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Author Correction: COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms

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Scientific data 2020年第1期7卷 247页

作者： Marek Ostaszewski Alexander Mazein Marc E Gillespie Inna Kuperstein Anna Niarakis Henning Hermjakob Alexander R Pico Egon L Willighagen Chris T Evelo Jan Hasenauer Falk Schreiber Andreas Dräger Emek Demir Olaf Wolkenhauer Laura I Furlong Emmanuel Barillot Joaquin Dopazo Aurelio Orta-Resendiz Francesco Messina Alfonso Valencia Akira Funahashi Hiroaki Kitano Charles Auffray Rudi Balling Reinhard Schneider Luxembourg Centre for Systems Biomedicine University of Luxembourg Belvaux Luxembourg. European Institute for Systems Biology and Medicine (EISBM) Vourles France. Ontario Institute for Cancer Research Toronto Canada. College of Pharmacy and Health Sciences St. John's University Queens NY USA. Institut Curie PSL Research University Mines Paris Tech Inserm Paris France. Department of Biology Univ. Évry University of Paris-Saclay Genopole 91025 Évry France. European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Hinxton UK. Institute of Data Science and Biotechnology Gladstone Institutes San Francisco United States. Department of Bioinformatics-BiGCaT NUTRIM Maastricht University Maastricht The Netherlands. Maastricht Centre for Systems Biology Maastricht University Maastricht The Netherlands. Helmholtz Zentrum München Institute of Computational Biology Neuherberg Germany. Center for Mathematics Technische Universität München Garching Germany. Faculty of Mathematics and Natural Sciences University of Bonn Bonn Germany. University of Konstanz Department of Computer and Information Science Konstanz Germany. Monash University Faculty of Information Technology Melbourne Australia. Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens Institute for Bioinformatics and Medical Informatics (IBMI) University of Tübingen 72076 Tübingen Germany. Department of Computer Science University of Tübingen 72076 Tübingen Germany. German Center for Infection Research (DZIF) partner site Tübingen Germany. Department of Molecular and Medical Genetics School of Medicine Oregon Health & Science University Portland USA. Department of Systems Biology & Bioinformatics University of Rostock Rostock Germany. Stellenbosch Institute of Advanced Study (STIAS) Wallenberg Research Centre at Stellenbosch University 7602 Stellenbosch South Africa. Research Programme on Biomedical informatics Hospital del Mar Medical Research

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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Africa-specific human genetic variation near CHD1L associates with HIV-1 load (vol 620, pg 1025, 2023)

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NATURE 2023年第7979期621卷 E42-E42页

作者： McLaren, Paul J. Porreca, Immacolata Iaconis, Gennaro Mok, Hoi Ping Mukhopadhyay, Subhankar Karakoc, Emre Cristinelli, Sara Pomilla, Cristina Bartha, Istvan Thorball, Christian W. Tough, Riley H. Angelino, Paolo Kiar, Cher S. Carstensen, Tommy Fatumo, Segun Porter, Tarryn Jarvis, Isobel Skarnes, William C. Bassett, Andrew DeGorter, Marianne K. Moorthy, Mohana Prasad Sathya Tuff, Jeffrey F. Kim, Eun-Young Walter, Miriam Simons, Lacy M. Bashirova, Arman Buchbinder, Susan Carrington, Mary Cossarizza, Andrea De Luca, Andrea Goedert, James J. Goldstein, David B. Haas, David W. Herbeck, Joshua T. Johnson, Eric O. Kaleebu, Pontiano Kilembe, William Kirk, Gregory D. Kootstra, Neeltje A. Kral, Alex H. Lambotte, Olivier Luo, Ma Mallal, Simon Martinez-Picado, Javier Meyer, Laurence Miro, Jose M. Moodley, Pravi Motala, Ayesha A. Mullins, James I. Nam, Kireem Obel, Niels Pirie, Fraser Plummer, Francis A. Poli, Guido Price, Matthew A. Rauch, Andri Theodorou, Ioannis Trkola, Alexandra Walker, Bruce D. Winkler, Cheryl A. Zagury, Jean-Francois Montgomery, Stephen B. Ciuffi, Angela Hultquist, Judd F. Wolinsky, Steven M. Dougan, Gordon Lever, Andrew M. L. Gurdasani, Deepti Groom, Harriet Sandhu, Manjinder S. Fellay, Jacques Sexually Transmitted and Blood-Borne Infections Division at JC Wilt Infectious Diseases Research Centre National Microbiology Laboratory Branch Public Health Agency of Canada Winnipeg Manitoba Canada Department of Medical Microbiology and Infectious Diseases University of Manitoba Winnipeg Manitoba Canada Vaccine and Therapeutics Laboratory Medical and Scientific Affairs National Microbiology Laboratory Branch Public Health Agency of Canada Winnipeg Manitoba Canada Wellcome Trust Sanger Institute Hinxton UK Department of Medicine University of Cambridge Cambridge UK Department of Medicine National University of Singapore Singapore Singapore Peter Gorer Department of Immunobiology School of Immunology and Microbial Sciences King’s College London London UK Institute of Microbiology Lausanne University Hospital and University of Lausanne Lausanne Switzerland Global Health Institute School of Life Sciences École Polytechnique Fédérale de Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics Lausanne Switzerland Precision Medicine Unit Biomedical Data Science Center Lausanne University Hospital (CHUV) and University of Lausanne Lausanne Switzerland The African Computational Genomics (TACG) Research Group MRC/UVRI and LSHTM Uganda Research Unit Entebbe Uganda Department of Non-Communicable Disease Epidemiology Faculty of Epidemiology and Population Health London School of Hygiene and Tropical Medicine London UK The Jackson Laboratory for Genomic Medicine Farmington CT USA Department of Pathology Stanford University School of Medicine Stanford CA USA Department of Genetics Stanford University School of Medicine Stanford CA USA Division of Infectious Diseases Feinberg School of Medicine Northwestern University Chicago IL USA Basic Science Program Frederick National Laboratory for Cancer Research National Cancer Institute Frederick MD USA Laboratory of Integrative Cancer Immunology Center for Cancer Research National Cancer Institute Bethesda

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Polygenic risk modeling for prediction of epithelial ovarian cancer risk (vol 30, pg 349, 2021)

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EUROPEAN JOURNAL OF HUMAN GENETICS 2022年第5期30卷 630-631页

作者： Dareng, Eileen O. Tyrer, Jonathan P. Barnes, Daniel R. Jones, Michelle R. Yang, Xin Aben, Katja K. H. Adank, Muriel A. Agata, Simona Andrulis, Irene L. Anton-Culver, Hoda Antonenkova, Natalia N. Aravantinos, Gerasimos Arun, Banu K. Augustinsson, Annelie Balmana, Judith Bandera, Elisa V. Barkardottir, Rosa B. Barrowdale, Daniel Beckmann, Matthias W. Beeghly-Fadiel, Alicia Benitez, Javier Bermisheva, Marina Bernardini, Marcus Q. Bjorge, Line Black, Amanda Bogdanova, Natalia V. Bonanni, Bernardo Borg, Ake Brenton, James D. Budzilowska, Agnieszka Butzow, Ralf Buys, Saundra S. Cai, Hui Caligo, Maria A. Campbell, Ian Cannioto, Rikki Cassingham, Hayley Chang-Claude, Jenny Chanock, Stephen J. Chen, Kexin Chiew, Yoke-Eng Chung, Wendy K. Claes, Kathleen B. M. Colonna, Sarah Cook, Linda S. Couch, Fergus J. Daly, Mary B. Dao, Fanny Davies, Eleanor de la Hoya, Miguel de Putter, Robin Dennis, Joe DePersia, Allison Devilee, Peter Diez, Orland Ding, Yuan Chun Doherty, Jennifer A. Domchek, Susan M. Dork, Thilo du Bois, Andreas Durst, Matthias Eccles, Diana M. Eliassen, Heather A. Engel, Christoph Evans, Gareth D. Fasching, Peter A. Flanagan, James M. Fortner, Renee T. Machackova, Eva Friedman, Eitan Ganz, Patricia A. Garber, Judy Gensini, Francesca Giles, Graham G. Glendon, Gord Godwin, Andrew K. Goodman, Marc T. Greene, Mark H. Gronwald, Jacek Hahnen, Eric Haiman, Christopher A. Hakansson, Niclas Hamann, Ute Hansen, Thomas V. O. Harris, Holly R. Hartman, Mikael Heitz, Florian Hildebrandt, Michelle A. T. Hogdall, Estrid Hogdall, Claus K. Hopper, John L. Huang, Ruea-Yea Huff, Chad Hulick, Peter J. Huntsman, David G. Imyanitov, Evgeny N. Isaacs, Claudine Jakubowska, Anna James, Paul A. Janavicius, Ramunas Jensen, Allan Johannsson, Oskar Th. John, Esther M. Jones, Michael E. Kang, Daehee Karlan, Beth Y. Karnezis, Anthony Kelemen, Linda E. Khusnutdinova, Elza Kiemeney, Lambertus A. Kim, Byoung-Gie Kjaer, Susanne K. Komenaka, Ian Kupryjanczyk, Jolanta Kurian, Allison W. Kwong, Ava Lambrechts, Diether Larson, Melissa C. Lazaro, Conxi L University of Cambridge Centre for Cancer Genetic Epidemiology Department of Public Health and Primary Care Cambridge UK University of Cambridge Centre for Cancer Genetic Epidemiology Department of Oncology Cambridge UK Center for Bioinformatics and Functional Genomics Cedars-Sinai Medical Center Los Angeles CA USA Radboud University Medical Center Radboud Institute for Health Sciences Nijmegen The Netherlands Netherlands Comprehensive Cancer Organisation Utrecht The Netherlands The Netherlands Cancer Institute—Antoni van Leeuwenhoek hospital Family Cancer Clinic Amsterdam The Netherlands Veneto Institute of Oncology IOV—IRCCS Immunology and Molecular Oncology Unit Padua Italy Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital Fred A. Litwin Center for Cancer Genetics Toronto ON Canada University of Toronto Department of Molecular Genetics Toronto ON Canada University of California Irvine Department of Epidemiology Genetic Epidemiology Research Institute Irvine CA USA N.N. Alexandrov Research Institute of Oncology and Medical Radiology Minsk Belarus ‘Agii Anargiri’ Cancer Hospital Athens Greece University of Texas MD Anderson Cancer Center Department of Breast Medical Oncology Houston TX USA Lund University Department of Cancer Epidemiology Clinical Sciences Lund Sweden Vall d’Hebron Institute of Oncology Hereditary cancer Genetics Group Barcelona Spain University Hospital of Vall d’Hebron Department of Medical Oncology Barcelona Spain Rutgers Cancer Institute of New Jersey Cancer Prevention and Control Program New Brunswick NJ USA Landspitali University Hospital Department of Pathology Reykjavik Iceland University of Iceland BMC (Biomedical Centre) Faculty of Medicine Reykjavik Iceland University Hospital Erlangen Friedrich-Alexander-University Erlangen-Nuremberg Department of Gynecology and Obstetrics Comprehensive Cancer Center ER-EMN Erlangen Germany Vanderbilt University School of Medicine Division of Epidemiology Department

Polygenic risk scores (PRS) for epithelial ovarian cancer (EOC) have the potential to improve risk stratification. Joint estimation of Single Nucleotide Polymorphism (SNP) effects in models could improve predictive performance over standard approaches of PRS construction. Here, we implemented computationally efficient, penalized, logistic regression models (lasso, elastic net, stepwise) to individual level genotype data and a Bayesian framework with continuous shrinkage, “select and shrink for summary statistics” (S4), to summary level data for epithelial non-mucinous ovarian cancer risk prediction. We developed the models in a dataset consisting of 23,564 non-mucinous EOC cases and 40,138 controls participating in the Ovarian Cancer Association Consortium (OCAC) and validated the best models in three populations of different ancestries: prospective data from 198,101 women of European ancestries; 7,669 women of East Asian ancestries; 1,072 women of African ancestries, and in 18,915 BRCA1 and 12,337 BRCA2 pathogenic variant carriers of European ancestries. In the external validation data, the model with the strongest association for non-mucinous EOC risk derived from the OCAC model development data was the S4 model (27,240 SNPs) with odds ratios (OR) of 1.38 (95% CI: 1.28–1.48, AUC: 0.588) per unit standard deviation, in women of European ancestries; 1.14 (95% CI: 1.08–1.19, AUC: 0.538) in women of East Asian ancestries; 1.38 (95% CI: 1.21–1.58, AUC: 0.593) in women of African ancestries; hazard ratios of 1.36 (95% CI: 1.29–1.43, AUC: 0.592) in BRCA1 pathogenic variant carriers and 1.49 (95% CI: 1.35–1.64, AUC: 0.624) in BRCA2 pathogenic variant carriers. Incorporation of the S4 PRS in risk prediction models for ovarian cancer may have clinical utility in ovarian cancer prevention programs.

关键词： Clinical genetics Genetic markers Risk factors Biomedicine general Human Genetics bioinformatics Gene Expression Cytogenetics

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Author Correction: Multi-ancestry genome-wide association analyses improve resolution of genes and pathways influencing lung function and chronic obstructive pulmonary disease risk

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Nature genetics 2023年第10期55卷 1778-1779页

作者： Nick Shrine Abril G Izquierdo Jing Chen Richard Packer Robert J Hall Anna L Guyatt Chiara Batini Rebecca J Thompson Chandan Pavuluri Vidhi Malik Brian D Hobbs Matthew Moll Wonji Kim Ruth Tal-Singer Per Bakke Katherine A Fawcett Catherine John Kayesha Coley Noemi Nicole Piga Alfred Pozarickij Kuang Lin Iona Y Millwood Zhengming Chen Liming Li Sara R A Wijnant Lies Lahousse Guy Brusselle Andre G Uitterlinden Ani Manichaikul Elizabeth C Oelsner Stephen S Rich R Graham Barr Shona M Kerr Veronique Vitart Michael R Brown Matthias Wielscher Medea Imboden Ayoung Jeong Traci M Bartz Sina A Gharib Claudia Flexeder Stefan Karrasch Christian Gieger Annette Peters Beate Stubbe Xiaowei Hu Victor E Ortega Deborah A Meyers Eugene R Bleecker Stacey B Gabriel Namrata Gupta Albert Vernon Smith Jian'an Luan Jing-Hua Zhao Ailin F Hansen Arnulf Langhammer Cristen Willer Laxmi Bhatta David Porteous Blair H Smith Archie Campbell Tamar Sofer Jiwon Lee Martha L Daviglus Bing Yu Elise Lim Hanfei Xu George T O'Connor Gaurav Thareja Omar M E Albagha Karsten Suhre Raquel Granell Tariq O Faquih Pieter S Hiemstra Annelies M Slats Benjamin H Mullin Jennie Hui Alan James John Beilby Karina Patasova Pirro Hysi Jukka T Koskela Annah B Wyss Jianping Jin Sinjini Sikdar Mikyeong Lee Sebastian May-Wilson Nicola Pirastu Katherine A Kentistou Peter K Joshi Paul R H J Timmers Alexander T Williams Robert C Free Xueyang Wang John L Morrison Frank D Gilliland Zhanghua Chen Carol A Wang Rachel E Foong Sarah E Harris Adele Taylor Paul Redmond James P Cook Anubha Mahajan Lars Lind Teemu Palviainen Terho Lehtimäki Olli T Raitakari Jaakko Kaprio Taina Rantanen Kirsi H Pietiläinen Simon R Cox Craig E Pennell Graham L Hall W James Gauderman Chris Brightling James F Wilson Tuula Vasankari Tarja Laitinen Veikko Salomaa Dennis O Mook-Kanamori Nicholas J Timpson Eleftheria Zeggini Josée Dupuis Caroline Hayward Ben Brumpton Claudia Langenberg Stefan Weiss Georg Homuth Carsten Oliver Schmidt Nicole Probst-Hensch Marjo-Riitta Jarvelin Alanna C Morrison Ozren Polasek Igor Department of Population Health Sciences University of Leicester Leicester UK. nick.shrine@leicester.ac.uk. Department of Population Health Sciences University of Leicester Leicester UK. Division of Respiratory Medicine and NIHR Nottingham Biomedical Research Centre University of Nottingham Nottingham UK. Leicester National Institute for Health and Care Research Biomedical Research Centre Glenfield Hospital Leicester UK. Channing Division of Network Medicine Division of Pulmonary and Critical Care Medicine Department of Medicine Brigham and Women's Hospital Boston MA USA. Harvard Medical School Boston MA USA. COPD Foundation Washington DC USA. Department of Clinical Science Unversity of Bergen Bergen Norway. Nuffield Department of Population Health University of Oxford Oxford UK. MRC Population Health Research Unit University of Oxford Oxford UK. Department of Epidemiology and Biostatistics School of Public Health Peking University Health Science Center Beijing China. Department of Respiratory Diseases Ghent Universital Hospital Ghent Belgium. Department of Bioanalysis Faculty of Pharmaceutical Sciences Ghent University Ghent Belgium. Department of Epidemiology Eramus Medical Center Rotterdam The Netherlands. Department of Internal Medicine Eramus Medical Center Rotterdam The Netherlands. Center for Public Health Genomics University of Virginia Charlottesville VA USA. Department of Medicine Columbia University Medical Center New York NY USA. Medical Research Council Human Genetics Unit Institute of Genetics and Cancer University of Edinburgh Edinburgh UK. Human Genetics Center Department of Epidemiology Human Genetics and Environmental Sciences School of Public Health The University of Texas Health Science Center at Houston Houston TX USA. MRC Centre for Environment and Health Department of Epidemiology and Biostatistics School of Public Health Imperial College London London UK. Department of Epidemiology and Public Health Swiss Tropical

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A short note on undirected fitch graphs

arXiv

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arXiv 2017年

作者： Geiss, Manuela Hellmuth, Marc Long, Yangjing Stadler, Peter F. Bioinformatics Group Department of Computer Science Universität Leipzig Härtelstrasse 16-18 LeipzigD-04107 Germany Department of Mathematics and Computer Science University of Greifswald Walther-Rathenau-Straße 47 GreifswaldD-17487 Germany Center for Bioinformatics Saarland University Building E 2.1 P.O. Box 151150 SaarbrückenD-66041 Germany Department of Mathematics and Computer Science University of Greifswald Walther-Rathenau-Straße 47 GreifswaldD-17487 Germany Halle-Jena-Leipzig Competence Center for Scalable Data Services and Solutions Dresden-Leipzig Leipzig Research Center for Civilization Diseases Centre for Biotechnology and Biomedicine Leipzig University Max Planck Institute for Mathematics in the Sciences Leipzig Germany Institute for Theoretical Chemistry University of Vienna Vienna Austria University of Copenhagen Santa Fe Institute Santa FeNM

The symmetric version of Fitch's xenology relation coincides with class of complete multipartite graph and thus cannot convey any non-trivial phylogenetic information. Copyright © 2017, The Authors. All right... 详细信息

关键词： Phylogenetic

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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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Dense sampling of bird diversity increases power of comparative genomics (vol 587, pg 252, 2020)

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NATURE 2021年第7856期592卷 E24-E24页

作者： Feng, Shaohong Stiller, Josefin Deng, Yuan Armstrong, Joel Fang, Qi Reeve, Andrew Hart Xie, Duo Chen, Guangji Guo, Chunxue Faircloth, Brant C. Petersen, Bent Wang, Zongji Zhou, Qi Diekhans, Mark Chen, Wanjun Andreu-Sanchez, Sergio Margaryan, Ashot Howard, Jason Travis Parent, Carole Pacheco, George Sinding, Mikkel-Holger S. Puetz, Lara Cavill, Emily Ribeiro, Angela M. Eckhart, Leopold Fjeldsa, Jon Hosner, Peter A. Brumfield, Robb T. Christidis, Les Bertelsen, Mads F. Sicheritz-Ponten, Thomas Tietze, Dieter Thomas Robertson, Bruce C. Song, Gang Borgia, Gerald Claramunt, Santiago Lovette, Irby J. Cowen, Saul J. Njoroge, Peter Dumbacher, John Philip Ryder, Oliver A. Fuchs, Jerome Bunce, Michael Burt, David W. Cracraft, Joel Meng, Guanliang Hackett, Shannon J. Ryan, Peter G. Jonsson, Knud Andreas Jamieson, Ian G. da Fonseca, Rute R. Braun, Edward L. Houde, Peter Mirarab, Siavash Suh, Alexander Hansson, Bengt Ponnikas, Suvi Sigeman, Hanna Stervander, Martin Frandsen, Paul B. van der Zwan, Henriette van der Sluis, Rencia Visser, Carina Balakrishnan, Christopher N. Clark, Andrew G. Fitzpatrick, John W. Bowman, Reed Chen, Nancy Cloutier, Alison Sackton, Timothy B. Edwards, Scott V. Foote, Dustin J. Shakya, Subir B. Sheldon, Frederick H. Vignal, Alain Soares, Andre E. R. Shapiro, Beth Gonzalez-Solis, Jacob Ferrer-Obiol, Joan Rozas, Julio Riutort, Marta Tigano, Anna Friesen, Vicki Dalen, Love Urrutia, Araxi O. Szekely, Tamas Liu, Yang Campana, Michael G. Corvelo, Andre Fleischer, Robert C. Rutherford, Kim M. Gemmell, Neil J. Dussex, Nicolas Mouritsen, Henrik Thiele, Nadine Delmore, Kira Liedvogel, Miriam Franke, Andre Hoeppner, Marc P. Krone, Oliver Fudickar, Adam M. Mila, Borja Ketterson, Ellen D. Fidler, Andrew Eric Friis, Guillermo Parody-Merino, Angela M. Battley, Phil F. Cox, Murray P. Lima, Nicholas Costa Barroso Prosdocimi, Francisco Parchman, Thomas Lee Schlinger, Barney A. Loiselle, Bette A. Blake, John G. Lim, Haw Chuan Day, Lainy B. Fuxjager, Matthew J. Baldwin, Maude W. Braun, Michael J. Wirthlin, Morgan Dikow, China National GeneBank BGI-Shenzhen Shenzhen China State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China BGI-Shenzhen Shenzhen China Villum Centre for Biodiversity Genomics Section for Ecology and Evolution Department of Biology University of Copenhagen Copenhagen Denmark BGI Education Center University of Chinese Academy of Sciences Shenzhen China MOE Laboratory of Biosystems Homeostasis and Protection Life Sciences Institute Zhejiang University Hangzhou China Department of Neuroscience and Developmental Biology University of Vienna Vienna Austria Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming China James D. Watson Institute of Genome Sciences Hangzhou China UC Santa Cruz Genomics Institute UC Santa Cruz Santa Cruz CA USA Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark Center for Macroecology Evolution and Climate GLOBE Institute University of Copenhagen Copenhagen Denmark Department of Biological Sciences Louisiana State University Baton Rouge LA USA Museum of Natural Science Louisiana State University Baton Rouge LA USA Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio) Faculty of Applied Sciences AIMST University Kedah Malaysia Section for Evolutionary Genomics The GLOBE Institute Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark Institute of Molecular Biology National Academy of Sciences Yerevan Armenia University Museum Norwegian University of Science and Technology Trondheim Norway Center for Reproductive Medicine The 2nd Affiliated Hospital School of Medicine Zhejiang University Hangzhou China Novogene Durham NC USA Duke University Medical Center Durham NC USA The Rockefeller University New York NY USA Howard Hughes Medical Institute Chevy Chase MD USA Department of Dermatology Medical University of Vienna Vienna Austria

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PO-329 Rejecting neutral tumour evolution across human cancer types

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ESMO Open 2018年 3卷 A357-A357页

作者： Tarabichi, M. Martincorena, I. Gerstung, M. Markowetz, F. Spellman, P. Morris, Q. Lingjærde, O.C. Wedge, D. Loo, P. Van Pcawg, W.G. The Francis Crick Institute Cancer Genomics London UK The Wellcome Trust Sanger Institute Inigo Martincorena lab Cambridge UK European Bioinformatics Institute EMBL – EBI- Wellcome Genome Campus Moritz Gerstung lab Cambridge UK CRUK Cancer Institute Markowetz lab Cambridge UK Oregon Health and Science University Spellman lab Portland USA Donnelly Centre for Cellular and Biomolecular Research- University of Toronto Morris lab Toronto Canada Centre for Computational Inference in Evolutionary Life Science- University of Oslo Department of statistics Oslo Norway Oxford Big Data Institute Wedge lab Oxford UK PCAWG PCAWG – working group 11 London UK

ABSTRACTIntroductionClusters of subclonal mutations attributed to subclonal expansions have been observed across most cancer types. To date it is not clear what fraction of these expansions can be ascribed to selective sweeps or genetic drifts. The widely held theory states that tumour expansion arises from a series of selective sweeps. However, Williams et al. (Nat. Genet. 48:238–224, 2016) recently claimed to have identified neutral tumour evolution in one third of 904 samples from The Cancer Genome Atlas (TCGA). Material and methodsFirst, using the same equations we simulated data of tumour undergoing selective sweeps. Second, we simulated data using branching processes, i.e. more realistic models. Third, we analysed the mutations from ~1600 exomes and ~1500 whole genomes of real tumours from TCGA and the International Cancer Genome Consortium, respectively. We grouped them into neutral and non-neutral tumours according to the rationale described by Williams et al. We then applied dN/dS, an orthogonal widely used approach to detect selection in non-synonymous mutations of coding regions. Finally, we ran dN/dS on subclonal mutations within individual cancer types. Results and discussionsApplication of the method described by Williams et al. led to over-calling of neutrality and led to random predictions (area under the curve~=50%) in simulations based on the deterministic or stochastic models, respectively. dN/dS analyses revealed significant and widespread positive selection in clonal and subclonal mutations within both neutral and non-neutral groups. Despite power limits, the subclonal mutations of many individual cancer types displayed dN/dS>1, evidence for positive selection. ConclusionAltogether, our results point to the lack of evidence for neutral tumour evolution and uncovered strong positive selection within subclonal mutations across cancers.

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Author Correction: Genome-wide analyses of ADHD identify 27 risk loci, refine the genetic architecture and implicate several cognitive domains

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Nature genetics 2023年第4期55卷 730页

作者： Ditte Demontis G Bragi Walters Georgios Athanasiadis Raymond Walters Karen Therrien Trine Tollerup Nielsen Leila Farajzadeh Georgios Voloudakis Jaroslav Bendl Biau Zeng Wen Zhang Jakob Grove Thomas D Als Jinjie Duan F Kyle Satterstrom Jonas Bybjerg-Grauholm Marie Bækved-Hansen Olafur O Gudmundsson Sigurdur H Magnusson Gisli Baldursson Katrin Davidsdottir Gyda S Haraldsdottir Esben Agerbo Gabriel E Hoffman Søren Dalsgaard Jonna Martin Marta Ribasés Dorret I Boomsma Maria Soler Artigas Nina Roth Mota Daniel Howrigan Sarah E Medland Tetyana Zayats Veera M Rajagopal Merete Nordentoft Ole Mors David M Hougaard Preben Bo Mortensen Mark J Daly Stephen V Faraone Hreinn Stefansson Panos Roussos Barbara Franke Thomas Werge Benjamin M Neale Kari Stefansson Anders D Børglum Department of Biomedicine - Human Genetics Aarhus University Aarhus Denmark. ditte@biomed.au.dk. The Lundbeck Foundation Initiative for Integrative Psychiatric Research iPSYCH Aarhus Denmark. ditte@biomed.au.dk. Center for Genomics and Personalized Medicine Aarhus Denmark. ditte@biomed.au.dk. deCODE Genetics/Amgen Reykjavik Iceland. Faculty of Medicine University of Iceland Reykjavik Iceland. The Lundbeck Foundation Initiative for Integrative Psychiatric Research iPSYCH Aarhus Denmark. Mental Health Centre Sct. Hans Capital Region of Denmark Institute of Biological Psychiatry Copenhagen University Hospital Copenhagen Denmark. Department of Evolutionary Biology Ecology and Environmental Sciences University of Barcelona Barcelona Spain. Analytic and Translational Genetics Unit Department of Medicine Massachusetts General Hospital and Harvard Medical School Boston MA USA. Stanley Center for Psychiatric Research Broad Institute of MIT and Harvard Cambridge MA USA. Center for Disease Neurogenomics Icahn School of Medicine at Mount Sinai New York NY USA. Icahn Institute for Data Science and Genomic Technology Icahn School of Medicine at Mount Sinai New York NY USA. Friedman Brain Institute Icahn School of Medicine at Mount Sinai New York NY USA. Department of Psychiatry Icahn School of Medicine at Mount Sinai New York NY USA. Department of Genetics and Genomic Science Icahn School of Medicine at Mount Sinai New York NY USA. Nash Family Department of Neuroscience Icahn School of Medicine at Mount Sinai New York NY USA. Department of Biomedicine - Human Genetics Aarhus University Aarhus Denmark. Center for Genomics and Personalized Medicine Aarhus Denmark. Bioinformatics Research Centre Aarhus University Aarhus Denmark. Center for Neonatal Screening Department for Congenital Disorders Statens Serum Institut Copenhagen Denmark. Department of Child and Adolescent Psychiatry National University Hospital Reykjavik Iceland. The Centre for Child Developme

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Genome-wide association study of long COVID

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Nature Genetics 2025年 1-16页

作者： Lammi, Vilma Nakanishi, Tomoko Jones, Samuel E. Andrews, Shea J. Karjalainen, Juha Cortés, Beatriz O’Brien, Heath E. Ochoa-Guzman, Ana Fulton-Howard, Brian E. Broberg, Martin Haapaniemi, Hele H. Kanai, Masahiro Pirinen, Matti Schmidt, Axel Mitchell, Ruth E. Mousas, Abdou Mangino, Massimo Huerta-Chagoya, Alicia Sinnott-Armstrong, Nasa Cirulli, Elizabeth T. Vaudel, Marc Kwong, Alex S. F. Maiti, Amit K. Marttila, Minttu M. Posner, Daniel C. Rodriguez, Alexis A. Batini, Chiara Minnai, Francesca Dearman, Anna R. Warmerdam, C. A. Robert Sequeros, Celia B. Winkler, Thomas W. Jordan, Daniel M. Rešcenko, Raimonds Miano, Lorenzo Lane, Jacqueline M. Chung, Ryan K. Guillen-Guio, Beatriz Leavy, Olivia C. Carvajal-Silva, Laura Aguilar-Valdés, Kevin Frangione, Erika Guare, Lindsay Vergasova, Ekaterina Marouli, Eirini Striano, Pasquale Zainulabid, Ummu Afeera Kumar, Ashutosh Ahmad, Hajar Fauzan Edahiro, Ryuya Azekawa, Shuhei Maj, Carlo Pensel, Max C. Miller, Abigail Nöthen, Markus M. Behzad, Pari Schultz, Sonja Heggemann, Julia Balla, Daniella Morrison, David R. Mooser, Vincent Perley, Danielle Ragoussis, Jiannis Rousseau, Simon Shi, Fangyi Lathrop, G. Mark Yanishevsky, Solomia Laurent, Laetitia Auld, Daniel Bertrand, Mylene Boisclair, Ariane Bourque, Guillaume Bujold, David Durand, Madeleine Adra, Darin St-Cyr, Janick Niemi, Mari E. K. Iyengar, Sudha K. Cai, Tianxi Cho, Kelly Sarvadhavabhatla, Sannidhi Donaire, Maria Sophia Valenzuela-Jorquera, Héctor Lamoza, Eduardo Arévalo, Tamara V. Retamales-Ortega, Rocío Sanhueza, Sergio Selman, Carolina S. Silva, Andrea X. Alarcon, Teresa A. Martínez, Matías F. Quiroga, Romina Zuñiga-Pacheco, Paula Zapata-Contreras, Daniela Yáñez, Cristian E. Quiñones, Luis A. Tobar-Calfucoy, Eduardo A. Monardes-Ramírez, Virginia A. Signore, Iskra A. Guajardo, Lissette G. Figueroa, Alvaro Oróstica, Karen Y. Muñoz, Christian A. Fuentes-Guajardo, Macarena Bocchieri, Pamela Cabrera, Camilo Echeverria, Cesar A. Cerpa, Leslie C. Donoso, Gerardo Gutiérrez-Richards, Scarlett Nova-Lamperti, Estefania Saez Hidalgo Institute for Molecular Medicine Finland (FIMM) Helsinki Institute of Life Science (HiLIFE) University of Helsinki Helsinki Finland Department of Human Genetics McGill University Montreal QC Canada Centre for Clinical Epidemiology Department of Medicine Lady Davis Institute Jewish General Hospital McGill University Montreal QC 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 Department of Psychiatry and Behavioral Sciences University of California San Francisco San Francisco CA United States Program in Medical and Population Genetics Broad Institute of Harvard and MIT Cambridge MA United States Stanley Center for Psychiatric Research Broad Institute of Harvard and MIT Cambridge MA United States Analytic and Translational Genetics Unit Massachusetts General Hospital Boston MA United States Genomes for Life-GCAT Lab CORE Program Germans Trias i Pujol Research Institute (IGTP) Badalona Spain Grup de REcerca en Impacte de les Malalties Cròniques i les seves Trajectòries (GRIMTra) Barcelona Spain Sano Genetics Limited London United Kingdom Unidad de Biología Molecular y Medicina Genómica Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán Mexico City Mexico Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai New York City NY United States Broad Institute Cambridge MA United States Analytical and Translational Genetics Unit Massachusetts General Hospital Harvard Medical School Boston MA United States Department of Mathematics and Statistics University of Helsinki Helsinki Finland Department of Public Health University of Helsinki Helsinki Finland Institute of Human Genetics University of Bonn School of Medicine and University Hospital Bonn Bonn Germany MRC Integrat

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 of FOXP4 with 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. © The Author(s) 2025.

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