular neuroscience Oligodendrocyte Transcriptomics Visual system

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The repertoire of mutational signatures in human cancer (vol 578, pg 94, 2020)

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NATURE 2023年第7948期614卷 E41-E41页

作者： Alexandrov, Ludmil B. Kim, Jaegil Haradhvala, Nicholas J. Huang, Mi Ni Ng, Alvin Wei Tian Wu, Yang Boot, Arnoud Covington, Kyle R. Gordenin, Dmitry A. Bergstrom, Erik N. Islam, S. M. Ashiqul Lopez-Bigas, Nuria Klimczak, Leszek J. McPherson, John R. Morganella, Sandro Sabarinathan, Radhakrishnan Wheeler, David A. Mustonen, Ville Getz, Gad Rozen, Steven G. Stratton, Michael R. Department of Cellular and Molecular Medicine Department of Bioengineering Moores Cancer Center University of California San Diego CA USA Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Department of Cellular and Molecular Medicine and Department of Bioengineering University of California San Diego La Jolla CA USA UC San Diego Moores Cancer Center San Diego CA USA University of California San Diego San Diego CA USA Broad Institute of MIT and Harvard Cambridge MA USA Center for Cancer Research Massachusetts General Hospital Boston MA USA Massachusetts General Hospital Boston MA USA Department of Pathology Massachusetts General Hospital Boston MA USA Harvard Medical School Boston MA USA Laboratory for Medical Science Mathematics RIKEN Center for Integrative Medical Sciences Yokohama Japan Computational Biology Program Ontario Institute for Cancer Research Toronto ON Canada Programme in Cancer & Stem Cell Biology Duke-NUS Medical School Singapore Singapore Centre for Computational Biology Duke-NUS Medical School Singapore Singapore Programme in Cancer and Stem Cell Biology Duke-NUS Medical School Singapore Singapore Programme in Cancer and Stem Cell Biology Centre for Computational Biology Duke-NUS Medical School Singapore Singapore SingHealth Duke-NUS Institute of Precision Medicine National Heart Centre Singapore Singapore Singapore Cancer Science Institute of Singapore National University of Singapore Singapore Singapore Institute of Molecular and Cell Biology Singapore Singapore Laboratory of Cancer Epigenome Division of Medical Science National Cancer Centre Singapore Singapore Singapore Duke-NUS Medical School Singapore Singapore Human Genome Sequencing Center Baylor College of Medicine Houston TX USA Dan L. Duncan Cancer Center Baylor College of Medicine Houston TX USA Department of Molecular and Human Genetics Baylor College of Medicine Houston TX USA Genome Integrity and Structural Biology Laboratory National Ins

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The evolutionary history of 2,658 cancers (vol 578, pg 122, 2020)

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NATURE 2023年第7948期614卷 E42-E42页

作者： Gerstung, Moritz Jolly, Clemency Leshchiner, Ignaty Dentro, Stefan C. Gonzalez, Santiago Rosebrock, Daniel Mitchell, Thomas J. Rubanova, Yulia Anur, Pavana Yu, Kaixian Tarabichi, Maxime Deshwar, Amit Wintersinger, Jeff Kleinheinz, Kortine Vazquez-Garcia, Ignacio Haase, Kerstin Jerman, Lara Sengupta, Subhajit Macintyre, Geoff Malikic, Salem Donmez, Nilgun Livitz, Dimitri G. Cmero, Marek Demeulemeester, Jonas Schumacher, Steven Fan, Yu Yao, Xiaotong Lee, Juhee Schlesner, Matthias Boutros, Paul C. Bowtell, David D. Zhu, Hongtu Getz, Gad Imielinski, Marcin Beroukhim, Rameen Sahinalp, S. Cenk Ji, Yuan Peifer, Martin Markowetz, Florian Mustonen, Ville Yuan, Ke Wang, Wenyi Morris, Quaid D. Spellman, Paul T. Wedge, David C. Van Loo, Peter European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Cambridge UK European Molecular Biology Laboratory Genome Biology Unit Heidelberg Germany Wellcome Sanger Institute Cambridge UK Genome Biology Unit European Molecular Biology Laboratory (EMBL) Heidelberg Germany University of Ljubljana Ljubljana Slovenia The Francis Crick Institute London UK Big Data Institute University of Oxford Oxford UK Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Big Data Institute Li Ka Shing Centre University of Oxford Oxford UK University of Cambridge Cambridge UK Cambridge University Hospitals NHS Foundation Trust Cambridge UK Department of Applied Mathematics and Theoretical Physics Centre for Mathematical Sciences University of Cambridge Cambridge UK Department of Epidemiology and Biostatistics Memorial Sloan Kettering Cancer Center New York NY USA Department of Statistics Columbia University New York NY USA Department of Haematology University of Cambridge Cambridge UK University of Leuven Leuven Belgium Broad Institute of MIT and Harvard Cambridge MA USA Center for Cancer Research Massachusetts General Hospital Charlestown MA USA Department of Pathology Massachusetts General Hospital Boston MA USA Harvard Medical School Boston MA USA Center for Cancer Research Massachusetts General Hospital Boston MA USA Dana-Farber Cancer Institute Boston MA USA Department of Medical Oncology Dana-Farber Cancer Institute Boston MA USA Department of Cancer Biology Dana-Farber Cancer Institute Boston MA USA Oxford NIHR Biomedical Research Centre Oxford UK Oxford NIHR Biomedical Research Centre University of Oxford Oxford UK University of Toronto Toronto Ontario Canada Vector Institute Toronto Ontario Canada Vector Institute Toronto ON Canada Department of Computer Science University of Toronto Toronto ON Canada Ontario Institute for Cancer Research Toronto Ontario Canada University of California Los Angeles

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Comparative cellular analysis of motor cortex in human, marmoset and mouse (vol 598, pg 111, 2021)

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NATURE 2022年第7904期604卷 E8-E8页

作者： Bakken, Trygve E. Jorstad, Nikolas L. Hu, Qiwen Lake, Blue B. Tian, Wei Kalmbach, Brian E. Crow, Megan Hodge, Rebecca D. Krienen, Fenna M. Sorensen, Staci A. Eggermont, Jeroen Yao, Zizhen Aevermann, Brian D. Aldridge, Andrew I. Bartlett, Anna Bertagnolli, Darren Casper, Tamara Castanon, Rosa G. Crichton, Kirsten Daigle, Tanya L. Dalley, Rachel Dee, Nick Dembrow, Nikolai Diep, Dinh Ding, Song-Lin Dong, Weixiu Fang, Rongxin Fischer, Stephan Goldman, Melissa Goldy, Jeff Graybuck, Lucas T. Herb, Brian R. Hou, Xiaomeng Kancherla, Jayaram Kroll, Matthew Lathia, Kanan van Lew, Baldur Li, Yang Eric Liu, Christine S. Liu, Hanqing Lucero, Jacinta D. Mahurkar, Anup McMillen, Delissa Miller, Jeremy A. Moussa, Marmar Nery, Joseph R. Nicovich, Philip R. Niu, Sheng-Yong Orvis, Joshua Osteen, Julia K. Owen, Scott Palmer, Carter R. Pham, Thanh Plongthongkum, Nongluk Poirion, Olivier Reed, Nora M. Rimorin, Christine Rivkin, Angeline Romanow, William J. Sedeno-Cortes, Adriana E. Siletti, Kimberly Somasundaram, Saroja Sulc, Josef Tieu, Michael Torkelson, Amy Tung, Herman Wang, Xinxin Xie, Fangming Yanny, Anna Marie Zhang, Renee Ament, Seth A. Behrens, M. Margarita Bravo, Hector Corrada Chun, Jerold Dobin, Alexander Gillis, Jesse Hertzano, Ronna Hof, Patrick R. Hollt, Thomas Horwitz, Gregory D. Keene, C. Dirk Kharchenko, Peter V. Ko, Andrew L. Lelieveldt, Boudewijn P. Luo, Chongyuan Mukamel, Eran A. Pinto-Duarte, Antonio Preiss, Sebastian Regev, Aviv Ren, Bing Scheuermann, Richard H. Smith, Kimberly Spain, William J. White, Owen R. Koch, Christof Hawrylycz, Michael Tasic, Bosiljka Macosko, Evan Z. McCarroll, Steven A. Ting, Jonathan T. Zeng, Hongkui Zhang, Kun Feng, Guoping Ecker, Joseph R. Linnarsson, Sten Lein, Ed S. Allen Institute for Brain Science Seattle WA USA Department of Physiology and Biophysics University of Washington Seattle WA USA Department of Biomedical Informatics Harvard Medical School Boston MA USA Department of Bioengineering University of California San Diego La Jolla CA USA The Salk Institute for Biological Studies La Jolla CA USA Epilepsy Center of Excellence Department of Veterans Affairs Medical Center Seattle WA USA Stanley Institute for Cognitive Genomics Cold Spring Harbor Laboratory Cold Spring Harbor NY USA Department of Genetics Harvard Medical School Boston MA USA Broad Institute of MIT and Harvard Cambridge MA USA LKEB Department of Radiology Leiden University Medical Center Leiden The Netherlands Pattern Recognition and Bioinformatics group Delft University of Technology Delft The Netherlands J. Craig Venter Institute La Jolla CA USA Department of Pathology University of California San Diego CA USA Division of Vaccine Discovery La Jolla Institute for Immunology La Jolla CA USA Genomic Analysis Laboratory The Salk Institute for Biological Studies La Jolla CA USA Computer Science and Engineering Program University of California San Diego La Jolla CA USA Howard Hughes Medical Institute The Salk Institute for Biological Studies La Jolla CA USA Bioinformatics and Systems Biology Graduate Program University of California San Diego La Jolla CA USA Institute for Genomes Sciences University of Maryland School of Medicine Baltimore MD USA Center for Epigenomics Department of Cellular and Molecular Medicine University of California San Diego La Jolla CA USA Ludwig Institute for Cancer Research La Jolla CA USA Department of Computer Science University of Maryland College Park College Park MD USA Sanford Burnham Prebys Medical Discovery Institute La Jolla CA USA Biomedical Sciences Program School of Medicine University of California San Diego La Jolla CA USA University of Connecticut Storrs CT USA Department

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Author Correction: Genomic footprints of activated telomere maintenance mechanisms in cancer (Dec, 10.1038/s41467-019-13824-9, 2022)

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NATURE COMMUNICATIONS 2022年第1期13卷 1-1页

作者： Sieverling, Lina Hong, Chen Koser, Sandra D. Ginsbach, Philip Kleinheinz, Kortine Hutter, Barbara Braun, Delia M. Cortes-Ciriano, Isidro Xi, Ruibin Kabbe, Rolf Park, Peter J. Eils, Roland Schlesner, Matthias Brors, Benedikt Rippe, Karsten Jones, David T. W. Feuerbach, Lars Division of Applied Bioinformatics German Cancer Research Center (DKFZ) 69120 Heidelberg Germany Faculty of Biosciences Heidelberg University 69120 Heidelberg Germany Division of Applied Bioinformatics German Cancer Research Center (DKFZ) Heidelberg Germany Faculty of Biosciences Heidelberg University Heidelberg Germany Division of Theoretical Bioinformatics German Cancer Research Center (DKFZ) 69120 Heidelberg Germany Department for Bioinformatics and Functional Genomics Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant 69120 Heidelberg Germany Division of Theoretical Bioinformatics German Cancer Research Center (DKFZ) Heidelberg Germany Institute of Pharmacy and Molecular Biotechnology and BioQuant Heidelberg University Heidelberg Germany German Cancer Consortium (DKTK) Heidelberg Germany National Center for Tumor Diseases (NCT) Heidelberg Heidelberg Germany Heidelberg Center for Personalized Oncology (DKFZ-HIPO) German Cancer Research Center (DKFZ) Heidelberg Germany German Cancer Consortium (DKTK) German Cancer Research Center (DKFZ) Heidelberg Germany Division of Chromatin Networks German Cancer Research Center (DKFZ) and BioQuant 69120 Heidelberg Germany Department of Biomedical Informatics Harvard Medical School Boston Massachusetts 02115 USA Department of Chemistry Centre for Molecular Science Informatics University of Cambridge Cambridge CB2 1EW UK Ludwig Center at Harvard Medical School Boston Massachusetts 02115 USA Department of Biomedical Informatics Harvard Medical School Boston MA USA Department of Chemistry Centre for Molecular Science Informatics University of Cambridge Cambridge UK Ludwig Center at Harvard Medical School Boston MA USA School of Mathematical Sciences and Center for Statistical Science Peking University Beijing 100871 China Heidelberg University Heidelberg Germany New BIH Digital Health Center Berlin Institute of Health (BIH) and Charité - Universitätsmedizin Berlin Berlin Germany Bioi

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Author Correction: Deciphering colorectal cancer genetics through multi-omic analysis of 100,204 cases and 154,587 controls of European and east Asian ancestries

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Nature genetics 2023年第3期55卷 519-520页

作者： Ceres Fernandez-Rozadilla Maria Timofeeva Zhishan Chen Philip Law Minta Thomas Stephanie Schmit Virginia Díez-Obrero Li Hsu Juan Fernandez-Tajes Claire Palles Kitty Sherwood Sarah Briggs Victoria Svinti Kevin Donnelly Susan Farrington James Blackmur Peter Vaughan-Shaw Xiao-Ou Shu Jirong Long Qiuyin Cai Xingyi Guo Yingchang Lu Peter Broderick James Studd Jeroen Huyghe Tabitha Harrison David Conti Christopher Dampier Mathew Devall Fredrick Schumacher Marilena Melas Gad Rennert Mireia Obón-Santacana Vicente Martín-Sánchez Ferran Moratalla-Navarro Jae Hwan Oh Jeongseon Kim Sun Ha Jee Keum Ji Jung Sun-Seog Kweon Min-Ho Shin Aesun Shin Yoon-Ok Ahn Dong-Hyun Kim Isao Oze Wanqing Wen Keitaro Matsuo Koichi Matsuda Chizu Tanikawa Zefang Ren Yu-Tang Gao Wei-Hua Jia John Hopper Mark Jenkins Aung Ko Win Rish Pai Jane Figueiredo Robert Haile Steven Gallinger Michael Woods Polly Newcomb David Duggan Jeremy Cheadle Richard Kaplan Timothy Maughan Rachel Kerr David Kerr Iva Kirac Jan Böhm Lukka-Pekka Mecklin Pekka Jousilahti Paul Knekt Lauri Aaltonen Harri Rissanen Eero Pukkala Johan Eriksson Tatiana Cajuso Ulrika Hänninen Johanna Kondelin Kimmo Palin Tomas Tanskanen Laura Renkonen-Sinisalo Brent Zanke Satu Männistö Demetrius Albanes Stephanie Weinstein Edward Ruiz-Narvaez Julie Palmer Daniel Buchanan Elizabeth Platz Kala Visvanathan Cornelia Ulrich Erin Siegel Stefanie Brezina Andrea Gsur Peter Campbell Jenny Chang-Claude Michael Hoffmeister Hermann Brenner Martha Slattery John Potter Konstantinos Tsilidis Matthias Schulze Marc Gunter Neil Murphy Antoni Castells Sergi Castellví-Bel Leticia Moreira Volker Arndt Anna Shcherbina Mariana Stern Bens Pardamean Timothy Bishop Graham Giles Melissa Southey Gregory Idos Kevin McDonnell Zomoroda Abu-Ful Joel Greenson Katerina Shulman Flavio Lejbkowicz Kenneth Offit Yu-Ru Su Robert Steinfelder Temitope Keku Bethany van Guelpen Thomas Hudson Heather Hampel Rachel Pearlman Sonja Berndt Richard Hayes Marie Elena Martinez Sushma Thomas Douglas Corley Paul Pharoah Susanna Larsson Yun Yen Heinz-Jo Edinburgh Cancer Research Centre Institute of Genomics and Cancer University of Edinburgh Edinburgh UK. Genomic Medicine Group Instituto de Investigacion Sanitaria de Santiago Santiago de Compostela Spain. Colon Cancer Genetics Group Medical Research Council Human Genetics Unit Institute of Genetics and Cancer University of Edinburgh Edinburgh UK. Danish Institute for Advanced Study Department of Public Health University of Southern Denmark Odense Denmark. Division of Epidemiology Department of Medicine Vanderbilt-Ingram Cancer Center Vanderbilt Epidemiology Center Vanderbilt University Medical Center Nashville TN USA. Division of Genetics and Epidemiology Institute of Cancer Research London UK. Public Health Sciences Division Fred Hutchinson Cancer Research Center Seattle WA USA. Genomic Medicine Institute Cleveland Clinic Cleveland OH USA. Population and Cancer Prevention Program Case Comprehensive Cancer Center Cleveland OH USA. Colorectal Cancer Group ONCOBELL Program Bellvitge Biomedical Research Institute Barcelona Spain. Oncology Data Analytics Program Catalan Institute of Oncology Barcelona Spain. Consortium for Biomedical Research in Epidemiology and Public Health Madrid Madrid Spain. Department of Clinical Sciences Faculty of Medicine University of Barcelona Barcelona Spain. Department of Biostatistics School of Public Health University of Washington Seattle WA USA. Institute of Cancer and Genomic Sciences College of Medical and Dental Sciences University of Birmingham Birmingham UK. Department of Public Health Richard Doll Building University of Oxford Oxford UK. Department of Biomedical Informatics Vanderbilt University School of Medicine Nashville TN USA. Department of Preventive Medicine USC Norris Comprehensive Cancer Center Keck School of Medicine University of Southern California Los Angeles CA USA. Center for Public Health Genomics Department of Public Health Sciences University of Virginia Charlottesville VA USA. De

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GWAS meta-analysis of over 29,000 people with epilepsy identifies 26 risk loci and subtype-specific genetic architecture

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Nature genetics 2023年第9期55卷 1471-1482页

作者： Remi Stevelink Dorothee Kasteleijn-Nolst Trenite Bobby P. C. Koeleman Dick Lindhout Anja C. M. Sonsma Ciarán Campbell Gianpiero L. Cavalleri Norman Delanty Hany El-Naggar Austin Lacey Peter Widdess-Walsh Colin P. Doherty Siwei Chen Claire Churchhouse Mark J. Daly Yen-Chen A. Feng Daniel P. Howrigan Mitja I. Kurki Benjamin M. Neale Aarno Palotie Wei Zhou Namrata Gupta Henrike O. Heyne Bassel Abou-Khalil Kevin F. Haas R. S. Taneja Oluyomi M. Adesoji Michael Nothnagel Peter Nürnberg Thomas Sander Zaid Afawi Ilan Blatt Amos D. Korczyn Elisabetta Amadori Ganna Balagura Antonella Riva Marcello Scala Paolo Scudieri Pasquale Striano Federico Zara Michele Iacomino Francesca Madia Alison Anderson Patrick Kwan Terence J. O’Brien Slavé Petrovski K. Meng Tan Marian Todaro Joseph Anderson Danielle M. Andrade Quratulain Zulfiqar Ali Grazia Annesi Pauls Auce Andreja Avbersek Simona Balestrini Vera Braatz Claudia B. Catarino Krishna Chinthapalli Jennifer Jamnadas-Khoda Dalia Kasperavičiūte Costin Leu Josemir W. Sander Sanjay M. Sisodiya Sara Zagaglia Melanie Bahlo Karen L. Oliver Mark D. Baker Beata Fonferko-Shadrach William O. Pickrell Carmen Barba Claudia Bianchini Viola Doccini Renzo Guerrini Davide Mei Martino Montomoli Elena Parrini Annalisa Vetro Karen Barboza Fabrice Bartolomei Thomas Bast Bernhard J. Steinhoff Larry Baum Stacey S. Cherny Pak Sham Tobias Baumgartner Christian E. Elger Kerstin Hallmann Wolfram S. Kunz Rainer Surges Randi von Wrede Gábor Zsurka Betül Baykan Nerses Bebek Yeşim Kesim Albert J. Becker Susanne Schoch Felicitas Becker Caitlin A. Bennett Samuel F. Berkovic Stephanie L. Leech Brigid M. Regan Ingrid E. Scheffer Bianca Berghuis Ahmad Beydoun Wassim Nasreddine Francesca Bisulli Lidia Di Vito Lorenzo Ferri Tania Giangregorio Laura Licchetta Raffaella Minardi Barbara Mostacci Carlotta Stipa Paolo Tinuper Lorenzo Muccioli Federica Pondrelli Dheeraj R. Bobbili Emadeldin Hassanin Roland Krause Zied Landoulsi Patrick May Ingo Borggraefe Christian Bosselmann Christian Hengsbach Josua Kegele Stephen Lauxmann Department of Genetics University Medical Center Utrecht Utrecht The Netherlands Stichting Epilepsie Instellingen Nederland (SEIN) Heemstede The Netherlands School of Pharmacy and Biomolecular Sciences The Royal College of Surgeons in Ireland Dublin Ireland The FutureNeuro Research Centre Dublin Ireland Department of Neurology Beaumont Hospital Dublin Ireland Department of Neurology St. James’s Hospital Dublin Ireland Analytic and Translational Genetics Unit Department of Medicine Massachusetts General Hospital and Harvard Medical School Boston MA USA Program in Medical and Population Genetics Broad Institute of MIT and Harvard Cambridge MA USA Stanley Center for Psychiatric Research Broad Institute of Harvard and M.I.T Cambridge MA USA Institute for Molecular Medicine Finland (FIMM) University of Helsinki Helsinki Finland Psychiatric & Neurodevelopmental Genetics Unit Department of Psychiatry Massachusetts General Hospital and Harvard Medical School Boston MA USA Division of Biostatistics Institute of Epidemiology and Preventive Medicine College of Public Health National Taiwan University Taipei Taiwan Hasso Plattner Institute Digital Health Center University of Potsdam Potsdam Germany Hasso Plattner Institute Mount Sinai School of Medicine New York City NY USA Department of Neurology Vanderbilt University Medical Center Nashville TN USA Cologne Center for Genomics (CCG) University of Cologne Faculty of Medicine and University Hospital Cologne Cologne Germany University Hospital Cologne Cologne Germany Department of Neurology Charité Universitaetsmedizin Berlin Campus Virchow-Clinic Berlin Germany Tel-Aviv University Sackler Faculty of Medicine Ramat Aviv Israel Department of Neurology Sheba Medical Center Ramat Gan Israel Department of Neurosciences Rehabilitation Ophthalmology Genetics Maternal and Child Health University of Genova Genova Italy IRCCS Istituto Giannina Gaslini Genova Italy Department of Medicine University of Melbour

Epilepsy is a highly heritable disorder affecting over 50 million people worldwide, of which about one-third are resistant to current treatments. Here we report a multi-ancestry genome-wide association study including 29,944 cases, stratified into three broad categories and seven subtypes of epilepsy, and 52,538 controls. We identify 26 genome-wide significant loci, 19 of which are specific to genetic generalized epilepsy (GGE). We implicate 29 likely causal genes underlying these 26 loci. SNP-based heritability analyses show that common variants explain between 39.6% and 90% of genetic risk for GGE and its subtypes. Subtype analysis revealed markedly different genetic architectures between focal and generalized epilepsies. Gene-set analyses of GGE signals implicate synaptic processes in both excitatory and inhibitory neurons in the brain. Prioritized candidate genes overlap with monogenic epilepsy genes and with targets of current antiseizure medications. Finally, we leverage our results to identify alternate drugs with predicted efficacy if repurposed for epilepsy treatment.

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Chronic obstructive pulmonary disease and related phenotypes: polygenic risk scores in population-based and case-control cohorts

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The Lancet Respiratory Medicine 2020年第7期8卷 696-708页

作者： Moll, Matthew Sakornsakolpat, Phuwanat Shrine, Nick Hobbs, Brian D DeMeo, Dawn L John, Catherine Guyatt, Anna L McGeachie, Michael J Gharib, Sina A Obeidat, Ma'en Lahousse, Lies Wijnant, Sara R A Brusselle, Guy Meyers, Deborah A Bleecker, Eugene R Li, Xingnan Tal-Singer, Ruth Manichaikul, Ani Rich, Stephen S Won, Sungho Kim, Woo Jin Do, Ah Ra Washko, George R Barr, R Graham Psaty, Bruce M Bartz, Traci M Hansel, Nadia N Barnes, Kathleen Hokanson, John E Crapo, James D Lynch, David Bakke, Per Gulsvik, Amund Hall, Ian P Wain, Louise Soler Artigas, María Jackson, Victoria E Strachan, David P Hui, Jennie James, Alan L Kerr, Shona M Polasek, Ozren Vitart, Veronique Marten, Jonathan Rudan, Igor Kähönen, Mika Surakka, Ida Gieger, Christian Karrasch, Stefan Rawal, Rajesh Schulz, Holger Deary, Ian J Harris, Sarah E Enroth, Stefan Gyllensten, Ulf Imboden, Medea Probst-Hensch, Nicole M Lehtimäki, Terho Raitakari, Olli T Langenberg, Claudia Luan, Jian'an Wareham, Nick Zhao, Jing Hua Hayward, Caroline Murray, Alison Porteous, David J Smith, Blair H Jarvelin, Marjo-Riitta Wielscher, Matthias Joshi, Peter K Kentistou, Katherine A Timmers, Paul RHJ Wilson, James F Cook, James P Lind, Lars Mahajan, Anubha Morris, Andrew P Ewert, Ralf Homuth, Georg Stubbe, Beate Weiss, Stefan Zeggini, Eleftheria Weiss, Scott T Silverman, Edwin K Dudbridge, Frank Tobin, Martin D Cho, Michael H Channing Division of Network Medicine Brigham and Women's Hospital Boston MA United States Division of Pulmonary and Critical Care Medicine Brigham and Women's Hospital Boston MA United States Department of Medicine Faculty of Medicine Siriraj Hospital Mahidol University Bangkok Thailand Genetic Epidemiology Group Department of Health Sciences University of Leicester Leicester United Kingdom Computational Medicine Core Center for Lung Biology Department of Medicine University of Washington Seattle WA United States Division of Pulmonary Critical Care and Sleep Medicine Department of Medicine University of Washington Seattle WA United States Cardiovascular Health Research Unit Department of Medicine University of Washington Seattle WA United States University of British Columbia Center for Heart Lung Innovation St Paul's Hospital Vancouver BC Canada Department of Epidemiology Erasmus Medical Centre Rotterdam Netherlands Department of Respiratory Medicine Erasmus Medical Centre Rotterdam Netherlands Department of Bioanalysis Faculty of Pharmaceutical Sciences Ghent University Ghent Belgium Department of Respiratory Medicine Ghent University Hospital Ghent Belgium Department of Medicine University of Arizona Tucson AZ United States GlaxoSmithKline Research and Development Collegeville PA United States Center for Public Health Genomics University of Virginia Charlottesville VA United States Department of Public Health Sciences University of Virginia Charlottesville VA United States Department of Public Health Sciences Graduate School of Public Health Seoul National University Seoul South Korea Interdisciplinary Program of Bioinformatics College of National Sciences Seoul National University Seoul South Korea Institute of Health and Environment Seoul National University Seoul South Korea Department of Internal Medicine Kangwon National University Chuncheon South Korea Department of Medicine and Department of Epidemiology Columbia Universit

Background: Genetic factors influence chronic obstructive pulmonary disease (COPD) risk, but the individual variants that have been identified have small effects. We hypothesised that a polygenic risk score using additional variants would predict COPD and associated phenotypes. Methods: We constructed a polygenic risk score using a genome-wide association study of lung function (FEV₁ and FEV₁/forced vital capacity [FVC]) from the UK Biobank and SpiroMeta. We tested this polygenic risk score in nine cohorts of multiple ethnicities for an association with moderate-to-severe COPD (defined as FEV₁/FVC <0·7 and FEV₁ <80% of predicted). Associations were tested using logistic regression models, adjusting for age, sex, height, smoking pack-years, and principal components of genetic ancestry. We assessed predictive performance of models by area under the curve. In a subset of studies, we also studied quantitative and qualitative CT imaging phenotypes that reflect parenchymal and airway pathology, and patterns of reduced lung growth. Findings: The polygenic risk score was associated with COPD in European (odds ratio [OR] per SD 1·81 [95% CI 1·74–1·88] and non-European (1·42 [1·34–1·51]) populations. Compared with the first decile, the tenth decile of the polygenic risk score was associated with COPD, with an OR of 7·99 (6·56–9·72) in European ancestry and 4·83 (3·45–6·77) in non-European ancestry cohorts. The polygenic risk score was superior to previously described genetic risk scores and, when combined with clinical risk factors (ie, age, sex, and smoking pack-years), showed improved prediction for COPD compared with a model comprising clinical risk factors alone (AUC 0·80 [0·79–0·81] vs 0·76 [0·75–0·76]). The polygenic risk score was associated with CT imaging phenotypes, including wall area percent, quantitative and qualitative measures of emphysema, local histogram emphysema patterns, and destructive emphysema subtypes. The po

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