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Paradigm shift in safety assessment using new approach methods: The EU-ToxRisk strategy

Current Opinion in Toxicology 2019年 15卷 33-39页

作者： Graepel, R. Ter Braak, B. Escher, S.E. Fisher, C. Gardner, I. Kamp, H. Kroese, D. Leist, M. Moné, M.J. Pastor, M. van de Water, B. Division of Drug Discovery and Safety Leiden Academic Centre for Drug Research Leiden University Einsteinweg 55 Leiden 2333 CC Netherlands Fraunhofer Institute of Toxicology and Experimental Medicine (ITEM) Hannover Germany Simcyp (A Certara Company) Sheffield United Kingdom BASF SE Experimental Toxicology and Ecology Ludwigshafen am Rhein Germany TNO (Department of Risk Analysis of Products in Development) Zeist Netherlands Fachbereich Biologie University of Konstanz Universitätsstrasse 1 Konstanz 78457 Germany Research Programme on Biomedical Informatics (GRIB) Institut Hospital del Mar d'Investigacions Mèdiques (IMIM) Department of Experimental and Health Sciences Universitat Pompeu Fabra Barcelona Spain

The EU-ToxRisk research project is an interdisciplinary research project that aims to advance the paradigm shift in toxicology towards new approach methodology (NAM)–based approaches for risk assessment. In this European research project, experts in the fields of in vitro and in silico techniques and risk assessment from academia, industry and regulatory agencies work together. Using a series of custom-designed case studies, the EU-ToxRisk battery of NAMs is being evaluated to learn how to carry out safety assessment using NAMs. This review article provides an overview of the project, its aims and approach and the methodologies that are being used. © 2019

关键词： Developmental and reproductive toxicity (DART) Hazard assessment in silico in vitro Mechanism-based testing Repeated dose toxicity (RDT)

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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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Patterns of somatic structural variation in human cancer genomes (vol 578, pg 112, 2020)

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NATURE 2023年第7948期614卷 E38-E38页

作者： Li, Yilong Roberts, Nicola D. Wala, Jeremiah A. Shapira, Ofer Schumacher, Steven E. Kumar, Kiran Khurana, Ekta Waszak, Sebastian Korbel, Jan O. Haber, James E. Imielinski, Marcin Weischenfeldt, Joachim Beroukhim, Rameen Campbell, Peter J. Cancer Genome Project Wellcome Trust Sanger Institute Hinxton UK Totient Inc Cambridge MA USA Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Department of Haematology University of Cambridge Cambridge UK Cambridge University Hospitals NHS Foundation Trust Cambridge UK Korea Advanced Institute of Science and Technology Daejeon South Korea Department of Zoology Genetics and Physical Anthropology University of Santiago de Compostela Santiago de Compostela Spain Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS) University of Santiago de Compostela Santiago de Compostela Spain The Biomedical Research Centre (CINBIO) University of Vigo Vigo Spain Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain Department of Zoology Genetics and Physical Anthropology (CiMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain The Biomedical Research Centre (CINBIO) Universidade de Vigo Vigo Spain The Broad Institute of Harvard and MIT Cambridge MA USA Bioinformatics and Integrative Genomics Harvard University Cambridge MA USA Department of Cancer Biology Dana-Farber Cancer Institute Boston MA USA Broad Institute of MIT and Harvard Cambridge MA USA Department of Medical Oncology Dana-Farber Cancer Institute Boston MA USA Harvard Medical School Boston MA USA Massachusetts General Hospital Center for Cancer Research Charlestown MA USA Dana-Farber Cancer Institute Boston MA USA Department of Biostatistics and Computational Biology Dana-Farber Cancer Institute and Harvard Medical School Boston MA USA Weill Cornell Medical College 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 Ne

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

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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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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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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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The overlapping burden of the three leading causes of disability and death in sub-Saharan African children

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Nature Communications 2022年第1期13卷 1-14页

作者： Reiner, Robert C. Welgan, Catherine A. Troeger, Christopher E. Baumann, Mathew M. Weiss, Daniel J. Deshpande, Aniruddha Blacker, Brigette F. Miller-Petrie, Molly K. Earl, Lucas Bhatt, Samir Abolhassani, Hassan Abosetugn, Akine Eshete Abu-Gharbieh, Eman Adekanmbi, Victor Adetokunboh, Olatunji O. Aghaali, Mohammad Aji, Budi Alahdab, Fares Al-Aly, Ziyad Alhassan, Robert Kaba Ali, Saqib Alizade, Hesam Aljunid, Syed Mohamed Almasi-Hashiani, Amir Al-Mekhlafi, Hesham M. Altirkawi, Khalid A. Alvis-Guzman, Nelson Amare, Azmeraw T. Amini, Saeed Amugsi, Dickson A. Ancuceanu, Robert Andrei, Catalina Liliana Ansari, Fereshteh Anvari, Davood Appiah, Seth Christopher Yaw Arabloo, Jalal Aremu, Olatunde Atout, Maha Moh’d Wahbi Ausloos, Marcel Ausloos, Floriane Ayanore, Martin Amogre Aynalem, Yared Asmare Azene, Zelalem Nigussie Badawi, Alaa Baig, Atif Amin Banach, Maciej Bedi, Neeraj Bhagavathula, Akshaya Srikanth Bhandari, Dinesh Bhardwaj, Nikha Bhardwaj, Pankaj Bhattacharyya, Krittika Bhutta, Zulfiqar A. Bijani, Ali Birhanu, Tesega Tesega Mengistu Bitew, Zebenay Workneh Boloor, Archith Brady, Oliver J. Butt, Zahid A. Car, Josip Carvalho, Felix Casey, Daniel C. Chattu, Vijay Kumar Chowdhury, Mohiuddin Ahsanul Kabir Chu, Dinh-Toi Coelho, Camila H. Cook, Aubrey J. Damiani, Giovanni Daoud, Farah Gela, Jiregna Darega Darwish, Amira Hamed Daryani, Ahmad Das, Jai K. Davis Weaver, Nicole Deribe, Kebede Desalew, Assefa Dharmaratne, Samath Dhamminda Dianatinasab, Mostafa Diaz, Daniel Djalalinia, Shirin Dorostkar, Fariba Dubljanin, Eleonora Duko, Bereket Dwyer-Lindgren, Laura Effiong, Andem El Sayed Zaki, Maysaa El Tantawi, Maha Enany, Shymaa Fattahi, Nazir Feigin, Valery L. Fernandes, Eduarda Ferrara, Pietro Fischer, Florian Foigt, Nataliya A. Folayan, Morenike Oluwatoyin Foroutan, Masoud Frostad, Joseph Jon Fukumoto, Takeshi Gaidhane, Abhay Motiramji Gebrekrstos, Hailemikael Gebrekidan G. K. Gebremeskel, Leake Gebreslassie, Assefa Ayalew Gething, Peter W. Gezae, Kebede Embaye Ghadiri, Keyghobad Ghashghaee, Ahmad Golechha, Mahaveer Gubar Institute for Health Metrics and Evaluation University of Washington Seattle WA United States Department of Health Metrics Sciences School of Medicine University of Washington Seattle WA United States Malaria Atlas Project University of Oxford Oxford United Kingdom Imperial College London London United Kingdom Department of Laboratory Medicine Karolinska University Hospital Huddinge Sweden Research Center for Immunodeficiencies Tehran University of Medical Sciences Tehran Iran Department of Public Health Debre Berhan University Debre Berhan Ethiopia Department of Clinical Sciences University of Sharjah Sharjah United Arab Emirates Population Health Sciences King’s College London London United Kingdom Centre of Excellence for Epidemiological Modelling and Analysis Stellenbosch University Stellenbosch South Africa Department of Global Health Stellenbosch University Cape Town South Africa Department of Epidemiology and Biostatistics Qom University of Medical Sciences Qom Iran Faculty of Medicine and Public Health Jenderal Soedirman University Purwokerto Indonesia Mayo Evidence-based Practice Center Mayo Clinic Foundation for Medical Education and Research Rochester MN United States John T. Milliken Department of Internal Medicine Washington University in St. Louis St. Louis MO United States Clinical Epidemiology Center Department of Veterans Affairs St Louis MO United States Institute of Health Research University of Health and Allied Sciences Ho Ghana Department of Information Systems College of Economics and Political Science Sultan Qaboos University Muscat Oman Infectious and Tropical Disease Research Center Hormozgan University of Medical Sciences Bandar Abbas Iran Department of Health Policy and Management Kuwait University Safat Kuwait International Centre for Casemix and Clinical Coding National University of Malaysia Bandar Tun Razak Malaysia Department of Epidemiology Arak University of Medical Sciences Arak Iran Medical Research Center

Despite substantial declines since 2000, lower respiratory infections (LRIs), diarrhoeal diseases, and malaria remain among the leading causes of nonfatal and fatal disease burden for children under 5 years of age (under 5), primarily in sub-Saharan Africa (SSA). The spatial burden of each of these diseases has been estimated subnationally across SSA, yet no prior analyses have examined the pattern of their combined burden. Here we synthesise subnational estimates of the burden of LRIs, diarrhoea, and malaria in children under-5 from 2000 to 2017 for 43 sub-Saharan countries. Some units faced a relatively equal burden from each of the three diseases, while others had one or two dominant sources of unit-level burden, with no consistent pattern geographically across the entire subcontinent. Using a subnational counterfactual analysis, we show that nearly 300 million DALYs could have been averted since 2000 by raising all units to their national average. Our findings are directly relevant for decision-makers in determining which and targeting where the most appropriate interventions are for increasing child survival. © 2022, The Author(s).

关键词： Biogeography Epidemiology Infectious diseases Malaria

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Author Correction: Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition

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Nature genetics 2023年第6期55卷 1080页

作者： Bernardo Rodriguez-Martin Eva G Alvarez Adrian Baez-Ortega Jorge Zamora Fran Supek Jonas Demeulemeester Martin Santamarina Young Seok Ju Javier Temes Daniel Garcia-Souto Harald Detering Yilong Li Jorge Rodriguez-Castro Ana Dueso-Barroso Alicia L Bruzos Stefan C Dentro Miguel G Blanco Gianmarco Contino Daniel Ardeljan Marta Tojo Nicola D Roberts Sonia Zumalave Paul A Edwards Joachim Weischenfeldt Montserrat Puiggròs Zechen Chong Ken Chen Eunjung Alice Lee Jeremiah A Wala Keiran M Raine Adam Butler Sebastian M Waszak Fabio C P Navarro Steven E Schumacher Jean Monlong Francesco Maura Niccolo Bolli Guillaume Bourque Mark Gerstein Peter J Park David C Wedge Rameen Beroukhim David Torrents Jan O Korbel Iñigo Martincorena Rebecca C Fitzgerald Peter Van Loo Haig H Kazazian Kathleen H Burns Peter J Campbell Jose M C Tubio Department of Zoology Genetics and Physical Anthropology Universidade de Santiago de Compostela Santiago de Compostela Spain. Biomedical Research Centre (CINBIO) University of Vigo Vigo Spain. Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain. Transmissible Cancer Group Department of Veterinary Medicine University of Cambridge Cambridge UK. The Biomedical Research Centre (CINBIO) Universidade de Vigo Vigo Spain. Wellcome Sanger Institute Wellcome Genome Campus Cambridge UK. Genome Data Science Institute for Research in Biomedicine (IRB Barcelona) The Barcelona Institute of Science and Technology (BIST) Barcelona Spain. Institucio Catalana de Recerca i Estudis Avançats (ICREA) Barcelona Spain. The Francis Crick Institute London UK. Department of Human Genetics University of Leuven Leuven Belgium. Genomes and Disease Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain. Graduate School of Medical Science and Engineering Korea Advanced Institute of Science and Technology Daejeon South Korea. Cancer Ageing and Somatic Mutation Programme Wellcome Sanger Institute Cambridge UK. Department of Biochemistry Genetics and Immunology University of Vigo Vigo Spain. Galicia Sur Health Research Institute Vigo Spain. Faculty of Science and Technology University of Vic-Central University of Catalonia (UVic-UCC) Vic Spain. Barcelona Supercomputing Center (BSC) Barcelona Spain. Experimental Cancer Genetics Wellcome Sanger Institute Cambridge UK. Oxford Big Data Institute University of Oxford Oxford UK. DNA Repair and Genome Integrity Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain. Department of Biochemistry and Molecular Biology Universidade de Santiago de Compostela Santiago de Compostela Spain. Medical R

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