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Deciphering colorectal cancer genetics through multi-omic analysis of 100,204 cases and 154,587 controls of European and east Asian ancestries (vol 55, pg 89, 2023)

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NATURE GENETICS 2023年第3期55卷 519-520页

作者： Fernandez-Rozadilla, Ceres Timofeeva, Maria Chen, Zhishan Law, Philip Thomas, Minta Schmit, Stephanie Diez-Obrero, Virginia Hsu, Li Fernandez-Tajes, Juan Palles, Claire Sherwood, Kitty Briggs, Sarah Svinti, Victoria Donnelly, Kevin Farrington, Susan Blackmur, James Vaughan-Shaw, Peter Shu, Xiao-ou Long, Jirong Cai, Qiuyin Guo, Xingyi Lu, Yingchang Broderick, Peter Studd, James Huyghe, Jeroen Harrison, Tabitha Conti, David Dampier, Christopher Devall, Mathew Schumacher, Fredrick Melas, Marilena Rennert, Gad Obon-Santacana, Mireia Martin-Sanchez, Vicente Moratalla-Navarro, Ferran Oh, Jae Hwan Kim, Jeongseon Jee, Sun Ha Jung, Keum Ji Kweon, Sun-Seog Shin, Min-Ho Shin, Aesun Ahn, Yoon-Ok Kim, Dong-Hyun Oze, Isao Wen, Wanqing Matsuo, Keitaro Matsuda, Koichi Tanikawa, Chizu Ren, Zefang Gao, Yu-Tang Jia, Wei-Hua Hopper, John Jenkins, Mark Win, Aung Ko Pai, Rish Figueiredo, Jane Haile, Robert Gallinger, Steven Woods, Michael Newcomb, Polly Duggan, David Cheadle, Jeremy Kaplan, Richard Maughan, Timothy Kerr, Rachel Kerr, David Kirac, Iva Bohm, Jan Mecklin, Lukka-Pekka Jousilahti, Pekka Knekt, Paul Aaltonen, Lauri Rissanen, Harri Pukkala, Eero Eriksson, Johan Cajuso, Tatiana Hanninen, Ulrika Kondelin, Johanna Palin, Kimmo Tanskanen, Tomas Renkonen-Sinisalo, Laura Zanke, Brent Mannisto, Satu Albanes, Demetrius Weinstein, Stephanie Ruiz-Narvaez, Edward Palmer, Julie Buchanan, Daniel Platz, Elizabeth Visvanathan, Kala Ulrich, Cornelia Siegel, Erin Brezina, Stefanie Gsur, Andrea Campbell, Peter Chang-Claude, Jenny Hoffmeister, Michael Brenner, Hermann Slattery, Martha Potter, John Tsilidis, Konstantinos Schulze, Matthias Gunter, Marc Murphy, Neil Castells, Antoni Castellvi-Bel, Sergi Moreira, Leticia Arndt, Volker Shcherbina, Anna Stern, Mariana Pardamean, Bens Bishop, Timothy Giles, Graham Southey, Melissa Idos, Gregory McDonnell, Kevin Abu-Ful, Zomoroda Greenson, Joel Shulman, Katerina Lejbkowicz, Flavio Offit, Kenneth Su, Yu-Ru Steinfelder, Robert Keku, Temitope van Guelpen, Bethany Hudson, Thomas Hampel, Heather Pearlman, Edinburgh Cancer Research Centre Institute of Genomics and Cancer University of Edinburgh Edinburgh UK Genomic Medicine Group Instituto de Investigacion Sanitaria de Santiago Santiago de Compostela Spain Colon Cancer Genetics Group Medical Research Council Human Genetics Unit Institute of Genetics and Cancer University of Edinburgh Edinburgh UK Danish Institute for Advanced Study Department of Public Health University of Southern Denmark Odense Denmark Division of Epidemiology Department of Medicine Vanderbilt-Ingram Cancer Center Vanderbilt Epidemiology Center Vanderbilt University Medical Center Nashville TN USA Division of Genetics and Epidemiology Institute of Cancer Research London UK Public Health Sciences Division Fred Hutchinson Cancer Research Center Seattle WA USA Genomic Medicine Institute Cleveland Clinic Cleveland OH USA Population and Cancer Prevention Program Case Comprehensive Cancer Center Cleveland OH USA Colorectal Cancer Group ONCOBELL Program Bellvitge Biomedical Research Institute Barcelona Spain Oncology Data Analytics Program Catalan Institute of Oncology Barcelona Spain Consortium for Biomedical Research in Epidemiology and Public Health Madrid Madrid Spain Department of Clinical Sciences Faculty of Medicine University of Barcelona Barcelona Spain Department of Biostatistics School of Public Health University of Washington Seattle WA USA Institute of Cancer and Genomic Sciences College of Medical and Dental Sciences University of Birmingham Birmingham UK Department of Public Health Richard Doll Building University of Oxford Oxford UK Department of Biomedical Informatics Vanderbilt University School of Medicine Nashville TN USA Department of Preventive Medicine USC Norris Comprehensive Cancer Center Keck School of Medicine University of Southern California Los Angeles CA USA Center for Public Health Genomics Department of Public Health Sciences University of Virginia Charlottesville VA USA Department of Populat

Colorectal cancer (CRC) is a leading cause of mortality worldwide. We conducted a genome-wide association study meta-analysis of 100,204 CRC cases and 154,587 controls of European and east Asian ancestry, identifying 205 independent risk associations, of which 50 were unreported. We performed integrative genomic, transcriptomic and methylomic analyses across large bowel mucosa and other tissues. Transcriptome- and methylome-wide association studies revealed an additional 53 risk associations. We identified 155 high-confidence effector genes functionally linked to CRC risk, many of which had no previously established role in CRC. These have multiple different functions and specifically indicate that variation in normal colorectal homeostasis, proliferation, cell adhesion, migration, immunity and microbial interactions determines CRC risk. Crosstissue analyses indicated that over a third of effector genes most probably act outside the colonic mucosa. Our findings provide insights into colorectal oncogenesis and highlight potential targets across tissues for new CRC treatment and chemoprevention strategies.

关键词： Colorectal cancer Epigenomics Genome-wide association studies Transcriptomics

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#4917 AN EXOME-WIDE STUDY OF RENAL OPERATIONAL TOLERANCE

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Nephrology Dialysis Transplantation 2023年第SUPPLEMENT_1期38卷

作者： Massart, Annick Danger, Richard Olsen, Catharina Emond, Mary Viklicky, Ondrej Jacquemin, Valérie Soblet, Julie Duerinckx, Sarah Croes, Didier Perazzolo, Camille Hruba, Petra Daneels, Dorien Caljon, Ben Sever, Mehmet Sukru Pascual, Julio Pirson, Isabelle Ghisdal, Lidia Smits, Guillaume Giral, Magali Abramowicz, Daniel Abramowicz, Marc Brouard, Sophie Department of Nephrology Antwerp University Hospital and Laboratory of Experimental Medicine University of Antwerp Belgium Institut de Recherche Interdisciplinaire en Biologie Humaine et moléculaire (IRIBHM) Human Genetics unit Université Libre de Bruxelles (ULB) Belgium Interuniversity Institute of Bioinformatics in Brussels (IB2) ULB-VUB Belgium Nantes Université INSERM Center for Research in Transplantation and Translational Immunology CRT2I France Center for Medical Genetics Reproduction and Genetics Reproduction Genetics and Regenerative Medicine Vrije Universiteit Brussel UZ Brussel Belgium United States of America Department of Biostatistics University of Washington United States of America Transplant Laboratory Institute for Clinical and Experimental Medicine Czech Republic Department of Genetics Hôpital Erasme ULB Center of Human Genetics Université Libre de Bruxelles Belgium Center for Human Genetics Clinique Universitaires Saint Luc Belgium Brussels Interuniversity Genomics High Throughput core (BRIGHTcore) VUB-ULB Belgium Istanbul School of Medicine Internal Medicine Nephrology Istanbul Tıp fakültesi Turkey Department of Nephrology Hospital Universitario 12 de Octubre Spain Department of Nephrology Hospital Centre EpiCURA Belgium CHU Nantes and Nantes Université INSERM Center for Research in Transplantation and Translational Immunology CRT2I France Department of Genetic Medicine and Development Faculty of Medicine Université de Genève Switzerland

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Predictive and prognostic value of excision repair cross-complementing group 1 in patients with advanced gastric cancer

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BJC reports 2024年第1期2卷 18页

作者： Yasuhide Yamada Kengo Nagashima Mizutomo Azuma Mitsuko Masutani Hitoshi Ichikawa Satoru Iwasa Naoki Takahashi Hidekazu Hirano Keisuke Kanato Nozomu Machida Takahiro Kinoshita Hiroaki Hata Hisato Kawakami Daisuke Takahari Narikazu Boku Yukinori Kurokawa Masanori Terashima Takaki Yoshikawa Shigeki Sekine Nobuyoshi Hiraoka Department of Medical Research National Center for Global Health and Medicine Tokyo 162-8655 Japan. yayamada@hosp.ncgm.go.jp. Biostatistics Unit Clinical and Translational Research Center Keio University Hospital Tokyo 160-8582 Japan. Department of Gastroenterology Kitasato University Hospital Sagamihara 252-0329 Japan. Molecular & Genomic Biomedicine Center for Bioinformatics and Molecular Medicine Nagasaki University Graduate School Nagasaki 852-8521 Japan. Department of Clinical Genomics National Cancer Center Research Institute Tokyo 104-0045 Japan. Department of Gastrointestinal Medical Oncology National Cancer Center Hospital Tokyo 104-0045 Japan. Department of Gastroenterology Saitama Cancer Center Saitama 362-0806 Japan. JCOG Data Center/ Operations Office National Cancer Center Tokyo 104-0045 Japan. Department of Gastroenterology Kanagawa Cancer Center Yokohama 241-8515 Japan. Department Gastric Surgery National Cancer Center Hospital East Chiba 241-8515 Japan. Department of Surgery Kyoto Medical Center Kyoto 612-0861 Japan. Department of Medical Oncology Kindai University Faculty of Medicine Osaka 577-8502 Japan. Department of Gastroenterological Chemotherapy Cancer Institute Hospital of JFCR Tokyo 135-8550 Japan. Department of Gastroenterological Surgery Osaka University Graduate School of Medicine Osaka 565-0871 Japan. Division of Gastric Surgery Shizuoka Cancer Center Shizuoka 411-8777 Japan. Department of Gastric Surgery National Cancer Center Hospital Tokyo 104-0045 Japan. Department of Pathology National Cancer Center Hospital Tokyo 104-0045 Japan.

BACKGROUND:To define the optimal chemotherapy regimen for each patient we therefore used tissue from patients to identify molecular prognostic or predictive biomarkers. METHODS:Endoscopic biopsy specimens from primary lesions and surgical specimens on a phase III trial in patients with unresectable advanced or recurrent gastric cancer treated with docetaxel with cisplatin plus S-1 (DCS) or cisplatin plus S-1 (CS), were collected. We measured the mRNA expression of ERCC1 and analyzed SNPs in GSTP1 and ERCC1. RESULTS:Low ERCC1 expression was associated with favorable prognosis for overall survival, OS by multivariable analysis (P = 0.001). There were significant interactions between the two treatment arms of DCS and CS, and ERCC1 mRNA expression. In patients with low ERCC1 expression of a favorable prognosis, DCS therapy was inferior to CS (P = 0.046). In addition to GSTP1 rs1695 (HR 1.728), ERCC1 rs3212980, ERCC1 rs2298881, ERCC1 rs3212964 with high expression of ERCC1 mRNA were associated with significantly worse prognosis with regard to OS. CONCLUSIONS:ERCC1 mRNA is an independent prognostic factor and predictive marker that can be used to guide the addition of docetaxel. The SNPs of ERCC1 and GSTP1 could be also prognostic or predictive factors.

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The importance of transparency and reproducibility in artificial intelligence research

arXiv

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arXiv 2020年

作者： Haibe-Kains, Benjamin Adam, George Alexandru Hosny, Ahmed Khodakarami, Farnoosh Waldron, Levi Wang, Bo McIntosh, Chris Kundaje, Anshul Greene, Casey S. Hoffman, Michael M. Leek, Jeffrey T. Huber, Wolfgang Brazma, Alvis Pineau, Joelle Tibshirani, Robert Hastie, Trevor Ioannidis, John P.A. Quackenbush, John Aerts, Hugo J.W.L. Princess Margaret Cancer Centre University Health Network TorontoON Canada Department of Medical Biophysics University of Toronto TorontoON Canada Department of Computer Science University of Toronto TorontoON Canada Ontario Institute for Cancer Research TorontoON Canada Vector Institute for Artificial Intelligence TorontoON Canada Program Brigham and Women's Hospital Harvard Medical School BostonMA United States Radiation Oncology and Radiology Dana-Farber Cancer Institute Brigham and Women's Department of Epidemiology and Biostatistics Institute for Implementation Science in Population Health CUNY Graduate School of Public Health and Health Policy New YorkNY United States Peter Munk Cardiac Centre University Health Network TorontoON Canada Hospital Harvard Medical School BostonMA United States Department of Genetics Stanford University School of Medicine StanfordCA United States Dept. of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Childhood Cancer Data Lab Alex's Lemonade Stand Foundation PhiladelphiaPA United States Department of Biostatistics Johns Hopkins Bloomberg School of Public Health BaltimoreMD United States European Molecular Biology Laboratory Genome Biology Unit Heidelberg Germany European Molecular Biology Laboratory European Bioinformatics Institute EMBL-EBI Hinxton United Kingdom McGill University MontrealQC Canada Montreal Institute for Learning Algorithms QC Canada StanfordCA United States Department of Biomedical Data Science Stanford University School of Medicine StanfordCA United States Departments of Medicine of Health Research and Policy and of Biomedical Data Science Stanford University School of Medicine StanfordCA United States Department of Statistics Stanford University School of Humanities and Sciences StanfordCA United States Department of Biostatistics Harvard T.H Chan School of Public Health BostonMA Un

In their study, McKinney et al. showed the high potential of artificial intelligence for breast cancer screening. However, the lack of detailed methods and computer code undermines its scientific value. We identify obstacles hindering transparent and reproducible AI research as faced by McKinney et al and provide solutions with implications for the broader field. Copyright © 2020, The Authors. All rights reserved.

关键词： Artificial intelligence

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The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic

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四川生理科学杂志 2022年第7期44卷 1246-1246页

作者： Michael Worobey Department of Ecology and Evolutionary Biology University of Arizona Tucson AZ 85721 USA. Department of Immunology and Microbiology The Scripps Research Institute La Jolla CA 92037 USA. W. Harry Feinstone Department of Molecular Microbiology and Immunology Johns Hopkins Bloomberg School of Public Health Baltimore MD 21205 USA. Bioinformatics and Systems Biology Graduate Program University of California San Diego La Jolla CA 92093 USA. Department of Biomedical Informatics University of California San Diego La Jolla CA 92093 USA. Department of Human Genetics University of Utah School of Medicine Salt Lake City UT 84112 USA. Vaccine and Infectious Disease Organization University of Saskatchewan Saskatoon SK S7N 5E3 Canada. Center for Global Health Science and Security Georgetown University Washington DC 20057 USA. Department of Zoology University of Oxford Oxford OX1 3SZ UK. Wildlife Conservation Research Unit Department of Zoology The Recanati-Kaplan Centre University of Oxford Oxford OX13 5QL UK. Pandemic and Disaster Preparedness Centre Erasmus University Medical Center 3015 CE Rotterdam Netherlands. Department of Viroscience Erasmus University Medical Center 3015 CE Rotterdam Netherlands. Department of Biostatistics Fielding School of Public Health University of California Los Angeles Los Angeles CA 90095 USA. Department of Human Genetics David Geffen School of Medicine University of California Los Angeles Los Angeles CA 90095 USA. Department of Computational Medicine David Geffen School of Medicine University of California Los Angeles Los Angeles CA 90095 USA. Department of Medicine University of California San Diego La Jolla CA 92093 USA. Department of Microbiology Immunology and Transplantation Rega Institute for Medical Research KU Leuven 3000 Leuven Belgium. Global Virus Network (GVN) Baltimore MD 21201 USA. MRC-University of Glasgow Center for Virus Research Glasgow G61 1QH UK. Tulane University School of Medicine Department of Mi

Understanding how severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)emerged in 2019 is critical to preventing zoonotic outbreaks before they become the next *** Huanan Seafood Wholesale Market in Wuhan,China,was identified as a likely source of cases in early reports but later this conclusion became *** show the earliest known COVID-19 cases from December 2019,including those without reported direct links,were geographically centered on this *** report that live SARS-CoV-2 susceptible mammals were sold at the market in late 2019 and,within the market,SARS-CoV-2-positive environmental samples were spatially associated with vendors selling live mammals.

关键词： Market likely Wuhan

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Natural variation in the parameters of innate immune cells is preferentially driven by genetic factors (vol 19, pg 302, 2018)

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NATURE IMMUNOLOGY 2018年第6期19卷 645-645页

作者： Patin, Etienne Hasan, Milena Bergstedt, Jacob Rouilly, Vincent Libri, Valentina Urrutia, Alejandra Alanio, Cecile Scepanovic, Petar Hammer, Christian Joensson, Friederike Beitz, Benoit Quach, Helene Lim, Yoong Wearn Hunkapiller, Julie Zepeda, Magge Green, Cherie Piasecka, Barbara Leloup, Claire Rogge, Lars Huetz, Francois Peguillet, Isabelle Lantz, Olivier Fontes, Magnus Di Santo, James P. Thomas, Stephanie Fellay, Jacques Duffy, Darragh Quintana-Murci, Lluis Albert, Matthew L. Unit of Human Evolutionary Genetics Department of Genomes & Genetics Institut Pasteur Paris France CNRS UMR 2000 Paris France Center of Bioinformatics Biostatistics and Integrative Biology Institut Pasteur Paris France Center for Translation Research Institut Pasteur Paris France Department of Automatic Control Lund University Lund Sweden International Group for Data Analysis Institut Pasteur Paris France Laboratory of Dendritic Cell Immunobiology Department of Immunology Institut Pasteur Paris France INSERM U1223 Paris France Department of Cancer Immunology Genentech South San Francisco USA School of Life Sciences École Polytechnique Fédérale de Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics Lausanne Switzerland Antibodies in Therapy and Pathology Department of Immunology Institut Pasteur Paris France INSERM U760 Paris France Department of Human Genetics Genentech South San Francisco USA Employee Donation Program Genentech South San Francisco USA Department of Development Sciences Genentech South San Francisco USA Immunoregulation Unit Department of Immunology Institut Pasteur Paris France INSERM U783 Faculté de Médecine Site Necker-Enfants Malades Université Paris Descartes Paris France Lymphocyte Population Biology CNRS URA 1961 Institut Pasteur Paris France Center of Clinical Investigations CIC-BT1428 IGR/Curie Paris France Department of Biopathology Institut Curie Paris France Equipe Labellisée de la Ligue de Lutte Contre le Cancer Institut Curie Paris France INSERM/Institut Curie U932 Paris France Centre for Mathematical Sciences Lund University Lund Sweden Innate Immunity Unit Institut Pasteur Paris France

The quantification and characterization of circulating immune cells provide key indicators of human health and disease. To identify the relative effects of environmental and genetic factors on variation in the parameters of innate and adaptive immune cells in homeostatic conditions, we combined standardized flow cytometry of blood leukocytes and genome-wide DNA genotyping of 1,000 healthy, unrelated people of Western European ancestry. We found that smoking, together with age, sex and latent infection with cytomegalovirus, were the main non-genetic factors that affected variation in parameters of human immune cells. Genome-wide association studies of 166 immunophenotypes identified 15 loci that showed enrichment for disease-associated variants. Finally, we demonstrated that the parameters of innate cells were more strongly controlled by genetic variation than were those of adaptive cells, which were driven by mainly environmental exposure. Our data establish a resource that will generate new hypotheses in immunology and highlight the role of innate immunity in susceptibility to common autoimmune diseases.

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The Impact of Genomic Variation on Function (IGVF) Consortium

arXiv

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arXiv 2023年

作者： Shendure, Jay Ahituv, Nadav Kircher, Martin Agarwal, Vikram Blair, Andrew Chalkiadakis, Theofilos Chardon, Florence M. Dash, Pyaree M. Deng, Chengyu Hamazaki, Nobuhiko Keukeleire, Pia Kubo, Connor Lalanne, Jean-Benoît Maass, Thorben Martin, Beth McDiarmid, Troy Nobuhara, Mai Page, Nicholas F. Regalado, Sam Schubach, Max Sims, Jasmine Ushiki, Aki Zhao, Jingjing Starita, Lea M. Fowler, Douglas M. Best, Sabrina M. Boyle, Gabe Camp, Nathan Casadei, Silvia Da, Estelle Y. Dawood, Moez Dawson, Samantha C. Fayer, Shawn Hamm, Audrey James, Richard G. Jarvik, Gail P. McEwen, Abbye E. Moore, Nick Muffley, Lara A. Pendyala, Sriram Popp, Nicholas A. Post, Mason Rubin, Alan F. Shendure, Jay Smith, Nahum T. Rubin, Alan F. Stone, Jeremy Tejura, Malvika Wang, Ziyu R. Wheelock, Melinda K. Woo, Ivan Zapp, Brendan D. Engreitz, Jesse M. Quertermous, Thomas Amgalan, Dulguun Aradhana, Aradhana Arana, Sophia M. Bassik, Michael C. Bauman, Julia R. Bhattacharya, Asmita Cai, Xiangmeng Shawn Chen, Ziwei Conley, Stephanie Deshpande, Salil Doughty, Benjamin R. Du, Peter P. Gifford, Casey Greenleaf, William J. Gschwind, Andreas R. Guo, Katherine Isobe, Sarasa Jagoda, Evelyn Jain, Nimit Jones, Hank Kang, Helen Y. Kim, Samuel H. Kim, YeEun Klemm, Sandy Kundaje, Anshul Kundu, Soumya Lago-Docampo, Mauro Lee-Yow, Yannick C. Levin-Konigsberg, Roni Li, Daniel Y. Lindenhofer, Dominik Rosa Ma, X. Marinov, Georgi K. Martyn, Gabriella E. Metzl-Raz, Eyal Monteiro, Joao P. Montgomery, Michael T. Mualim, Kristy S. Munger, Chad Munson, Glen Nguyen, Tri C. Nguyen, Trieu Palmisano, Brian T. Pampari, Anusri Park, Chong Y. Rabinovitch, Marlene Ramste, Markus Ray, Judhajeet Roy, Kevin R. Rubio, Oriane M. Schaepe, Julia M. Schnitzler, Gavin Schreiber, Jacob Sharma, Disha Sheth, Maya U. Shi, Huitong Singh, Vasundhara Sinha, Riya Steinmetz, Lars M. Tan, Jason Tan, Anthony Tycko, Josh Valbuena, Raeline C. Pour Amiri, Valeh Valiollah van Kooten, Mariëlle J.F.M. Vaughan-Jackson, Alun Venida, Anthony Weldy, Chad S. Yao, David Zeng, Tony Zhou, Ronghao Vidal, Marc Calderw Department of Genome Sciences University of Washington SeattleWA United States Department of Bioengineering and Therapeutic Sciences Institute for Human Genetics University of California San Francisco San FranciscoCA United States Institute of Human Genetics University Medical Center Schleswig-Holstein University of Lübeck Lübeck23562 Germany Exploratory Diagnostic Sciences Berlin Institute of Health Charité-Universitätsmedizin Berlin Berlin10117 Germany Brotman Baty Institute for Precision Medicine SeattleWA United States Center of immunotherapy and Immunity Seattle Children's Research Institute SeattleWA United States Bioinformatics Division WEHI ParkvilleVIC Australia Human Genome Sequencing Center Baylor College of Medicine HoustonTX United States Department of Laboratory Medicine and Pathology University of Washington SeattleWA United States Department of Genetics Stanford University School of Medicine StanfordCA United States Basic Science and Engineering Initiative Stanford Children’s Health Betty Irene Moore Children’s Heart Center StanfordCA United States The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease Broad Institute of MIT and Harvard CambridgeMA United States Division of Cardiovascular Medicine School of Medicine Stanford University United States Department of Computer Science Stanford University School of Medicine StanfordCA United States Institute for Computational and Mathematical Engineering Stanford University StanfordCA United States Department of Pediatrics Stanford University School of Medicine StanfordCA United States Institute for Stem Cell Biology and Regenerative Medicine Stanford University School of Medicine StanfordCA United States Division of Pediatric Cardiology Cardiovascular Institute Stanford University School of Medicine Stanford University United States Genome Biology Unit Heidelberg Germany Department of Biology Stanford University StanfordCA United States Stanford Genome Techn

Our genomes influence nearly every aspect of human biology from molecular and cellular functions to phenotypes in health and disease. Human genetics studies have now associated hundreds of thousands of differences in our DNA sequence ("genomic variation") with disease risk and other phenotypes, many of which could reveal novel mechanisms of human biology and uncover the basis of genetic predispositions to diseases, thereby guiding the development of new diagnostics and therapeutics. Yet, understanding how genomic variation alters genome function to influence phenotype has proven challenging. To unlock these insights, we need a systematic and comprehensive catalog of genome function and the molecular and cellular effects of genomic variants. Toward this goal, the Impact of Genomic Variation on Function (IGVF) Consortium will combine approaches in single-cell mapping, genomic perturbations, and predictive modeling to investigate the relationships among genomic variation, genome function, and phenotypes. Through systematic comparisons and benchmarking of experimental and computational methods, we aim to create maps across hundreds of cell types and states describing how coding variants alter protein activity, how noncoding variants change the regulation of gene expression, and how both coding and noncoding variants may connect through gene regulatory and protein interaction networks. These experimental data, computational predictions, and accompanying standards and pipelines will be integrated into an open resource that will catalyze community efforts to explore genome function and the impact of genetic variation on human biology and disease across populations. © 2023, CC BY.

关键词： Genome

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Author Correction: Genomic footprints of activated telomere maintenance mechanisms in cancer (Dec, 10.1038/s41467-019-13824-9, 2022)

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NATURE COMMUNICATIONS 2022年第1期13卷 1页

作者： Sieverling, Lina Hong, Chen Koser, Sandra D. Ginsbach, Philip Kleinheinz, Kortine Hutter, Barbara Braun, Delia M. Cortes-Ciriano, Isidro Xi, Ruibin Kabbe, Rolf Park, Peter J. Eils, Roland Schlesner, Matthias Brors, Benedikt Rippe, Karsten Jones, David T. W. Feuerbach, Lars Division of Applied Bioinformatics German Cancer Research Center (DKFZ) 69120 Heidelberg Germany Faculty of Biosciences Heidelberg University 69120 Heidelberg Germany Division of Applied Bioinformatics German Cancer Research Center (DKFZ) Heidelberg Germany Faculty of Biosciences Heidelberg University Heidelberg Germany German Cancer Consortium (DKTK) Heidelberg Germany National Center for Tumor Diseases (NCT) Heidelberg Heidelberg Germany German Cancer Consortium (DKTK) German Cancer Research Center (DKFZ) Heidelberg Germany Wellcome Sanger Institute Wellcome Genome Campus Hinxton Cambridge CB10 1SA UK Korea Advanced Institute of Science and Technology Daejeon 34141 South Korea Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Korea Advanced Institute of Science and Technology Daejeon South Korea Division of Chromatin Networks German Cancer Research Center (DKFZ) and BioQuant 69120 Heidelberg Germany Division of Theoretical Bioinformatics German Cancer Research Center (DKFZ) 69120 Heidelberg Germany Department for Bioinformatics and Functional Genomics Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant 69120 Heidelberg Germany Division of Theoretical Bioinformatics German Cancer Research Center (DKFZ) Heidelberg Germany Institute of Pharmacy and Molecular Biotechnology and BioQuant Heidelberg University Heidelberg Germany Heidelberg University Heidelberg Germany New BIH Digital Health Center Berlin Institute of Health (BIH) and Charité - Universitätsmedizin Berlin Berlin Germany Heidelberg Center for Personalized Oncology (DKFZ-HIPO) German Cancer Research Center (DKFZ) Heidelberg Germany Department of Biomedical Informatics Harvard Medical School Boston MA USA Ludwig Center at Harvard Medical School Boston MA USA Department of Biomedical Informatics Harvard Medical School Boston Massachusetts 02115 USA Ludwig Center at Harvard Medical School Boston Massachusetts 02115 USA Broad Institute of MIT and Harvard

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Enhancing Discovery of Genetic Variants for Posttraumatic Stress Disorder Through Integration of Quantitative Phenotypes and Trauma Exposure Information (vol 91, pg 626, 2022)

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BIOLOGICAL PSYCHIATRY 2022年第7期91卷 690-690页

作者： Maihofer, Adam X. Vinkers, Christiaan H. Department of Psychiatry University of California San Diego La Jolla California Department of Family Medicine and Public Health University of California San Diego La Jolla California Center of Excellence for Stress and Mental Health Veterans Affairs Healthcare System San Diego California. Electronic address: amaihofer@health.ucsd.edu. Department of Epidemiology Harvard T.H. Chan School of Public Health Boston Massachusetts Department of Psychiatry Massachusetts General Hospital Boston Massachusetts. Social Genetic and Developmental Psychiatry Centre Institute of Psychiatry Psychology and Neuroscience King's College London London United Kingdom National Institute of Health Research Maudsley Biomedical Research Centre King's College London London United Kingdom. Department of Psychiatry Harvard Medical School Boston Massachusetts Stanley Center for Psychiatric Research Broad Institute of MIT and Harvard Cambridge Massachusetts Center of Excellence in Depression and Anxiety Disorders Belmont Massachusetts. Department of Epidemiology Harvard T.H. Chan School of Public Health Boston Massachusetts Stanley Center for Psychiatric Research Broad Institute of MIT and Harvard Cambridge Massachusetts. Department of Psychiatry University of California San Diego La Jolla California Center of Excellence for Stress and Mental Health Veterans Affairs Healthcare System San Diego California Research Service Veterans Affairs Healthcare System San Diego California. Duke Molecular Physiology Institute Duke University School of Medicine Durham North Carolina. Department of Psychiatry Veterans Affairs Connecticut Healthcare System West Haven Connecticut Department of Psychiatry Yale University School of Medicine New Haven Connecticut. Department of Epidemiology Harvard T.H. Chan School of Public Health Boston Massachusetts Department of Epidemiology Columbia University Mailman School of Public Health New York. Division of Mental Health Atlanta Veterans Affairs Medical Center

BACKGROUND: Posttraumatic stress disorder (PTSD) is heritable and a potential consequence of exposure to traumatic stress. Evidence suggests that a quantitative approach to PTSD phenotype measurement and incorporation of lifetime trauma exposure (LTE) information could enhance the discovery power of PTSD genome-wide association studies (GWASs). METHODS: A GWAS on PTSD symptoms was performed in 51 cohorts followed by a fixed-effects meta-analysis (N = 182,199 European ancestry participants). A GWAS of LTE burden was performed in the UK Biobank cohort (N = 132,988). Genetic correlations were evaluated with linkage disequilibrium score regression. Multivariate analysis was performed using Multi-Trait Analysis of GWAS. Functional mapping and annotation of leading loci was performed with FUMA. Replication was evaluated using the Million Veteran Program GWAS of PTSD total symptoms. RESULTS: GWASs of PTSD symptoms and LTE burden identified 5 and 6 independent genome-wide significant loci, respectively. There was a 72% genetic correlation between PTSD and LTE. PTSD and LTE showed largely similar patterns of genetic correlation with other traits, albeit with some distinctions. Adjusting PTSD for LTE reduced PTSD heritability by 31%. Multivariate analysis of PTSD and LTE increased the effective sample size of the PTSD GWAS by 20% and identified 4 additional loci. Four of these 9 PTSD loci were independently replicated in the Million Veteran Program. CONCLUSIONS: Through using a quantitative trait measure of PTSD, we identified novel risk loci not previously identified using prior case-control analyses. PTSD and LTE have a high genetic overlap that can be leveraged to increase discovery power through multivariate methods.

关键词： GWAS Genetics Heritability PTSD PheWAS Trauma

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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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