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Sequence data and association statistics from 12,940 type 2 diabetes cases and controls

Scientific data 2017年第1期4卷 170179页

作者： Jason Flannick Christian Fuchsberger Anubha Mahajan Tanya M Teslovich Vineeta Agarwala Kyle J Gaulton Lizz Caulkins Ryan Koesterer Clement Ma Loukas Moutsianas Davis J McCarthy Manuel A Rivas John R B Perry Xueling Sim Thomas W Blackwell Neil R Robertson N William Rayner Pablo Cingolani Adam E Locke Juan Fernandez Tajes Heather M Highland Josee Dupuis Peter S Chines Cecilia M Lindgren Christopher Hartl Anne U Jackson Han Chen Jeroen R Huyghe Martijn van de Bunt Richard D Pearson Ashish Kumar Martina Müller-Nurasyid Niels Grarup Heather M Stringham Eric R Gamazon Jaehoon Lee Yuhui Chen Robert A Scott Jennifer E Below Peng Chen Jinyan Huang Min Jin Go Michael L Stitzel Dorota Pasko Stephen C J Parker Tibor V Varga Todd Green Nicola L Beer Aaron G Day-Williams Teresa Ferreira Tasha Fingerlin Momoko Horikoshi Cheng Hu Iksoo Huh Mohammad Kamran Ikram Bong-Jo Kim Yongkang Kim Young Jin Kim Min-Seok Kwon Juyoung Lee Selyeong Lee Keng-Han Lin Taylor J Maxwell Yoshihiko Nagai Xu Wang Ryan P Welch Joon Yoon Weihua Zhang Nir Barzilai Benjamin F Voight Bok-Ghee Han Christopher P Jenkinson Teemu Kuulasmaa Johanna Kuusisto Alisa Manning Maggie C Y Ng Nicholette D Palmer Beverley Balkau Alena Stančáková Hanna E Abboud Heiner Boeing Vilmantas Giedraitis Dorairaj Prabhakaran Omri Gottesman James Scott Jason Carey Phoenix Kwan George Grant Joshua D Smith Benjamin M Neale Shaun Purcell Adam S Butterworth Joanna M M Howson Heung Man Lee Yingchang Lu Soo-Heon Kwak Wei Zhao John Danesh Vincent K L Lam Kyong Soo Park Danish Saleheen Wing Yee So Claudia H T Tam Uzma Afzal David Aguilar Rector Arya Tin Aung Edmund Chan Carmen Navarro Ching-Yu Cheng Domenico Palli Adolfo Correa Joanne E Curran Dennis Rybin Vidya S Farook Sharon P Fowler Barry I Freedman Michael Griswold Daniel Esten Hale Pamela J Hicks Chiea-Chuen Khor Satish Kumar Benjamin Lehne Dorothée Thuillier Wei Yen Lim Jianjun Liu Marie Loh Solomon K Musani Sobha Puppala William R Scott Loïc Yengo Sian-Tsung Tan Herman A Taylor Farook Thameem Gregory Wilson Tien Yin Wong Pål Rasmu Department of Molecular Biology Massachusetts General Hospital Boston Massachusetts USA. Program in Medical and Population Genetics Broad Institute Cambridge Massachusetts USA. Department of Biostatistics and Center for Statistical Genetics University of Michigan Ann Arbor Michigan USA. Wellcome Trust Centre for Human Genetics Nuffield Department of Medicine University of Oxford Oxford UK. Harvard-MIT Division of Health Sciences and Technology Massachusetts Institute of Technology Cambridge Massachusetts USA. Department of Statistics University of Oxford Oxford UK. Genetics of Complex Traits University of Exeter Medical School University of Exeter Exeter UK. MRC Epidemiology Unit Institute of Metabolic Science University of Cambridge Cambridge UK. Department of Twin Research and Genetic Epidemiology King's College London London UK. Oxford Centre for Diabetes Endocrinology and Metabolism Radcliffe Department of Medicine University of Oxford Oxford UK. Department of Human Genetics Wellcome Trust Sanger Institute Hinxton Cambridgeshire UK. School of Computer Science McGill University Montreal Quebec Canada. McGill University and Génome Québec Innovation Centre Montreal Quebec Canada. Human Genetics Center The University of Texas Graduate School of Biomedical Sciences at Houston The University of Texas Health Science Center at Houston Houston Texas USA. Department of Biostatistics Boston University School of Public Health Boston Massachusetts USA. National Heart Lung and Blood Institute's Framingham Heart Study Framingham Massachusetts USA. Medical Genomics and Metabolic Genetics Branch National Human Genome Research Institute National Institutes of Health Bethesda Maryland USA. Department of Biostatistics Harvard School of Public Health Boston Massachusetts USA. Chronic Disease Epidemiology Swiss Tropical and Public Health Institute University of Basel Basel Switzerland. Institute of Genetic Epidemiology Helmholtz Zentrum München German R

To investigate the genetic basis of type 2 diabetes (T2D) to high resolution, the GoT2D and T2D-GENES consortia catalogued variation from whole-genome sequencing of 2,657 European individuals and exome sequencing of 12,940 individuals of multiple ancestries. Over 27M SNPs, indels, and structural variants were identified, including 99% of low-frequency (minor allele frequency [MAF] 0.1-5%) non-coding variants in the whole-genome sequenced individuals and 99.7% of low-frequency coding variants in the whole-exome sequenced individuals. Each variant was tested for association with T2D in the sequenced individuals, and, to increase power, most were tested in larger numbers of individuals (>80% of low-frequency coding variants in ~82 K Europeans via the exome chip, and ~90% of low-frequency non-coding variants in ~44 K Europeans via genotype imputation). The variants, genotypes, and association statistics from these analyses provide the largest reference to date of human genetic information relevant to T2D, for use in activities such as T2D-focused genotype imputation, functional characterization of variants or genes, and other novel analyses to detect associations between sequence variation and T2D.

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Identification of host interactions for phenotypic antimalarial hits

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Journal of cheminformatics 2014年第SUPPL 1期6卷 O12页

作者： Andreas Spitzmüller Jordi Mestres Chemotargets SL and Systems Pharmacology Group Research Programme on Biomedical Informatics (GRIB) IMIM Hospital del Mar Research Institute and Universitat Pompeu Fabra Parc de Recerca Biomèdica Doctor Aiguader 88 08003 Barcelona Catalonia Spain.

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British Society of Breast Radiology Annual Scientific Meeting 2016

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Breast Cancer research 2016年第1期18卷 1-20页

作者： Ameerah Mohd Azmil Matthew Wallis Gaurav Jyoti Bansal Eleri Davies Susan Astley Fleur Kilburn-Toppin Mohamad Hajaj Sian Taylor-Phillip Anne Buckley Nuala Healy Aine Quinn Sylvia O’Keeffe Teri Ang Anthony Maxwell Yit Y. Lim Elaine Harkness Soujanya Gadde Richard Emsley Guy Stevens Kate Gower Thomas Jennifer Ferguson Robert Hills Sabrina Rajan Nisha Sharma Ajit Kishore John O’ Dowd Claire Murphy Ken Lindsay Guneesh Dadayal Anne Nielsen Moody Madeleine Whitaker Stephen Wolstenhulme Jane Bull Anne-Marie Culpan Natalia Roszkowski Alexis Grima Michaela Stahnke Caroline Rubin Ruth Walker Rachel Oeppen Srikanth Puttagunta Karen Gray Shama Puri Anne Turnbull Mark Bagnall Joanne York Stuart Benney Amit Goyal Rebecca Millican-Slater Sana Pascaline Janet Flinn Kim Thomson Beatrix Elsberger Ashley Topps Simon Barr Panagiotis Pikoulas Susan Pritchard Muthyala Sreenivas Sophie Greenhalgh Anju Nandhra Sheetal Sharma Archita Gulati Furhan Razzaq Sana Khan Jacqueline McKillen Rupert Larkin Sachin Kamat Carla Goncalves Alan Tan Asha Eleti Nithya Vidyaprakash Michelle A. McMahon Barbara J. G. Dall Faisal Majid Ramachadra Rattehalli Vandana Gaur Alistair Mackenzie Lucy Warren Mishal Patel Mark Halling-Brown Kenneth Young Louise Wilkinson James Tanner Rachael Currie Sharron Balyes Julie Wragg Georgiana Zamfir Pallavi Ayra Max Marsden James Butterworth Shona Sinha Anil Desai Anna Metafa Anne Nielsen-Moody Laura Ward Samantha Heller Sue Hudson Kathryn Taylor Elizabeth Orlowski Argyro Xyda Steven Allen Kate Downey Richard Sidebottom Ahmad Lodhi Anthony Howell Gareth Evans Yit Lim Yan Chen Elizabeth Lepine-Williams Steven Henderson Janet Litherland Naveed Altaf Yvonne Bury Nerys Forester Mei Chan Chin Caroline Taylor Pippa Skippage Aneet Sian Rita McAvinchey Tom Evans Sian Nisbet Alex Murray Raquel Clark Castillo Hannah Markham Timothy Thomas Anil Jain Joseph Wan Jaanilka Molderson Helen Newman Simon Lowes Linsley Lunt Sadia Sultana Varun Chillal Rebecca Dalton David Reeves Jamie Sergeant Liz Edwards Kate Jenkins Shaheeda Shaikh Elizabeth Cardiff University Cardiff UK Cambridge Breast Unit Cambridge UK Cambridge University Hospitals NHS Foundation Trust Cambridge UK The Breast Centre University Hospital of Llandough Cardiff UK Nightingale Centre and Genesis Prevention Centre University Hospital of South Manchester Manchester UK Centre for Imaging Sciences Institute of Population Health University of Manchester Manchester UK University of Manchester Manchester UK The Nightingale Centre University Hospital of South Manchester Manchester UK Division of Informatics Imaging and Data Sciences School of Health Sciences University of Manchester Manchester UK University of Warwick Coventry UK Department of Diagnostic Radiology St. James’s Hospital Dublin Ireland Manchester Medical School University of Manchester Manchester UK University Hospital of South Manchester NHS Foundation Trust Manchester UK Centre for Biostatistics Institute of Population Health University of Manchester Manchester UK Breast Test Wales Cardiff UK Public Health Wales Wales UK Cardiff University School of Medicine Cardiff UK Leeds Teaching Hospitals NHS Trust Leeds UK Leeds teaching Hospitals NHS Trust Leeds UK Leeds Teaching Hospitals Leeds UK The Leeds Teaching Hospitals NHS Trust Leeds UK St James’s University Hospital Leeds UK Leeds Teaching Hospitals Trust Leeds UK Airedale General Hospital Keighley/West Yorkshire UK University of Leeds Leeds UK University Hospital Southampton Southampton UK Hairmyres Hospital Lanarkshire Scotland UK Royal Derby Hospital Derby UK Kettering General Hospital Kettering UK Ninewells Hospital Dundee UK University Hospitals of Coventry and Warwickshire Coventry West Midlands UK University Hospitals Coventry and Warwickshire NHS Trust Coventry UK UHCW NHS Trust Coventry West Midlands UK University Hospital Coventry and Warwickshire Coventry UK Warwick Medical School Coventry West Midlands UK Queen Elizabeth Hospital Gateshead Gateshead UK Royal Liverpool University

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Erratum to: Methods for evaluating medical tests and biomarkers

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Diagnostic and prognostic research 2017年第1期1卷 11页

作者： Gowri Gopalakrishna Miranda Langendam Rob Scholten Patrick Bossuyt Mariska Leeflang Anna Noel-Storr James Thomas Iain Marshall Byron Wallace Penny Whiting Clare Davenport Gowri GopalaKrishna Isabel de Salis Sue Mallett Robert Wolff Richard Riley Marie Westwood Jos Kleinen Gary Collins Hans Reitsma Karel Moons Antonia Zapf Annika Hoyer Katharina Kramer Oliver Kuss J Ensor J J Deeks E C Martin R D Riley Gerta Rücker Susanne Steinhauser Martin Schumacher Joie Ensor Kym Snell Brian Willis Thomas Debray Jon Deeks Lavinia Ferrante di Ruffano Sian Taylor-Phillips Chris Hyde Stuart A Taylor Gauraang Batnagar Lavinia Ferrante Di Ruffano Farah Seedat Aileen Clarke Sarah Byron Frances Nixon Rebecca Albrow Thomas Walker Carla Deakin Zhivko Zhelev Harriet Hunt Yaling Yang Lucy Abel James Buchanan Thomas Fanshawe Bethany Shinkins Laure Wynants Jan Verbakel Sabine Van Huffel Dirk Timmerman Ben Van Calster Aeliko Zwinderman Jason Oke Jack O'Sullivan Rafael Perera Brian Nicholson Hannah L Bromley Tracy E Roberts Adele Francis Denniis Petrie G Bruce Mann Kinga Malottki Holly Smith Lucinda Billingham Alice Sitch Oke Gerke Mie Holm-Vilstrup Eivind Antonsen Segtnan Ulrich Halekoh Poul Flemming Høilund-Carlsen Bernard G Francq Jac Dinnes Julie Parkes Walter Gregory Jenny Hewison Doug Altman William Rosenberg Peter Selby Julien Asselineau Paul Perez Aïssatou Paye Emilie Bessede Cécile Proust-Lima Christiana Naaktgeboren Joris de Groot Anne Rutjes Johannes Reitsma Emmanuel Ogundimu Jonathan Cook Yannick Le Manach Yvonne Vergouwe Romin Pajouheshnia Rolf Groenwold Karen Moons Linda Peelen Daan Nieboer Bavo De Cock Micael J Pencina Ewout W Steyerberg Jennifer Cooper Nick Parsons Chris Stinton Steve Smith Andy Dickens Rachel Jordan Alexandra Enocson David Fitzmaurice Peymane Adab Charles Boachie Gaj Vidmar Karoline Freeman Martin Connock Rachel Court Carl Moons Jessica Harris Andrew Mumford Zoe Plummer Kurtis Lee Barnaby Reeves Chris Rogers Veerle Verheyden Gianni D Angelini Gavin J Murphy Jeremy Huddy Melody Ni Katherine Good Graham Cooke 1Department of Clinical Epidemiology Biostatistics & Bioinformatics Academic Medical Center University of Amsterdam Amsterdam The Netherlands. 2Cochrane Netherlands Julius Center for Health Sciences and Primary Care University Medical Center Utrecht Utrecht Netherlands. 234Department of Clinical Epidemiology Biostatistics & Bioinformatics Academic Medical Center University of Amsterdam Amsterdam The Netherlands. 49Department of Clinical Epidemiology Biostatistics & Bioinformatics Academic Medical Center University of Amsterdam Amsterdam The Netherlands. 3Cochrane Dementia and Cognitive Improvement Group University of Oxford Oxford UK. 4EPPI-Centre Department of Social Science University College London London UK. 5Division of Health and Social Care Research King's College London London UK. 6College of Computer and Information Science Northeastern University Boston USA. 13University Hospitals Bristol NHS Foundation Trust School of Social and Community Medicine Bristol UK. 275Institute of Applied Health Research University of Birmingham Birmingham UK. 9Department of Clinical Epidemiology Biostatistics & Bioinformatics Academic Medical Center University of Amsterdam Amsterdam The Netherlands. 10School of Social and Community Medicine University of Bristol Bristol UK. 179Institute of Applied Health Research University of Birmingham Birmingham UK. 12Kleijnen Systematic Reviews Ltd York UK. 25Research Institute for Primary Care and Health Sciences Keele University Keele UK. 188Centre for Statistics in Medicine Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences University of Oxford Oxford UK. 191Julius Center for Health Sciences and Primary Care University Medical Center Utrecht 3584 CG Utrecht Netherlands. 237Julius Center for Health Sciences and Primary Care University Medical Center Utrecht 3584 CG Utrecht Netherlands. 18Department of Medical Statistics University Medical Center Göttingen Göttingen Germany. 19Institute for B

[This corrects the article DOI: 10.1186/s41512-016-0001-y.].

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Erratum to: Scaling up strategies of the chronic respiratory disease programme of the European Innovation Partnership on Active and Healthy Ageing (Action Plan B3: Area 5)

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Clinical and translational allergy 2017年第1期7卷 5页

作者： J Bousquet J Farrell G Crooks P Hellings E H Bel M Bewick N H Chavannes J Correia de Sousa A A Cruz T Haahtela G Joos N Khaltaev J Malva A Muraro M Nogues S Palkonen S Pedersen C Robalo-Cordeiro B Samolinski T Strandberg A Valiulis A Yorgancioglu T Zuberbier A Bedbrook W Aberer M Adachi A Agusti C A Akdis M Akdis J Ankri A Alonso I Annesi-Maesano I J Ansotegui J M Anto S Arnavielhe H Arshad C Bai I Baiardini C Bachert A K Baigenzhin C Barbara E D Bateman B Beghé A Ben Kheder K S Bennoor M Benson K C Bergmann T Bieber C Bindslev-Jensen L Bjermer H Blain F Blasi A L Boner M Bonini S Bonini S Bosnic-Anticevitch L P Boulet R Bourret P J Bousquet F Braido A H Briggs C E Brightling J Brozek R Buhl P G Burney A Bush F Caballero-Fonseca D Caimmi M A Calderon P M Calverley P A M Camargos G W Canonica T Camuzat K H Carlsen W Carr A Carriazo T Casale A M Cepeda Sarabia L Chatzi Y Z Chen R Chiron E Chkhartishvili A G Chuchalin K F Chung G Ciprandi I Cirule L Cox D J Costa A Custovic R Dahl S E Dahlen U Darsow G De Carlo F De Blay T Dedeu D Deleanu E De Manuel Keenoy P Demoly J A Denburg P Devillier A Didier A T Dinh-Xuan R Djukanovic D Dokic H Douagui G Dray R Dubakiene S R Durham M S Dykewicz Y El-Gamal R Emuzyte L M Fabbri M Fletcher A Fiocchi A Fink Wagner J Fonseca W J Fokkens F Forastiere P Frith M Gaga A Gamkrelidze J Garces J Garcia-Aymerich B Gemicioğlu J E Gereda S González Diaz M Gotua I Grisle L Grouse Z Gutter M A Guzmán L G Heaney B Hellquist-Dahl D Henderson A Hendry J Heinrich D Heve F Horak J O' B Hourihane P Howarth M Humbert M E Hyland M Illario J C Ivancevich J R Jardim E J Jares C Jeandel C Jenkins S L Johnston O Jonquet K Julge K S Jung J Just I Kaidashev M R Khaitov O Kalayci A F Kalyoncu T Keil P K Keith L Klimek B Koffi N'Goran V Kolek G H Koppelman M L Kowalski I Kull P Kuna V Kvedariene B Lambrecht S Lau D Larenas-Linnemann D Laune L T T Le P Lieberman B Lipworth J Li K Lodrup Carlsen R Louis W MacNee Y Magard A Magnan B Mahboub A Mair I Majer M J Makela P Manning S Mara G D Marshall M R Masjedi P M CHRU University Hospital 371 Avenue du Doyen Gaston Giraud 34295 Montpellier Cedex 5 France. MACVIA-LR Contre les MAladies Chroniques pour un VIeillissement Actif en Languedoc Roussilon European Innovation Partnership on Active and Healthy Ageing Reference Site Montpellier France. INSERM VIMA: Ageing and Chronic Diseases Epidemiological and Public Health Approaches U1168 Paris France. UVSQ UMR-S 1168 Université Versailles St-Quentin-en-Yvelines Paris France. Department of Health Social Services and Public Safety Belfast Northern Ireland UK. EIP on AHA European Innovation Partnership on Active and Healthy Ageing Reference Site Scottish Centre for Telehealth and Telecare NHS 24 Glasgow UK. Laboratory of Clinical Immunology Department of Microbiology and Immunology KU Leuven Louvain Belgium. European Academy of Allergy and Clinical Immunology Zurich Switzerland. Department of Respiratory Medicine Academic Medical Center (AMC) University of Amsterdam Amsterdam The Netherlands. European Respiratory Society Lausanne Switzerland. iQ4U Consultants Ltd London UK. Department of Public Health and Primary Care Leiden University Medical Center Leiden The Netherlands. Global Alliance Against Chronic Respiratory Diseases (GARD) Cape Town South Africa. International Primary Care Respiratory Group Westhill UK. Life and Health Sciences Research Institute ICVS School of Health Sciences University of Minho Braga Portugal. ProAR - Nucleo de Excelencia em Asma Federal University of Bahia Bahia Brazil. GARD Executive Committee Bahia Brazil. EIP on AHA Commitment for Action Lisbon Portugal. Skin and Allergy Hospital Helsinki University Hospital Helsinki Finland. Department of Respiratory Medicine Ghent University Hospital Ghent Belgium. Faculty of Medicine University of Coimbra Coimbra Portugal. Ageing@Coimbra Reference Site Coimbra Portugal. Food Allergy Referral Centre Veneto Region Department of Women and Child Health Padua General University Hospital Padua It

[This corrects the article DOI: 10.1186/s13601-016-0116-9.].

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Assessment of NER solutions against the first and second CALBC Silver Standard Corpus

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Journal of biomedical Semantics 2011年第5期2卷 1-12页

作者： Rebholz-Schuhmann, Dietrich Yepes, Antonio Jimeno Li, Chen Kafkas, Senay Lewin, Ian Kang, Ning Corbett, Peter Milward, David Buyko, Ekaterina Beisswanger, Elena Hornbostel, Kerstin Kouznetsov, Alexandre Witte, René Laurila, Jonas B Baker, Christopher JO Kuo, Cheng-Ju Clematide, Simone Rinaldi, Fabio Farkas, Richárd Móra, György Hara, Kazuo Furlong, Laura I Rautschka, Michael Neves, Mariana Lara Pascual-Montano, Alberto Wei, Qi Collier, Nigel Chowdhury, Md Faisal Mahbub Lavelli, Alberto Berlanga, Rafael Morante, Roser Van Asch, Vincent Daelemans, Walter Marina, José Luís van Mulligen, Erik Kors, Jan Hahn, Udo European Bioinformatics Institute EMBL Outstation Hinxton Cambridge CB10 1SD United Kingdom Erasmus University Medical Center Dept. of Medical Informatics Rotterdam Netherlands St. John's Innovation Centre Linguamatics Ltd Cambridge United Kingdom Friedrich-Schiller-Universität Language and Information Engineering (JULIE) Lab Jena Germany University of New Brunswick Dept. of Computer Science and Applied Statistics Canada Concordia University Dept. of Computer Science and Software Engineering Montreal Canada Academia Sinica Institute of Information Science Taipei 115 Taiwan University of Zürich Switzerland Hungarian Academy of Sciences Research Group on Artificial Intelligence Hungary Nara Institute of Science and Technology Nara Japan IMIM (Hospital del Mar Research Institute) Universitat Pompeu Fabra Research Programme on Biomedical Informatics (GRIB) Barcelona Spain National Center for Biotechnology-CSIC Madrid Spain National Institute of Informatics Tokyo Japan Fondazione Bruno Kessler Trento Italy Universitat Jaume I Spain University of Antwerp CLiPS Belgium Complutense University of Madrid Spain

Background: Competitions in text mining have been used to measure the performance of automatic text processing solutions against a manually annotated gold standard corpus (GSC). The preparation of the GSC is time-consuming and costly and the final corpus consists at the most of a few thousand documents annotated with a limited set of semantic groups. To overcome these shortcomings, the CALBC project partners (PPs) have produced a large-scale annotated biomedical corpus with four different semantic groups through the harmonisation of annotations from automatic text mining solutions, the first version of the Silver Standard Corpus (SSC-I). The four semantic groups are chemical entities and drugs (CHED), genes and proteins (PRGE), diseases and disorders (DISO) and species (SPE). This corpus has been used for the First CALBC Challenge asking the participants to annotate the corpus with their text processing solutions. Results: All four PPs from the CALBC project and in addition, 12 challenge participants (CPs) contributed annotated data sets for an evaluation against the SSC-I. CPs could ignore the training data and deliver the annotations from their genuine annotation system, or could train a machine-learning approach on the provided pre-annotated data. In general, the performances of the annotation solutions were lower for entities from the categories CHED and PRGE in comparison to the identification of entities categorized as DISO and SPE. The best performance over all semantic groups were achieved from two annotation solutions that have been trained on the SSC-I. The data sets from participants were used to generate the harmonised Silver Standard Corpus II (SSC-II), if the participant did not make use of the annotated data set from the SSC-I for training purposes. The performances of the participants' solutions were again measured against the SSC-II. The performances of the annotation solutions showed again better results for DISO and SPE in comparison to CHED and P

关键词： Chemical Entity Cosine Similarity Semantic Type Semantic Group Annotate Corpus

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