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The genome of the model beetle and pest Tribolium castaneum

NATURE 2008年第7190期452卷 949-955页

作者： Richards, Stephen Gibbs, Richard A. Weinstock, George M. Brown, Susan J. Denell, Robin Beeman, Richard W. Gibbs, Richard Bucher, Gregor Friedrich, Markus Grimmelikhuijzen, Cornelis J. P. Klingler, Martin Lorenzen, Marce D. Roth, Siegfried Schroeder, Reinhard Tautz, Diethard Zdobnov, Evgeny M. Muzny, Donna Attaway, Tony Bell, Stephanie Buhay, Christian J. Chandrabose, Mimi N. Chavez, Dean Clerk-Blankenburg, Kerstin P. Cree, Andrew Dao, Marvin Davis, Clay Chacko, Joseph Dinh, Huyen Dugan-Rocha, Shannon Fowler, Gerald Garner, Toni T. Garnes, Jeffrey Gnirke, Andreas Hawes, Alica Hernandez, Judith Hines, Sandra Holder, Michael Hume, Jennifer Jhangiani, Shalini N. Joshi, Vandita Khan, Ziad Mohid Jackson, LaRonda Kovar, Christie Kowis, Andrea Lee, Sandra Lewis, Lora R. Margolis, Jon Morgan, Margaret Nazareth, Lynne V. Nguyen, Ngoc Okwuonu, Geoffrey Parker, David Ruiz, San-Juana Santibanez, Jireh Savard, Joel Scherer, Steven E. Schneider, Brian Sodergren, Erica Vattahil, Selina Villasana, Donna White, Courtney S. Wright, Rita Park, Yoonseong Lord, Jeff Oppert, Brenda Brown, Susan Wang, Liangjiang Savard, Joel Liu, Yue Worley, Kim Elsik, Christine G. Reese, Justin T. Elhaik, Eran Landan, Giddy Graur, Dan Arensburger, Peter Atkinson, Peter Beidler, Jim Demuth, Jeffery P. Drury, Douglas W. Du, Yu-Zhou Fujiwara, Haruhiko Maselli, Vincenza Osanai, Mizuko Robertson, Hugh M. Tu, Zhijian Wang, Jian-Jun Wang, Suzhi Song, Henry Zhang, Lan Sodergren, Erica Werner, Doreen Stanke, Mario Morgenstern, Burkhard Solovyev, Victor Kosarev, Peter Brown, Garth Chen, Hsiu-Chuan Ermolaeva, Olga Hlavina, Wratko Kapustin, Yuri Kiryutin, Boris Kitts, Paul Maglott, Donna Pruitt, Kim Sapojnikov, Victor Souvorov, Alexandre Mackey, Aaron J. Waterhouse, Robert M. Wyder, Stefan Zdobnov, Evgeny M. Kriventseva, Evgenia V. Kadowaki, Tatsuhiko Bork, Peer Aranda, Manuel Bao, Riyue Beermann, Anke Berns, Nicola Bolognesi, Renata Bonneton, Francois Bopp, Daniel Butts, Thomas Chaumot, Arnaud Denell, Robin E. Ferrier, David E. K. Gordon, Cassondra M. Jindra, Mar Baylor Coll Med Human Genome Sequencing Ctr Houston TX 77030 USA Baylor Coll Med Dept Mol & Human Genet Houston TX 77030 USA Kansas State Univ Div Biol Manhattan KS 66506 USA ARS Grain Mkt & Prod Res Ctr USDA Manhattan KS 66502 USA Univ Gottingen Johann Friedrich Blumenbach Inst Dept Dev Biol D-37077 Gottingen Germany Wayne State Univ Dept Biol Sci Detroit MI 48202 USA Univ Copenhagen Ctr Funct & Comparat Insect Genom DK-2100 Copenhagen Denmark Univ Copenhagen Dept Cell Biol & Comparat Zool Inst Biol DK-2100 Copenhagen Denmark Friedrich Alexander Univ Erlangen Dept Dev Biol Inst Biol D-91058 Erlangen Germany Univ Cologne Inst Dev Biol D-50674 Cologne Germany Univ Tubingen Interfac Inst Cell Biol D-72076 Tubingen Germany Univ Cologne Dept Genet D-50674 Cologne Germany Univ Geneva Med Sch Dept Genet Med & Dev CH-1211 Geneva Switzerland Swiss Inst Bioinformat CH-1211 Geneva Switzerland Univ London Imperial Coll Sci Technol & Med London SW7 2AZ England Childrens Hosp Oakland Res Inst BACPAC Resources Oakland CA 94609 USA MIT Broad Inst Cambridge MA 02142 USA Harvard Univ Cambridge Ctr 7 Cambridge MA 02142 USA AgraQuest Inc Davis CA 95616 USA Kansas State Univ Dept Entomol Manhattan KS 66506 USA Texas A&M Univ Dept Anim Sci College Stn TX 77843 USA Univ Houston Dept Biol & Biochem Houston TX 77204 USA Univ Calif Dept Entomol Riverside CA 92521 USA Virginia Tech Dept Biochem Blacksburg VA 24061 USA Univ Texas Arlington Dept Biol Arlington TX 76019 USA Indiana Univ Dept Biol Bloomington IN 47405 USA Yangzhou Univ Dept Plant Protect Yangzhou 225009 Peoples R China Univ Tokyo Grad Sch Frontier Sci Dept Integrated Biosci Chiba 2778562 Japan European Sch Mol Med I-80131 Naples Italy Telethon Inst Genet & Med I-80131 Naples Italy Univ Illinois Dept Entomol Urbana IL 61801 USA Univ Gottingen Dept Bioinformat Inst Microbiol & Genet D-37077 Gottingen Germany Univ London Dept Comp Sci Surrey TW20 0EX England Softberry Inc Mt Ki

Tribolium castaneum is a member of the most species-rich eukaryotic order, a powerful model organism for the study of generalized insect development, and an important pest of stored agricultural products. We describe its genome sequence here. This omnivorous beetle has evolved the ability to interact with a diverse chemical environment, as shown by large expansions in odorant and gustatory receptors, as well as P450 and other detoxification enzymes. Development in Tribolium is more representative of other insects than is Drosophila, a fact reflected in gene content and function. For example, Tribolium has retained more ancestral genes involved in cell - cell communication than Drosophila, some being expressed in the growth zone crucial for axial elongation in short- germ development. Systemic RNA interference in T. castaneum functions differently from that in Caenorhabditis elegans, but nevertheless offers similar power for the elucidation of gene function and identification of targets for selective insect control.

关键词： Disease genetics Protein folding Structural biology

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Pan-cancer analysis of whole genomes

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NATURE 2020年第7793期578卷 82-+页

作者： Campbell, Peter J. Getz, Gad Korbel, Jan O. Stuart, Joshua M. Jennings, Jennifer L. Stein, Lincoln D. Perry, Marc D. Nahal-Bose, Hardeep K. Ouellette, B. F. Francis Li, Constance H. Rheinbay, Esther Nielsen, G. Petur Sgroi, Dennis C. Wu, Chin-Lee Faquin, William C. Deshpande, Vikram Boutros, Paul C. Lazar, Alexander J. Hoadley, Katherine A. Louis, David N. Dursi, L. Jonathan Yung, Christina K. Bailey, Matthew H. Saksena, Gordon Raine, Keiran M. Buchhalter, Ivo Kleinheinz, Kortine Schlesner, Matthias Zhang, Junjun Wang, Wenyi Wheeler, David A. Ding, Li Simpson, Jared T. O'Connor, Brian D. Yakneen, Sergei Ellrott, Kyle Miyoshi, Naoki Butler, Adam P. Royo, Romina Shorser, Solomon, I Vazquez, Miguel Rausch, Tobias Tiao, Grace Waszak, Sebastian M. Rodriguez-Martin, Bernardo Shringarpure, Suyash Wu, Dai-Ying Demidov, German M. Delaneau, Olivier Hayashi, Shuto Imoto, Seiya Habermann, Nina Segre, Ayellet, V Garrison, Erik Cafferkey, Andy Alvarez, Eva G. Maria Heredia-Genestar, Jose Muyas, Francesc Drechsel, Oliver Bruzos, Alicia L. Temes, Javier Zamora, Jorge Baez-Ortega, Adrian Kim, Hyung-Lae Mashl, R. Jay Ye, Kai DiBiase, Anthony Huang, Kuan-lin Letunic, Ivica McLellan, Michael D. Newhouse, Steven J. Shmaya, Tal Kumar, Sushant Wedge, David C. Wright, Mark H. Yellapantula, Venkata D. Gerstein, Mark Khurana, Ekta Marques-Bonet, Tomas Navarro, Arcadi Bustamante, Carlos D. Siebert, Reiner Nakagawa, Hidewaki Easton, Douglas F. Ossowski, Stephan Tubio, Jose M. C. De La Vega, Francisco M. Estivill, Xavier Yuen, Denis Mihaiescu, George L. Omberg, Larsson Ferretti, Vincent Sabarinathan, Radhakrishnan Pich, Oriol Gonzalez-Perez, Abel Weiner, Amaro Taylor Fittall, Matthew W. Demeulemeester, Jonas Tarabichi, Maxime Roberts, Nicola D. Van Loo, Peter Cortes-Ciriano, Isidro Urban, Lara Park, Peter Bin Zhu Pitkaenen, Esa Li, Yilong Saini, Natalie Klimczak, Leszek J. Weischenfeldt, Joachim Sidiropoulos, Nikos Alexandrov, Ludmil B. Rabionet, Raquel Escaramis, Georgia Bosio, Mattia Holik, Aliaksei Z. Susak, Hana Prasad, Aparna Erkek, Ser Wellcome Sanger Inst Hinxton England Univ Cambridge Dept Haematol Cambridge England Broad Inst MIT & Harvard Cambridge MA 02142 USA Massachusetts Gen Hosp Ctr Canc Res Boston MA 02114 USA Massachusetts Gen Hosp Dept Pathol Boston MA 02114 USA Harvard Med Sch Boston MA 02115 USA European Bioinformat Inst EMBL European Mol Biol Lab EMBL EBI Hinxton England European Mol Biol Lab EMBL Genome Biol Unit Heidelberg Germany Univ Calif Santa Cruz Biomol Engn Dept Santa Cruz CA 95064 USA Ontario Inst Canc Res Adapt Oncol Initiat Toronto ON Canada ICGC Accelerating Res Genom Oncol ICGC ARGO Secre Int Canc Genome Consortium ICGC Toronto ON Canada Ontario Inst Canc Res Computat Biol Program Toronto ON Canada Univ Toronto Dept Mol Genet Toronto ON Canada Univ Calif San Francisco Dept Radiat Oncol San Francisco CA USA Ontario Inst Canc Res Genome Informat Program Toronto ON Canada Univ Toronto Dept Cell & Syst Biol Toronto ON Canada Ontario Inst Canc Res Genome Informat Toronto ON Canada Univ Toronto Dept Med Biophys Toronto ON Canada Massachusetts Gen Hosp Boston MA 02114 USA Univ Toronto Dept Pharmacol Toronto ON Canada Univ Calif Los Angeles Los Angeles CA USA Univ Texas MD Anderson Canc Ctr Dept Pathol Dept Genom Med Houston TX 77030 USA Univ Texas MD Anderson Canc Ctr Dept Pathol Dept Translat Mol Pathol Houston TX 77030 USA Univ North Carolina Dept Genet Chapel Hill NC 27515 USA Univ North Carolina Lineberger Comprehens Canc Ctr Chapel Hill NC 27515 USA Hosp Sick Children Toronto ON Canada Washington Univ Sch Med Alvin J Siteman Canc Ctr St Louis MO USA Washington Univ McDonnell Genome Inst St Louis MO 63110 USA German Canc Res Ctr Div Theoret Bioinformat Heidelberg Germany German Canc Res Ctr Heidelberg Ctr Personalized Oncol DKFZ HIPO Heidelberg Germany Heidelberg Univ Inst Pharm & Mol Biotechnol Heidelberg Germany Heidelberg Univ BioQuant Heidelberg Germany German Canc Res Ctr Bioinformat & Omics Data Analyt Heidelb

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements;however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution;in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4);identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6);analyses timings and patterns of tumour evolution(7);describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9);and evaluates a range of more-specialized features of cancer genomes(8,10-18).

关键词： Science Humanities and Social Sciences multidisciplinary

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A draft genome sequence of the elusive giant squid, Architeuthis dux

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GIGASCIENCE 2020年第1期9卷 giz152页

作者： da Fonseca, Rute R. Couto, Alvarina Machado, Andre M. Brejova, Brona Albertin, Carolin B. Silva, Filipe Gardner, Paul Baril, Tobias Hayward, Alex Campos, Alexandre Ribeiro, Angela M. Barrio-Hernandez, Inigo Hoving, Henk-Jan Tafur-Jimenez, Ricardo Chu, Chong Frazao, Barbara Petersen, Bent Penaloza, Fernando Musacchia, Francesco Alexander, Graham C., Jr. Osorio, Hugo Winkelmann, Inger Simakov, Oleg Rasmussen, Simon Rahman, M. Ziaur Pisani, Davide Vinther, Jakob Jarvis, Erich Zhang, Guojie Strugnell, Jan M. Castro, L. Filipe C. Fedrigo, Olivier Patricio, Mateus Li, Qiye Rocha, Sara Antunes, Agostinho Wu, Yufeng Ma, Bin Sanges, Remo Vinar, Tomas Blagoev, Blagoy Sicheritz-Ponten, Thomas Nielsen, Rasmus Gilbert, M. Thomas P. Univ Copenhagen GLOBE Inst CMEC Univ Pk 15 DK-2100 Copenhagen Denmark Univ Copenhagen Dept Biol Bioinformat Ctr Ole Maaloes Vej 5 DK-2200 Copenhagen Denmark Univ Vigo Dept Biochem Genet & Immunol Vigo 36310 Spain Univ Porto Interdisciplinary Ctr Marine & Environm Res CIIMAR Av Gen Norton Matos P-4450208 Matosinhos Portugal Comenius Univ Fac Math Phys & Informat Bratislava 84248 Slovakia Marine Biol Lab Eugene Bell Ctr Regenerat Biol & Tissue Engn Woods Hole MA 02543 USA Univ Otago Dept Biochem 710 Cumberland St Dunedin 9016 New Zealand Univ Exeter Ctr Ecol & Conservat Penryn Campus Penryn TR10 9FE Cornwall England Univ Southern Denmark Dept Biochem & Mol Biol Campusvej 55 DK-5230 Odense M Denmark GEOMAR Helmholtz Ctr Ocean Res Kiel Wischhofstr 1-3 D-24148 Kiel Germany Inst Mar Peru Esq Gamarra & Gral Valle Chucuito Apartado 22 Callao Peru Harvard Med Sch Dept Biomed Informat Boston MA 02115 USA IPMA Fitoplancton Lab Rua C Aeroporto P-1749077 Lisbon Portugal AIMST Univ Fac Sci Appl Ctr Excellence Omics Driven Computat Biodiscovery Batu 3 1-2 Bedong 08100 Kedah Malaysia Univ Copenhagen Globe Inst Evolutionary Genom Sect Oster Farimagsgade 5 DK-1353 Copenhagen Denmark Univ Nacl Autonoma Mexico Inst Invest Biomed Inst Nacl Cancerol Unidad Invest Biomed Canc Mexico City DF Mexico Telethon Inst Genet & Med Genom Med Via Campi Flegrei 34 I-80078 Naples Italy Duke Univ GCB Sequencing & Genom Technol Shared Resource CIEMAS 101 Sci Dr Durham NC 27708 USA Univ Porto I3S Rua Alfredo Allen 208 P-4200135 Porto Portugal Univ Porto IPATIMUP Inst Mol Pathol & Immunol Rua Julio Amaral de Carvalho 45 P-4200135 Porto Portugal Univ Porto Fac Med Alameda Prof Hernani Monteiro P-4200319 Porto Portugal Univ Copenhagen GLOBE Inst Sect GeoGenet Oster Voldgade 5-7 DK-1350 Copenhagen Denmark Univ Vienna Dept Mol Evolut & Dev Althanstr 14 UZA1 A-1090 Vienna Austria Univ Copenhagen Fac Hlth & Med Sci Ctr Prot Res Novo Nordisk Fdn Blegdamsvej 3

Background: The giant squid (Architeuthis dux;Steenstrup, 1857) is an enigmatic giant mollusc with a circumglobal distribution in the deep ocean, except in the high Arctic and Antarctic waters. The elusiveness of the species makes it difficult to study. Thus, having a genome assembled for this deep-sea-dwelling species will allow several pending evolutionary questions to be unlocked. Findings: We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long reads, and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from 3 different tissue types from 3 other species of squid (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein-coding genes supported by evidence, and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome. Conclusions: This annotated draft genome of A. dux provides a critical resource to investigate the unique traits of this species, including its gigantism and key adaptations to deep-sea environments.

关键词： cephalopod invertebrate genome assembly

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Global Climate

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BULLETIN OF THE AMERICAN METEOROLOGICAL SOCIETY 2023年第9期104卷 S20-S145页

作者： Dunn, Robert J. H. Aldred, Freya Gobron, Nadine Miller, John B. Willett, Kate M. Ades, Melanie Adler, Robert Allan, R. P. Anderson, John Anneville, Orlane Aono, Yasuyuki Arguez, Anthony Arosio, Carlo Augustine, John A. Azorin-Molina, Cesar Barichivich, Jonathan Basu, Aman Beck, Hylke E. Bellouin, Nicolas Benedetti, Angela Blagrave, Kevin Blenkinsop, Stephen Bock, Olivier Bodin, Xavier Bosilovich, Michael G. Boucher, Olivier Bove, Gerald Buechler, Dennis Buehler, Stefan A. Carrea, Laura Chang, Kai-Lan Christiansen, Hanne H. Christy, John R. Chung, Eui-Seok Ciasto, Laura M. Coldewey-Egbers, Melanie Cooper, Owen R. Cornes, Richard C. Covey, Curt Cropper, Thomas Crotwell, Molly Cusicanqui, Diego Davis, Sean M. de Jeu, Richard A. M. Degenstein, Doug Delaloye, Reynald Donat, Markus G. Dorigo, Wouter A. Durre, Imke Dutton, Geoff S. Duveiller, Gregory Elkins, James W. Estilow, Thomas W. Fedaeff, Nava Fereday, David Fioletov, Vitali E. Flemming, Johannes Foster, Michael J. Frith, Stacey M. Froidevaux, Lucien Fullekrug, Martin Garforth, Judith Garg, Jay Gentry, Matthew Goodman, Steven Gou, Qiqi Granin, Nikolay Guglielmin, Mauro Hahn, Sebastian Haimberger, Leopold Hall, Brad D. Harris, Ian Hemming, Debbie L. Hirschi, Martin Ho, Shu-pen (Ben) Holzworth, Robert Hrbacek, Filip Hubert, Daan Hulsman, Petra Hurst, Dale F. Inness, Antje Isaksen, Ketil John, Viju O. Jones, Philip D. Junod, Robert Kaab, Andreas Kaiser, Johannes W. Kaufmann, Viktor Kellerer-Pirklbauer, Andreas Kent, Elizabeth C. Kidd, Richard Kim, Hyungiun Kipling, Zak Koppa, Akash L'Abee-Lund, Jan Henning Lan, Xin Lantz, Kathleen O. Lavers, David Loeb, Norman G. Loyola, Diego Madelon, Remi Malmquist, Hilmar J. Marszelewski, Wlodzimierz Mayer, Michael McCabe, Matthew F. McVicar, Tim R. Mears, Carl A. Menzel, Annette Merchant, Christopher J. Miralles, Diego G. Montzka, Stephen A. Morice, Colin Moesinger, Leander Muhle, Jens Nicolas, Julien P. Noetzli, Jeannette Noges, Tiina Noll, Ben O'Keefe, John Osborn, Tim J. Park, Taejin Pellet, Cecile Pelto, Maury S. Perkins-Kirk Met Off Hadley Ctr Exeter Devon England European Commiss Joint Res Ctr Ispra Italy NOAA Global Monitoring Lab Boulder CO USA European Ctr Medium Range Weather Forecasts Reading Berks England Univ Maryland CMNS Earth Syst Sci Interdisciplinary Ctr College Pk MD 20742 USA Univ Reading Dept Meteorol Reading Berks England Univ Reading Natl Ctr Earth Observat Reading Berks England Hampton Univ Dept Atmospher & Planetary Sci Hampton VA 23668 USA Univ Savoie Mt Blanc Natl Res Inst Agr Food & Environm INRAE CARRTEL Thonon Les Bains France Osaka Prefecture Univ Grad Sch Life & Environm Sci Sakai Osaka Japan NOAA NESDIS Natl Ctr Environm Informat Asheville NC USA Univ Bremen Bremen Germany Spanish Natl Res Council CIDE Ctr Invest Desertificac CSIC UV Generalitat Valenciana Climate Atmosphere & Ocean Lab Climatoc Lab Valencia Spain Pontificia Univ Catolica Valparaiso Inst Geog Valparaiso Chile Univ East Anglia Sch Environm Sci Climat Res Unit Norwich Norfolk England York Univ Toronto ON Canada European Commiss Joint Res Ctr Ispra Italy GloH2O Almere Netherlands Univ Reading Reading Berks England Newcastle Univ Sch Engn Newcastle Upon Tyne Tyne & Wear England Univ Paris Cite CNRS Inst Phys Globe Paris IGN F-7500 Paris France Univ Savoie Mt Blanc Lab EDYTEM CNRS Le Bourget Du Lac France NASA Goddard Space Flight Ctr Global Modeling & Assimilat Off Greenbelt MD USA Sorbonne Univ Paris France Univ Virgin Isl St Thomas VI USA Univ Huntsville Alabama Huntsville AL USA Univ Hamburg Meteorol Inst CEN Fachbereich Erdsyst Wissensch Hamburg Germany Univ Colorado Cooperat Inst Res Environm Sci Boulder CO 80309 USA NOAA Chem Sci Lab Boulder CO USA Univ Ctr Svalbard Dept Geol Longyearbyen Norway Univ Alabama Huntsville AL 35899 USA IBS Ctr Climate Phys Busan South Korea NOAA Climate Predict Ctr College Pk MD USA DLR German Aerosp Ctr Oberpfaffenhofen Wessling Germany Natl Oceanog Ctr Southampton Hants England Lawrence Livermore Natl

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Mapping subnational HIV mortality in six Latin American countries with incomplete vital registration systems

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BMC MEDICINE 2021年第1期19卷 4-4页

作者： Cork, Michael A. Henry, Nathaniel J. Watson, Stefanie Croneberger, Andrew J. Baumann, Mathew Letourneau, Ian D. Yang, Mingyou Serfes, Audrey L. Abbas, Jaffar Abbasi, Nooshin Abbastabar, Hedayat Abreu, Lucas G. Abu-Gharbieh, Eman Achappa, Basavaprabhu Adabi, Maryam Adal, Tadele G. Adegbosin, Adeyinka E. Adekanmbi, Victor Adetokunboh, Olatunji O. Agudelo-Botero, Marcela Ahinkorah, Bright O. Ahmadi, Keivan Ahmed, Muktar B. Alhassan, Robert K. Alipour, Vahid Almasi-Hashiani, Amir Alvis-Guzman, Nelson Ancuceanu, Robert Andrei, Tudorel Anvari, Davood Aqeel, Muhammad Arabloo, Jalal Aremu, Olatunde Asaad, Malke Atnafu, Desta D. Atreya, Alok Quintanilla, Beatriz Paulina Ayala Azari, Samad Darshan, B. B. Baig, Atif A. Banach, Maciej Bante, Simachew A. Barboza, Miguel A. Basu, Sanjay Bedi, Neeraj Bejarano Ramirez, Diana F. Bensenor, Isabela M. Beyene, Fentahun Y. Bezabih, Yihienew M. Bhagavathula, Akshaya S. Bhardwaj, Nikha Bhardwaj, Pankaj Bhattacharyya, Krittika Bhutta, Zulfiqar A. Bijani, Ali Birlik, Sait M. Bitew, Zebenay W. Bohlouli, Somayeh Boloor, Archith Brunoni, Andre R. Butt, Zahid A. Cardenas, Rosario Carvalho, Felix Castaldelli-Maia, Joao Mauricio Castaneda-Orjuela, Carlos A. Charan, Jaykaran Chatterjee, Souranshu Chattu, Vijay Kumar Chattu, Soosanna Kumary Chowdhury, Mohiuddin Ahsanul Kabir Christopher, Devasahayam J. Chu, Dinh-Toi Cook, Aubrey J. Cormier, Natalie M. Dahlawi, Saad M. A. Daoud, Farah Davila Cervantes, Claudio A. Weaver, Nicole Davis De la Hoz, Fernando P. Demeke, Feleke M. Denova-Gutierrez, Edgar Deribe, Kebede Deuba, Keshab Dharmaratne, Samath D. Dhungana, Govinda P. Diaz, Daniel Djalalinia, Shirin Duraes, Andre R. Eagan, Arielle W. Earl, Lucas Effiong, Andem Zaki, Maysaa El Sayed El Tantawi, Maha Elayedath, Rajesh El-Jaafary, Shaimaa I. Faraon, Emerito Jose A. Faro, Andre Fattahi, Nazir Fauk, Nelsensius K. Fernandes, Eduarda Filip, Irina Fischer, Florian Foigt, Nataliya A. Foroutan, Masoud Fukumoto, Takeshi Gad, Mohamed M. Gebremariam, Tesfay B. B. Gebremedhin, Ketema B. Gebremeskel, Gebreamla Univ Washington Inst Hlth Metr & Evaluat Seattle WA 98195 USA Univ Oxford Big Data Inst Oxford England Shanghai Jiao Tong Univ Antai Coll Econ Shanghai Peoples R China McGill Univ Montreal Neurol Inst Montreal PQ Canada Univ Tehran Med Sci Adv Diagnost & Intervent Radiol Res Ctr Tehran Iran Univ Fed Minas Gerais Dept Pediat Dent Belo Horizonte MG Brazil Univ Sharjah Dept Clin Sci Sharjah U Arab Emirates Manipal Acad Higher Educ Dept Internal Med Mangalore India Hamadan Univ Med Sci Hamadan Iran Wolkite Univ Dept Publ Hlth Wolkite Ethiopia Griffith Univ Sch Med Gold Coast Qld Australia Kings Coll London Dept Populat Hlth Sci London England Stellenbosch Univ Ctr Excellence Epidemiol Modelin & Anal Stellenbosch South Africa Stellenbosch Univ Dept Global Hlth Cape Town South Africa Univ Nacl Autonoma Mexico Ctr Policy Populat & Hlth Res Mexico City DF Mexico Univ Technol Sydney Australian Ctr Publ & Populat Hlth Res ACPP HR Sydney NSW Australia Univ Nottingham Lincoln Med Sch Lincoln England Univ Lincoln Lincoln Med Sch Lincoln England Jimma Univ Dept Epidemiol Jimma Ethiopia Univ South Australia Australian Ctr Precis Hlth Adelaide SA Australia Univ Hlth & Allied Sci Inst Hlth Res Ho Ghana Iran Univ Med Sci Hlth Management & Econ Res Ctr Tehran Iran Iran Univ Med Sci Hlth Econ Dept Tehran Iran Arak Univ Med Sci Dept Epidemiol Arak Iran Univ Cartagena Res Grp Hlth Econ Cartagena Colombia ALZAK Fdn Res Grp Hosp Management & Hlth Policies Cartagena Colombia Carol Davila Univ Med & Pharm Bucharest Romania Bucharest Univ Econ Studies Stat & Econometr Dept Bucharest Romania Mazandaran Univ Med Sci Dept Parasitol Sari Iran Iranshahr Univ Med Sci Dept Parasitol Iranshahr Iran Fdn Univ Islamabad Dept Psychol Rawalpandi Pakistan Birmingham City Univ Dept Publ Hlth Birmingham W Midlands England Univ Texas Houston Dept Plast Surg Houston TX USA Bahir Dar Univ Dept Hlth Syst & Hlth Econ Bahir Dar Ethiopia Lumbini Med Coll D

BackgroundHuman immunodeficiency virus (HIV) remains a public health priority in Latin America. While the burden of HIV is historically concentrated in urban areas and high-risk groups, subnational estimates that cover multiple countries and years are missing. This paucity is partially due to incomplete vital registration (VR) systems and statistical challenges related to estimating mortality rates in areas with low numbers of HIV deaths. In this analysis, we address this gap and provide novel estimates of the HIV mortality rate and the number of HIV deaths by age group, sex, and municipality in Brazil, Colombia, Costa Rica, Ecuador, Guatemala, and *** performed an ecological study using VR data ranging from 2000 to 2017, dependent on individual country data availability. We modeled HIV mortality using a Bayesian spatially explicit mixed-effects regression model that incorporates prior information on VR completeness. We calibrated our results to the Global Burden of Disease Study *** countries displayed over a 40-fold difference in HIV mortality between municipalities with the highest and lowest age-standardized HIV mortality rate in the last year of study for men, and over a 20-fold difference for women. Despite decreases in national HIV mortality in all countries-apart from Ecuador-across the period of study, we found broad variation in relative changes in HIV mortality at the municipality level and increasing relative inequality over time in all countries. In all six countries included in this analysis, 50% or more HIV deaths were concentrated in fewer than 10% of municipalities in the latest year of study. In addition, national age patterns reflected shifts in mortality to older age groups-the median age group among decedents ranged from 30 to 45years of age at the municipality level in Brazil, Colombia, and Mexico in *** subnational estimates of HIV mortality revealed significant spatial variation and diverging local tre

关键词： HIV AIDS Latin America HIV mortality Vital registration Small area estimation Mapping Spatial statistics

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Analysis of shared heritability in common disorders of the brain

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SCIENCE 2018年第6395期360卷 1313-+页

作者： Anttila, Verneri Bulik-Sullivan, Brendan Finucane, Hilary K. Walters, Raymond K. Bras, Jose Duncan, Laramie Escott-Price, Valentina Falcone, Guido J. Gormley, Padhraig Malik, Rainer Patsopoulos, Nikolaos A. Ripke, Stephan Wei, Zhi Yu, Dongmei Lee, Phil H. Turley, Patrick Grenier-Boley, Benjamin Chouraki, Vincent Kamatani, Yoichiro Berr, Claudine Letenneur, Luc Hannequin, Didier Amouyel, Philippe Boland, Anne Deleuze, Jean-Francois Duron, Emmanuelle Vardarajan, Badri N. Reitz, Christiane Goate, Alison M. Huentelman, Matthew J. Kamboh, M. Ilyas Larson, Eric B. Rogaeva, Ekaterina St George-Hyslop, Peter Hakonarson, Hakon Kukull, Walter A. Farrer, Lindsay A. Barnes, Lisa L. Beach, Thomas G. Demirci, F. Yesim Head, Elizabeth Hulette, Christine M. Jicha, Gregory A. Kauwe, John S. K. Kaye, Jeffrey A. Leverenz, James B. Levey, Allan I. Lieberman, Andrew P. Pankratz, Vernon S. Poon, Wayne W. Quinn, Joseph F. Saykin, Andrew J. Schneider, Lon S. Smith, Amanda G. Sonnen, Joshua A. Stern, Robert A. Van Deerlin, Vivianna M. Van Eldik, Linda J. Harold, Denise Russo, Giancarlo Rubinsztein, David C. Bayer, Anthony Tsolaki, Magda Proitsi, Petra Fox, Nick C. Hampel, Harald Owen, Michael J. Mead, Simon Passmore, Peter Morgan, Kevin Noethen, Markus M. Rossor, Martin Lupton, Michelle K. Hoffmann, Per Kornhuber, Johannes Lawlor, Brian McQuillin, Andrew Al-Chalabi, Ammar Bis, Joshua C. Ruiz, Agustin Boada, Merce Seshadri, Sudha Beiser, Alexa Rice, Kenneth van der Lee, Sven J. De Jager, Philip L. Geschwind, Daniel H. Riemenschneider, Matthias Riedel-Heller, Steffi Rotter, Jerome I. Ransmayr, Gerhard Hyman, Bradley T. Cruchaga, Carlos Alegret, Montserrat Winsvold, Bendik Palta, Priit Farh, Kai-How Cuenca-Leon, Ester Furlotte, Nicholas Kurth, Tobias Ligthart, Lannie Terwindt, Gisela M. Freilinger, Tobias Ran, Caroline Gordon, Scott D. Borck, Guntram Adams, Hieab H. H. Lehtimaki, Terho Wedenoja, Juho Buring, Julie E. Schuerks, Markus Hrafnsdottir, Maria Hottenga, Jouke-Jan Penninx, Brenda Artto, Ville Kaunisto, Mari Vepsalainen, Salli Marti Massachusetts Gen Hosp Analyt Translat Genet Unit Boston MA 02114 USA Harvard Med Sch Boston MA 02115 USA Broad Inst MIT & Harvard Stanley Ctr Psychiat Res Cambridge MA 02142 USA Broad Inst MIT & Harvard Program Med & Populat Genet Cambridge MA 02142 USA MIT Dept Math Cambridge MA 02139 USA Harvard TH Chan Sch Publ Hlth Dept Epidemiol Boston MA USA UCL UK Dementia Res Inst London England UCL Dept Mol Neurosci Inst Neurol London England Stanford Univ Dept Psychiat & Behav Sci Stanford CA 94305 USA Cardiff Univ Med Res Council Ctr Neuropsychiat Genet & Genom Inst Psychol Med & Clin Neurosci Cardiff S Glam Wales Cardiff Univ Dementia Res Inst Cardiff S Glam Wales Massachusetts Gen Hosp Ctr Genom Med Boston MA 02114 USA Massachusetts Gen Hosp Dept Neurol Boston MA 02114 USA Harvard Med Sch Boston MA USA Ludwig Maximilians Univ Munchen Univ Hosp Inst Stroke & Dementia Res ISD Munich Germany Harvard Med Sch Dept Neurol Brigham & Womens Hosp Boston MA USA Charite Univ Med Berlin Berlin Germany New Jersey Inst Technol Dept Comp Sci Newark NJ 07102 USA INSERM U1167 LabEx DISTALZ Lille France Inst Pasteur U1167 Lille France Univ Lille Risk Factors & Mol Determinants Aging Related Dis U1167 RIDAGE Lille France Ctr Hosp Univ Lille France RIKEN Ctr Integrat Med Sci Lab Stat Anal Yokohama Kanagawa Japan Kyoto Univ Grad Sch Med Ctr Genom Med Kyoto Japan INSERM U1061 Neuropsychiat Epidemiol & Clin Res Montpellier France Univ Montpellier Montpellier France Montpellier Univ Hosp Gui Chauliac Memory Res & Resources Ctr Dept Neurol Montpellier France INSERM UMR 1219 Bordeaux France Univ Bordeaux Bordeaux France Rouen Univ Hosp Rouen France INSERM U1245 Rouen France CEA Inst Biol Francois Jacob CNRGH Evry France Hop Broca AP HP Dept Gerontol Paris France Univ Paris Sud XI Hop Paul Brousse Le Kremlin Bicetre Paris France Columbia Univ Gertrude H Sergievsky Ctr New York NY USA Columbia Univ Dept Neurol New York NY USA

Disorders of the brain can exhibit considerable epidemiological comorbidity and often share symptoms, provoking debate about their etiologic overlap. We quantified the genetic sharing of 25 brain disorders from genome-wide association studies of 265,218 patients and 784,643 control participants and assessed their relationship to 17 phenotypes from 1,191,588 individuals. Psychiatric disorders share common variant risk, whereas neurological disorders appear more distinct from one another and from the psychiatric disorders. We also identified significant sharing between disorders and a number of brain phenotypes, including cognitive measures. Further, we conducted simulations to explore how statistical power, diagnostic misclassification, and phenotypic heterogeneity affect genetic correlations. These results highlight the importance of common genetic variation as a risk factor for brain disorders and the value of heritability-based methods in understanding their etiology.

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