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Genome-wide association study of long COVID

Nature Genetics 2025年 1-16页

作者： Vilma Lammi Tomoko Nakanishi Samuel E. Jones Juha Karjalainen Martin Broberg Hele H. Haapaniemi Matti Pirinen Mari E. K. Niemi Mattia Cordioli Mark J. Daly Andrea Ganna Hanna M. Ollila J. Brent Richards Yukinori Okada Shea J. Andrews Beatriz Cortés Rafael de Cid Susana Iraola-Guzmán Natalia Blay Xavier Farré Heath E. O’Brien Thompson Hannah Patrick J. Short Ana Ochoa-Guzman Michelle Duran-Gomez Brian E. Fulton-Howard Masahiro Kanai Axel Schmidt Daniella Balla Julia Heggemann Sonja Schultz Pari Behzad Markus M. Nöthen Abigail Miller Kerstin U. Ludwig Ruth E. Mitchell George Davey Smith Nicholas J. Timpson Abdou Mousas Evangelos Evangelou Evangelia Ntzani Konstantinos K. Tsilidis Massimo Mangino Alicia Huerta-Chagoya Nasa Sinnott-Armstrong Elizabeth T. Cirulli Francisco Tanudjaja Efren Sandoval Nicole L. Washington Simon White Alexandre Bolze Kelly M. Schiabor Barrett Marc Vaudel Alex S. F. Kwong Amit K. Maiti Minttu M. Marttila Daniel C. Posner Alexis A. Rodriguez Chiara Batini Beatriz Guillen-Guio Olivia C. Leavy Anna L. Guyatt Catherine John Louise V. Wain Francesca Minnai Anna R. Dearman Benedict Hignell Meena Kumari C. A. Robert Warmerdam Lude H. Franke Celia B. Sequeros Søren Brunak David Westergaard Karina Banasik Thomas W. Winkler Iris M. Heid Daniel M. Jordan Ryan C. Thompson Alexander W. Charney Laura G. Sloofman Nicole W. Simons Noam D. Beckmann Raimonds Rešcenko Vita Rovite Peculis Raitis Monta Briviba Janis Klovinš Laura Ansone Lorenzo Miano Flora Peyvandi Francesco Malvestiti Nicola Montano Alessandra Bandera Francesco Bruno Arturo Blasi Jacqueline M. Lane Jakob M. Cherry Ryan K. Chung Laura Carvajal-Silva Kevin Aguilar-Valdés Leslie C. Cerpa Tamara V. Arévalo Eduardo Lamoza Alicia Colombo Ricardo A. Verdugo Erika Frangione Xu Xinyi Jennifer Taher Jordan Lerner-Ellis Lindsay Guare Shefali S. Verma Ekaterina Vergasova Michil Trofimov Layal Shaheen Nikolay Plotnikov Anna Kim Dmitrii Kharitonov Alexei Kamelin Alexander Rakitko Eirini Marouli Pasquale Striano Ummu Afeera Zainulabid Ashutosh Kumar Hajar Fa Institute for Molecular Medicine Finland (FIMM) Helsinki Institute of Life Science (HiLIFE) University of Helsinki Helsinki Finland Department of Human Genetics McGill University Montreal Quebec Canada Centre for Clinical Epidemiology Department of Medicine Lady Davis Institute Jewish General Hospital McGill University Montreal Quebec Canada Kyoto-McGill International Collaborative Program in Genomic Medicine Graduate School of Medicine Kyoto University Kyoto Japan Department of Genome Informatics Graduate School of Medicine the University of Tokyo Tokyo Japan Research Fellow Japan Society for the Promotion of Science Tokyo Japan Program in Medical and Population Genetics Broad Institute of Harvard and MIT Cambridge MA USA Stanley Center for Psychiatric Research Broad Institute of Harvard and MIT Cambridge MA USA Analytic and Translational Genetics Unit Massachusetts General Hospital Boston MA USA Department of Mathematics and Statistics University of Helsinki Helsinki Finland Department of Public Health University of Helsinki Helsinki Finland Broad Institute Cambridge MA USA Analytical and Translational Genetics Unit Massachusetts General Hospital Harvard Medical School Boston MA USA Center for Genomic Medicine Massachusetts General Hospital Boston MA USA Anesthesia Critical Care and Pain Medicine Massachusetts General Hospital and Harvard Medical School Boston MA USA Broad Institute of MIT and Harvard Cambridge MA USA Department of Twin Research King’s College London London UK 5 Prime Sciences Inc Montreal Quebec Canada Department of Epidemiology Biostatistics and Occupational Health McGill University Montreal Quebec Canada Department of Statistical Genetics Osaka University Graduate School of Medicine Suita Japan Laboratory for Systems Genetics RIKEN Center for Integrative Medical Sciences Yokohama Japan Laboratory of Statistical Immunology Immunology Frontier Research Center (WPI-IFReC) Osaka University Suita Japan Departmen

Infections can lead to persistent symptoms and diseases such as shingles after varicella zoster or rheumatic fever after streptococcal infections. Similarly, severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) infection can result in long coronavirus disease (COVID), typically manifesting as fatigue, pulmonary symptoms and cognitive dysfunction. The biological mechanisms behind long COVID remain unclear. We performed a genome-wide association study for long COVID including up to 6,450 long COVID cases and 1,093,995 population controls from 24 studies across 16 countries. We discovered an association ofFOXP4with long COVID, independent of its previously identified association with severe COVID-19. The signal was replicated in 9,500 long COVID cases and 798,835 population controls. Given the transcription factor FOXP4’s role in lung physiology and pathology, our findings highlight the importance of lung function in the pathophysiology of long COVID.

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The mutational constraint spectrum quantified from variation in 141,456 humans (vol 581, pg 434, 2020)

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NATURE 2021年第7874期597卷 E3-E4页

作者： Gudmundsson, Sanna Karczewski, Konrad J. Francioli, Laurent C. Tiao, Grace Cummings, Beryl B. Alfoldi, Jessica Wang, Qingbo Collins, Ryan L. Laricchia, Kristen M. Ganna, Andrea Birnbaum, Daniel P. Gauthier, Laura D. Brand, Harrison Solomonson, Matthew Watts, Nicholas A. Rhodes, Daniel Singer-Berk, Moriel England, Eleina M. Seaby, Eleanor G. Kosmicki, Jack A. Walters, Raymond K. Tashman, Katherine Farjoun, Yossi Banks, Eric Poterba, Timothy Wang, Arcturus Seed, Cotton Whiffin, Nicola Chong, Jessica X. Samocha, Kaitlin E. Pierce-Hoffman, Emma Zappala, Zachary O'Donnell-Luria, Anne H. Minikel, Eric Vallabh Weisburd, Ben Lek, Monkol Ware, James S. Vittal, Christopher Armean, Irina M. Bergelson, Louis Cibulskis, Kristian Connolly, Kristen M. Covarrubias, Miguel Donnelly, Stacey Ferriera, Steven Gabriel, Stacey Gentry, Jeff Gupta, Namrata Jeandet, Thibault Kaplan, Diane Llanwarne, Christopher Munshi, Ruchi Novod, Sam Petrillo, Nikelle Roazen, David Ruano-Rubio, Valentin Saltzman, Andrea Schleicher, Molly Soto, Jose Tibbetts, Kathleen Tolonen, Charlotte Wade, Gordon Talkowski, Michael E. Neale, Benjamin M. Daly, Mark J. MacArthur, Daniel G. Program in Medical and Population Genetics Broad Institute of MIT and Harvard Cambridge MA USA Analytic and Translational Genetics Unit Massachusetts General Hospital Boston MA USA Division of Genetics and Genomics Boston Children’s Hospital Boston MA USA Program in Biological and Biomedical Sciences Harvard Medical School Boston MA USA Program in Bioinformatics and Integrative Genomics Harvard Medical School Boston MA USA Center for Genomic Medicine Massachusetts General Hospital Boston MA USA Institute for Molecular Medicine Finland Helsinki Finland Stanley Center for Psychiatric Research Broad Institute of MIT and Harvard Cambridge MA USA National Heart & Lung Institute and MRC London Institute of Medical Sciences Imperial College London London UK Cardiovascular Research Centre Royal Brompton & Harefield Hospitals NHS Trust London UK Vertex Pharmaceuticals Inc Boston MA USA Department of Pediatrics Harvard Medical School Boston MA USA Broad Genomics Broad Institute of MIT and Harvard Cambridge MA USA Department of Neurology Harvard Medical School Boston MA USA Cardiac Arrhythmia Service and Cardiovascular Research Center Massachusetts General Hospital Boston MA USA Estonian Genome Center Institute of Genomics University of Tartu Tartu Estonia Data Sciences Platform Broad Institute of MIT and Harvard Cambridge MA USA Diabetes Unit Massachusetts General Hospital Boston MA USA Program in Metabolism Broad Institute of MIT and Harvard Cambridge MA USA Department of Medicine Harvard Medical School Boston MA USA Division of General Internal Medicine Massachusetts General Hospital Boston MA USA Department of Public Health Faculty of Medicine University of Helsinki Helsinki Finland Cardiovascular Disease Initiative and Program in Medical and Population Genetics Broad Institute of MIT and Harvard Cambridge MA USA Genomics Diabetes and Endocrinology Lund University Lund Sweden Folkhälsan Institute of Genetics Folkhälsan Research C

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The mutational constraint spectrum quantified from variation in 141,456 humans (vol 581, pg 434, 2020)

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NATURE 2021年第7846期590卷 E53-E53页

作者： Karczewski, Konrad J. Francioli, Laurent C. Tiao, Grace Cummings, Beryl B. Alfoldi, Jessica Wang, Qingbo Collins, Ryan L. Laricchia, Kristen M. Ganna, Andrea Birnbaum, Daniel P. Gauthier, Laura D. Brand, Harrison Solomonson, Matthew Watts, Nicholas A. Rhodes, Daniel Singer-Berk, Moriel England, Eleina M. Seaby, Eleanor G. Kosmicki, Jack A. Walters, Raymond K. Tashman, Katherine Farjoun, Yossi Banks, Eric Poterba, Timothy Wang, Arcturus Seed, Cotton Whiffin, Nicola Chong, Jessica X. Samocha, Kaitlin E. Pierce-Hoffman, Emma Zappala, Zachary O'Donnell-Luria, Anne H. Minikel, Eric Vallabh Weisburd, Ben Lek, Monkol Ware, James S. Vittal, Christopher Armean, Irina M. Bergelson, Louis Cibulskis, Kristian Connolly, Kristen M. Covarrubias, Miguel Donnelly, Stacey Ferriera, Steven Gabriel, Stacey Gentry, Jeff Gupta, Namrata Jeandet, Thibault Kaplan, Diane Llanwarne, Christopher Munshi, Ruchi Novod, Sam Petrillo, Nikelle Roazen, David Ruano-Rubio, Valentin Saltzman, Andrea Schleicher, Molly Soto, Jose Tibbetts, Kathleen Tolonen, Charlotte Wade, Gordon Talkowski, Michael E. Aggregation, Genome Neale, Benjamin M. Daly, Mark J. MacArthur, Daniel G. Program in Medical and Population Genetics Broad Institute of MIT and Harvard Cambridge MA USA Analytic and Translational Genetics Unit Massachusetts General Hospital Boston MA USA Program in Biological and Biomedical Sciences Harvard Medical School Boston MA USA Program in Bioinformatics and Integrative Genomics Harvard Medical School Boston MA USA Center for Genomic Medicine Massachusetts General Hospital Boston MA USA Institute for Molecular Medicine Finland Helsinki Finland Stanley Center for Psychiatric Research Broad Institute of MIT and Harvard Cambridge MA USA National Heart & Lung Institute and MRC London Institute of Medical Sciences Imperial College London London UK Cardiovascular Research Centre Royal Brompton & Harefield Hospitals NHS Trust London UK Vertex Pharmaceuticals Inc Boston MA USA Division of Genetics and Genomics Boston Children’s Hospital Boston MA USA Department of Pediatrics Harvard Medical School Boston MA USA Broad Genomics Broad Institute of MIT and Harvard Cambridge MA USA Department of Neurology Harvard Medical School Boston MA USA Cardiac Arrhythmia Service and Cardiovascular Research Center Massachusetts General Hospital Boston MA USA Estonian Genome Center Institute of Genomics University of Tartu Tartu Estonia Data Sciences Platform Broad Institute of MIT and Harvard Cambridge MA USA Diabetes Unit Massachusetts General Hospital Boston MA USA Program in Metabolism Broad Institute of MIT and Harvard Cambridge MA USA Department of Medicine Harvard Medical School Boston MA USA Division of General Internal Medicine Massachusetts General Hospital Boston MA USA Department of Public Health Faculty of Medicine University of Helsinki Helsinki Finland Cardiovascular Disease Initiative and Program in Medical and Population Genetics Broad Institute of MIT and Harvard Cambridge MA USA Genomics Diabetes and Endocrinology Lund University Lund Sweden Folkhälsan Institute of Genetics Folkhälsan Research C

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Variant interpretation using population databases: lessons from gnomAD

arXiv

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arXiv 2021年

作者： Gudmundsson, Sanna Singer-Berk, Moriel Watts, Nicholas A. Phu, William Goodrich, Julia K. Solomonson, Matthew Rehm, Heidi L. MacArthur, Daniel G. O'Donnell-Luria, Anne Abreu, Maria Aguilar Salinas, Carlos A. Ahmad, Tariq Albert, Christine M. Alföldi, Jessica Ardissino, Diego Armean, Irina M. Atzmon, Gil Banks, Eric Barnard, John Baxter, Samantha M. Beaugerie, Laurent Benjamin, Emelia J. Benjamin, David Bergelson, Louis Boehnke, Michael Bonnycastle, Lori L. Bottinger, Erwin P. Bowden, Donald W. Bown, Matthew J. Brant, Steven Calvo, Sarah E. Campos, Hannia Chambers, John C. Chan, Juliana C. Chao, Katherine R. Chapman, Sinéad Chasman, Daniel Chisholm, Rex Cho, Judy Chowdhury, Rajiv Chung, Mina K. Chung, Wendy Cibulskis, Kristian Cohen, Bruce Collins, Ryan L. Connolly, Kristen M. Correa, Adolfo Covarrubias, Miguel Cummings, Beryl Dabelea, Dana Daly, Mark J. Danesh, John Darbar, Dawood Denny, Joshua Donnelly, Stacey Duggirala, Ravindranath Dupuis, Josée Ellinor, Patrick T. Elosua, Roberto Emery, James England, Eleina Erdmann, Jeanette Esko, Tõnu Evangelista, Emily Farjoun, Yossi Fatkin, Diane Ferriera, Steven Florez, Jose Francioli, Laurent Franke, Andre Färkkilä, Martti Gabriel, Stacey Garimella, Kiran Gauthier, Laura D. Gentry, Jeff Getz, Gad Glahn, David C. Glaser, Benjamin Glatt, Stephen J. Goldstein, David Gonzalez, Clicerio Goodrich, Julia Groop, Leif Gudmundsson, Sanna Gupta, Namrata Haessly, Andrea Haiman, Christopher Hall, Ira Hanis, Craig Harms, Matthew Hiltunen, Mikko Holi, Matti M. Hultman, Christina M. Jalas, Chaim Jeandet, Thibault Kallela, Mikko Kaplan, Diane Kaprio, Jaakko Karczewski, Konrad J. Kathiresan, Sekar Kenny, Eimear Kim, Bong-Jo Kim, Young Jin Kirov, George Kooner, Jaspal Koskinen, Seppo Krumholz, Harlan M. Kugathasan, Subra Kwak, Soo Heon Laakso, Markku Lake, Nicole Langsford, Trevyn Laricchia, Kristen M. Lehtimäki, Terho Lek, Monkol Lipscomb, Emily Llanwarne, Christopher Loos, Ruth J.F. Lubitz, Steven A. Luna, Teresa Tusie Ma, Ronald C.W. MacArthur, Daniel G. Marcus, Gregory M. Marrugat, Ja University of Miami Miller School of Medicine Gastroenterology Miami United States Unidad de Investigacion de Enfermedades Metabolicas Instituto Nacional de Ciencias Medicas y Nutricion Mexico City Mexico Peninsula College of Medicine and Dentistry Exeter United Kingdom Division of Preventive Medicine Brigham and Women's Hospital BostonMA United States Division of Cardiovascular Medicine Brigham and Women's Hospital Harvard Medical School BostonMA United States Program in Medical and Population Genetics Broad Institute of MIT and Harvard CambridgeMA United States Analytic and Translational Genetics Unit Massachusetts General Hospital BostonMA United States Department of Cardiology University Hospital Parma Italy European Molecular Biology Laboratory European Bioinformatics Institute Wellcome Genome Campus Hinxton Cambridge United Kingdom Department of Biology Faculty of Natural Sciences University of Haifa Haifa Israel Department of Medicine and Genetics Albert Einstein College of Medicine BronxNY United States Data Science Platform Broad Institute of MIT and Harvard CambridgeMA United States Department of Quantitative Health Sciences Lerner Research Institute Cleveland Clinic ClevelandOH United States Sorbonne Université APHP Gastroenterology Department Saint Antoine Hospital Paris France NHLBI Boston University's Framingham Heart Study FraminghamMA United States Department of Medicine Boston University School of Medicine BostonMA United States Department of Epidemiology Boston University School of Public Health BostonMA United States Department of Biostatistics and Center for Statistical Genetics University of Michigan Ann ArborMS United States National Human Genome Research Institute National Institutes of Health BethesdaMD United States The Charles Bronfman Institute for Personalized Medicine Icahn School of Medicine at Mount Sinai New YorkNY United States Department of Biochemistry Wake Forest School of Medicine Winston-SalemNC

Reference population databases are an essential tool in variant and gene interpretation. Their use guides the identification of pathogenic variants amidst the sea of benign variation present in every human genome, and supports the discovery of new disease-gene relationships. The Genome Aggregation database (gnomAD) is currently the largest and most widely used publicly available collection of population variation from harmonized sequencing data. The data is available through the online gnomAD browser (https://***/) that enables rapid and intuitive variant analysis. This review provides guidance on the content of the gnomAD browser, and its usage for variant and gene interpretation. We introduce key features including allele frequency, per-base expression levels, constraint scores, and variant co-occurrence, alongside guidance on how to use these in analysis, with a focus on the interpretation of candidate variants and novel genes in rare disease. © 2021, CC BY.

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Stroke genetics informs drug discovery and risk prediction across ancestries (vol 611, pg 115, 2022)

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NATURE 2022年第7938期612卷 E7-E7页

作者： Mishra, Aniket Malik, Rainer Hachiya, Tsuyoshi Jurgenson, Tuuli Namba, Shinichi Posner, Daniel C. Kamanu, Frederick K. Koido, Masaru Le Grand, Quentin Shi, Mingyang He, Yunye Georgakis, Marios K. Caro, Ilana Krebs, Kristi Liaw, Yi-Ching Vaura, Felix C. Lin, Kuang Winsvold, Bendik Slagsvold Srinivasasainagendra, Vinodh Parodi, Livia Bae, Hee-Joon Chauhan, Ganesh Chong, Michael R. Tomppo, Liisa Akinyemi, Rufus Roshchupkin, Gennady V. Habib, Naomi Jee, Yon Ho Thomassen, Jesper Qvist Abedi, Vida Carcel-Marquez, Jara Nygaard, Marianne Leonard, Hampton L. Yang, Chaojie Yonova-Doing, Ekaterina Knol, Maria J. Lewis, Adam J. Judy, Renae L. Ago, Tetsuro Amouyel, Philippe Armstrong, Nicole D. Bakker, Mark K. Bartz, Traci M. Bennett, David A. Bis, Joshua C. Bordes, Constance Borte, Sigrid Cain, Anael Ridker, Paul M. Cho, Kelly Chen, Zhengming Cruchaga, Carlos Cole, John W. de Jager, Phil L. de Cid, Rafael Endres, Matthias Ferreira, Leslie E. Geerlings, Mirjam I. Gasca, Natalie C. Gudnason, Vilmundur Hata, Jun He, Jing Heath, Alicia K. Ho, Yuk-Lam Havulinna, Aki S. Hopewell, Jemma C. Hyacinth, I. Hyacinth Inouye, Michael Jacob, Mina A. Jeon, Christina E. Jern, Christina Kamouchi, Masahiro Keene, Keith L. Kitazono, Takanari Kittner, Steven J. Konuma, Takahiro Kumar, Amit Lacaze, Paul Launer, Lenore J. Lee, Keon-Joo Lepik, Kaido Li, Jiang Li, Liming Manichaikul, Ani Markus, Hugh S. Marston, Nicholas A. Meitinger, Thomas Mitchell, Braxton D. Montellano, Felipe A. Morisaki, Takayuki Mosley, Thomas H. Nalls, Mike A. Nordestgaard, Borge G. O'Donnell, Martin J. Okada, Yukinori Onland-Moret, N. Charlotte Ovbiagele, Bruce Peters, Annette Psaty, Bruce M. Rich, Stephen S. Rosand, Jonathan Sabatine, Marc S. Sacco, Ralph L. Saleheen, Danish Sandset, Else Charlotte Salomaa, Veikko Sargurupremraj, Muralidharan Sasaki, Makoto Satizabal, Claudia L. Schmidt, Carsten O. Shimizu, Atsushi Smith, Nicholas L. Sloane, Kelly L. Sutoh, Yoichi Sun, Yan V. Tanno, Kozo Tiedt, Steffen Tatlisumak, Turgut Torres-Aguila, Nuria P. Tiwari, Hemant K. Tregouet, Bordeaux Population Health Research Center University of Bordeaux Inserm UMR 1219 Bordeaux France Department of Public Health Bordeaux University Hospital Bordeaux France Department of Neurology Memory Clinic Bordeaux University Hospital Bordeaux France Department of Neurology Institute for Neurodegenerative Diseases CHU de Bordeaux Bordeaux France Institute for Stroke and Dementia Research (ISD) University Hospital LMU Munich Munich Germany Center for Genomic Medicine Massachusetts General Hospital Boston MA USA Program in Medical and Population Genetics Broad Institute of Harvard and the Massachusetts Institute of Technology Cambridge MA USA Munich Cluster for Systems Neurology Munich Germany German Center for Neurodegenerative Diseases (DZNE) Munich Germany Iwate Tohoku Medical Megabank Organization Iwate Medical University Iwate Japan Estonian Genome Centre Institute of Genomics University of Tartu Tartu Estonia Institute of Mathematics and Statistics University of Tartu Tartu Estonia Department of Computational Biology University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics Lausanne Switzerland University Center for Primary Care and Public Health Lausanne Switzerland Department of Statistical Genetics Osaka University Graduate School of Medicine Suita Japan Department of Genome Informatics Graduate School of Medicine The University of Tokyo Tokyo Japan Laboratory for Systems Genetics RIKEN Center for Integrative Medical Sciences Yokohama Japan Laboratory of Statistical Immunology Immunology Frontier Research Center (WPI-IFReC) Osaka University Suita Japan Integrated Frontier Research for Medical Science Division Institute for Open and Transdisciplinary Research Initiatives Osaka University Suita Japan Center for Infectious Disease Education and Research (CiDER) Osaka University Suita Japan Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC) VA Boston Healthcare System Boston MA USA TIMI S

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Global burden of 369 diseases and injuries in 204 countries and territories, 1990–2019: a systematic analysis for the Global Burden of Disease Study 2019

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The Lancet 2020年第10258期396卷 1204-1222页

作者： Abbafati, Cristiana Abbas, Kaja M. Abbasi, Mohammad Abbasifard, Mitra Abbasi-Kangevari, Mohsen Abbastabar, Hedayat Abd-Allah, Foad Abdelalim, Ahmed Abdollahi, Mohammad Abdollahpour, Ibrahim Abedi, Aidin Abedi, Parisa Abegaz, Kedir Hussein Abolhassani, Hassan Abosetugn, Akine Eshete Aboyans, Victor Abrams, Elissa M. Abreu, Lucas Guimarães Abrigo, Michael R.M. Abu Haimed, Abdulaziz Khalid Abualhasan, Ahmed Abu-Gharbieh, Eman Abu-Raddad, Laith Jamal Abushouk, Abdelrahman I. Acebedo, Alyssa Ackerman, Ilana N. Adabi, Maryam Adair, Tim Adamu, Abdu A. Adebayo, Oladimeji M. Adedeji, Isaac Akinkunmi Adekanmbi, Victor Adelson, Jaimie D. Adeoye, Abiodun Moshood Adetokunboh, Olatunji O. Adham, Davoud Advani, Shailesh M. Afarideh, Mohsen Afshari, Mahdi Afshin, Ashkan Agardh, Emilie E. Agarwal, Gina Agasthi, Pradyumna Agesa, Kareha M. Aghaali, Mohammad Aghamir, Seyed Mohammad Kazem Agrawal, Anurag Ahmad, Tauseef Ahmadi, Alireza Ahmadi, Keivan Ahmadi, Mehdi Ahmadieh, Hamid Ahmadpour, Ehsan Ahmed, Muktar Beshir Aji, Budi Akalu, Temesgen Yihunie Akinyemi, Rufus Olusola Akinyemiju, Tomi Akombi, Blessing Akunna, Chisom Joyqueenet Alahdab, Fares Al-Aly, Ziyad Alam, Khurshid Alam, Noore Alam, Samiah Alam, Tahiya Alanezi, Fahad Mashhour Alanzi, Turki M. Albertson, Samuel B. Alcalde-Rabanal, Jacqueline Elizabeth Alema, Niguse Meles Alemu, Biresaw Wassihun Alemu, Yihun Mulugeta Alhabib, Khalid F. Alhassan, Robert Kaba Ali, Muhammad Ali, Saqib Alicandro, Gianfranco Alijanzadeh, Mehran Alinia, Cyrus Alipour, Vahid Alizade, Hesam Aljunid, Syed Mohamed Alla, François Allebeck, Peter Almadi, Majid Abdulrahman Hamad Almasi, Ali Almasi-Hashiani, Amir Almasri, Nihad A. Al-Mekhlafi, Hesham M. Almulhim, Abdulaziz M. Alonso, Jordi Al-Raddadi, Rajaa M. Altirkawi, Khalid A. Alumran, Arwa Khalid Alvis-Guzman, Nelson Alvis-Zakzuk, Nelson J. Amare, Azmeraw T. Amare, Bekalu Amini, Saeed Amini-Rarani, Mostafa Aminorroaya, Arya Amiri, Fatemeh Amit, Arianna Maever L. Amugsi, Dickson A. Amul, Gianna Gayle Herrera Anbesu, Etsay Woldu Ancuceanu, Robert Anderl Department of Juridical and Economic Studies La Sapienza University Rome Italy Department of Infectious Disease Epidemiology London School of Hygiene and Tropical Medicine London United Kingdom Social Determinants of Health Research Center Tehran Iran Department of Neurology Cairo University Cairo Egypt School of Pharmacy Tehran Iran The Institute of Pharmaceutical Sciences (TIPS) Tehran Iran Neuroscience Research Center Isfahan University of Medical Sciences Isfahan Iran Biostatistics Department Near East University Nicosia Cyprus Biostatistics and Health Informatics Madda Walabu University Bale Robe Ethiopia Research Center for Immunodeficiencies Tehran Iran Karolinska University Hospital Huddinge Sweden Department of Cardiology Dupuytren University Hospital Limoges France University of Limoges Limoges France Department of Pediatric Dentistry Federal University of Minas Gerais Belo Horizonte Brazil Department of Research Philippine Institute for Development Studies Quezon City Philippines Department of Healthcare Policy and Research Weill Cornell Medical College in Qatar Doha Qatar Harvard Medical School Boston MA United States Department of Medicine Ain Shams University Cairo Egypt Hamadan University of Medical Sciences Hamadan Iran School of Medicine Cardiff University Cardiff United Kingdom School of Laboratory Medicine and Science University College Hospital Ibadan Ibadan Nigeria Institute of Cardiovascular Diseases University of Ibadan Ibadan Nigeria Centre of Excellence for Epidemiological Modelling and Analysis Stellenbosch University Cape Town South Africa Department of Global Health Stellenbosch University Cape Town South Africa School of Health Ardabil University of Medical Science Ardabil Iran Social Behavioral Research Branch National Institute of Health Bethesda MD United States Department of Oncology Georgetown University Washington DC DC United States Department of Health Metrics Sciences School of Medicine Seattle WA

Background: In an era of shifting global agendas and expanded emphasis on non-communicable diseases and injuries along with communicable diseases, sound evidence on trends by cause at the national level is essential. The Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) provides a systematic scientific assessment of published, publicly available, and contributed data on incidence, prevalence, and mortality for a mutually exclusive and collectively exhaustive list of diseases and injuries. Methods: GBD estimates incidence, prevalence, mortality, years of life lost (YLLs), years lived with disability (YLDs), and disability-adjusted life-years (DALYs) due to 369 diseases and injuries, for two sexes, and for 204 countries and territories. Input data were extracted from censuses, household surveys, civil registration and vital statistics, disease registries, health service use, air pollution monitors, satellite imaging, disease notifications, and other sources. Cause-specific death rates and cause fractions were calculated using the Cause of Death Ensemble model and spatiotemporal Gaussian process regression. Cause-specific deaths were adjusted to match the total all-cause deaths calculated as part of the GBD population, fertility, and mortality estimates. Deaths were multiplied by standard life expectancy at each age to calculate YLLs. A Bayesian meta-regression modelling tool, DisMod-MR 2.1, was used to ensure consistency between incidence, prevalence, remission, excess mortality, and cause-specific mortality for most causes. Prevalence estimates were multiplied by disability weights for mutually exclusive sequelae of diseases and injuries to calculate YLDs. We considered results in the context of the Socio-demographic Index (SDI), a composite indicator of income per capita, years of schooling, and fertility rate in females younger than 25 years. Uncertainty intervals (UIs) were generated for every metric using the 25th and 975th ordered 1000 draw value

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Identifying the best machine learning algorithms for brain tumor segmentation, progression assessment, and overall survival prediction in the BRATS challenge

arXiv

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arXiv 2018年

作者： Bakas, Spyridon Reyes, Mauricio Jakab, Andras Bauer, Stefan Rempfler, Markus Crimi, Alessandro Shinohara, Russell Takeshi Berger, Christoph Ha, Sung Min Rozycki, Martin Prastawa, Marcel Alberts, Esther Lipkova, Jana Freymann, John Kirby, Justin Bilello, Michel Fathallah-Shaykh, Hassan M. Wiest, Roland Kirschke, Jan Wiestler, Benedikt Colen, Rivka Kotrotsou, Aikaterini Lamontagne, Pamela Marcus, Daniel Milchenko, Mikhail Nazeri, Arash Weber, Marc-Andr Mahajan, Abhishek Baid, Ujjwal Gerstner, Elizabeth Kwon, Dongjin Acharya, Gagan Agarwal, Manu Alam, Mahbubul Albiol, Alberto Albiol, Antonio Albiol, Francisco J. Alex, Varghese Allinson, Nigel Amorim, Pedro H.A. Amrutkar, Abhijit Anand, Ganesh Andermatt, Simon Arbel, Tal Arbelaez, Pablo Avery, Aaron Azmat, Muneeza Pranjal, B. Bai, Wenjia Banerjee, Subhashis Barth, Bill Batchelder, Thomas Batmanghelich, Kayhan Battistella, Enzo Beers, Andrew Belyaev, Mikhail Bendszus, Martin Benson, Eze Bernal, Jose Bharath, Halandur Nagaraja Biros, George Bisdas, Sotirios Brown, James Cabezas, Mariano Cao, Shilei Cardoso, Jorge M. Carver, Eric N. Casamitjana, Adri Castillo, Laura Silvana Cat, Marcel Cattin, Philippe Cérigues, Albert Chagas, Vinicius S. Chandra, Siddhartha Chang, Yi-Ju Chang, Shiyu Chang, Ken Chazalon, Joseph Chen, Shengcong Chen, Wei Chen, Jefferson W. Chen, Zhaolin Cheng, Kun Choudhury, Ahana Roy Chylla, Roger Clrigues, Albert Colleman, Steven Colmeiro, Ramiro German Rodriguez Combalia, Marc Costa, Anthony Cui, Xiaomeng Dai, Zhenzhen Dai, Lutao Daza, Laura Alexandra Deutsch, Eric Ding, Changxing Dong, Chao Dong, Shidu Dudzik, Wojciech Eaton-Rosen, Zach Egan, Gary Escudero, Guilherme Estienne, Tho Everson, Richard Fabrizio, Jonathan Fan, Yong Fang, Longwei Feng, Xue Ferrante, Enzo Fidon, Lucas Fischer, Martin French, Andrew P. Fridman, Naomi Fu, Huan Fuentes, David Gao, Yaozong Gates, Evan Gering, David Gholami, Amir Gierke, Willi Glocker, Ben Gong, Mingming Gonzlez-Vill, Sandra Grosges, T. Guan, Yuanfang Guo, Sheng Gupta, Sudeep Han, Woo-Sup Han, Il Song Harmuth, Ko Center for Biomedical Image Computing and Analytics University of Pennsylvania PhiladelphiaPA United States Department of Radiology Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Institute for Surgical Technology and Biomechanics University of Bern Bern Switzerland Center for MR-Research University Children's Hospital Zurich Zurich Switzerland Support Centre for Advanced Neuroimaging Inselspital Institute for Diagnostic and Interventional Neuroradiology Bern University Hospital Bern Switzerland University Hospital of Zurich Zurich Switzerland Center for Clinical Epidemiology and Biostatistics University of Pennsylvania Philadelphia United States Image-Based Biomedical Modeling Group Technical University of Munich Munich Germany Icahn School of Medicine Mount Sinai Health System New YorkNY United States Leidos Biomedical Research Inc. Frederick National Laboratory for Cancer Research FrederickMD21701 United States Cancer Imaging Program National Cancer Institute National Institutes of Health BethesdaMD20814 United States Department of Neurology University of Alabama at Birmingham BirminghamAL United States Department of Diagnostic Radiology University of Texas MD Anderson Cancer Center HoustonTX United States Department of Psychology Washington University St. LouisMO United States Neuroimaging Informatics and Analysis Center Washington University St. LouisMO United States Department of Radiology Washington University St. LouisMO United States Institute of Diagnostic and Interventional Radiology Pediatric Radiology and Neuroradiology University Medical Center Rostock Ernst-Heydemann-Str. 6 Rostock18057 Germany Tata Memorial Centre Homi Bhabha National Institute Mumbai India Shri Guru Gobind Singhji Institute of Engineering and Technology Nanded India NVIDIA Santa Clara

Gliomas are the most common primary brain malignancies, with different degrees of aggressiveness, variable prognosis and various heterogeneous histologic sub-regions, i.e., peritumoral edematous/invaded tissue, necrotic core, active and non-enhancing core. This intrinsic heterogeneity is also portrayed in their radio-phenotype, as their sub-regions are depicted by varying intensity profiles disseminated across multi-parametric magnetic resonance imaging (mpMRI) scans, reflecting varying biological properties. Their heterogeneous shape, extent, and location are some of the factors that make these tumors difficult to resect, and in some cases inoperable. The amount of resected tumor is a factor also considered in longitudinal scans, when evaluating the apparent tumor for potential diagnosis of progression. Furthermore, there is mounting evidence that accurate segmentation of the various tumor sub-regions can offer the basis for quantitative image analysis towards prediction of patient overall survival. This study assesses the state-of-the-art machine learning (ML) methods used for brain tumor image analysis in mpMRI scans, during the last seven instances of the International Brain Tumor Segmentation (BraTS) challenge, i.e., 2012-2018. Specifically, we focus on i) evaluating segmentations of the various glioma sub-regions in pre-operative mpMRI scans, ii) assessing potential tumor progression by virtue of longitudinal growth of tumor sub-regions, beyond use of the RECIST/RANO criteria, and iii) predicting the overall survival from pre-operative mpMRI scans of patients that underwent gross total resection. Finally, we investigate the challenge of identifying the best ML algorithms for each of these tasks, considering that apart from being diverse on each instance of the challenge, the multi-institutional mpMRI BraTS dataset has also been a continuously evolving/growing dataset. Copyright © 2018, The Authors. All rights reserved.

关键词： Tumors

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Evaluating drug targets through human loss-of-function genetic variation (vol 581, pg 459, 2020)

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NATURE 2021年第7846期590卷 E56-E56页

作者： Minikel, Eric Vallabh Karczewski, Konrad J. Martin, Hilary C. Cummings, Beryl B. Whiffin, Nicola Rhodes, Daniel Alfoldi, Jessica Trembath, Richard C. van Heel, David A. Daly, Mark J. Schreiber, Stuart L. MacArthur, Daniel G. Program in Medical and Population Genetics Broad Institute of MIT and Harvard Cambridge MA USA Stanley Center for Psychiatric Research Broad Institute of MIT and Harvard Cambridge MA USA Chemical Biology and Therapeutics Science Program Broad Institute of MIT and Harvard Cambridge MA USA Analytical and Translational Genetics Unit Massachusetts General Hospital Boston MA USA Program in Biological and Biomedical Sciences Harvard Medical School Boston MA USA Henry and Allison McCance Center for Brain Health Massachusetts General Hospital Boston MA USA Department of Neurology Massachusetts General Hospital Boston MA USA Prion Alliance Cambridge MA USA National Heart and Lung Institute and MRC London Institute of Medical Sciences Imperial College London London UK National Heart & Lung Institute and MRC London Institute of Medical Sciences Imperial College London London UK Cardiovascular Research Centre Royal Brompton & Harefield Hospitals NHS Trust London UK European Molecular Biology Laboratory European Bioinformatics Institute Wellcome Genome Campus Hinxton Cambridge UK Center for Genomic Medicine Massachusetts General Hospital Boston MA USA Program in Bioinformatics and Integrative Genomics Harvard Medical School Boston MA USA Broad Genomics Broad Institute of MIT and Harvard Cambridge MA USA Division of Genetics and Genomics Boston Children’s Hospital Boston MA USA Department of Pediatrics Harvard Medical School Boston MA USA Cardiac Arrhythmia Service and Cardiovascular Research Center Massachusetts General Hospital Boston MA USA Estonian Genome Center Institute of Genomics University of Tartu Tartu Estonia Department of Medicine Harvard Medical School Boston MA USA Cardiac Arrhythmia Service Massachusetts General Hospital Boston MA USA Centre for Population Genomics Garvan Institute of Medical Research and UNSW Sydney Sydney Australia Centre for Population Genomics Murdoch Children’s Research Institute Melbourne Australia Divi

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Author Correction: A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response

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Nature genetics 2021年第12期53卷 1722页

作者： Yang Luo Masahiro Kanai Wanson Choi Xinyi Li Saori Sakaue Kenichi Yamamoto Kotaro Ogawa Maria Gutierrez-Arcelus Peter K Gregersen Philip E Stuart James T Elder Lukas Forer Sebastian Schönherr Christian Fuchsberger Albert V Smith Jacques Fellay Mary Carrington David W Haas Xiuqing Guo Nicholette D Palmer Yii-Der Ida Chen Jerome I Rotter Kent D Taylor Stephen S Rich Adolfo Correa James G Wilson Sekar Kathiresan Michael H Cho Andres Metspalu Tonu Esko Yukinori Okada Buhm Han Paul J McLaren Soumya Raychaudhuri Center for Data Sciences Brigham and Women's Hospital Harvard Medical School Boston MA USA. yangluo@***. Division of Rheumatology Immunology and Immunity Brigham and Women's Hospital Harvard Medical School Boston MA USA. yangluo@***. Division of Genetics Brigham and Women's Hospital Harvard Medical School Boston MA USA. yangluo@***. Department of Biomedical Informatics Harvard Medical School Boston MA USA. yangluo@***. Broad Institute of MIT and Harvard Cambridge MA USA. yangluo@***. Department of Biomedical Informatics Harvard Medical School Boston MA USA. Broad Institute of MIT and Harvard Cambridge MA USA. Analytic and Translational Genetics Unit Massachusetts General Hospital Boston MA USA. Stanley Center for Psychiatric Research Broad Institute of Harvard and MIT Cambridge MA USA. Department of Statistical Genetics Osaka University Graduate School of Medicine Suita Japan. Department of Biomedical Sciences Seoul National University College of Medicine Seoul South Korea. Committee on Genetics Genomics and Systems Biology University of Chicago Chicago IL USA. Center for Data Sciences Brigham and Women's Hospital Harvard Medical School Boston MA USA. Division of Rheumatology Immunology and Immunity Brigham and Women's Hospital Harvard Medical School Boston MA USA. Division of Genetics Brigham and Women's Hospital Harvard Medical School Boston MA USA. Department of Pediatrics Osaka University Graduate School of Medicine Osaka Japan. Department of Neurology Osaka University Graduate School of Medicine Osaka Japan. The Robert S. Boas Center for Genomics and Human Genetics Feinstein Institute for Medical ResearchNorth Short LIJ Health System Manhasset NY USA. Department of Dermatology University of Michigan Ann Arbor MI USA. Ann Arbor Veterans Affairs Hospital Ann Arbor MI USA. Institute of Genetic Epidemiology Department of Genetics and Pharmacology Medical University of Innsbruck Innsbruck Austria. Department of Biostatistics

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Publisher Correction: Shared heritability and functional enrichment across six solid cancers

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Nature communications 2019年第1期10卷 4386页

作者： Xia Jiang Hilary K Finucane Fredrick R Schumacher Stephanie L Schmit Jonathan P Tyrer Younghun Han Kyriaki Michailidou Corina Lesseur Karoline B Kuchenbaecker Joe Dennis David V Conti Graham Casey Mia M Gaudet Jeroen R Huyghe Demetrius Albanes Melinda C Aldrich Angeline S Andrew Irene L Andrulis Hoda Anton-Culver Antonis C Antoniou Natalia N Antonenkova Susanne M Arnold Kristan J Aronson Banu K Arun Elisa V Bandera Rosa B Barkardottir Daniel R Barnes Jyotsna Batra Matthias W Beckmann Javier Benitez Sara Benlloch Andrew Berchuck Sonja I Berndt Heike Bickeböller Stephanie A Bien Carl Blomqvist Stefania Boccia Natalia V Bogdanova Stig E Bojesen Manjeet K Bolla Hiltrud Brauch Hermann Brenner James D Brenton Mark N Brook Joan Brunet Hans Brunnström Daniel D Buchanan Barbara Burwinkel Ralf Butzow Gabriella Cadoni Trinidad Caldés Maria A Caligo Ian Campbell Peter T Campbell Géraldine Cancel-Tassin Lisa Cannon-Albright Daniele Campa Neil Caporaso André L Carvalho Andrew T Chan Jenny Chang-Claude Stephen J Chanock Chu Chen David C Christiani Kathleen B M Claes Frank Claessens Judith Clements J Margriet Collée Marcia Cruz Correa Fergus J Couch Angela Cox Julie M Cunningham Cezary Cybulski Kamila Czene Mary B Daly Anna deFazio Peter Devilee Orland Diez Manuela Gago-Dominguez Jenny L Donovan Thilo Dörk Eric J Duell Alison M Dunning Miriam Dwek Diana M Eccles Christopher K Edlund Digna R Velez Edwards Carolina Ellberg D Gareth Evans Peter A Fasching Robert L Ferris Triantafillos Liloglou Jane C Figueiredo Olivia Fletcher Renée T Fortner Florentia Fostira Silvia Franceschi Eitan Friedman Steven J Gallinger Patricia A Ganz Judy Garber José A García-Sáenz Simon A Gayther Graham G Giles Andrew K Godwin Mark S Goldberg David E Goldgar Ellen L Goode Marc T Goodman Gary Goodman Kjell Grankvist Mark H Greene Henrik Gronberg Jacek Gronwald Pascal Guénel Niclas Håkansson Per Hall Ute Hamann Freddie C Hamdy Robert J Hamilton Jochen Hampe Aage Haugen Florian Heitz Rolando Herrero Peter Hillemanns Michael Hoffmeister Estrid Høgdall Yun-Ch Program in Genetic Epidemiology and Statistical Genetics Harvard T.H. Chan School of Public Health 677 Huntington Ave Boston MA 02115 USA. xiajiang@hsph.harvard.edu. Unit of Cardiovascular Epidemiology Institute of Environmental Medicine Karolinska Institutet Nobels vagen 13 17177 Stockholm Sweden. xiajiang@hsph.harvard.edu. Department of Epidemiology Harvard T.H. Chan School of Public Health 677 Huntington Ave Boston MA 02115 USA. Program in Medical and Population Genetics Broad Institute of MIT and Harvard 75 Ames St Cambridge MA 02142 USA. Department of Population and Quantitative Health Sciences Case Western Reserve University 10900 Eucid Avenue Cleveland OH 44106 USA. Seidman Cancer Center University Hospitals Cleveland OH 44106 USA. Department of Cancer Epidemiology H. Lee Moffitt Cancer Center and Research Institute 12902 Magnolia Dr. MRC-CANCONT Tampa FL 33612 USA. Department of Gastrointestinal Oncology H. Lee Moffitt Cancer Center and Research Institute 12902 Magnolia Dr. MRC-CANCONT Tampa FL 33612 USA. Centre for Cancer Genetic Epidemiology Department of Oncology University of Cambridge 2 Worts' Causeway Cambridge CB1 8RN UK. Department of Biomedical Data Science The Geisel School of Medicine at Dartmouth 1 Medical Center Drive Lebanon NH 03756 USA. Centre for Cancer Genetic Epidemiology Department of Public Health and Primary Care University of Cambridge 2 Worts' Causeway Cambridge CB1 8RN UK. Department of Electron Microscopy/Molecular Pathology The Cyprus Institute of Neurology and Genetics 1683 Nicosia Cyprus. Genetic Epidemiology Group International Agency for Research on Cancer 150 Cours Albert Thomas 69008 Lyon France. Section of Genetics International Agency for Research on Cancer 150 cours Albert Thomas 69008 Lyon France. Division of Psychiatry University College London Maple House 149 Tottenham Court Road London W1T 7NF UK. UCL Genetics Institute University College London Gower Street London WC1E 6BT UK.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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