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

NATURE 2023年第7948期614卷 E41-E41页

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

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MIFA: Metadata, Incentives, Formats, and Accessibility guidelines to improve the reuse of AI datasets for bioimage analysis

arXiv

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arXiv 2023年

作者： Zulueta-Coarasa, Teresa Jug, Florian Mathur, Aastha Moore, Josh Muñoz-Barrutia, Arrate Anita, Liviu Babalola, Kola Bankhead, Pete Gilloteaux, Perrine Gogoberidze, Nodar Jones, Martin Kleywegt, Gerard J. Korir, Paul Kreshuk, Anna Yoldaş, Aybüke Küpcü Marconato, Luca Narayan, Kedar Norlin, Nils Oezdemir, Bugra Riesterer, Jessica Rzepka, Norman Sarkans, Ugis Serrano, Beatriz Tischer, Christian Uhlmann, Virginie Ulman, Vladimír Hartley, Matthew European Molecular Biology Laboratory European Bioinformatics Institute Hinxton United Kingdom Human Technopole V.le Rita Levi-Montalcini 1 Milan20017 Italy Heidelberg Meyerhofstraße 1 Heidelberg69117 Germany German BioImaging Gesellschaft für Mikroskopie und Bildanalyse e.V. Konstanz Germany Universidad Carlos III de Madrid Leganés Madrid Spain Instituto de Investigación Sanitaria Gregorio Marañón Madrid Spain Edinburgh Pathology Centre for Genomic and Experimental Medicine CRUK Scotland Centre University of Edinburgh Edinburgh United Kingdom Nantes Université CHU Nantes CNRS Inserm BioCore US16 SFR Bonamy NantesF 44000 France Imaging Platform Broad Institute Cambridge United States Francis Crick Institute London United Kingdom Cell Biology and Biophysics Unit European Molecular Biology Laboratory Heidelberg69117 Germany Genome Biology Unit Heidelberg Germany Heidelberg Germany Collaboration for joint PhD degree between EMBL and Heidelberg University Faculty of Biosciences Germany Center for Molecular Microscopy Center for Cancer Research National Cancer Institute NIH BethesdaMD United States Cancer Research Technology Program Frederick National Laboratory for Cancer Research FrederickMD United States Lund University 221 00 Sweden Knight Cancer Institute Oregon Health & Science University PortlandOR United States Scalable Minds GmbH Potsdam Germany European Molecular Biology Laboratory Heidelberg Germany IT4Innovations VSB – Technical University of Ostrava Ostrava-Poruba Czech Republic

Artificial Intelligence methods are powerful tools for biological image analysis and processing. High-quality annotated images are key to training and developing new methods, but access to such data is often hindered by the lack of standards for sharing datasets. We brought together community experts in a workshop to develop guidelines to improve the reuse of bioimages and annotations for AI applications. These include standards on data formats, metadata, data presentation and sharing, and incentives to generate new datasets. We are positive that the MIFA (Metadata, Incentives, Formats, and Accessibility) recommendations will accelerate the development of AI tools for bioimage analysis by facilitating access to high quality training data. © 2023, CC BY.

关键词： Metadata

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Correction: New insights into epigenetic regulation of resistance to PD-1/PD-L1 blockade cancer immunotherapy: mechanisms and therapeutic opportunities

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Experimental hematology & oncology 2022年第1期11卷 106页

作者： Mengyuan Dai Miao Liu Hua Yang Can Küçük Hua You Laboratory for Excellence in Systems Biomedicine of Pediatric Oncology Department of Hematology and Oncology Pediatric Research Institute Chongqing Key Laboratory of Pediatrics Ministry of Education Key Laboratory of Child Development and Disorders International Science and Technology Cooperation Base of Child Development and Critical Disorders National Clinical Research Center for Child Health and Disorders Children's Hospital of Chongqing Medical University 136 Zhongshan Second Road Yuzhong District Chongqing 401122 China. Department of Pathology Brigham and Women's Hospital Harvard Medical School Boston USA. Department of Basic Medicine and Biomedical Engineering School of Medical Foshan University Foshan China. İzmir International Biomedicine and Genome Institute Dokuz Eylül University İzmir Türkiye. Basic and Translational Research Program İzmir Biomedicine and Genome Center İzmir Türkiye. Department of Medical Biology Faculty of Medicine Dokuz Eylül University İzmir Türkiye. Laboratory for Excellence in Systems Biomedicine of Pediatric Oncology Department of Hematology and Oncology Pediatric Research Institute Chongqing Key Laboratory of Pediatrics Ministry of Education Key Laboratory of Child Development and Disorders International Science and Technology Cooperation Base of Child Development and Critical Disorders National Clinical Research Center for Child Health and Disorders Children's Hospital of Chongqing Medical University 136 Zhongshan Second Road Yuzhong District Chongqing 401122 China. youhua307@***.

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Mapping the Human Body at Cellular Resolution -- The NIH Common Fund Human BioMolecular Atlas program

arXiv

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arXiv 2019年

作者： Snyder, Michael P. Lin, Shin Posgai, Amanda Atkinson, Mark Regev, Aviv Rood, Jennifer Rozenblatt-Rosen, Orit Gaffney, Leslie Hupalowska, Anna Satija, Rahul Gehlenborg, Nils Shendure, Jay Laskin, Julia Harbury, Pehr Nystrom, Nicholas A. Bar-Joseph, Ziv Zhang, Kun Börner, Katy Lin, Yiing Conroy, Richard Procaccini, Dena Roy, Ananda L. Pillai, Ajay Brown, Marishka Galis, Zorina S. Cai, Long Shendure, Jay Trapnell, Cole Lin, Shin Jackson, Dana Snyder, Michael P. Nolan, Garry Greenleaf, William James Lin, Yiing Plevritis, Sylvia Ahadi, Sara Lee, Hayan Nevins, Stephanie Esplin, Ed Horning, Aaron Bahmani, Amir Zhang, Kun Sun, Xin Jain, Sanjay Hagood, James Kharchenko, Peter Atkinson, Mark Bodenmiller, Bernd Brusko, Todd Clare-Salzler, Michael Nick, Harry Otto, Kevin Posgai, Amanda Wasserfall, Clive Maffioletti, Sergio Caprioli, Richard M. Spraggins, Jeffrey M. Gutierrez, Danielle Patterson, Nathan Heath Neumann, Elizabeth K. Harris, Raymond deCaestecker, Mark de Plas, Raf Van Lau, Ken Cai, Long Yuan, Guo-Cheng Zhu, Qian Dries, Ruben Yin, Peng Saka, Sinem K. Kishi, Jocelyn Y. Wang, Yu Goldaracena, Isabel Laskin, Julia Ye, DongHye Burnum-Johnson, Kristin E. Piehowski, Paul D. Ansong, Charles Zhu, Ying Harbury, Pehr Desai, Tushar Mulye, Jay Chou, Peter Nagendran, Monica Bar-Joseph, Ziv Teichmann, Sarah A. Paten, Benedict Murphy, Robert F. Ma, Jian Kiselev, Vladimir Yu Kingsford, Carl Ricarte, Allyson Ruffalo, Matthew Gehlenborg, Nils Kharchenko, Peter Vella, Margaret McCallum, Chuck Börner, Katy Cross, Leonard E. Friedman, Samuel H. Heiland, Randy Herr, Bruce Macklin, Paul Quardokus, Ellen M. Record, Lisel Sluka, James P. Weber, Griffin M. Nystrom, Nicholas A. Silverstein, Jonathan C. Blood, Philip D. Ropelewski, Alexander J. Shirey, William E. Mabee, Paula Lenhardt, W. Christopher Robasky, Kimberly Michailidis, Stavros Satija, Rahul Marioni, John Regev, Aviv Butler, Andrew Stuart, Tim Fisher, Eyal Ghazanfar, Shila Rood, Jennifer Gaffney, Leslie Ersalan, Gokcen Biancalani, Tommaso Conroy, Richard Procaccini, Dena Roy, Anan School of Medicine Stanford University 300 Pasteur Drive United States Department of Genetics Stanford School of Medicine StanfordCA94305 United States Department of Medicine University of Washington SeattleWA98195 United States Department of Pathology University of Florida Diabetes Institute GainesvilleFL32610 United States Klarman Cell Observatory Broad Institute of MIT and Harvard CambridgeMA02142 United States Howard Hughes Medical Institute Koch Institute of Integrative Cancer Research Department of Biology Massachusetts Institute of Technology CambridgeMA02140 United States New York Genome Center New York CityNY10013 United States New York University New YorkNY10012 United States Department of Biomedical Informatics Harvard Medical School BostonMA02115 United States Department of Genome Sciences University of Washington SeattleWA98105 United States Department of Chemistry Purdue University West LafayetteIN47907 United States Department of Biochemistry Stanford University School of Medicine StanfordCA94305 United States Pittsburgh Supercomputing Center Carnegie Mellon University PittsburghPA15213 United States Department of Computational Biology School of Computer Science Carnegie Mellon University PittsburghPA15213 United States Department of Bioengineering University of California San Diego La JollaCA92093 United States Department of Intelligent Systems Engineering School of Informatics Computing and Engineering Indiana University BloomingtonIN47408 United States Department of Surgery Washington University School of Medicine St LouisMO63110 United States Division of Program Coordination Planning and Strategic Initiatives National Institutes of Health BethesdaMD20892 United States National Human Genome Research Institute National Institutes of Health BethesdaMD20892 United States National Heart Lung and Blood Institute National Institutes of Health BethesdaMD20892 United States Caltech-UW TMC Departmen

Transformative technologies are enabling the construction of three dimensional (3D) maps of tissues with unprecedented spatial and molecular resolution. Over the next seven years, the NIH Common Fund Human Biomolecular Atlas program (HuBMAP) intends to develop a widely accessible framework for comprehensively mapping the human body at single-cell resolution by supporting technology development, data acquisition, and detailed spatial mapping. HuBMAP will integrate its efforts with other funding agencies, programs, consortia, and the biomedical research community at large towards the shared vision of a comprehensive, accessible 3D molecular and cellular atlas of the human body, in health and various disease settings. Copyright © 2019, The Authors. All rights reserved.

关键词： Mapping

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genome-wide analyses identify 30 loci associated with obsessive–compulsive disorder

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Nature Genetics 2025年 1-13页

作者： Strom, Nora I. Gerring, Zachary F. Galimberti, Marco Yu, Dongmei Halvorsen, Matthew W. Abdellaoui, Abdel Rodriguez-Fontenla, Cristina Sealock, Julia M. Bigdeli, Tim Coleman, Jonathan R. Mahjani, Behrang Thorp, Jackson G. Bey, Katharina Burton, Christie L. Luykx, Jurjen J. Zai, Gwyneth Alemany, Silvia Andre, Christine Askland, Kathleen D. Bäckman, Julia Banaj, Nerisa Barlassina, Cristina Nissen, Judith Becker Bienvenu, O. Joseph Black, Donald Bloch, Michael H. Børte, Sigrid Bosch, Rosa Breen, Michael Brennan, Brian P. Brentani, Helena Buxbaum, Joseph D. Bybjerg-Grauholm, Jonas Byrne, Enda M. Cabana-Dominguez, Judit Camarena, Beatriz Camarena, Adrian Cappi, Carolina Carracedo, Angel Casas, Miguel Cavallini, Maria Cristina Ciullo, Valentina Cook, Edwin H. Crosby, Jesse Cullen, Bernadette A. De Schipper, Elles J. Delorme, Richard Djurovic, Srdjan Elias, Jason A. Estivill, Xavier Falkenstein, Martha J. Fundin, Bengt T. Garner, Lauryn Gironda, Christina Goes, Fernando S. Grados, Marco A. Grove, Jakob Guo, Wei Haavik, Jan Hagen, Kristen Harrington, Kelly Havdahl, Alexandra Höffler, Kira D. Hounie, Ana G. Hucks, Donald Hultman, Christina Janecka, Magdalena Jenike, Eric Karlsson, Elinor K. Kelley, Kara Klawohn, Julia Krasnow, Janice E. Krebs, Kristi Lange, Christoph Lanzagorta, Nuria Levey, Daniel Lindblad-Toh, Kerstin Macciardi, Fabio Maher, Brion Mathes, Brittany McArthur, Evonne McGregor, Nathaniel McLaughlin, Nicole C. Meier, Sandra Miguel, Euripedes C. Mulhern, Maureen Nestadt, Paul S. Nurmi, Erika L. O’Connell, Kevin S. Osiecki, Lisa Ousdal, Olga Therese Palviainen, Teemu Pedersen, Nancy L. Piras, Federica Potluri, Sriramya Rabionet, Raquel Ramirez, Alfredo Rauch, Scott Reichenberg, Abraham Riddle, Mark A. Ripke, Stephan Rosário, Maria C. Sampaio, Aline S. Schiele, Miriam A. Skogholt, Anne Heidi Sloofman, Laura G. Smit, Jan Artigas, María Soler Thomas, Laurent F. Tifft, Eric Vallada, Homero van Kirk, Nathanial Veenstra-VanderWeele, Jeremy Vulink, Nienke N. Walker, Christopher P. Wang, Ying Wendland, Jens R. Winsvold Department of Psychology Humboldt-Universität zu Berlin Berlin Germany Department of Psychiatric Phenomics and Genomics (IPPG) Ludwig-Maximilians University Munich Munich Germany Centre for Psychiatry Research Department of Clinical Neuroscience Karolinska Institutet and Stockholm Health Services Region Stockholm Stockholm Sweden Department of Biomedicine Aarhus University Aarhus Denmark University Hospital of Psychiatry and Psychotherapy University of Bern Bern Switzerland Department of Mental Health and Neuroscience Translational Neurogenomics QIMR Berghofer Medical Research Institute Brisbane QLD Australia Department of Population Health and Immunity Healthy Development and Ageing Walter and Eliza Hall Institute of Medical Research Melbourne VIC Australia Department of Psychiatry Human Genetics Yale University New Haven CT United States VA Connecticut Healthcare System West Haven CT United States Department of Center for Genomic Medicine Psychiatric and Neurodevelopmental Genetics Unit Massachusetts General Hospital Boston MA United States Stanley Center for Psychiatric Research Broad Institute of MIT and Harvard Cambridge MA United States Department of Genetics University of North Carolina at Chapel Hill Chapel Hill NC United States Department of Psychiatry Amsterdam University Medical Centers University of Amsterdam Amsterdam Netherlands Center for Research in Molecular Medicine and Chronic Diseases (CiMUS) Genomics and Bioinformatics University of Santiago de Compostela Santiago de Compostela Spain Grupo de Medicina Xenómica Genetics Instituto de Investigación Sanitaria de Santiago de Compostela (FIDIS) Santiago de Compostela Spain Vanderbilt Genetics Institute Vanderbilt University Nashville TN United States Department of Psychiatry and Behavioral Sciences SUNY Downstate Health Sciences University Brooklyn NY United States VA NY Harbor Healthcare System Brooklyn NY United States Social Genetic and Developmental Psychiatry Centre Insti

Obsessive–compulsive disorder (OCD) affects ~1% of children and adults and is partly caused by genetic factors. We conducted a genome-wide association study (GWAS) meta-analysis combining 53,660 OCD cases and 2,044,417 controls and identified 30 independent genome-wide significant loci. Gene-based approaches identified 249 potential effector genes for OCD, with 25 of these classified as the most likely causal candidates, including WDR6, DALRD3 and CTNND1 and multiple genes in the major histocompatibility complex (MHC) region. We estimated that ~11,500 genetic variants explained 90% of OCD genetic heritability. OCD genetic risk was associated with excitatory neurons in the hippocampus and the cortex, along with D₁ and D₂ type dopamine receptor-containing medium spiny neurons. OCD genetic risk was shared with 65 of 112 additional phenotypes, including all the psychiatric disorders we examined. In particular, OCD shared genetic risk with anxiety, depression, anorexia nervosa and Tourette syndrome and was negatively associated with inflammatory bowel diseases, educational attainment and body mass index. © The Author(s) 2025.

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

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NATURE 2023年第7948期614卷 E42-E42页

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

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Penetrance of neurodevelopmental copy number variants is associated with variations in cortical morphology

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Biological psychiatry. Cognitive neuroscience and neuroimaging 2025年

作者： Ana I Silva Ida E Sønderby George Kirov Abdel Abdellaoui Ingrid Agartz David Ames Nicola J Armstrong Eric Artiges Tobias Banaschewski Anne S Bassett Carrie E Bearden John Blangero Rune Boen Dorret I Boomsma Robin Bülow Nancy J Butcher Vince Calhoun Linda E Campbell Eva W C Chow Simone Ciufolini Michael C Craig Benedicto Crespo-Farroco Adam C Cunningham Shareefa Dalvie Eileen Daly Paola Dazzan Eco J C de Geus Greig I de Zubicaray Joanne L Doherty Gary Donohoe Mark Drakesmith Thomas Espeseth Vincent Frouin Hugh Garavan David C Glahn Naomi J Goodrich-Hunsaker Penny A Gowland Hans J Grabe Antoine Grigis Maria Gudbrandsen Boris A Gutman Jan Haavik Asta K Håberg Jeremy Hall Andreas Heinz Sarah Hohmann Jouke-Jan Hottenga Sébastien Jacquemont Neda Jahanshad Rachel K Jonas Derek K Jones Erik G Jönsson Sanne Koops Kuldeep Kumar Stephanie Le Hellard Herve Lemaitre Jingyu Liu Astri J Lundervold Jean-Luc Martinot Karen A Mather Donna M McDonald-McGinn Katie L McMahon Allan F McRae Sarah E Medland Clara A Moreau Kieran C Murphy Declan Murphy Robin M Murray Frauke Nees Michael J Owen Marie-Laure Paillère Martinot Diimitri Papadopoulos Orfanos Tomas Paus Luise Poustka Tiago Reis Marques David R Roalf Perminder S Sachdev Freda Scheffler J Eric Schmitt Gunter Schumann Vidar M Steen Dan J Stein Lachlan T Strike Alexander Teumer Anbupalam Thalamuthu Sophia I Thomopoulos Diana Tordesillas-Gutiérrez Julian N Trollor Anne Uhlmann Ariana Vajdi Dennis van 't Ent Therese van Amelsvoort Marianne B M van den Bree Dennis van der Meer Javier Vázquez-Bourgon Julio E Villalón-Reina Uwe Völker Henry Völzke Jacob A S Vorstman Lars T Westlye Nigel Williams Katharina Wittfeld Margaret J Wright Paul M Thompson Ole A Andreassen David E J Linden School for Mental Health and Neuroscience Department of Psychiatry and Neuropsychology Faculty of Health Medicine and Life Sciences Maastricht University Maastricht The Netherlands Neuroscience and Mental Health Innovation Institute Cardiff University Cardiff United Kingdom Center for Magnetic Resonance Research Department of Radiology University of Minnesota Minneapolis MN USA. Electronic address: silvaai@um.edu. Centre for Precision Psychiatry Institute of Clinical Medicine University of Oslo Oslo Norway Department of Medical Genetics Oslo University Hospital Oslo Norway KG Jebsen Centre for Neurodevelopmental Disorders University of Oslo Oslo Norway. Division of Psychological Medicine and Clinical Neurosciences Cardiff University Cardiff United Kingdom Centre for Neuropsychiatric Genetics and Genomics School of Medicine Cardiff University Cardiff United Kingdom. Department of Psychiatry Amsterdam UMC University of Amsterdam Amsterdam the Netherlands. Norwegian Centre for Mental Disorders Research (NORMENT) Institute of Clinical Medicine University of Oslo Oslo Norway Centre for Psychiatry Research Department of Clinical Neuroscience Karolinska Institutet & Stockholm Health Care Services Stockholm Region Stockholm Sweden Department of Psychiatric Research Diakonhjemmet Hospital Oslo Norway. University of Melbourne Academic Unit for Psychiatry of Old Age Kew Victoria Australia. Mathematics and Statistics Curtin University Perth WA Australia. Institut National de la Santé et de la Recherche Médicale INSERM U1299 "Trajectoires développementales et psychiatrie" Université Paris-Saclay Ecole Normale supérieure Paris-Saclay CNRS Centre Borelli Gif-sur-Yvette France Psychiatry Department EPS Barthélémy Durand Etampes Île-de-France France. Department of Child and Adolescent Psychiatry and Psychotherapy Central Institute of Mental Health Medical Faculty Mannheim University of Heidelberg Mannheim Germany. Clinical Genetics Research Program Centre for

BACKGROUND:Copy number variants (CNVs) increase risk for neurodevelopmental conditions. The neurobiological mechanisms linking these high-risk genetic variants to clinical phenotypes are largely unknown. An important question is whether brain abnormalities in individuals carrying CNVs are associated with their degree of penetrance. METHODS:We investigated if increased CNV-penetrance for schizophrenia and other developmental disorders was associated with variations in cortical and subcortical morphology. We pooled T1-weighted brain magnetic resonance imaging and genetic data from 22 cohorts from the ENIGMA-CNV consortium. In the main analyses, we included 9,268 individuals (aged 7 to 90 years, 54% females), from which we identified 398 carriers of 36 neurodevelopmental CNVs at 20 distinct loci. A secondary analysis was performed including additional neuroimaging data from the ENIGMA-22q consortium, including 274 carriers of the 22q11.2 deletion and 291 non-carriers. CNV-penetrance was estimated through penetrance scores that were previously generated from large cohorts of patients and controls. These scores represent the probability risk to develop either schizophrenia or other developmental disorders (including developmental delay, autism spectrum disorder and congenital malformations). RESULTS:For both schizophrenia and developmental disorders, increased penetrance scores were associated with lower surface area in the cerebral cortex and lower intracranial volume. For both conditions, associations between CNV-penetrance scores and cortical surface area were strongest in regions of the occipital lobes, specifically in the cuneus and lingual gyrus. CONCLUSIONS:Our findings link global and regional cortical morphometric features with CNV-penetrance, providing new insights into neurobiological mechanisms of genetic risk for schizophrenia and other developmental disorders.

关键词： autism neuroimaging psychiatric disorders schizophrenia structural imaging

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Correction: Gender differences among patients with drug resistant tuberculosis and HIV co-infection in Uganda: a countrywide retrospective cohort study

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BMC infectious diseases 2023年第1期23卷 44页

作者： Joseph Baruch Baluku David Mukasa Felix Bongomin Anna M Stadelman Edwin Nuwagira Sabine Haller Kauthrah Ntabadde Stavia Turyahabwe Division of Pulmonology Kiruddu National Referral Hospital Kampala Uganda. bbjoe18@***. Makerere University Lung Institute PO Box 26343 Kampala Uganda. bbjoe18@***. Complex Diseases and Genome Epidemiology Graduate School of Public Health Seoul National University Seoul South Korea. Department of Medical Microbiology & Immunology Faculty of Medicine Gulu University Gulu Uganda. Division of Epidemiology and Community Health School of Public Health University of Minnesota Minneapolis MN USA. Infectious Diseases Unit Department of Medicine Mbarara University of Science and Technology Mbarara Uganda. Department of Public and Global Health Epidemiology Biostatistics & Prevention Institute University of Zurich Zurich Switzerland. MRC/UVRI & LSHTM Uganda Research Unit Entebbe Uganda. National Tuberculosis and Leprosy Control Program Ministry of Health Kampala Uganda.

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

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NATURE 2023年第7948期614卷 E37-E37页

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

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Analysis of more than 400,000 women provides case-control evidence for BRCA1 and BRCA2 variant classification

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Nature Communications 2025年第1期16卷 1-18页

作者： Maria Zanti Denise G. O’Mahony Kristia Yiangou Kyriaki Michailidou Michael T. Parsons Amanda B. Spurdle Leila Dorling Joe Dennis Marc Naven Antonis C. Antoniou Manjeet K. Bolla Qin Wang Douglas F. Easton Nicholas J. Boddicker Wenan Chen Chunling Hu Steven N. Hart Fergus J. Couch Thomas U. Ahearn Jonine D. Figueroa Montserrat García-Closas Christine B. Ambrosone Song Yao Irene L. Andrulis Gord Glendon Paul L. Auer Caroline Baynes Don M. Conroy Alison M. Dunning Craig Luccarini Clara Bodelon James M. Hodge Alpa V. Patel Lauren R. Teras Natalia V. Bogdanova Stig E. Bojesen Kristen D. Brantley Nicola J. Camp Archie Campbell Jose E. Castelao Melissa H. Cessna Jenny Chang-Claude Fei Chen Christopher A. Haiman Georgia Chenevix-Trench Kamila Czene Arcangela De Nicolo Susan M. Domchek Katherine L. Nathanson Thilo Dörk A. Heather Eliassen D. Gareth Evans Peter A. Fasching Henrik Flyger Manuela Gago-Dominguez Anna González-Neira Rocio Nuñez-Torres Felix Grassmann Andreas Hadjisavvas Mihalis I. Panayiotidis Ute Hamann Muhammad U. Rashid Diana Torres Mikael B. A. Hartman Weang-Kee Ho Reiner Hoppe Sacha J. Howell Anna Jakubowska Elza K. Khusnutdinova Yon-Dschun Ko Peter Kraft Vessela N. Kristensen James V. Lacey Jingmei Li Geok Hoon Lim Veronique Kiak-Mien Tan Sara Lindström Artitaya Lophatananon Kenneth Muir Arto Mannermaa Maria Elena Martinez Dimitrios Mavroudis Roger L. Milne Melissa C. Southey Nadia Obi Janet E. Olson Celine M. Vachon Julie R. Palmer Gary R. Zirpoli Paul D. P. Pharoah Eric C. Polley Kathryn J. Ruddy Siddhartha Yadav Emmanouil Saloustros Elinor J. Sawyer Marjanka K. Schmidt Soo Hwang Teo Amy Trentham-Dietz Thérèse Truong Jeffrey N. Weitzel Melissa S. Cline Peter Devilee Sean V. Tavtigian David E. Goldgar Biostatistics Unit The Cyprus Institute of Neurology & Genetics Nicosia Cyprus Department of Medical Genetics Oslo University Hospital Oslo Norway Population Health Program QIMR Berghofer Medical Research Institute Brisbane Queensland Australia Centre for Cancer Genetic Epidemiology Department of Public Health and Primary Care University of Cambridge Cambridge UK Centre for Cancer Genetic Epidemiology Department of Oncology University of Cambridge Cambridge UK Department of Quantitative Health Sciences Division of Computational Biology Mayo Clinic Rochester MN USA Department of Laboratory Medicine and Pathology Mayo Clinic Rochester MN USA Division of Cancer Epidemiology and Genetics National Cancer Institute National Institutes of Health Department of Health and Human Services Bethesda MD USA Usher Institute of Population Health Sciences and Informatics The University of Edinburgh Edinburgh UK Cancer Research UK Edinburgh Centre The University of Edinburgh Edinburgh UK Department of Cancer Prevention and Control Roswell Park Comprehensive Cancer Institute Buffalo NY USA Fred A. Litwin Center for Cancer Genetics Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital Toronto Ontario Canada Department of Molecular Genetics University of Toronto Toronto Ontario Canada Division of Biostatistics Data Science Institute and Cancer Center Medical College of Wisconsin Milwaukee WI USA Department of Population Science American Cancer Society Atlanta GA USA Radiation Oncology Research Unit Hannover Medical School Hannover Germany Copenhagen General Population Study Herlev and Gentofte Hospital Copenhagen University Hospital Herlev Denmark Department of Clinical Biochemistry Herlev and Gentofte Hospital Copenhagen University Hospital Herlev Denmark Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark Department of Medical Oncology Dana-Farber Cancer Institute Boston MA USA Department of Internal Medicine and Hu

Clinical genetic testing identifies variants causal for hereditary cancer, information that is used for risk assessment and clinical management. Unfortunately, some variants identified are of uncertain clinical significance (VUS), complicating patient management. Case-control data is one evidence type used to classify VUS. As an initiative of the Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) Analytical Working Group we analyze germline sequencing data ofBRCA1andBRCA2from 96,691 female breast cancer cases and 302,116 controls from three studies: the BRIDGES study of the Breast Cancer Association Consortium, the Cancer Risk Estimates Related to Susceptibility consortium, and the UK Biobank. We observe 11,207BRCA1andBRCA2variants, with 6909 being coding, covering 23.4% ofBRCA1andBRCA2VUS in ClinVar and 19.2% of ClinVar curated (likely) benign or pathogenic variants. Case-control likelihood ratio (ccLR) evidence is highly consistent with ClinVar assertions for (likely) benign or pathogenic variants; exhibiting 99.1% sensitivity and 95.3% specificity forBRCA1and 93.3% sensitivity and 86.6% specificity forBRCA2. This approach provides case-control evidence for 787 unclassified variants; these include 579 with strong or moderate benign evidence and 10 with strong pathogenic evidence for which ccLR evidence is sufficient to alter clinical classification.

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