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Erratum to: The whole genome sequence of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann), reveals insights into the biology and adaptive evolution of a highly invasive pest species

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Genome biology 2017年第1期18卷 11页

作者： Alexie Papanicolaou Marc F Schetelig Peter Arensburger Peter W Atkinson Joshua B Benoit Kostas Bourtzis Pedro Castañera John P Cavanaugh Hsu Chao Christopher Childers Ingrid Curril Huyen Dinh HarshaVardhan Doddapaneni Amanda Dolan Shannon Dugan Markus Friedrich Giuliano Gasperi Scott Geib Georgios Georgakilas Richard A Gibbs Sarah D Giers Ludvik M Gomulski Miguel González-Guzmán Ana Guillem-Amat Yi Han Artemis G Hatzigeorgiou Pedro Hernández-Crespo Daniel S T Hughes Jeffery W Jones Dimitra Karagkouni Panagiota Koskinioti Sandra L Lee Anna R Malacrida Mosè Manni Kostas Mathiopoulos Angela Meccariello Monica Munoz-Torres Shwetha C Murali Terence D Murphy Donna M Muzny Georg Oberhofer Félix Ortego Maria D Paraskevopoulou Monica Poelchau Jiaxin Qu Martin Reczko Hugh M Robertson Andrew J Rosendale Andrew E Rosselot Giuseppe Saccone Marco Salvemini Grazia Savini Patrick Schreiner Francesca Scolari Paolo Siciliano Sheina B Sim George Tsiamis Enric Ureña Ioannis S Vlachos John H Werren Ernst A Wimmer Kim C Worley Antigone Zacharopoulou Stephen Richards Alfred M Handler Hawkesbury Institute for the Environment Western Sydney University Sydney Australia. Justus-Liebig-University Giessen Institute for Insect Biotechnology 35394 Giessen Germany. Department of Biological Sciences Cal Poly Pomona Pomona CA 91768 USA. Department of Entomology and Center for Disease Vector Research University of California Riverside Riverside CA 92521 USA. Interdepartmental Graduate Program in Genetics Genomics & Bioinformatics University of California Riverside Riverside CA 92521 USA. Department of Biological Sciences University of Cincinnati Cincinnati OH 45221 USA. Insect Pest Control Laboratory Joint FAO/IAEA Programme of Nuclear Techniques in Food and Agriculture Seibersdorf Vienna Austria. Department of Environmental and Natural Resources Management University of Patras Agrinio Greece. Department of Environmental Biology Centro de Investigaciones Biológicas CSIC 28040 Madrid Spain. Human Genome Sequencing Center Department of Human and Molecular Genetics Baylor College of Medicine 77030 Houston TX USA. National Agricultural Library USDA 20705 Beltsville MD USA. Georg-August-Universität Göttingen Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie 37077 Göttingen Germany. Department of Biology University of Rochester 14627 Rochester NY USA. Department of Biological Sciences Wayne State University 48202 Detroit MI USA. Department of Biology and Biotechnology University of Pavia 27100 Pavia Italy. USDA-ARS Pacific Basin Agricultural Research Center 96720 Hilo HI USA. DIANA-Lab Department of Electrical & Computer Engineering University of Thessaly 382 21 Volos Greece and Hellenic Pasteur Institute 11521 Athens Greece. Department of Entomology University of Illinois at Urbana-Champaign 61801 Urbana IL USA. Department of Biological Sciences Oakland University 48309 Rochester MI USA. Department of Biochemistry and Biotechnology University of Thessaly Larissa Greece. Department of Biology Univer

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

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

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

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

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

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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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Author Correction: Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition

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Nature genetics 2023年第6期55卷 1080页

作者： Bernardo Rodriguez-Martin Eva G Alvarez Adrian Baez-Ortega Jorge Zamora Fran Supek Jonas Demeulemeester Martin Santamarina Young Seok Ju Javier Temes Daniel Garcia-Souto Harald Detering Yilong Li Jorge Rodriguez-Castro Ana Dueso-Barroso Alicia L Bruzos Stefan C Dentro Miguel G Blanco Gianmarco Contino Daniel Ardeljan Marta Tojo Nicola D Roberts Sonia Zumalave Paul A Edwards Joachim Weischenfeldt Montserrat Puiggròs Zechen Chong Ken Chen Eunjung Alice Lee Jeremiah A Wala Keiran M Raine Adam Butler Sebastian M Waszak Fabio C P Navarro Steven E Schumacher Jean Monlong Francesco Maura Niccolo Bolli Guillaume Bourque Mark Gerstein Peter J Park David C Wedge Rameen Beroukhim David Torrents Jan O Korbel Iñigo Martincorena Rebecca C Fitzgerald Peter Van Loo Haig H Kazazian Kathleen H Burns Peter J Campbell Jose M C Tubio Department of Zoology Genetics and Physical Anthropology Universidade de Santiago de Compostela Santiago de Compostela Spain. Biomedical Research Centre (CINBIO) University of Vigo Vigo Spain. Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain. Transmissible Cancer Group Department of Veterinary Medicine University of Cambridge Cambridge UK. The Biomedical Research Centre (CINBIO) Universidade de Vigo Vigo Spain. Wellcome Sanger Institute Wellcome Genome Campus Cambridge UK. Genome Data Science Institute for Research in Biomedicine (IRB Barcelona) The Barcelona Institute of Science and Technology (BIST) Barcelona Spain. Institucio Catalana de Recerca i Estudis Avançats (ICREA) Barcelona Spain. The Francis Crick Institute London UK. Department of Human Genetics University of Leuven Leuven Belgium. Genomes and Disease Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain. Graduate School of Medical Science and Engineering Korea Advanced Institute of Science and Technology Daejeon South Korea. Cancer Ageing and Somatic Mutation Programme Wellcome Sanger Institute Cambridge UK. Department of Biochemistry Genetics and Immunology University of Vigo Vigo Spain. Galicia Sur Health Research Institute Vigo Spain. Faculty of Science and Technology University of Vic-Central University of Catalonia (UVic-UCC) Vic Spain. Barcelona Supercomputing Center (BSC) Barcelona Spain. Experimental Cancer Genetics Wellcome Sanger Institute Cambridge UK. Oxford Big Data Institute University of Oxford Oxford UK. DNA Repair and Genome Integrity Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain. Department of Biochemistry and Molecular Biology Universidade de Santiago de Compostela Santiago de Compostela Spain. Medical R

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

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NATURE 2021年第7846期590卷 E56-E56页

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

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

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NATURE 2021年第7846期590卷 E53-E53页

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

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

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NATURE 2021年第7874期597卷 E3-E4页

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

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Transcript expression-aware annotation improves rare variant interpretation (vol 581, pg 452, 2020)

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NATURE 2021年第7846期590卷 E54-E54页

作者： Cummings, Beryl B. Karczewski, Konrad J. Kosmicki, Jack A. Seaby, Eleanor G. Watts, Nicholas A. Singer-Berk, Moriel Mudge, Jonathan M. Karjalainen, Juha Satterstrom, F. Kyle O'Donnell-Luria, Anne H. Poterba, Timothy Seed, Cotton Solomonson, Matthew Alfoldi, Jessica Daly, Mark J. MacArthur, Daniel G. Program in Medical and Population Genetics Broad Institute of MIT and Harvard Cambridge MA USA Analytical and Translational Genetics Unit Massachusetts General Hospital Boston MA USA Program in Biological and Biomedical Sciences Harvard Medical School Boston MA USA Program in Bioinformatics and Integrative Genomics Harvard Medical School Boston MA USA Genomic Informatics Group University Hospital Southampton Southampton UK Stanley Center for Psychiatric Research Broad Institute of MIT and Harvard Cambridge MA USA Division of Genetics and Genomics Boston Children’s Hospital Boston MA USA Department of Pediatrics Harvard Medical School Boston MA USA European Molecular Biology Laboratory European Bioinformatics Institute Wellcome Genome Campus Hinxton Cambridge UK Center for Genomic Medicine Massachusetts General Hospital Boston MA USA Broad Genomics Broad Institute of MIT and Harvard Cambridge MA USA National Heart & Lung Institute and MRC London Institute of Medical Sciences Imperial College London London UK Cardiovascular Research Centre Royal Brompton & Harefield Hospitals NHS Trust London UK Cardiac Arrhythmia Service and Cardiovascular Research Center Massachusetts General Hospital Boston MA USA Estonian Genome Center Institute of Genomics University of Tartu Tartu Estonia Department of Medicine Harvard Medical School Boston MA USA Cardiac Arrhythmia Service Massachusetts General Hospital Boston MA USA Division of General Internal Medicine Massachusetts General Hospital Boston MA USA Institute for Molecular Medicine FIMM University of Helsinki Helsinki Finland Department of Public Health Faculty of Medicine University of Helsinki Helsinki Finland Department of Genetics Harvard Medical School Boston MA USA Data Sciences Platform Broad Institute of MIT and Harvard Cambridge MA USA Genomics Platform Broad Institute of MIT and Harvard Cambridge MA USA Wellcome Sanger Institute Hinxton Cambridgeshire UK Unidad de Investigaci

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A structural variation reference for medical and population genetics (vol 581, pg 444, 2020)

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NATURE 2021年第7846期590卷 E55-E55页

作者： Collins, Ryan L. Brand, Harrison Karczewski, Konrad J. Zhao, Xuefang Alfoldi, Jessica Francioli, Laurent C. Khera, Amit V. Lowther, Chelsea Gauthier, Laura D. Wang, Harold Watts, Nicholas A. Solomonson, Matthew O'Donnell-Luria, Anne Baumann, Alexander Munshi, Ruchi Walker, Mark Whelan, Christopher W. Huang, Yongqing Brookings, Ted Sharpe, Ted Stone, Matthew R. Valkanas, Elise Fu, Jack Tiao, Grace Laricchia, Kristen M. Ruano-Rubio, Valentin Stevens, Christine Gupta, Namrata Cusick, Caroline Margolin, Lauren Taylor, Kent D. Lin, Henry J. Rich, Stephen S. Post, Wendy S. Chen, Yii-Der Ida Rotter, Jerome I. Nusbaum, Chad Philippakis, Anthony Lander, Eric Gabriel, Stacey Neale, Benjamin M. Kathiresan, Sekar Daly, Mark J. Banks, Eric MacArthur, Daniel G. Talkowski, Michael E. Program in Medical and Population Genetics Broad Institute of MIT and Harvard Cambridge MA USA Center for Genomic Medicine Massachusetts General Hospital Boston MA USA Division of Medical Sciences Harvard Medical School Boston MA USA Department of Neurology Massachusetts General Hospital and Harvard Medical School Boston MA USA Analytical and Translational Genetics Unit Massachusetts General Hospital Boston MA USA Analytic and Translational Genetics Unit Massachusetts General Hospital Boston MA USA Department of Medicine Harvard Medical School Boston MA USA Data Science Platform Broad Institute of MIT and Harvard Cambridge MA USA Broad Genomics Broad Institute of MIT and Harvard Cambridge MA USA European Molecular Biology Laboratory European Bioinformatics Institute Wellcome Genome Campus Hinxton Cambridge UK Stanley Center for Psychiatric Research Broad Institute of MIT and Harvard Cambridge MA USA Division of Genetics and Genomics Boston Children’s Hospital Boston MA USA Department of Pediatrics Harvard Medical School Boston MA USA National Heart & Lung Institute and MRC London Institute of Medical Sciences Imperial College London London UK Cardiovascular Research Centre Royal Brompton & Harefield Hospitals NHS Trust London UK Cardiac Arrhythmia Service Cardiovascular Research Center Massachusetts General Hospital Boston MA USA Estonian Genome Center Institute of Genomics University of Tartu Tartu Estonia Diabetes Unit Massachusetts General Hospital Boston MA USA Program in Metabolism Broad Institute of MIT and Harvard Cambridge MA USA Division of Cardiology Massachusetts General Hospital Boston MA USA Cardiovascular Disease Initiative Broad Institute of MIT and Harvard Cambridge MA USA Division of General Internal Medicine Massachusetts General Hospital Boston MA USA Institute for Molecular Medicine Finland (FIMM) HiLIFE University of Helsinki Helsinki Finland Department of Public Health Faculty of Medicine University

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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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