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A second update on mapping the human genetic architecture of COVID-19

Nature 2023年第7977期621卷 E7-E26页

作者： Masahiro Kanai Christine Stevens Benjamin M. Neale Mark Daly Andrea Ganna Amy Trankiem Mary K. Balaconis Samuli Ripatti Lindo Nkambul Mark J. Daly Sam Bryant Matthew Solomonson Shea J. Andrews Mattia Cordioli Juha Karjalainen Juha Mehtonen Matti Pirinen Andrea Corbetta Bradley Jermy Kati Donner Katja Kivinen Aarno Palotie Mari Kaunisto Kumar Veerapen Konrad J. Karczewski Alicia R. Martin Elizabeth G. Atkinson Kristin Tsuo Nikolas Baya Rahul Gupta Raymond K. Walters Duncan S. Palmer Gopal Sarma Nathan Cheng Wenhan Lu Claire Churchhouse Jacqueline I. Goldstein Daniel King Wei Zhou Cotton Seed Hilary Finucane F. Kyle Satterstrom Gita A. Pathak Akiko Iwasaki Karolina Chwialkowska Karolina Chwiałkowska Brooke N. Wolford Hajar Fauzan Ahmad Shea Andrews Kathrin Aprile von Hohenstaufen Puoti Palwende R. Boua Guillaume Butler-Laporte Celia M. T. Greenwood Bartha M. Knoppers Mark Lathrop Carmen L. Cadilla Francesca Colombo Nicole Dueker Chloe Kirk Atanu Kumar Dutta Yasser M. El-Sherbiny Jehan J. El-Jawhari Doaa Shahin Ahmed Elzeiny Tamer A. Mansour Madonna M. Eltoukhy Attia A. S. Mohamed Sahar Esmaeeli Annika Faucon Israel Fernández Cadenas Israel Fernandez-Cadenas Laia Llucià-Carol Natalia Cullell Elena Muiño Jara Cárcel-Márquez Margherita Francescatto Laurent Francioli Lindokuhle Nkambule Jatin Arora Soumya Raychaudhuri Caroline Cusick Lude Franke Macarena Fuentes Macarena Fuentes-Guajardo David Gómez Cabrero Emi N. Harry Philip Jansen József L. Szentpéteri Réka Várnai Elżbieta Kaja Athanasios Kousathanas Dorote Pasko Mark J. Caulfield Alex Stuckey Christopher A. Odhams Susan Walker Daniel Rhodes Richard H. Scott Loukas Moutsianas Afshan Siddiq Peter Goddard Sally Donovan Tala Zainy Fiona Maleady-Crowe Linda Todd Shahla Salehi Greg Elgar Georgia Chan Prabhu Arumugam Christine Patch Augusto Rendon Tom A. Fowler Jose E. Krieger Sanjay K. Patel Audrey Lemaçon Sophie Limou Pietro Lió Eirini Marouli Charles Hinds Minttu M. Marttila Carolina Medina-Gómez Isabelle Migeotte Soumyajit Mondal Andrés Moreno-Estrada Leire Moya Tomok Broad Institute of MIT and Harvard Cambridge MA USA Analytic and Translational Genetics Unit Massachusetts General Hospital Boston MA USA Program in Medical and Population Genetics Broad Institute of MIT and Harvard Cambridge MA USA Department of Biomedical Informatics Harvard Medical School Boston MA USA Program in Bioinformatics and Integrative Genomics Harvard Medical School Boston MA USA Institute for Molecular Medicine Finland (FIMM) University of Helsinki Helsinki Finland Institute for Molecular Medicine Finland University of Helsinki Helsinki Finland Institute for Molecular Medicine Finland (FIMM) HiLIFE University of Helsinki Helsinki Finland Public Health Faculty of Medicine University of Helsinki Helsinki Finland Analytic & Translational Genetics Unit Massachusetts General Hospital Boston MA USA Stanley Center for Psychiatric Research & Program in Medical and Population Genetics Cambridge UK Institute for Molecular Medicine Finland (FIMM) Univerisity of Helsinki Helsinki Finland University of California San Francisco San Francisco CA USA Department of Molecular and Human Genetics Baylor College of Medicine Houston TX USA Program in Biological and Biomedical Sciences Harvard Medical School Boston MA USA Department of Psychiatry School of Medicine Yale University New Haven CT USA Veteran Affairs Connecticut Healthcare System West Haven CT USA Yale University New Haven CT USA Centre for Bioinformatics and Data Analysis Medical University of Bialystok Bialystok Poland Department of Computational Medicine and Bioinformatics University of Michigan Ann Arbor MI USA Faculty of Industrial Sciences and Technology Universiti Malaysia Pahang Pahang Malaysia Icahn School of Medicine at Mount Sinai New York NY USA Genolier Innovation Network and Hub Swiss Medical Network Genolier Healthcare Campus Genolier Switzerland Immediate Independent Multidisciplinary Med & Biotech Research Association Milan Italy Clinical Research Unit of Nanor

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BioTIME 2.0: Expanding and Improving a Database of Biodiversity Time Series

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Global Ecology and Biogeography 2025年第5期34卷

作者： Maria Dornelas Laura H. Antão Amanda E. Bates Viviana Brambilla Jonathan M. Chase Cher F. Y. Chow Ada Fontrodona-Eslava Anne E. Magurran Inês S. Martins Faye Moyes Alban Sagouis Samuel Adu-Acheampong Daniel Acquah-Lamptey Dušan Adam Penelope A. Ajani Aitor Albaina Pablo Almaraz Jeongseop An Roger Sigismund Anderson Madelaine Jean Robertson Anderson Alexsander Z. Antunes Ivan Arismendi Linda Armbrecht Pedro Aros-Mardones Sreejith Kalpuzha Ashtamoorthy Narayanan Ayyappan Gal Badihi Joseph J. Bailey Andrew H. Baird Mark Edward Baird Sreekumar Vadakkethil Balakrishnan José António L. Barão-Nóbrega Adi Barash Miguel Barbosa Jos Barlow Claus Bässler Matthieu Beaumont Natalie Beenaerts Tiago Octavio Begot Wallace Beiroz Ricardo Beldade David M. Bell Alecia Bellgrove Jonathan Belmaker Lisandro Benedetti-Cecchi Cassandra E. Benkwitt Pamela Medina-van Berkum Brandon T. Bestelmeyer Matthew G. Betts Maxwell Kelvin Billah Anne D. Bjorkman Magdalena Błażewicz Christopher P. Bloch Shane A. Blowes Antonio Bode Juliano A. Bogoni Thomas Bolger Timothy C. Bonebrake Erik Bonsdorff Roberta Bottarin Luke N. Brokensha Rob W. Brooker Andrew J. Brooks Helge Bruelheide Thiago Almeida Bueno Claire Laguionie Mariana Lopes Campagnoli James Cant Erica Pellegrini Caramaschi Alexandre Caron Tadhg Carroll Tancredi Caruso Juan Carvajal-Quintero Giuseppe Castaldelli Edward Castañeda-Moya Pedro V. Castilho Sonia Zanini Cechin Shahar Chaikin Uchangi Manjunatha Chandrashekara Tory J. Chase Chaolun Allen Chen Jorge José Cherem Sei-Woong Choi Erica M. Christensen Alexander V. Christianini Jackson Wing Four Chu Peter Coad Carl Van Colen Lise Comte Elisabeth J. Cooper J. Hans C. Cornelissen Eddy Cosson Unai Cotano Luc Crevecoeur Shannan Kyle Crow Graeme S. Cumming Vanessa S. Daga Gabriella Damasceno Gergana N. Daskalova Claire H. Davies Robert A. Davis Frank P. Day Sussy De-La-Zerda Amy Elizabeth Deacon Indradatta de Castro-Arrazola Steven Degraer Kharran Deonarinesingh Juan C. Diaz-Ricaurte Christopher R. Dickman Tara Dirilgen Ciaran John Dolan J. Emmet Centre for Biological Diversity School of Biology University of St Andrews Fife UK MARE—Centro de Ciências do Mar e do Ambiente Faculdade de Ciências Universidade de Lisboa Lisboa Portugal Research Centre for Ecological Change Organismal and Evolutionary Biology Research Programme Faculty of Biological and Environmental Sciences University of Helsinki Helsinki Finland Department of Biology University of Victoria Victoria British Columbia Canada German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig Leipzig Germany Department of Computer Science Martin Luther University Halle-Wittenberg Halle (Saale) Germany Leverhulme Centre for Anthropocene Biodiversity Department of Biology University of York York UK Department of Animal Biology and Conservation Science University of Ghana Accra Ghana Philipps Universität Marburg Marburg Germany Department of Forest Ecology Silva Tarouca Research Institute Brno Czech Republic School of Life Sciences University of Technology Sydney Sydney New South Wales Australia Zoology and Animal Cell Biology Department University of the Basque Country (UPV/EHU) Leioa Spain Grupo de Oceanografía de Ecosistemas Instituto de Ciencias Marinas de Andalucía CSIC Campus Universitario de Puerto Real Puerto Real Spain National Institute of Ecology Seocheon Republic of Korea African Regional Postgraduate Programme in Insect Science University of Ghana Accra Ghana Département de Biologie Université de Sherbrooke Sherbrooke Quebec Canada Núcleo de Conservação da Biodiversidade Instituto de Pesquisas Ambientais Secretaria de Meio Ambiente Infraestrutura e Logística do Estado de São Paulo São Paulo Brazil Department of Fisheries Wildlife and Conservation Sciences Oregon State University Corvallis Oregon USA Institute for Marine and Antarctic Studies Ecology & Biodiversity Centre University of Tasmania Hobart Tasmania Australia Graduate Program in Oceanography Department of Oceanography Faculty of Natural Scienc

Motivation Here, we make available a second version of the BioTIME database, which compiles records of abundance estimates for species in sample events of ecological assemblages through time. The updated version expands version 1.0 of the database by doubling the number of studies and includes substantial additional curation to the taxonomic accuracy of the records, as well as the metadata. Moreover, we now provide an R package (BioTIMEr) to facilitate use of the database. Main Types of Variables Included The database is composed of one main data table containing the abundance records and 11 metadata tables. The data are organised in a hierarchy of scales where 11,989,233 records are nested in 1,603,067 sample events, from 553,253 sampling locations, which are nested in 708 studies. A study is defined as a sampling methodology applied to an assemblage for a minimum of 2 years. Spatial Location and Grain Sampling locations in BioTIME are distributed across the planet, including marine, terrestrial and freshwater realms. Spatial grain size and extent vary across studies depending on sampling methodology. We recommend gridding of sampling locations into areas of consistent size. Time Period and Grain The earliest time series in BioTIME start in 1874, and the most recent records are from 2023. Temporal grain and duration vary across studies. We recommend doing sample-level rarefaction to ensure consistent sampling effort through time before calculating any diversity metric. Major Taxa and Level of Measurement The database includes any eukaryotic taxa, with a combined total of 56,400 taxa. Software Format csv and. SQL.

关键词： assemblage biodiversity community database ecoinformatics species taxa time

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Correction to: 2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

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Archives of virology 2021年第12期166卷 3567-3579页

作者： Jens H Kuhn Scott Adkins Bernard R Agwanda Rim Al Kubrusli Sergey V Alkhovsky Gaya K Amarasinghe Tatjana Avšič-Županc María A Ayllón Justin Bahl Anne Balkema-Buschmann Matthew J Ballinger Christopher F Basler Sina Bavari Martin Beer Nicolas Bejerman Andrew J Bennett Dennis A Bente Éric Bergeron Brian H Bird Carol D Blair Kim R Blasdell Dag-Ragnar Blystad Jamie Bojko Wayne B Borth Steven Bradfute Rachel Breyta Thomas Briese Paul A Brown Judith K Brown Ursula J Buchholz Michael J Buchmeier Alexander Bukreyev Felicity Burt Carmen Büttner Charles H Calisher Mengji Cao Inmaculada Casas Kartik Chandran Rémi N Charrel Qi Cheng Yuya Chiaki Marco Chiapello Il-Ryong Choi Marina Ciuffo J Christopher S Clegg Ian Crozier Elena Dal Bó Juan Carlos de la Torre Xavier de Lamballerie Rik L de Swart Humberto Debat Nolwenn M Dheilly Emiliano Di Cicco Nicholas Di Paola Francesco Di Serio Ralf G Dietzgen Michele Digiaro Olga Dolnik Michael A Drebot J Felix Drexler William G Dundon W Paul Duprex Ralf Dürrwald John M Dye Andrew J Easton Hideki Ebihara Toufic Elbeaino Koray Ergünay Hugh W Ferguson Anthony R Fooks Marco Forgia Pierre B H Formenty Jana Fránová Juliana Freitas-Astúa Jingjing Fu Stephanie Fürl Selma Gago-Zachert George Fú Gāo María Laura García Adolfo García-Sastre Aura R Garrison Thomas Gaskin Jean-Paul J Gonzalez Anthony Griffiths Tony L Goldberg Martin H Groschup Stephan Günther Roy A Hall John Hammond Tong Han Jussi Hepojoki Roger Hewson Jiang Hong Ni Hong Seiji Hongo Masayuki Horie John S Hu Tao Hu Holly R Hughes Florian Hüttner Timothy H Hyndman M Ilyas Risto Jalkanen Dàohóng Jiāng Gilda B Jonson Sandra Junglen Fujio Kadono Karia H Kaukinen Michael Kawate Boris Klempa Jonas Klingström Gary Kobinger Igor Koloniuk Hideki Kondō Eugene V Koonin Mart Krupovic Kenji Kubota Gael Kurath Lies Laenen Amy J Lambert Stanley L Langevin Benhur Lee Elliot J Lefkowitz Eric M Leroy Shaorong Li Longhui Li Jiànróng Lǐ Huazhen Liu Igor S Lukashevich Piet Maes William Marciel de Souza Marco Marklewitz Sergio H Marshall Shin-Yi L Marzano Se Integrated Research Facility at Fort Detrick National Institute of Allergy and Infectious Diseases National Institutes of Health Frederick MD USA. kuhnjens@mail.nih.gov. United States Department of Agriculture Agricultural Research Service US Horticultural Research Laboratory Fort Pierce FL USA. Zoology Department National Museums of Kenya Nairobi Kenya. Jomo Kenyatta University of Agriculture & Technology Nairobi Kenya. Division Phytomedicine Faculty of Life Sciences Humboldt-Universität zu Berlin Berlin Germany. D.I. Ivanovsky Institute of Virology of N.F. Gamaleya National Center on Epidemiology and Microbiology of Ministry of Health of Russian Federation Moscow Russia. Department of Pathology and Immunology Washington University School of Medicine St. Louis MO USA. Faculty of Medicine University of Ljubljana Ljubljana Slovenia. Centro de Biotecnología y Genómica de Plantas Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria Campus de Montegancedo Pozuelo de Alarcón Madrid Spain. Departamento de Biotecnología-Biología Vegetal Escuela Técnica Superior de Ingeniería Agronómica Alimentaria y de Biosistemas Universidad Politécnica de Madrid Madrid Spain. Center for Ecology of Infectious Diseases Department of Infectious Diseases Department of Epidemiology and Biostatistics Insitute of Bioinformatics University of Georgia Athens GA USA. Institute of Novel and Emerging Infectious Diseases Friedrich-Loeffler-Institut Federal Research Institute for Animal Health Greifswald-Insel Riems Germany. Department of Biological Sciences Mississippi State University Mississippi State MS USA. Center for Microbial Pathogenesis Institute for Biomedical Sciences Georgia State University Atlanta GA USA. Edge BioInnovation Consulting and Mgt Frederick MD USA. Institute of Diagnostic Virology Friedrich-Loeffler-Institut Greifswald-Insel Riems Germany. UFyMA INTA-CONICET Cordoba Argentina. Genomics and Bioinformatics D

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Author Correction: A case-only study to identify genetic modifiers of breast cancer risk for BRCA1/BRCA2 mutation carriers

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Nature communications 2021年第1期12卷 2986页

作者： Juliette Coignard Michael Lush Jonathan Beesley Tracy A O'Mara Joe Dennis Jonathan P Tyrer Daniel R Barnes Lesley McGuffog Goska Leslie Manjeet K Bolla Muriel A Adank Simona Agata Thomas Ahearn Kristiina Aittomäki Irene L Andrulis Hoda Anton-Culver Volker Arndt Norbert Arnold Kristan J Aronson Banu K Arun Annelie Augustinsson Jacopo Azzollini Daniel Barrowdale Caroline Baynes Heko Becher Marina Bermisheva Leslie Bernstein Katarzyna Białkowska Carl Blomqvist Stig E Bojesen Bernardo Bonanni Ake Borg Hiltrud Brauch Hermann Brenner Barbara Burwinkel Saundra S Buys Trinidad Caldés Maria A Caligo Daniele Campa Brian D Carter Jose E Castelao Jenny Chang-Claude Stephen J Chanock Wendy K Chung Kathleen B M Claes Christine L Clarke J Margriet Collée Don M Conroy Kamila Czene Mary B Daly Peter Devilee Orland Diez Yuan Chun Ding Susan M Domchek Thilo Dörk Isabel Dos-Santos-Silva Alison M Dunning Miriam Dwek Diana M Eccles A Heather Eliassen Christoph Engel Mikael Eriksson D Gareth Evans Peter A Fasching Henrik Flyger Florentia Fostira Eitan Friedman Lin Fritschi Debra Frost Manuela Gago-Dominguez Susan M Gapstur Judy Garber Vanesa Garcia-Barberan Montserrat García-Closas José A García-Sáenz Mia M Gaudet Simon A Gayther Andrea Gehrig Vassilios Georgoulias Graham G Giles Andrew K Godwin Mark S Goldberg David E Goldgar Anna González-Neira Mark H Greene Pascal Guénel Lothar Haeberle Eric Hahnen Christopher A Haiman Niclas Håkansson Per Hall Ute Hamann Patricia A Harrington Steven N Hart Wei He Frans B L Hogervorst Antoinette Hollestelle John L Hopper Darling J Horcasitas Peter J Hulick David J Hunter Evgeny N Imyanitov Agnes Jager Anna Jakubowska Paul A James Uffe Birk Jensen Esther M John Michael E Jones Rudolf Kaaks Pooja Middha Kapoor Beth Y Karlan Renske Keeman Elza Khusnutdinova Johanna I Kiiski Yon-Dschun Ko Veli-Matti Kosma Peter Kraft Allison W Kurian Yael Laitman Diether Lambrechts Loic Le Marchand Jenny Lester Fabienne Lesueur Tricia Lindstrom Adria Lopez-Fernández Jennifer T Loud Craig Luccarini Arto Mannermaa Siranou Genetic Epidemiology of Cancer team Inserm U900 Paris France. Institut Curie Paris Paris France. Mines ParisTech Fontainebleau Paris France. Centre for Cancer Genetic Epidemiology Department of Public Health and Primary Care University of Cambridge Cambridge UK. PSL University Paris Paris France. Paris Sud University Orsay France. Department of Genetics and Computational Biology QIMR Berghofer Medical Research Institute Brisbane QLD Australia. Centre for Cancer Genetic Epidemiology Department of Oncology University of Cambridge Cambridge UK. Family Cancer Clinic The Netherlands Cancer Institute Antoni van Leeuwenhoek hospital Amsterdam The Netherlands. Immunology and Molecular Oncology Unit Veneto Institute of Oncology IOV - IRCCS Padua Italy. Division of Cancer Epidemiology and Genetics National Cancer Institute National Institutes of Health Department of Health and Human Services Bethesda MD USA. Department of Clinical Genetics Helsinki University Hospital University of Helsinki Helsinki Finland. Fred A. Litwin Center for Cancer Genetics Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital Toronto ON Canada. Department of Molecular Genetics University of Toronto Toronto ON Canada. Department of Epidemiology Genetic Epidemiology Research Institute University of California Irvine Irvine CA USA. Division of Clinical Epidemiology and Aging Research German Cancer Research Center (DKFZ) Heidelberg Germany. Department of Gynaecology and Obstetrics University Hospital of Schleswig-Holstein Campus Kiel Christian-Albrechts University Kiel Kiel Germany. Institute of Clinical Molecular Biology University Hospital of Schleswig-Holstein Campus Kiel Christian-Albrechts University Kiel Kiel Germany. Department of Public Health Sciences and Cancer Research Institute Queen's University Kingston ON Canada. Department of Breast Medical Oncology University of Texas MD Anderson Cancer Center Houston TX USA. Department of Cancer Epidemiology Clinical Sciences

A Correction to this paper has been published: https://***/10.1038/s41467-021-23162-4.

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Erratum to: The real cost of sequencing: scaling computation to keep pace with data generation

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Genome biology 2016年第1期17卷 78页

作者： Paul Muir Shantao Li Shaoke Lou Daifeng Wang Daniel J Spakowicz Leonidas Salichos Jing Zhang George M Weinstock Farren Isaacs Joel Rozowsky Mark Gerstein Department of Molecular Cellular and Developmental Biology Yale University New Haven CT 06520 USA. Systems Biology Institute Yale University West Haven CT 06516 USA. Integrated Graduate Program in Physical and Engineering Biology Yale University New Haven CT 06520 USA. Program in Computational Biology and Bioinformatics Yale University New Haven CT 06520 USA. Department of Molecular Biophysics and Biochemistry Yale University New Haven CT 06520 USA. The Jackson Laboratory for Genomic Medicine Farmington CT 06032 USA. Program in Computational Biology and Bioinformatics Yale University New Haven CT 06520 USA. mark@***. Department of Molecular Biophysics and Biochemistry Yale University New Haven CT 06520 USA. mark@***. Department of Computer Science Yale University New Haven CT 06520 USA. mark@***.

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Gene expression imputation across multiple brain regions provides insights into schizophrenia risk (vol 51, pg 659, 2019)

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NATURE GENETICS 2019年第6期51卷 1068-1068页

作者： Huckins, Laura M. Dobbyn, Amanda Ruderfer, Douglas M. Hoffman, Gabriel Wang, Weiqing Pardinas, Antonio F. Rajagopal, Veera M. Als, Thomas D. Nguyen, Hoang T. Girdhar, Kiran Boocock, James Roussos, Panos Fromer, Menachem Kramer, Robin Domenici, Enrico Gamazon, Eric R. Purcell, Shaun Demontis, Ditte Borglum, Anders D. Walters, James T. R. O'Donovan, Michael C. Sullivan, Patrick Owen, Michael J. Devlin, Bernie Sieberts, Solveig K. Cox, Nancy J. Im, Hae Kyung Sklar, Pamela Stahl, Eli A. Pamela Sklar Division of Psychiatric Genomics Icahn School of Medicine at Mount Sinai New York NY USA Department of Genetics and Genomics 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 Icahn Institute for Genomics and Multiscale Biology Icahn School of Medicine at Mount Sinai New York NY USA Vanderbilt University Medical Center Nashville TN USA MRC Centre for Neuropsychiatric Genetics and Genomics Cardiff University Cardiff UK Department of Biomedicine Aarhus University Aarhus Denmark The Lundbeck Foundation Initiative for Integrative Psychiatric Research iPSYCH Denmark Center for Integrative Sequencing Aarhus University Aarhus Denmark Department of Human Genetics David Geffen School of Medicine University of California Los Angeles Los Angeles CA USA Human Brain Collection Core National Institute of Mental Health Bethesda MD USA Laboratory of Neurogenomic Biomarkers Centre for Integrative Biology (CIBIO) University of Trento Trento Italy Clare Hall University of Cambridge Cambridge UK University of North Carolina at Chapel Hill Chapel Hill NC USA Karolinska Institutet Stockholm Sweden Department of Psychiatry University of Pittsburgh Pittsburgh PA USA Systems Biology Sage Bionetworks Seattle WA USA Section of Genetic Medicine Department of Medicine University of Chicago Chicago IL USA Integrated Technology Research Laboratories Pharmaceutical Research Division Takeda Pharmaceutical Company Limited Fujisawa Japan Neuropsychiatry Section Department of Psychiatry Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Neuropsychiatric Signaling Program Department of Psychiatry Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Psychiatry JJ Peters Virginia Medical Center Bronx NY USA Department of Neuroscience Icahn School of Medicine at Mount Sinai New York New York NY USA Friedman Brain Institute

Transcriptomic imputation approaches combine eQTL reference panels with large-scale genotype data in order to test associations between disease and gene expression. These genic associations could elucidate signals in complex genome-wide association study (GWAS) loci and may disentangle the role of different tissues in disease development. We used the largest eQTL reference panel for the dorso-lateral prefrontal cortex (DLPFC) to create a set of gene expression predictors and demonstrate their utility. We applied DLPFC and 12 GTEx-brain predictors to 40,299 schizophrenia cases and 65,264 matched controls for a large transcriptomic imputation study of schizophrenia. We identified 413 genic associations across 13 brain regions. Stepwise conditioning identified 67 non-MHC genes, of which 14 did not fall within previous GWAS loci. We identified 36 significantly enriched pathways, including hexosaminidase-A deficiency, and multiple porphyric disorder pathways. We investigated developmental expression patterns among the 67 non-MHC genes and identified specific groups of pre- and postnatal expression.

关键词： Gene expression Genome-wide association studies Schizophrenia Transcriptomics

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Abstracts from the 8th International Conference on cGMP Generators, Effectors and Therapeutic Implications : Bamberg, Germany. 23-25 June, 2017

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BMC pharmacology & toxicology 2017年第SUPPL 1期18卷 64-64页

作者： Todd Milne, G. Sandner, Peter Lincoln, Kathleen A. Harrison, Paul C. Chen, Hongxing Wang, Hong Clifford, Holly Qian, Hu Sheng Wong, Diane Sarko, Chris Fryer, Ryan Richman, Jeremy Reinhart, Glenn A. Boustany, Carine M. Pullen, Steven S. Andresen, Henriette Moltzau, Lise Román Cataliotti, Alessandro Levy, Finn Olav Lukowski, Robert Frankenreiter, Sandra Friebe, Andreas Calamaras, Timothy Baumgartner, Robert McLaughlin, Angela Aronovitz, Mark Baur, Wendy Wang, Guang-Rong Kapur, Navin Karas, Richard Blanton, Robert Hell, Stefan Waldman, Scott A. Lin, Jieru E. Colon-Gonzalez, Francheska Kim, Gilbert W. Blomain, Erik S. Merlino, Dante Snook, Adam Erdmann, Jeanette Wobst, Jana Kessler, Thorsten Schunkert, Heribert Walter, Ulrich Pagel, Oliver Walter, Elena Gambaryan, Stepan Smolenski, Albert Jurk, Kerstin Zahedi, Rene Klinger, James R. Benza, Raymond L. Corris, Paul A. Langleben, David Naeije, Robert Simonneau, Gérald Meier, Christian Colorado, Pablo Chang, Mi Kyung Busse, Dennis Hoeper, Marius M. Masferrer, Jaime L. Jacobson, Sarah Liu, Guang Sarno, Renee Bernier, Sylvie Zhang, Ping Flores-Costa, Roger Currie, Mark Hall, Katherine Möhrle, Dorit Reimann, Katrin Wolter, Steffen Wolters, Markus Mergia, Evanthia Eichert, Nicole Geisler, Hyun-Soon Ruth, Peter Feil, Robert Zimmermann, Ulrike Koesling, Doris Knipper, Marlies Rüttiger, Lukas Tanaka, Yasutake Okamoto, Atsuko Nojiri, Takashi Kumazoe, Motofumi Tokudome, Takeshi Miura, Koichi Hino, Jun Hosoda, Hiroshi Miyazato, Mikiya Kangawa, Kenji Kapil, Vikas Ahluwalia, Amrita Paolocci, Nazareno Eaton, Philip Campbell, James C. Henning, Philipp Franz, Eugen Sankaran, Banumathi Herberg, Friedrich W. Kim, Choel Wittwer, M. Luo, Q. Kaila, V. Dames, S. A. Tobin, Andrew Alam, Mahmood Rudyk, Olena Krasemann, Susanne Hartmann, Kristin Prysyazhna, Oleksandra Zhang, Min Zhao, Lan Weiss, Astrid Schermuly, Ralph Moyes, Amie J. Chu, Sandy M. Baliga, Reshma S. Hobbs, Adrian J. Michalakis, Stylianos Mühlfriedel, Regine Schön, Christian Fischer, Dominik M. Wilhelm, Barbara Zobor, Ditta Kohl, Ironwood Pharmaceuticals Cambridge USA Bayer AG Drug Discovery - Cardiovascular Research Wuppertal Germany Department of Cardiometabolic Diseases Research Boehringer Ingelheim Pharmaceuticals Ridgefield USA Department of Small Molecule Drug Research Boehringer Ingelheim Pharmaceuticals Ridgefield USA Department of Pharmacology University of Oslo and Oslo University Hospital Oslo Norway Institute of Experimental Medical Research University of Oslo and Oslo University Hospital Oslo Norway Center for Heart Failure Research University of Oslo and Oslo University Hospital Oslo Norway Department of Pharmacology Toxicology and Clinical Pharmacy Institute of Pharmacy University of Tuebingen Tuebingen Germany Physiologisches Institut Universität Würzburg Würzburg Germany Molecular Cardiology Research Institute Tufts Medical Center Boston USA Present Affiliation: Division of Cardiology University of Pittsburgh Medical Center Pittsburgh USA Present Affiliation: Department of Medicine Brown University School of Medicine Providence USA Division of Cardiology Tufts Medical Center Boston USA Max Planck Institute for Biophysical Chemistry Göttingen and German Cancer Research Center (DKFZ) Heidelberg Germany Department of Pharmacology and Experimental Therapeutics Thomas Jefferson University Philadelphia USA Institut für Kardiogenetik and Universitäres Herzzentrum Lübeck Universität zu Lübeck Lübeck Germany & DZHK e.V. (German Center for Cardiovascular Research) Partner Site Hamburg/Kiel/Lübeck Lübeck Germany Deutsches Herzzentrum München Klinik für Herz- und Kreislauferkrankungen Technische Universität München Munich Germany Center for Thrombosis & Hemostasis Universitätsklinikum der Johannes Gutenberg-Universität Mainz Mainz Germany Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V Dortmund Germany Sechenov Institute of Evolutionary Physiology and Biochemistry Russian Academy of Sciences St. Petersburg Russia UCD Conway Institute UCD School of Medicine

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Expression, purification, crystallization, and preliminary X-ray crystallographic studies of the human adiponectin receptors, AdipoR1 and AdipoR2

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Journal of Structural and Functional Genomics 2015年第1期16卷 11-23页

作者： Tanabe, Hiroaki Motoyama, Kanna Ikeda, Mariko Wakiyama, Motoaki Terada, Takaho Ohsawa, Noboru Hosaka, Toshiaki Hato, Masakatsu Fujii, Yoshifumi Nakamura, Yoshihiro Ogasawara, Satoshi Hino, Tomoya Murata, Takeshi Iwata, So Okada-Iwabu, Miki Iwabu, Masato Hirata, Kunio Kawano, Yoshiaki Yamamoto, Masaki Kimura-Someya, Tomomi Shirouzu, Mikako Yamauchi, Toshimasa Kadowaki, Takashi Yokoyama, Shigeyuki RIKEN Systems and Structural Biology Center 1-7-22 Suehiro-cho Tsurumi-ku Yokohama 230-0045 Japan Department of Biophysics and Biochemistry and Laboratory of Structural Biology Graduate School of Science The University of Tokyo Hongo Bunkyo-ku Tokyo 113-0033 Japan Division of Structural and Synthetic Biology RIKEN Center for Life Science Technologies 1-7-22 Suehiro-cho Tsurumi-ku Yokohama 230-0045 Japan RIKEN Structural Biology Laboratory 1-7-22 Suehiro-cho Tsurumi-ku Yokohama 230-0045 Japan Department of Cell Biology Graduate School of Medicine Kyoto University Yoshida-Konoe-cho Sakyo-ku Kyoto 606-8501 Japan JST Research Acceleration Program Membrane Protein Crystallography Project Yoshida-Konoe-cho Sakyo-ku Kyoto 606-8501 Japan Department of Chemistry Graduate School of Science Chiba University Yayoi-cho Inage Chiba 263-8522 Japan Division of Molecular Biosciences Membrane Protein Crystallography Group Imperial College London SW7 2AZ United Kingdom Diamond Light Source Harwell Science and Innovation Campus Chilton Didcot Oxfordshire OX11 0DE United Kingdom RIKEN SPring-8 Center Harima Institute Kouto Sayo 679-5148 Hyogo Japan Department of Diabetes and Metabolic Diseases Graduate School of Medicine The University of Tokyo Hongo Bunkyo-ku Tokyo 113-0033 Japan Department of Integrated Molecular Science on Metabolic Diseases 22nd Century Medical and Research Center The University of Tokyo Hongo Bunkyo-ku Tokyo 113-0033 Japan CREST Japan Science and Technology Agency Kawaguchi 332-0012 Saitama Japan

The adiponectin receptors (AdipoR1 and AdipoR2) are membrane proteins with seven transmembrane helices. These receptors regulate glucose and fatty acid metabolism, thereby ameliorating type 2 diabetes. The full-length human AdipoR1 and a series of N-terminally truncated mutants of human AdipoR1 and AdipoR2 were expressed in insect cells. In small-scale size exclusion chromatography, the truncated mutants AdipoR1Δ88 (residues 89–375) and AdipoR2Δ99 (residues 100–386) eluted mostly in the intact monodisperse state, while the others eluted primarily as aggregates. However, gel filtration chromatography of the large-scale preparation of the tag-affinity-purified AdipoR1Δ88 revealed the presence of an excessive amount of the aggregated state over the intact state. Since aggregation due to contaminating nucleic acids may have occurred during the sample concentration step, anion-exchange column chromatography was performed immediately after affinity chromatography, to separate the intact AdipoR1Δ88 from the aggregating species. The separated intact AdipoR1Δ88 did not undergo further aggregation, and was successfully purified to homogeneity by gel filtration chromatography. The purified AdipoR1Δ88 and AdipoR2Δ99 proteins were characterized by thermostability assays with 7-diethylamino-3-(4-maleimidophenyl)-4-methyl coumarin, thin layer chromatography of bound lipids, and surface plasmon resonance analysis of ligand binding, demonstrating their structural integrities. The AdipoR1Δ88 and AdipoR2Δ99 proteins were crystallized with the anti-AdipoR1 monoclonal antibody Fv fragment, by the lipidic mesophase method. X-ray diffraction data sets were obtained at resolutions of 2.8 and 2.4 Å, respectively. © 2015, The Author(s).

关键词： Adiponectin receptors AdipoR1 and AdipoR2 Antibody Crystallization Lipidic mesophase Membrane protein Purification

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Global, regional, and national sex-specific burden and control of the HIV epidemic, 1990–2019, for 204 countries and territories: the Global Burden of Diseases Study 2019

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The Lancet HIV 2021年第10期8卷 e633-e651页

作者： Jahagirdar, Deepa Walters, Magdalene K. Novotney, Amanda Brewer, Edmond D. Frank, Tahvi D. Carter, Austin Biehl, Molly H. Abbastabar, Hedayat Abhilash, E.S. Abu-Gharbieh, Eman Abu-Raddad, Laith Jamal Adekanmbi, Victor Adeyinka, Daniel Adedayo Adnani, Qorinah Estiningtyas Sakilah Afzal, Saira Aghababaei, Soodabeh Ahinkorah, Bright Opoku Ahmad, Sajjad Ahmadi, Keivan Ahmadi, Sepideh Ahmadpour, Ehsan Ahmed, Muktar Beshir Rashid, Tarik Ahmed Salih, Yusra Ahmed Aklilu, Addis Akram, Tayyaba Akunna, Chisom Joyqueenet Al Hamad, Hanadi Alahdab, Fares Alanezi, Fahad Mashhour Aleksandrova, Ekaterina A. Alene, Kefyalew Addis Ali, Liaqat Alipour, Vahid Almustanyir, Sami Alvis-Guzman, Nelson Ameyaw, Edward Kwabena Amu, Hubert Andrei, Catalina Liliana Andrei, Tudorel Anvari, Davood Arabloo, Jalal Aremu, Olatunde Arulappan, Judie Atnafu, Desta Debalkie Quintanilla, Beatriz Paulina Ayala Ayza, Muluken Altaye Azari, Samad Darshan, B.B. Banach, Maciej Bärnighausen, Till Winfried Barra, Fabio Barrow, Amadou Basu, Sanjay Bazargan-Hejazi, Shahrzad Belay, Habtamu Gebrehana Berheto, Tezera Moshago Bezabhe, Woldesellassie Mequanint Bezabih, Yihienew Mequanint Bhagavathula, Akshaya Srikanth Bhardwaj, Nikha Bhardwaj, Pankaj Bhattacharyya, Krittika Bibi, Sadia Bijani, Ali Bisignano, Catherine Bolarinwa, Obasanjo Afolabi Boloor, Archith Boltaev, Azizbek A. Briko, Nikolay Ivanovich Buonsenso, Danilo Burkart, Katrin Butt, Zahid A. Cao, Chao Charan, Jaykaran Chatterjee, Souranshu Chattu, Soosanna Kumary Chattu, Vijay Kumar Choudhari, Sonali Gajanan Chu, Dinh-Toi Couto, Rosa A.S. Cowden, Richard G. Dachew, Berihun Assefa Dadras, Omid Dagnew, Amare Belachew Dahlawi, Saad M.A. Dai, Xiaochen Dandona, Lalit Dandona, Rakhi das Neves, José Degenhardt, Louisa Demeke, Feleke Mekonnen Desta, Abebaw Alemayehu Deuba, Keshab Dhamnetiya, Deepak Dhungana, Govinda Prasad Dianatinasab, Mostafa Diaz, Daniel Djalalinia, Shirin Doan, Linh Phuong Dorostkar, Fariba Edinur, Hisham Atan Effiong, Andem Eftekharzadeh, Sahar El Sayed Zaki, Maysaa Elayedath, Rajesh Elhadi, 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 Division of Allergy and Infectious Diseases University of Washington Seattle WA United States Department of Global Health University of Washington Seattle WA United States School of Social Work University of Washington Seattle WA United States Department of Medicine University of Washington Seattle WA United States Vagelos College of Physicians and Surgeones Columbia University Medical Center New York NY United States Division of Data Analytics and Delivery for Impact WHO Geneva Switzerland Advanced Diagnostic and Interventional Radiology Research Centre Tehran University of Medical Sciences Tehran Iran Multiple Sclerosis Research Centre Tehran University of Medical Sciences Tehran Iran School of Public Health Tehran University of Medical Sciences Tehran Iran Department of Epidemiology and Biostatistics Tehran University of Medical Sciences Tehran Iran Paediatric Chronic Kidney Disease Research Centre Tehran University of Medical Sciences Tehran Iran Department of Psychiatry Tehran University of Medical Sciences Tehran Iran Metabolomics and Genomics Research Centre Tehran University of Medical Sciences Tehran Iran Sina Trauma and Surgery Research Centre Tehran University of Medical Sciences Tehran Iran Research Centre for Immunodeficiencies Tehran University of Medical Sciences Tehran Iran Non-Communicable Diseases Research Centre Tehran University of Medical Sciences Tehran Iran Department of Botany Sree Narayana Guru College Chelannur Kozhikode India Clinical Sciences Department University of Sharjah Sharjah United Arab Emirates Mass Communication Department University of Sharjah Sharjah United Arab Emirates Department of Health-Care Policy and Research Weill Cornell Medical College in Qatar Doha Qatar Department of Population Medicine Ca

Background: The sustainable development goals (SDGs) aim to end HIV/AIDS as a public health threat by 2030. Understanding the current state of the HIV epidemic and its change over time is essential to this effort. This study assesses the current sex-specific HIV burden in 204 countries and territories and measures progress in the control of the epidemic. Methods: To estimate age-specific and sex-specific trends in 48 of 204 countries, we extended the Estimation and Projection Package Age-Sex Model to also implement the spectrum paediatric model. We used this model in cases where age and sex specific HIV-seroprevalence surveys and antenatal care-clinic sentinel surveillance data were available. For the remaining 156 of 204 locations, we developed a cohort-incidence bias adjustment to derive incidence as a function of cause-of-death data from vital registration systems. The incidence was input to a custom Spectrum model. To assess progress, we measured the percentage change in incident cases and deaths between 2010 and 2019 (threshold >75% decline), the ratio of incident cases to number of people living with HIV (incidence-to-prevalence ratio threshold <0·03), and the ratio of incident cases to deaths (incidence-to-mortality ratio threshold <1·0). Findings: In 2019, there were 36·8 million (95% uncertainty interval [UI] 35·1–38·9) people living with HIV worldwide. There were 0·84 males (95% UI 0·78–0·91) per female living with HIV in 2019, 0·99 male infections (0·91–1·10) for every female infection, and 1·02 male deaths (0·95–1·10) per female death. Global progress in incident cases and deaths between 2010 and 2019 was driven by sub-Saharan Africa (with a 28·52% decrease in incident cases, 95% UI 19·58–35·43, and a 39·66% decrease in deaths, 36·49–42·36). Elsewhere, the incidence remained stable or increased, whereas deaths generally decreased. In 2019, the global incidence-to-prevalence ratio was 0·05 (95% UI 0·05–0·06) and the global incidence-to-mortality ratio was

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Association between GWAS-identified lung adenocarcinoma susceptibility loci and EGFR mutations in never-smoking Asian women, and comparison with findings from Western populations

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Human molecular genetics 2017年第2期26卷 454-465页

作者： Wei Jie Seow Keitaro Matsuo Chao Agnes Hsiung Kouya Shiraishi Minsun Song Hee Nam Kim Maria Pik Wong Yun-Chul Hong H Dean Hosgood Zhaoming Wang I-Shou Chang Jiu-Cun Wang Nilanjan Chatterjee Margaret Tucker Hu Wei Tetsuya Mitsudomi Wei Zheng Jin Hee Kim Baosen Zhou Neil E Caporaso Demetrius Albanes Min-Ho Shin Lap Ping Chung She-Juan An Ping Wang Hong Zheng Yasushi Yatabe Xu-Chao Zhang Young Tae Kim Xiao-Ou Shu Young-Chul Kim Bryan A Bassig Jiang Chang James Chung Man Ho Bu-Tian Ji Michiaki Kubo Yataro Daigo Hidemi Ito Yukihide Momozawa Kyota Ashikawa Yoichiro Kamatani Takayuki Honda Hiromi Sakamoto Hideo Kunitoh Koji Tsuta Shun-Ichi Watanabe Hiroshi Nokihara Yohei Miyagi Haruhiko Nakayama Shingo Matsumoto Masahiro Tsuboi Koichi Goto Zhihua Yin Jianxin Shi Atsushi Takahashi Akiteru Goto Yoshihiro Minamiya Kimihiro Shimizu Kazumi Tanaka Tangchun Wu Fusheng Wei Jason Y Y Wong Fumihiko Matsuda Jian Su Yeul Hong Kim In-Jae Oh Fengju Song Victor Ho Fun Lee Wu-Chou Su Yuh-Min Chen Gee-Chen Chang Kuan-Yu Chen Ming-Shyan Huang Pan-Chyr Yang Hsien-Chih Lin Yong-Bing Xiang Adeline Seow Jae Yong Park Sun-Seog Kweon Chien-Jen Chen Haixin Li Yu-Tang Gao Chen Wu Biyun Qian Daru Lu Jianjun Liu Hyo-Sung Jeon Chin-Fu Hsiao Jae Sook Sung Ying-Huang Tsai Yoo Jin Jung Huan Guo Zhibin Hu Wen-Chang Wang Charles C Chung Charles Lawrence Laurie Burdett Meredith Yeager Kevin B Jacobs Amy Hutchinson Sonja I Berndt Xingzhou He Wei Wu Junwen Wang Yuqing Li Jin Eun Choi Kyong Hwa Park Sook Whan Sung Li Liu Chang Hyun Kang Lingmin Hu Chung-Hsing Chen Tsung-Ying Yang Jun Xu Peng Guan Wen Tan Chih-Liang Wang Alan Dart Loon Sihoe Ying Chen Yi Young Choi Jen-Yu Hung Jun Suk Kim Ho-Il Yoon Qiuyin Cai Chien-Chung Lin In Kyu Park Ping Xu Jing Dong Christopher Kim Qincheng He Reury-Perng Perng Chih-Yi Chen Roel Vermeulen Junjie Wu Wei-Yen Lim Kun-Chieh Chen John K C Chan Minjie Chu Yao-Jen Li Jihua Li Hongyan Chen Chong-Jen Yu Li Jin Yen-Li Lo Ying-Hsiang Chen Joseph F Fraumeni Jie Liu Taiki Yamaji Yang Yang Belynda Hicks Kathleen Wyatt Shengchao A Li Division of Cancer Epidemiology and Genetics National Cancer Institute Bethesda MD USA. Saw Swee Hock School of Public Health National University of Singapore and National University Health System Singapore. Division of Molecular Medicine Aichi Cancer Center Research Institute Nagoya Japan. Institute of Population Health Sciences National Health Research Institutes Zhunan Taiwan. Division of Genome Biology National Cancer Center Research Institute Tokyo Japan. Department of Statistics Sookmyung Women's University Seoul Republic of Korea. Department of Preventive Medicine Chonnam National University Medical School Gwangju Republic of Korea. Department of Pathology The University of Hong Kong Queen Mary Hospital Hong Kong. Department of Preventive Medicine Seoul National University College of Medicine Seoul Republic of Korea. Department of Epidemiology and Population Health Albert Einstein College of Medicine Bronx NY USA. Department of Computational Biology St. Jude Children's Research Hospital Memphis TN 38105 USA. National Institute of Cancer Research National Health Research Institutes Zhunan Taiwan. Ministry of Education Key Laboratory of Contemporary Anthropology School of Life Sciences Fudan University Shanghai People's Republic of China. State Key Laboratory of Genetic Engineering School of Life Sciences Fudan University Shanghai People's Republic of China. Division of Thoracic Surgery Kinki University School of Medicine Sayama Japan. Division of Epidemiology Department of Medicine Vanderbilt University Medical Center and Vanderbilt-Ingram Cancer Center Nashville TN USA. Department of Integrative Bioscience & Biotechnology Sejong University Seoul Republic of Korea. Department of Epidemiology School of Public Health China Medical University Shenyang People's Republic of China. Guangdong Lung Cancer Institute Medical Research Center and Cancer Center of Guangdong General Hospital Guangdong Academy of Medical Sciences Guangzhou People's Republic

To evaluate associations by EGFR mutation status for lung adenocarcinoma risk among never-smoking Asian women, we conducted a meta-analysis of 11 loci previously identified in genome-wide association studies (GWAS). Genotyping in an additional 10,780 never-smoking cases and 10,938 never-smoking controls from Asia confirmed associations with eight known single nucleotide polymorphisms (SNPs). Two new signals were observed at genome-wide significance (P < 5 × 10-8), namely, rs7216064 (17q24.3, BPTF), for overall lung adenocarcinoma risk, and rs3817963 (6p21.3, BTNL2) which is specific to cases with EGFR mutations. In further sub-analyses by EGFR status, rs9387478 (ROS1/DCBLD1) and rs2179920 (HLA-DPB1) showed stronger estimated associations in EGFR-positive compared to EGFR-negative cases. Comparison of the overall associations with published results in Western populations revealed that the majority of these findings were distinct, underscoring the importance of distinct contributing factors for smoking and non-smoking lung cancer. Our results extend the catalogue of regions associated with lung adenocarcinoma in non-smoking Asian women and highlight the importance of how the germline could inform risk for specific tumour mutation patterns, which could have important translational implications.

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