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Furness K, Harris M, Lassemillante A, Keenan S, Smith N, Desneves KJ, King S. Patient Mealtime Experience: Capturing Patient Perceptions Using a Novel Patient Mealtime Experience Tool. Nutrients 2023; 15:2747. [PMID: 37375651 DOI: 10.3390/nu15122747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 05/23/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
INTRODUCTION The aim of this study is to describe the mealtime experience using the qualitative components of the Austin Health Patient Mealtime Experience Tool (AHPMET) to complement the quantitative findings of this tool. METHODS A multiphase, cross-sectional study was undertaken across all sites of Austin Health (Victoria, Australia) between March 2020 and November 2021. Patient mealtime experience was measured using the AHPMET. Descriptive statistics and a deductive thematic analysis approach described the patients' mealtime experiences. RESULTS Questionnaire data were collected from 149 participants. Patients were most satisfied with staff interactions, and least satisfied with dimensions of food quality, specifically, flavour, presentation, and menu variety. Clinical symptoms, nutrition impact symptoms and the patient's position were barriers to consumption. DISCUSSION Food quality was perceived as the poorest aspect of patient satisfaction with the hospital foodservice, particularly flavour, presentation, and menu variety. Future foodservice quality improvements must prioritise improving food quality to have the greatest impact on patient satisfaction. While clinical and organisational systems have a role in improving mealtime experience and oral intake, communicating patient perceptions of the mealtime experience is critical for responding to current perceptions of hospital food quality. CONCLUSION Mealtime experience in the hospital has a significant impact on oral intake and patients' wider perception of hospital services. Questionnaires have been used to capture patient satisfaction with foodservice in the hospital; however, no comprehensive questionnaires including qualitative questions that capture the broader mealtime experience have been validated across different hospital settings. The tool developed through this study can be implemented in any acute and subacute health service to provide feedback and improve the mealtime experience of patients. This has the capacity to improve mealtime intake, mitigate malnutrition, and improve quality of life and patient outcomes.
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Affiliation(s)
- Kate Furness
- Department Sport, Exercise and Nutrition Sciences, School of Allied Health, Human Services and Sport, La Trobe University, Bundoora, VIC 3086, Australia
- School of Health Sciences, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
| | - Melina Harris
- School of Health Sciences, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
| | - Annie Lassemillante
- Department Sport, Exercise and Nutrition Sciences, School of Allied Health, Human Services and Sport, La Trobe University, Bundoora, VIC 3086, Australia
- School of Health Sciences, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
| | - Stephen Keenan
- School of Health Sciences, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
| | - Natasha Smith
- School of Health Sciences, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
- Austin Health, Nutrition and Dietetics Department, Division of Allied Health, Heidelberg, VIC 3084, Australia
| | - Katherine J Desneves
- Austin Health, Nutrition and Dietetics Department, Division of Allied Health, Heidelberg, VIC 3084, Australia
| | - Sam King
- Austin Health, Nutrition and Dietetics Department, Division of Allied Health, Heidelberg, VIC 3084, Australia
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Roaldsen MB, Eltoft A, Wilsgaard T, Christensen H, Engelter ST, Indredavik B, Jatužis D, Karelis G, Kõrv J, Lundström E, Petersson J, Putaala J, Søyland MH, Tveiten A, Bivard A, Johnsen SH, Mazya MV, Werring DJ, Wu TY, De Marchis GM, Robinson TG, Mathiesen EB, Valente M, Chen A, Sharobeam A, Edwards L, Blair C, Christensen L, Ægidius K, Pihl T, Fassel-Larsen C, Wassvik L, Folke M, Rosenbaum S, Gharehbagh SS, Hansen A, Preisler N, Antsov K, Mallene S, Lill M, Herodes M, Vibo R, Rakitin A, Saarinen J, Tiainen M, Tumpula O, Noppari T, Raty S, Sibolt G, Nieminen J, Niederhauser J, Haritoncenko I, Puustinen J, Haula TM, Sipilä J, Viesulaite B, Taroza S, Rastenyte D, Matijosaitis V, Vilionskis A, Masiliunas R, Ekkert A, Chmeliauskas P, Lukosaitis V, Reichenbach A, Moss TT, Nilsen HY, Hammer-Berntzen R, Nordby LM, Weiby TA, Nordengen K, Ihle-Hansen H, Stankiewiecz M, Grotle O, Nes M, Thiemann K, Særvold IM, Fraas M, Størdahl S, Horn JW, Hildrum H, Myrstad C, Tobro H, Tunvold JA, Jacobsen O, Aamodt N, Baisa H, Malmberg VN, Rohweder G, Ellekjær H, Ildstad F, Egstad E, Helleberg BH, Berg HH, Jørgensen J, Tronvik E, Shirzadi M, Solhoff R, Van Lessen R, Vatne A, Forselv K, Frøyshov H, Fjeldstad MS, Tangen L, Matapour S, Kindberg K, Johannessen C, Rist M, Mathisen I, Nyrnes T, Haavik A, Toverud G, Aakvik K, Larsson M, Ytrehus K, Ingebrigtsen S, Stokmo T, Helander C, Larsen IC, Solberg TO, Seljeseth YM, Maini S, Bersås I, Mathé J, Rooth E, Laska AC, Rudberg AS, Esbjörnsson M, Andler F, Ericsson A, Wickberg O, Karlsson JE, Redfors P, Jood K, Buchwald F, Mansson K, Gråhamn O, Sjölin K, Lindvall E, Cidh Å, Tolf A, Fasth O, Hedström B, Fladt J, Dittrich TD, Kriemler L, Hannon N, Amis E, Finlay S, Mitchell-Douglas J, McGee J, Davies R, Johnson V, Nair A, Robinson M, Greig J, Halse O, Wilding P, Mashate S, Chatterjee K, Martin M, Leason S, Roberts J, Dutta D, Ward D, Rayessa R, Clarkson E, Teo J, Ho C, Conway S, Aissa M, Papavasileiou V, Fry S, Waugh D, Britton J, Hassan A, Manning L, Khan S, Asaipillai A, Fornolles C, Tate ML, Chenna S, Anjum T, Karunatilake D, Foot J, VanPelt L, Shetty A, Wilkes G, Buck A, Jackson B, Fleming L, Carpenter M, Jackson L, Needle A, Zahoor T, Duraisami T, Northcott K, Kubie J, Bowring A, Keenan S, Mackle D, England T, Rushton B, Hedstrom A, Amlani S, Evans R, Muddegowda G, Remegoso A, Ferdinand P, Varquez R, Davis M, Elkin E, Seal R, Fawcett M, Gradwell C, Travers C, Atkinson B, Woodward S, Giraldo L, Byers J, Cheripelli B, Lee S, Marigold R, Smith S, Zhang L, Ghatala R, Sim CH, Ghani U, Yates K, Obarey S, Willmot M, Ahlquist K, Bates M, Rashed K, Board S, Andsberg G, Sundayi S, Garside M, Macleod MJ, Manoj A, Hopper O, Cederin B, Toomsoo T, Gross-Paju K, Tapiola T, Kestutis J, Amthor KF, Heermann B, Ottesen V, Melum TA, Kurz M, Parsons M, Valente M, Chen A, Sharobeam A, Edwards L, Blair C. Safety and efficacy of tenecteplase in patients with wake-up stroke assessed by non-contrast CT (TWIST): a multicentre, open-label, randomised controlled trial. Lancet Neurol 2023; 22:117-126. [PMID: 36549308 DOI: 10.1016/s1474-4422(22)00484-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Current evidence supports the use of intravenous thrombolysis with alteplase in patients with wake-up stroke selected with MRI or perfusion imaging and is recommended in clinical guidelines. However, access to advanced imaging techniques is often scarce. We aimed to determine whether thrombolytic treatment with intravenous tenecteplase given within 4·5 h of awakening improves functional outcome in patients with ischaemic wake-up stroke selected using non-contrast CT. METHODS TWIST was an investigator-initiated, multicentre, open-label, randomised controlled trial with blinded endpoint assessment, conducted at 77 hospitals in ten countries. We included patients aged 18 years or older with acute ischaemic stroke symptoms upon awakening, limb weakness, a National Institutes of Health Stroke Scale (NIHSS) score of 3 or higher or aphasia, a non-contrast CT examination of the head, and the ability to receive tenecteplase within 4·5 h of awakening. Patients were randomly assigned (1:1) to either a single intravenous bolus of tenecteplase 0·25 mg per kg of bodyweight (maximum 25 mg) or control (no thrombolysis) using a central, web-based, computer-generated randomisation schedule. Trained research personnel, who conducted telephone interviews at 90 days (follow-up), were masked to treatment allocation. Clinical assessments were performed on day 1 (at baseline) and day 7 of hospital admission (or at discharge, whichever occurred first). The primary outcome was functional outcome assessed by the modified Rankin Scale (mRS) at 90 days and analysed using ordinal logistic regression in the intention-to-treat population. This trial is registered with EudraCT (2014-000096-80), ClinicalTrials.gov (NCT03181360), and ISRCTN (10601890). FINDINGS From June 12, 2017, to Sept 30, 2021, 578 of the required 600 patients were enrolled (288 randomly assigned to the tenecteplase group and 290 to the control group [intention-to-treat population]). The median age of participants was 73·7 years (IQR 65·9-81·1). 332 (57%) of 578 participants were male and 246 (43%) were female. Treatment with tenecteplase was not associated with better functional outcome, according to mRS score at 90 days (adjusted OR 1·18, 95% CI 0·88-1·58; p=0·27). Mortality at 90 days did not significantly differ between treatment groups (28 [10%] patients in the tenecteplase group and 23 [8%] in the control group; adjusted HR 1·29, 95% CI 0·74-2·26; p=0·37). Symptomatic intracranial haemorrhage occurred in six (2%) patients in the tenecteplase group versus three (1%) in the control group (adjusted OR 2·17, 95% CI 0·53-8·87; p=0·28), whereas any intracranial haemorrhage occurred in 33 (11%) versus 30 (10%) patients (adjusted OR 1·14, 0·67-1·94; p=0·64). INTERPRETATION In patients with wake-up stroke selected with non-contrast CT, treatment with tenecteplase was not associated with better functional outcome at 90 days. The number of symptomatic haemorrhages and any intracranial haemorrhages in both treatment groups was similar to findings from previous trials of wake-up stroke patients selected using advanced imaging. Current evidence does not support treatment with tenecteplase in patients selected with non-contrast CT. FUNDING Norwegian Clinical Research Therapy in the Specialist Health Services Programme, the Swiss Heart Foundation, the British Heart Foundation, and the Norwegian National Association for Public Health.
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Affiliation(s)
- Melinda B Roaldsen
- Department of Clinical Research, University Hospital of North Norway, Tromsø, Norway
| | - Agnethe Eltoft
- Department of Neurology, University Hospital of North Norway, Tromsø, Norway; Department of Clinical Medicine, UiT the Arctic University of Norway, Tromsø, Norway
| | - Tom Wilsgaard
- Department of Community Medicine, UiT the Arctic University of Norway, Tromsø, Norway
| | - Hanne Christensen
- Department of Neurology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Stefan T Engelter
- Department of Neurology, University Hospital Basel, Basel, Switzerland; Department of Neurology and Neurorehabilitation, University of Basel, Basel, Switzerland; University Department of Geriatric Medicine Felix Platter, University of Basel, Basel, Switzerland
| | - Bent Indredavik
- Department of Medicine, St Olavs Hospital Trondheim University Hospital, Trondheim, Norway; Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Dalius Jatužis
- Faculty of Medicine, Vilnius University, Center of Neurology, Vilnius, Lithuania
| | - Guntis Karelis
- Department of Neurology and Neurosurgery, Riga East University Hospital, Riga, Latvia; Rīga Stradiņš University, Riga, Latvia
| | - Janika Kõrv
- Department of Neurology and Neurosurgery, University of Tartu, Tartu, Estonia
| | - Erik Lundström
- Department of Medicine and Neurology, Uppsala University, Uppsala, Sweden
| | - Jesper Petersson
- Department of Neurology, Lund University, Institute for Clinical Sciences Lund, Lund, Sweden
| | - Jukka Putaala
- Department of Neurology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Mary-Helen Søyland
- Department of Clinical Medicine, UiT the Arctic University of Norway, Tromsø, Norway; Department of Neurology, Hospital of Southern Norway, Kristiansand, Norway
| | - Arnstein Tveiten
- Department of Neurology, Hospital of Southern Norway, Kristiansand, Norway
| | - Andrew Bivard
- Department of Medicine, Royal Melbourne Hospital, Melbourne Brain Centre, Melbourne, VIC, Australia
| | - Stein Harald Johnsen
- Department of Neurology, University Hospital of North Norway, Tromsø, Norway; Department of Clinical Medicine, UiT the Arctic University of Norway, Tromsø, Norway
| | - Michael V Mazya
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden; Department of Neurology, Karolinska University Hospital, Stockholm, Sweden
| | - David J Werring
- Department of Brain Repair and Rehabilitation, UCL Queen Square Institute of Neurology, London, UK
| | - Teddy Y Wu
- Department of Neurology, Christchurch Hospital, Christchurch, New Zealand
| | - Gian Marco De Marchis
- Department of Neurology, University Hospital Basel, Basel, Switzerland; Department of Neurology, University of Basel, Basel, Switzerland
| | - Thompson G Robinson
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Ellisiv B Mathiesen
- Department of Neurology, University Hospital of North Norway, Tromsø, Norway; Department of Clinical Medicine, UiT the Arctic University of Norway, Tromsø, Norway.
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Proietti M, Romiti GF, Vitolo M, Harrison SL, Lane DA, Fauchier L, Marin F, Näbauer M, Potpara TS, Dan GA, Maggioni AP, Cesari M, Boriani G, Lip GYH, Ekmekçiu U, Paparisto V, Tase M, Gjergo H, Dragoti J, Goda A, Ciutea M, Ahadi N, el Husseini Z, Raepers M, Leroy J, Haushan P, Jourdan A, Lepiece C, Desteghe L, Vijgen J, Koopman P, Van Genechten G, Heidbuchel H, Boussy T, De Coninck M, Van Eeckhoutte H, Bouckaert N, Friart A, Boreux J, Arend C, Evrard P, Stefan L, Hoffer E, Herzet J, Massoz M, Celentano C, Sprynger M, Pierard L, Melon P, Van Hauwaert B, Kuppens C, Faes D, Van Lier D, Van Dorpe A, Gerardy A, Deceuninck O, Xhaet O, Dormal F, Ballant E, Blommaert D, Yakova D, Hristov M, Yncheva T, Stancheva N, Tisheva S, Tokmakova M, Nikolov F, Gencheva D, Shalganov T, Kunev B, Stoyanov M, Marchov D, Gelev V, Traykov V, Kisheva A, Tsvyatkov H, Shtereva R, Bakalska-Georgieva S, Slavcheva S, Yotov Y, Kubíčková M, Marni Joensen A, Gammelmark A, Hvilsted Rasmussen L, Dinesen P, Riahi S, Krogh Venø S, Sorensen B, Korsgaard A, Andersen K, Fragtrup Hellum C, Svenningsen A, Nyvad O, Wiggers P, May O, Aarup A, Graversen B, Jensen L, Andersen M, Svejgaard M, Vester S, Hansen S, Lynggaard V, Ciudad M, Vettus R, Muda P, Maestre A, Castaño S, Cheggour S, Poulard J, Mouquet V, Leparrée S, Bouet J, Taieb J, Doucy A, Duquenne H, Furber A, Dupuis J, Rautureau J, Font M, Damiano P, Lacrimini M, Abalea J, Boismal S, Menez T, Mansourati J, Range G, Gorka H, Laure C, Vassalière C, Elbaz N, Lellouche N, Djouadi K, Roubille F, Dietz D, Davy J, Granier M, Winum P, Leperchois-Jacquey C, Kassim H, Marijon E, Le Heuzey J, Fedida J, Maupain C, Himbert C, Gandjbakhch E, Hidden-Lucet F, Duthoit G, Badenco N, Chastre T, Waintraub X, Oudihat M, Lacoste J, Stephan C, Bader H, Delarche N, Giry L, Arnaud D, Lopez C, Boury F, Brunello I, Lefèvre M, Mingam R, Haissaguerre M, Le Bidan M, Pavin D, Le Moal V, Leclercq C, Piot O, Beitar T, Martel I, Schmid A, Sadki N, Romeyer-Bouchard C, Da Costa A, Arnault I, Boyer M, Piat C, Fauchier L, Lozance N, Nastevska S, Doneva A, Fortomaroska Milevska B, Sheshoski B, Petroska K, Taneska N, Bakrecheski N, Lazarovska K, Jovevska S, Ristovski V, Antovski A, Lazarova E, Kotlar I, Taleski J, Poposka L, Kedev S, Zlatanovik N, Jordanova S, Bajraktarova Proseva T, Doncovska S, Maisuradze D, Esakia A, Sagirashvili E, Lartsuliani K, Natelashvili N, Gumberidze N, Gvenetadze R, Etsadashvili K, Gotonelia N, Kuridze N, Papiashvili G, Menabde I, Glöggler S, Napp A, Lebherz C, Romero H, Schmitz K, Berger M, Zink M, Köster S, Sachse J, Vonderhagen E, Soiron G, Mischke K, Reith R, Schneider M, Rieker W, Boscher D, Taschareck A, Beer A, Oster D, Ritter O, Adamczewski J, Walter S, Frommhold A, Luckner E, Richter J, Schellner M, Landgraf S, Bartholome S, Naumann R, Schoeler J, Westermeier D, William F, Wilhelm K, Maerkl M, Oekinghaus R, Denart M, Kriete M, Tebbe U, Scheibner T, Gruber M, Gerlach A, Beckendorf C, Anneken L, Arnold M, Lengerer S, Bal Z, Uecker C, Förtsch H, Fechner S, Mages V, Martens E, Methe H, Schmidt T, Schaeffer B, Hoffmann B, Moser J, Heitmann K, Willems S, Willems S, Klaus C, Lange I, Durak M, Esen E, Mibach F, Mibach H, Utech A, Gabelmann M, Stumm R, Ländle V, Gartner C, Goerg C, Kaul N, Messer S, Burkhardt D, Sander C, Orthen R, Kaes S, Baumer A, Dodos F, Barth A, Schaeffer G, Gaertner J, Winkler J, Fahrig A, Aring J, Wenzel I, Steiner S, Kliesch A, Kratz E, Winter K, Schneider P, Haag A, Mutscher I, Bosch R, Taggeselle J, Meixner S, Schnabel A, Shamalla A, Hötz H, Korinth A, Rheinert C, Mehltretter G, Schön B, Schön N, Starflinger A, Englmann E, Baytok G, Laschinger T, Ritscher G, Gerth A, Dechering D, Eckardt L, Kuhlmann M, Proskynitopoulos N, Brunn J, Foth K, Axthelm C, Hohensee H, Eberhard K, Turbanisch S, Hassler N, Koestler A, Stenzel G, Kschiwan D, Schwefer M, Neiner S, Hettwer S, Haeussler-Schuchardt M, Degenhardt R, Sennhenn S, Steiner S, Brendel M, Stoehr A, Widjaja W, Loehndorf S, Logemann A, Hoskamp J, Grundt J, Block M, Ulrych R, Reithmeier A, Panagopoulos V, Martignani C, Bernucci D, Fantecchi E, Diemberger I, Ziacchi M, Biffi M, Cimaglia P, Frisoni J, Boriani G, Giannini I, Boni S, Fumagalli S, Pupo S, Di Chiara A, Mirone P, Fantecchi E, Boriani G, Pesce F, Zoccali C, Malavasi VL, Mussagaliyeva A, Ahyt B, Salihova Z, Koshum-Bayeva K, Kerimkulova A, Bairamukova A, Mirrakhimov E, Lurina B, Zuzans R, Jegere S, Mintale I, Kupics K, Jubele K, Erglis A, Kalejs O, Vanhear K, Burg M, Cachia M, Abela E, Warwicker S, Tabone T, Xuereb R, Asanovic D, Drakalovic D, Vukmirovic M, Pavlovic N, Music L, Bulatovic N, Boskovic A, Uiterwaal H, Bijsterveld N, De Groot J, Neefs J, van den Berg N, Piersma F, Wilde A, Hagens V, Van Es J, Van Opstal J, Van Rennes B, Verheij H, Breukers W, Tjeerdsma G, Nijmeijer R, Wegink D, Binnema R, Said S, Erküner Ö, Philippens S, van Doorn W, Crijns H, Szili-Torok T, Bhagwandien R, Janse P, Muskens A, van Eck M, Gevers R, van der Ven N, Duygun A, Rahel B, Meeder J, Vold A, Holst Hansen C, Engset I, Atar D, Dyduch-Fejklowicz B, Koba E, Cichocka M, Sokal A, Kubicius A, Pruchniewicz E, Kowalik-Sztylc A, Czapla W, Mróz I, Kozlowski M, Pawlowski T, Tendera M, Winiarska-Filipek A, Fidyk A, Slowikowski A, Haberka M, Lachor-Broda M, Biedron M, Gasior Z, Kołodziej M, Janion M, Gorczyca-Michta I, Wozakowska-Kaplon B, Stasiak M, Jakubowski P, Ciurus T, Drozdz J, Simiera M, Zajac P, Wcislo T, Zycinski P, Kasprzak J, Olejnik A, Harc-Dyl E, Miarka J, Pasieka M, Ziemińska-Łuć M, Bujak W, Śliwiński A, Grech A, Morka J, Petrykowska K, Prasał M, Hordyński G, Feusette P, Lipski P, Wester A, Streb W, Romanek J, Woźniak P, Chlebuś M, Szafarz P, Stanik W, Zakrzewski M, Kaźmierczak J, Przybylska A, Skorek E, Błaszczyk H, Stępień M, Szabowski S, Krysiak W, Szymańska M, Karasiński J, Blicharz J, Skura M, Hałas K, Michalczyk L, Orski Z, Krzyżanowski K, Skrobowski A, Zieliński L, Tomaszewska-Kiecana M, Dłużniewski M, Kiliszek M, Peller M, Budnik M, Balsam P, Opolski G, Tymińska A, Ozierański K, Wancerz A, Borowiec A, Majos E, Dabrowski R, Szwed H, Musialik-Lydka A, Leopold-Jadczyk A, Jedrzejczyk-Patej E, Koziel M, Lenarczyk R, Mazurek M, Kalarus Z, Krzemien-Wolska K, Starosta P, Nowalany-Kozielska E, Orzechowska A, Szpot M, Staszel M, Almeida S, Pereira H, Brandão Alves L, Miranda R, Ribeiro L, Costa F, Morgado F, Carmo P, Galvao Santos P, Bernardo R, Adragão P, Ferreira da Silva G, Peres M, Alves M, Leal M, Cordeiro A, Magalhães P, Fontes P, Leão S, Delgado A, Costa A, Marmelo B, Rodrigues B, Moreira D, Santos J, Santos L, Terchet A, Darabantiu D, Mercea S, Turcin Halka V, Pop Moldovan A, Gabor A, Doka B, Catanescu G, Rus H, Oboroceanu L, Bobescu E, Popescu R, Dan A, Buzea A, Daha I, Dan G, Neuhoff I, Baluta M, Ploesteanu R, Dumitrache N, Vintila M, Daraban A, Japie C, Badila E, Tewelde H, Hostiuc M, Frunza S, Tintea E, Bartos D, Ciobanu A, Popescu I, Toma N, Gherghinescu C, Cretu D, Patrascu N, Stoicescu C, Udroiu C, Bicescu G, Vintila V, Vinereanu D, Cinteza M, Rimbas R, Grecu M, Cozma A, Boros F, Ille M, Tica O, Tor R, Corina A, Jeewooth A, Maria B, Georgiana C, Natalia C, Alin D, Dinu-Andrei D, Livia M, Daniela R, Larisa R, Umaar S, Tamara T, Ioachim Popescu M, Nistor D, Sus I, Coborosanu O, Alina-Ramona N, Dan R, Petrescu L, Ionescu G, Popescu I, Vacarescu C, Goanta E, Mangea M, Ionac A, Mornos C, Cozma D, Pescariu S, Solodovnicova E, Soldatova I, Shutova J, Tjuleneva L, Zubova T, Uskov V, Obukhov D, Rusanova G, Soldatova I, Isakova N, Odinsova S, Arhipova T, Kazakevich E, Serdechnaya E, Zavyalova O, Novikova T, Riabaia I, Zhigalov S, Drozdova E, Luchkina I, Monogarova Y, Hegya D, Rodionova L, Rodionova L, Nevzorova V, Soldatova I, Lusanova O, Arandjelovic A, Toncev D, Milanov M, Sekularac N, Zdravkovic M, Hinic S, Dimkovic S, Acimovic T, Saric J, Polovina M, Potpara T, Vujisic-Tesic B, Nedeljkovic M, Zlatar M, Asanin M, Vasic V, Popovic Z, Djikic D, Sipic M, Peric V, Dejanovic B, Milosevic N, Stevanovic A, Andric A, Pencic B, Pavlovic-Kleut M, Celic V, Pavlovic M, Petrovic M, Vuleta M, Petrovic N, Simovic S, Savovic Z, Milanov S, Davidovic G, Iric-Cupic V, Simonovic D, Stojanovic M, Stojanovic S, Mitic V, Ilic V, Petrovic D, Deljanin Ilic M, Ilic S, Stoickov V, Markovic S, Kovacevic S, García Fernandez A, Perez Cabeza A, Anguita M, Tercedor Sanchez L, Mau E, Loayssa J, Ayarra M, Carpintero M, Roldán Rabadan I, Leal M, Gil Ortega M, Tello Montoliu A, Orenes Piñero E, Manzano Fernández S, Marín F, Romero Aniorte A, Veliz Martínez A, Quintana Giner M, Ballesteros G, Palacio M, Alcalde O, García-Bolao I, Bertomeu Gonzalez V, Otero-Raviña F, García Seara J, Gonzalez Juanatey J, Dayal N, Maziarski P, Gentil-Baron P, Shah D, Koç M, Onrat E, Dural IE, Yilmaz K, Özin B, Tan Kurklu S, Atmaca Y, Canpolat U, Tokgozoglu L, Dolu AK, Demirtas B, Sahin D, Ozcan Celebi O, Diker E, Gagirci G, Turk UO, Ari H, Polat N, Toprak N, Sucu M, Akin Serdar O, Taha Alper A, Kepez A, Yuksel Y, Uzunselvi A, Yuksel S, Sahin M, Kayapinar O, Ozcan T, Kaya H, Yilmaz MB, Kutlu M, Demir M, Gibbs C, Kaminskiene S, Bryce M, Skinner A, Belcher G, Hunt J, Stancombe L, Holbrook B, Peters C, Tettersell S, Shantsila A, Lane D, Senoo K, Proietti M, Russell K, Domingos P, Hussain S, Partridge J, Haynes R, Bahadur S, Brown R, McMahon S, Y H Lip G, McDonald J, Balachandran K, Singh R, Garg S, Desai H, Davies K, Goddard W, Galasko G, Rahman I, Chua Y, Payne O, Preston S, Brennan O, Pedley L, Whiteside C, Dickinson C, Brown J, Jones K, Benham L, Brady R, Buchanan L, Ashton A, Crowther H, Fairlamb H, Thornthwaite S, Relph C, McSkeane A, Poultney U, Kelsall N, Rice P, Wilson T, Wrigley M, Kaba R, Patel T, Young E, Law J, Runnett C, Thomas H, McKie H, Fuller J, Pick S, Sharp A, Hunt A, Thorpe K, Hardman C, Cusack E, Adams L, Hough M, Keenan S, Bowring A, Watts J, Zaman J, Goffin K, Nutt H, Beerachee Y, Featherstone J, Mills C, Pearson J, Stephenson L, Grant S, Wilson A, Hawksworth C, Alam I, Robinson M, Ryan S, Egdell R, Gibson E, Holland M, Leonard D, Mishra B, Ahmad S, Randall H, Hill J, Reid L, George M, McKinley S, Brockway L, Milligan W, Sobolewska J, Muir J, Tuckis L, Winstanley L, Jacob P, Kaye S, Morby L, Jan A, Sewell T, Boos C, Wadams B, Cope C, Jefferey P, Andrews N, Getty A, Suttling A, Turner C, Hudson K, Austin R, Howe S, Iqbal R, Gandhi N, Brophy K, Mirza P, Willard E, Collins S, Ndlovu N, Subkovas E, Karthikeyan V, Waggett L, Wood A, Bolger A, Stockport J, Evans L, Harman E, Starling J, Williams L, Saul V, Sinha M, Bell L, Tudgay S, Kemp S, Brown J, Frost L, Ingram T, Loughlin A, Adams C, Adams M, Hurford F, Owen C, Miller C, Donaldson D, Tivenan H, Button H, Nasser A, Jhagra O, Stidolph B, Brown C, Livingstone C, Duffy M, Madgwick P, Roberts P, Greenwood E, Fletcher L, Beveridge M, Earles S, McKenzie D, Beacock D, Dayer M, Seddon M, Greenwell D, Luxton F, Venn F, Mills H, Rewbury J, James K, Roberts K, Tonks L, Felmeden D, Taggu W, Summerhayes A, Hughes D, Sutton J, Felmeden L, Khan M, Walker E, Norris L, O’Donohoe L, Mozid A, Dymond H, Lloyd-Jones H, Saunders G, Simmons D, Coles D, Cotterill D, Beech S, Kidd S, Wrigley B, Petkar S, Smallwood A, Jones R, Radford E, Milgate S, Metherell S, Cottam V, Buckley C, Broadley A, Wood D, Allison J, Rennie K, Balian L, Howard L, Pippard L, Board S, Pitt-Kerby T. Epidemiology and impact of frailty in patients with atrial fibrillation in Europe. Age Ageing 2022; 51:6670566. [PMID: 35997262 DOI: 10.1093/ageing/afac192] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 06/08/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Frailty is a medical syndrome characterised by reduced physiological reserve and increased vulnerability to stressors. Data regarding the relationship between frailty and atrial fibrillation (AF) are still inconsistent. OBJECTIVES We aim to perform a comprehensive evaluation of frailty in a large European cohort of AF patients. METHODS A 40-item frailty index (FI) was built according to the accumulation of deficits model in the AF patients enrolled in the ESC-EHRA EORP-AF General Long-Term Registry. Association of baseline characteristics, clinical management, quality of life, healthcare resources use and risk of outcomes with frailty was examined. RESULTS Among 10,177 patients [mean age (standard deviation) 69.0 (11.4) years, 4,103 (40.3%) females], 6,066 (59.6%) were pre-frail and 2,172 (21.3%) were frail, whereas only 1,939 (19.1%) were considered robust. Baseline thromboembolic and bleeding risks were independently associated with increasing FI. Frail patients with AF were less likely to be treated with oral anticoagulants (OACs) (odds ratio 0.70, 95% confidence interval 0.55-0.89), especially with non-vitamin K antagonist OACs and managed with a rhythm control strategy, compared with robust patients. Increasing frailty was associated with a higher risk for all outcomes examined, with a non-linear exponential relationship. The use of OAC was associated with a lower risk of outcomes, except in patients with very/extremely high frailty. CONCLUSIONS In this large cohort of AF patients, there was a high burden of frailty, influencing clinical management and risk of adverse outcomes. The clinical benefit of OAC is maintained in patients with high frailty, but not in very high/extremely frail ones.
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Affiliation(s)
- Marco Proietti
- Liverpool Centre for Cardiovascular Science, University of Liverpool and Liverpool Heart & Chest Hospital, Liverpool, UK.,Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy.,Geriatric Unit, IRCCS Istituti Clinici Scientifici Maugeri, Milan, Italy
| | - Giulio Francesco Romiti
- Liverpool Centre for Cardiovascular Science, University of Liverpool and Liverpool Heart & Chest Hospital, Liverpool, UK.,Department of Translational and Precision Medicine, Sapienza - University of Rome, Italy
| | - Marco Vitolo
- Liverpool Centre for Cardiovascular Science, University of Liverpool and Liverpool Heart & Chest Hospital, Liverpool, UK.,Cardiology Division, Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Policlinico di Modena, Modena, Italy.,Clinical and Experimental Medicine PhD Program, University of Modena and Reggio Emilia, Modena, Italy
| | - Stephanie L Harrison
- Liverpool Centre for Cardiovascular Science, University of Liverpool and Liverpool Heart & Chest Hospital, Liverpool, UK
| | - Deirdre A Lane
- Liverpool Centre for Cardiovascular Science, University of Liverpool and Liverpool Heart & Chest Hospital, Liverpool, UK.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Laurent Fauchier
- Service de Cardiologie, Centre Hospitalier Universitaire Trousseau, Tours, France
| | - Francisco Marin
- Department of Cardiology, Hospital Universitario Virgen de la Arrixaca, IMIB-Arrixaca, University of Murcia, CIBER-CV, Murcia, Spain
| | - Michael Näbauer
- Department of Cardiology, Ludwig-Maximilians-University, Munich, Germany
| | - Tatjana S Potpara
- School of Medicine, University of Belgrade, Belgrade, Serbia.,Clinical Center of Serbia, Belgrade, Serbia
| | - Gheorghe-Andrei Dan
- University of Medicine, 'Carol Davila', Colentina University Hospital, Bucharest, Romania
| | - Aldo P Maggioni
- ANMCO Research Center, Heart Care Foundation, Florence, Italy
| | - Matteo Cesari
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy.,Geriatric Unit, IRCCS Istituti Clinici Scientifici Maugeri, Milan, Italy
| | - Giuseppe Boriani
- Cardiology Division, Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Policlinico di Modena, Modena, Italy
| | - Gregory Y H Lip
- Liverpool Centre for Cardiovascular Science, University of Liverpool and Liverpool Heart & Chest Hospital, Liverpool, UK.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
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Keenan S, Cooke M, Wu S, Hassan EB, Meyer D, Chen WS, Sullivan J, Duque G, Belski R. The Effect Of Continuous Energy Restriction Vs Intermittent Fasting, With Resistance Training, On Lean Mass. Med Sci Sports Exerc 2020. [DOI: 10.1249/01.mss.0000684652.42236.55] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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5
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Fiume M, Cupak M, Keenan S, Rambla J, de la Torre S, Dyke SOM, Brookes AJ, Carey K, Lloyd D, Goodhand P, Haeussler M, Baudis M, Stockinger H, Dolman L, Lappalainen I, Törnroos J, Linden M, Spalding JD, Ur-Rehman S, Page A, Flicek P, Sherry S, Haussler D, Varma S, Saunders G, Scollen S. Publisher Correction: Federated discovery and sharing of genomic data using Beacons. Nat Biotechnol 2019; 37:480. [PMID: 30894680 PMCID: PMC7608460 DOI: 10.1038/s41587-019-0094-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | - Stephen Keenan
- Global Alliance for Genomics and Health, Toronto, Ontario, Canada.,European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | | | - Stephanie O M Dyke
- Centre of Genomics and Policy, Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | | | | | - David Lloyd
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Peter Goodhand
- Global Alliance for Genomics and Health, Toronto, Ontario, Canada.,Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Michael Baudis
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Lena Dolman
- Global Alliance for Genomics and Health, Toronto, Ontario, Canada.,Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Ilkka Lappalainen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,CSC - IT Center for Science Ltd, Espoo, Finland
| | | | | | - J Dylan Spalding
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Saif Ur-Rehman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Angela Page
- Global Alliance for Genomics and Health, Toronto, Ontario, Canada.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Stephen Sherry
- National Center for Biotechnology Information, US National Library of Medicine, Bethesda, MD, USA
| | - David Haussler
- Genomics Institute, University of California at Santa Cruz, Santa Cruz, CA, USA
| | - Susheel Varma
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Gary Saunders
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Serena Scollen
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, UK
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6
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McAdam L, Greenspoon D, Bell K, English K, Keenan S, McPherson A. REGISTRIES AND CARE OF NEUROMUSCULAR DISORDERS. Neuromuscul Disord 2018. [DOI: 10.1016/j.nmd.2018.06.326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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7
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Belski R, Staley K, Keenan S, Skiadopoulos A, Randle E, Donaldson A, O'Halloran P, Kappelides P, O'Neil S, Nicholson M. The impact of coaches providing healthy snacks at junior sport training. Aust N Z J Public Health 2017; 41:561-566. [PMID: 29044878 DOI: 10.1111/1753-6405.12724] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 06/01/2017] [Accepted: 07/01/2017] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVE Sports clubs provide an opportunity to tackle childhood obesity rates through targeted interventions. Our study aimed to investigate if coaches providing healthy snacks to participants before junior netball sessions at five clubs in Melbourne, Australia, increased consumption of healthy foods and influenced coach perceptions of participants' attention/participation levels. METHODS Coaches provided healthy snacks to participants before each netball session for one school term. Children's food consumption was observed at one session before, during and after the intervention. Parents attending the observed session completed pre- and post-intervention questionnaires. Coaches rated participants' attention/participation at the observed sessions before and during the intervention, and completed a questionnaire post-intervention. RESULTS Baseline: Ice cream and cake were the most frequently consumed snacks. During intervention: Fruit, cheese and crackers and vegetables were the most frequently consumed snacks. Coaches ratings of participants' attention/participation increased significantly (baseline: 6.4 ± 0.17, intervention: 7.5 ± 0.36; p=0.02) where the same coach undertook ratings at both time points. CONCLUSIONS Coaches providing healthy snacks before sessions at sports clubs increased consumption of nutrient-dense foods at the session, and may have positively affected participants' attention/participation. Implications for public health: This study highlights how a simple intervention could improve the diet of Australian children.
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Affiliation(s)
- Regina Belski
- Department of Health Professions, Swinburne University of Technology, Victoria.,Centre for Sport and Social Impact, La Trobe University, Victoria
| | - Kiera Staley
- Centre for Sport and Social Impact, La Trobe University, Victoria
| | - Stephen Keenan
- Centre for Sport and Social Impact, La Trobe University, Victoria
| | | | - Erica Randle
- Centre for Sport and Social Impact, La Trobe University, Victoria
| | - Alex Donaldson
- Centre for Sport and Social Impact, La Trobe University, Victoria
| | - Paul O'Halloran
- Centre for Sport and Social Impact, La Trobe University, Victoria
| | - Pam Kappelides
- Centre for Sport and Social Impact, La Trobe University, Victoria
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8
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Ruffier M, Kähäri A, Komorowska M, Keenan S, Laird M, Longden I, Proctor G, Searle S, Staines D, Taylor K, Vullo A, Yates A, Zerbino D, Flicek P. Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation. Database (Oxford) 2017; 2017:3074789. [PMID: 28365736 PMCID: PMC5467575 DOI: 10.1093/database/bax020] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 02/07/2017] [Accepted: 02/20/2017] [Indexed: 01/09/2023]
Abstract
The Ensembl software resources are a stable infrastructure to store, access and manipulate genome assemblies and their functional annotations. The Ensembl 'Core' database and Application Programming Interface (API) was our first major piece of software infrastructure and remains at the centre of all of our genome resources. Since its initial design more than fifteen years ago, the number of publicly available genomic, transcriptomic and proteomic datasets has grown enormously, accelerated by continuous advances in DNA-sequencing technology. Initially intended to provide annotation for the reference human genome, we have extended our framework to support the genomes of all species as well as richer assembly models. Cross-referenced links to other informatics resources facilitate searching our database with a variety of popular identifiers such as UniProt and RefSeq. Our comprehensive and robust framework storing a large diversity of genome annotations in one location serves as a platform for other groups to generate and maintain their own tailored annotation. We welcome reuse and contributions: our databases and APIs are publicly available, all of our source code is released with a permissive Apache v2.0 licence at http://github.com/Ensembl and we have an active developer mailing list ( http://www.ensembl.org/info/about/contact/index.html ). Database URL http://www.ensembl.org.
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Affiliation(s)
- Magali Ruffier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andreas Kähäri
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Monika Komorowska
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Stephen Keenan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Matthew Laird
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ian Longden
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Glenn Proctor
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Steve Searle
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Daniel Staines
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kieron Taylor
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Alessandro Vullo
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andrew Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel Zerbino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
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9
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Aken BL, Achuthan P, Akanni W, Amode MR, Bernsdorff F, Bhai J, Billis K, Carvalho-Silva D, Cummins C, Clapham P, Gil L, Girón CG, Gordon L, Hourlier T, Hunt SE, Janacek SH, Juettemann T, Keenan S, Laird MR, Lavidas I, Maurel T, McLaren W, Moore B, Murphy DN, Nag R, Newman V, Nuhn M, Ong CK, Parker A, Patricio M, Riat HS, Sheppard D, Sparrow H, Taylor K, Thormann A, Vullo A, Walts B, Wilder SP, Zadissa A, Kostadima M, Martin FJ, Muffato M, Perry E, Ruffier M, Staines DM, Trevanion SJ, Cunningham F, Yates A, Zerbino DR, Flicek P. Ensembl 2017. Nucleic Acids Res 2016; 45:D635-D642. [PMID: 27899575 PMCID: PMC5210575 DOI: 10.1093/nar/gkw1104] [Citation(s) in RCA: 409] [Impact Index Per Article: 51.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Revised: 10/25/2016] [Accepted: 10/28/2016] [Indexed: 12/12/2022] Open
Abstract
Ensembl (www.ensembl.org) is a database and genome browser for enabling research on vertebrate genomes. We import, analyse, curate and integrate a diverse collection of large-scale reference data to create a more comprehensive view of genome biology than would be possible from any individual dataset. Our extensive data resources include evidence-based gene and regulatory region annotation, genome variation and gene trees. An accompanying suite of tools, infrastructure and programmatic access methods ensure uniform data analysis and distribution for all supported species. Together, these provide a comprehensive solution for large-scale and targeted genomics applications alike. Among many other developments over the past year, we have improved our resources for gene regulation and comparative genomics, and added CRISPR/Cas9 target sites. We released new browser functionality and tools, including improved filtering and prioritization of genome variation, Manhattan plot visualization for linkage disequilibrium and eQTL data, and an ontology search for phenotypes, traits and disease. We have also enhanced data discovery and access with a track hub registry and a selection of new REST end points. All Ensembl data are freely released to the scientific community and our source code is available via the open source Apache 2.0 license.
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Affiliation(s)
- Bronwen L Aken
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Premanand Achuthan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Wasiu Akanni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - M Ridwan Amode
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Friederike Bernsdorff
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jyothish Bhai
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Denise Carvalho-Silva
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Carla Cummins
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Peter Clapham
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Laurent Gil
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Carlos García Girón
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Leo Gordon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sarah E Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sophie H Janacek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thomas Juettemann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Stephen Keenan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Matthew R Laird
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ilias Lavidas
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thomas Maurel
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - William McLaren
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Benjamin Moore
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel N Murphy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Rishi Nag
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Victoria Newman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Michael Nuhn
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Chuang Kee Ong
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Anne Parker
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mateus Patricio
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Harpreet Singh Riat
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel Sheppard
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Helen Sparrow
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kieron Taylor
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Anja Thormann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Alessandro Vullo
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Brandon Walts
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Steven P Wilder
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Amonida Zadissa
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Myrto Kostadima
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Matthieu Muffato
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Emily Perry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Magali Ruffier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel M Staines
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Stephen J Trevanion
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andrew Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel R Zerbino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK .,Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
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10
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Yates A, Akanni W, Amode MR, Barrell D, Billis K, Carvalho-Silva D, Cummins C, Clapham P, Fitzgerald S, Gil L, Girón CG, Gordon L, Hourlier T, Hunt SE, Janacek SH, Johnson N, Juettemann T, Keenan S, Lavidas I, Martin FJ, Maurel T, McLaren W, Murphy DN, Nag R, Nuhn M, Parker A, Patricio M, Pignatelli M, Rahtz M, Riat HS, Sheppard D, Taylor K, Thormann A, Vullo A, Wilder SP, Zadissa A, Birney E, Harrow J, Muffato M, Perry E, Ruffier M, Spudich G, Trevanion SJ, Cunningham F, Aken BL, Zerbino DR, Flicek P. Ensembl 2016. Nucleic Acids Res 2016; 44:D710-6. [PMID: 26687719 PMCID: PMC4702834 DOI: 10.1093/nar/gkv1157] [Citation(s) in RCA: 1066] [Impact Index Per Article: 133.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Revised: 10/19/2015] [Accepted: 10/19/2015] [Indexed: 01/17/2023] Open
Abstract
The Ensembl project (http://www.ensembl.org) is a system for genome annotation, analysis, storage and dissemination designed to facilitate the access of genomic annotation from chordates and key model organisms. It provides access to data from 87 species across our main and early access Pre! websites. This year we introduced three newly annotated species and released numerous updates across our supported species with a concentration on data for the latest genome assemblies of human, mouse, zebrafish and rat. We also provided two data updates for the previous human assembly, GRCh37, through a dedicated website (http://grch37.ensembl.org). Our tools, in particular the VEP, have been improved significantly through integration of additional third party data. REST is now capable of larger-scale analysis and our regulatory data BioMart can deliver faster results. The website is now capable of displaying long-range interactions such as those found in cis-regulated datasets. Finally we have launched a website optimized for mobile devices providing views of genes, variants and phenotypes. Our data is made available without restriction and all code is available from our GitHub organization site (http://github.com/Ensembl) under an Apache 2.0 license.
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Affiliation(s)
- Andrew Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Wasiu Akanni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - M Ridwan Amode
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel Barrell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Denise Carvalho-Silva
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Carla Cummins
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Peter Clapham
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Stephen Fitzgerald
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Laurent Gil
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Carlos García Girón
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Leo Gordon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sarah E Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sophie H Janacek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nathan Johnson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thomas Juettemann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Stephen Keenan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ilias Lavidas
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thomas Maurel
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - William McLaren
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel N Murphy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Rishi Nag
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Michael Nuhn
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Anne Parker
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mateus Patricio
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Miguel Pignatelli
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Matthew Rahtz
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Harpreet Singh Riat
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel Sheppard
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kieron Taylor
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Anja Thormann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Alessandro Vullo
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Steven P Wilder
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Amonida Zadissa
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jennifer Harrow
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Matthieu Muffato
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Emily Perry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Magali Ruffier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Giulietta Spudich
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Stephen J Trevanion
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Bronwen L Aken
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel R Zerbino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
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11
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Gerhardt S, McCallum A, McDougall C, Keenan S, Rigby P. The goal of making friends for youth with disabilities: creating a goal menu. Child Care Health Dev 2015; 41:1018-29. [PMID: 25891293 DOI: 10.1111/cch.12251] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/15/2015] [Indexed: 11/29/2022]
Abstract
BACKGROUND Clinicians working with youth with disabilities have acknowledged making friends as a commonly identified client goal. Clinicians find this goal difficult to address, as there are no measures that provide a breakdown of making friends into functional steps. In addition, research on friendship has traditionally focused on characteristics and quality of friendships rather than the friend-making process as a whole. A goal menu, comprised of a variety of steps that address the goal of making friends, would provide guidance to clinicians challenged with this goal in practice. PURPOSE To develop an understanding of the friend-making process as a first step towards the development of a goal menu for the goal of making friends. METHODS A literature review, youth focus group and expert clinician semi-structured interviews and consultation were used to generate a comprehensive data set. Established qualitative methods were used to sort and group the data into categories. A thematic analysis of the categories was performed. RESULTS Analysis revealed four themes integral to the friend-making process: person factors influencing friend-making, making friend-making a priority, opportunity for friend-making and motivation to make friends. An additional theme identified as occasionally involved in the process was a little bit of luck in making friends. CONCLUSIONS The themes generated by this research indicate that actionable target areas exist for the somewhat abstract notion of friend-making and the authors recommend that clinicians explore beyond person factors when addressing the goal of making friends. As a next step, the identified themes will provide the foundation for a goal menu, ultimately enabling clinicians to address the goal of making friends in a more efficient and effective manner.
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Affiliation(s)
- S Gerhardt
- Faculty of Medicine, Department of Occupational Science and Occupational Therapy, The University of Toronto, Toronto, ON, Canada
| | - A McCallum
- Faculty of Medicine, Department of Occupational Science and Occupational Therapy, The University of Toronto, Toronto, ON, Canada
| | - C McDougall
- Faculty of Medicine, Department of Occupational Science and Occupational Therapy, The University of Toronto, Toronto, ON, Canada.,Holland Bloorview Kids Rehabilitation Hospital, Toronto, ON, Canada
| | - S Keenan
- Holland Bloorview Kids Rehabilitation Hospital, Toronto, ON, Canada.,Bloorview Research Institute, Holland Bloorview Kids Rehabilitation Hospital, Toronto, ON, Canada
| | - P Rigby
- Faculty of Medicine, Department of Occupational Science and Occupational Therapy, The University of Toronto, Toronto, ON, Canada.,Bloorview Research Institute, Holland Bloorview Kids Rehabilitation Hospital, Toronto, ON, Canada
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12
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Keenan S, Snyder B, Xiao H, Robertson A, Ahlijanian M, Bristow L, Devidze N. Phenotypic differences in mdx mice on C57Bl/10 and DBA/2 backgrounds. Neuromuscul Disord 2015. [DOI: 10.1016/j.nmd.2015.06.385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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13
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Cunningham F, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S, Gil L, Girón CG, Gordon L, Hourlier T, Hunt SE, Janacek SH, Johnson N, Juettemann T, Kähäri AK, Keenan S, Martin FJ, Maurel T, McLaren W, Murphy DN, Nag R, Overduin B, Parker A, Patricio M, Perry E, Pignatelli M, Riat HS, Sheppard D, Taylor K, Thormann A, Vullo A, Wilder SP, Zadissa A, Aken BL, Birney E, Harrow J, Kinsella R, Muffato M, Ruffier M, Searle SMJ, Spudich G, Trevanion SJ, Yates A, Zerbino DR, Flicek P. Ensembl 2015. Nucleic Acids Res 2014; 43:D662-9. [PMID: 25352552 PMCID: PMC4383879 DOI: 10.1093/nar/gku1010] [Citation(s) in RCA: 961] [Impact Index Per Article: 96.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Ensembl (http://www.ensembl.org) is a genomic interpretation system providing the most up-to-date annotations, querying tools and access methods for chordates and key model organisms. This year we released updated annotation (gene models, comparative genomics, regulatory regions and variation) on the new human assembly, GRCh38, although we continue to support researchers using the GRCh37.p13 assembly through a dedicated site (http://grch37.ensembl.org). Our Regulatory Build has been revamped to identify regulatory regions of interest and to efficiently highlight their activity across disparate epigenetic data sets. A number of new interfaces allow users to perform large-scale comparisons of their data against our annotations. The REST server (http://rest.ensembl.org), which allows programs written in any language to query our databases, has moved to a full service alongside our upgraded website tools. Our online Variant Effect Predictor tool has been updated to process more variants and calculate summary statistics. Lastly, the WiggleTools package enables users to summarize large collections of data sets and view them as single tracks in Ensembl. The Ensembl code base itself is more accessible: it is now hosted on our GitHub organization page (https://github.com/Ensembl) under an Apache 2.0 open source license.
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Affiliation(s)
- Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - M Ridwan Amode
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel Barrell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Kathryn Beal
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Simon Brent
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Denise Carvalho-Silva
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Peter Clapham
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Guy Coates
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Stephen Fitzgerald
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Laurent Gil
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Carlos García Girón
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Leo Gordon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sarah E Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sophie H Janacek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nathan Johnson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thomas Juettemann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andreas K Kähäri
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Stephen Keenan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thomas Maurel
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - William McLaren
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel N Murphy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Rishi Nag
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Bert Overduin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Anne Parker
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mateus Patricio
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Emily Perry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Miguel Pignatelli
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Harpreet Singh Riat
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel Sheppard
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kieron Taylor
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Anja Thormann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Alessandro Vullo
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Steven P Wilder
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Amonida Zadissa
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Bronwen L Aken
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jennifer Harrow
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Rhoda Kinsella
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Matthieu Muffato
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Magali Ruffier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Stephen M J Searle
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Giulietta Spudich
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Stephen J Trevanion
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andy Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel R Zerbino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
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Yates A, Beal K, Keenan S, McLaren W, Pignatelli M, Ritchie GRS, Ruffier M, Taylor K, Vullo A, Flicek P. The Ensembl REST API: Ensembl Data for Any Language. ACTA ACUST UNITED AC 2014; 31:143-5. [PMID: 25236461 PMCID: PMC4271150 DOI: 10.1093/bioinformatics/btu613] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
MOTIVATION We present a Web service to access Ensembl data using Representational State Transfer (REST). The Ensembl REST server enables the easy retrieval of a wide range of Ensembl data by most programming languages, using standard formats such as JSON and FASTA while minimizing client work. We also introduce bindings to the popular Ensembl Variant Effect Predictor tool permitting large-scale programmatic variant analysis independent of any specific programming language. AVAILABILITY AND IMPLEMENTATION The Ensembl REST API can be accessed at http://rest.ensembl.org and source code is freely available under an Apache 2.0 license from http://github.com/Ensembl/ensembl-rest.
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Affiliation(s)
- Andrew Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Kathryn Beal
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Stephen Keenan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - William McLaren
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Miguel Pignatelli
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Graham R S Ritchie
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Magali Ruffier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Kieron Taylor
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Alessandro Vullo
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
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15
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Flicek P, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S, Gil L, Girón CG, Gordon L, Hourlier T, Hunt S, Johnson N, Juettemann T, Kähäri AK, Keenan S, Kulesha E, Martin FJ, Maurel T, McLaren WM, Murphy DN, Nag R, Overduin B, Pignatelli M, Pritchard B, Pritchard E, Riat HS, Ruffier M, Sheppard D, Taylor K, Thormann A, Trevanion SJ, Vullo A, Wilder SP, Wilson M, Zadissa A, Aken BL, Birney E, Cunningham F, Harrow J, Herrero J, Hubbard TJ, Kinsella R, Muffato M, Parker A, Spudich G, Yates A, Zerbino DR, Searle SM. Ensembl 2014. Nucleic Acids Res 2013; 42:D749-55. [PMID: 24316576 PMCID: PMC3964975 DOI: 10.1093/nar/gkt1196] [Citation(s) in RCA: 1056] [Impact Index Per Article: 96.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Ensembl (http://www.ensembl.org) creates tools and data resources to facilitate genomic analysis in chordate species with an emphasis on human, major vertebrate model organisms and farm animals. Over the past year we have increased the number of species that we support to 77 and expanded our genome browser with a new scrollable overview and improved variation and phenotype views. We also report updates to our core datasets and improvements to our gene homology relationships from the addition of new species. Our REST service has been extended with additional support for comparative genomics and ontology information. Finally, we provide updated information about our methods for data access and resources for user training.
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Affiliation(s)
- Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- *To whom correspondence should be addressed. Tel: +44 1223 492 581; Fax: +44 1223 494 494;
| | - M. Ridwan Amode
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Daniel Barrell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Kathryn Beal
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Simon Brent
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Denise Carvalho-Silva
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Peter Clapham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Guy Coates
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Stephen Fitzgerald
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Laurent Gil
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Carlos García Girón
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Leo Gordon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Sarah Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Nathan Johnson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Thomas Juettemann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Andreas K. Kähäri
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Stephen Keenan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Eugene Kulesha
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Fergal J. Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Thomas Maurel
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - William M. McLaren
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Daniel N. Murphy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Rishi Nag
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Bert Overduin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Miguel Pignatelli
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Bethan Pritchard
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Emily Pritchard
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Harpreet S. Riat
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Magali Ruffier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Daniel Sheppard
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Kieron Taylor
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Anja Thormann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Stephen J. Trevanion
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Alessandro Vullo
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Steven P. Wilder
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Mark Wilson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Amonida Zadissa
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Bronwen L. Aken
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Jennifer Harrow
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Javier Herrero
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Tim J.P. Hubbard
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Rhoda Kinsella
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Matthieu Muffato
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Anne Parker
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Giulietta Spudich
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Andy Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Daniel R. Zerbino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Stephen M.J. Searle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
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Bewick BM, Bell D, Crosby S, Edlin B, Keenan S, Marshall K, Savva G. Promoting improvements in public health: Using a Social Norms Approach to reduce use of alcohol, tobacco and other drugs. Drugs: Education, Prevention and Policy 2013. [DOI: 10.3109/09687637.2013.766150] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Flicek P, Ahmed I, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S, Gil L, García-Girón C, Gordon L, Hourlier T, Hunt S, Juettemann T, Kähäri AK, Keenan S, Komorowska M, Kulesha E, Longden I, Maurel T, McLaren WM, Muffato M, Nag R, Overduin B, Pignatelli M, Pritchard B, Pritchard E, Riat HS, Ritchie GRS, Ruffier M, Schuster M, Sheppard D, Sobral D, Taylor K, Thormann A, Trevanion S, White S, Wilder SP, Aken BL, Birney E, Cunningham F, Dunham I, Harrow J, Herrero J, Hubbard TJP, Johnson N, Kinsella R, Parker A, Spudich G, Yates A, Zadissa A, Searle SMJ. Ensembl 2013. Nucleic Acids Res 2012. [PMID: 23203987 PMCID: PMC3531136 DOI: 10.1093/nar/gks1236] [Citation(s) in RCA: 787] [Impact Index Per Article: 65.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Ensembl project (http://www.ensembl.org) provides genome information for sequenced chordate genomes with a particular focus on human, mouse, zebrafish and rat. Our resources include evidenced-based gene sets for all supported species; large-scale whole genome multiple species alignments across vertebrates and clade-specific alignments for eutherian mammals, primates, birds and fish; variation data resources for 17 species and regulation annotations based on ENCODE and other data sets. Ensembl data are accessible through the genome browser at http://www.ensembl.org and through other tools and programmatic interfaces.
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Affiliation(s)
- Paul Flicek
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK.
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18
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Flicek P, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S, Gil L, Gordon L, Hendrix M, Hourlier T, Johnson N, Kähäri AK, Keefe D, Keenan S, Kinsella R, Komorowska M, Koscielny G, Kulesha E, Larsson P, Longden I, McLaren W, Muffato M, Overduin B, Pignatelli M, Pritchard B, Riat HS, Ritchie GRS, Ruffier M, Schuster M, Sobral D, Tang YA, Taylor K, Trevanion S, Vandrovcova J, White S, Wilson M, Wilder SP, Aken BL, Birney E, Cunningham F, Dunham I, Durbin R, Fernández-Suarez XM, Harrow J, Herrero J, Hubbard TJP, Parker A, Proctor G, Spudich G, Vogel J, Yates A, Zadissa A, Searle SMJ. Ensembl 2012. Nucleic Acids Res 2011; 40:D84-90. [PMID: 22086963 PMCID: PMC3245178 DOI: 10.1093/nar/gkr991] [Citation(s) in RCA: 806] [Impact Index Per Article: 62.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The Ensembl project (http://www.ensembl.org) provides genome resources for chordate genomes with a particular focus on human genome data as well as data for key model organisms such as mouse, rat and zebrafish. Five additional species were added in the last year including gibbon (Nomascus leucogenys) and Tasmanian devil (Sarcophilus harrisii) bringing the total number of supported species to 61 as of Ensembl release 64 (September 2011). Of these, 55 species appear on the main Ensembl website and six species are provided on the Ensembl preview site (Pre!Ensembl; http://pre.ensembl.org) with preliminary support. The past year has also seen improvements across the project.
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Affiliation(s)
- Paul Flicek
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK.
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Flicek P, Amode MR, Barrell D, Beal K, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, Gordon L, Hendrix M, Hourlier T, Johnson N, Kähäri A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Kulesha E, Larsson P, Longden I, McLaren W, Overduin B, Pritchard B, Riat HS, Rios D, Ritchie GRS, Ruffier M, Schuster M, Sobral D, Spudich G, Tang YA, Trevanion S, Vandrovcova J, Vilella AJ, White S, Wilder SP, Zadissa A, Zamora J, Aken BL, Birney E, Cunningham F, Dunham I, Durbin R, Fernández-Suarez XM, Herrero J, Hubbard TJP, Parker A, Proctor G, Vogel J, Searle SMJ. Ensembl 2011. Nucleic Acids Res 2011; 39:D800-6. [PMID: 21045057 PMCID: PMC3013672 DOI: 10.1093/nar/gkq1064] [Citation(s) in RCA: 564] [Impact Index Per Article: 43.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Accepted: 10/13/2010] [Indexed: 11/13/2022] Open
Abstract
The Ensembl project (http://www.ensembl.org) seeks to enable genomic science by providing high quality, integrated annotation on chordate and selected eukaryotic genomes within a consistent and accessible infrastructure. All supported species include comprehensive, evidence-based gene annotations and a selected set of genomes includes additional data focused on variation, comparative, evolutionary, functional and regulatory annotation. The most advanced resources are provided for key species including human, mouse, rat and zebrafish reflecting the popularity and importance of these species in biomedical research. As of Ensembl release 59 (August 2010), 56 species are supported of which 5 have been added in the past year. Since our previous report, we have substantially improved the presentation and integration of both data of disease relevance and the regulatory state of different cell types.
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Affiliation(s)
- Paul Flicek
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
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Morgan NV, Morris MR, Cangul H, Gleeson D, Straatman-Iwanowska A, Davies N, Keenan S, Pasha S, Rahman F, Gentle D, Vreeswijk MPG, Devilee P, Knowles MA, Ceylaner S, Trembath RC, Dalence C, Kismet E, Köseoğlu V, Rossbach HC, Gissen P, Tannahill D, Maher ER. Mutations in SLC29A3, encoding an equilibrative nucleoside transporter ENT3, cause a familial histiocytosis syndrome (Faisalabad histiocytosis) and familial Rosai-Dorfman disease. PLoS Genet 2010; 6:e1000833. [PMID: 20140240 PMCID: PMC2816679 DOI: 10.1371/journal.pgen.1000833] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2009] [Accepted: 01/04/2010] [Indexed: 11/19/2022] Open
Abstract
The histiocytoses are a heterogeneous group of disorders characterised by an excessive number of histiocytes. In most cases the pathophysiology is unclear and treatment is nonspecific. Faisalabad histiocytosis (FHC) (MIM 602782) has been classed as an autosomal recessively inherited form of histiocytosis with similarities to Rosai-Dorfman disease (RDD) (also known as sinus histiocytosis with massive lymphadenopathy (SHML)). To elucidate the molecular basis of FHC, we performed autozygosity mapping studies in a large consanguineous family and identified a novel locus at chromosome 10q22.1. Mutation analysis of candidate genes within the target interval identified biallelic germline mutations in SLC29A3 in the FHC kindred and in two families reported to have familial RDD. Analysis of SLC29A3 expression during mouse embryogenesis revealed widespread expression by e14.5 with prominent expression in the central nervous system, eye, inner ear, and epithelial tissues including the gastrointestinal tract. SLC29A3 encodes an intracellular equilibrative nucleoside transporter (hENT3) with affinity for adenosine. Recently germline mutations in SLC29A3 were also described in two rare autosomal recessive disorders with overlapping phenotypes: (a) H syndrome (MIM 612391) that is characterised by cutaneous hyperpigmentation and hypertrichosis, hepatomegaly, heart anomalies, hearing loss, and hypogonadism; and (b) PHID (pigmented hypertrichosis with insulin-dependent diabetes mellitus) syndrome. Our findings suggest that a variety of clinical diagnoses (H and PHID syndromes, FHC, and familial RDD) can be included in a new diagnostic category of SLC29A3 spectrum disorder. The histiocytoses are a group of systemic disorders usually confined to childhood and are caused by an excessive number of histiocytes which phagocytose other cells and process antigens. Although nearly a century has passed since histiocytic disorders were recognised, their pathophysiology remains largely unclear, and treatment is nonspecific. The identification of SLC29A3 mutations as the molecular basis for a familial form of syndromic histiocytosis (FHC/RDD) confirms a direct link between Faisalabad histiocytosis and Rosai-Dorfman disease and links these disorders to other SLC29A3-associated phenotypes.
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Affiliation(s)
- Neil V. Morgan
- Wellchild Paediatric Research Centre and Department of Medical and Molecular Genetics, University of Birmingham College of Medical and Dental Sciences, Edgbaston, Birmingham, United Kingdom
| | - Mark R. Morris
- Wellchild Paediatric Research Centre and Department of Medical and Molecular Genetics, University of Birmingham College of Medical and Dental Sciences, Edgbaston, Birmingham, United Kingdom
- Cancer Research UK Renal Molecular Oncology Group, Department of Medical and Molecular Genetics, University of Birmingham College of Medical and Dental Sciences, Edgbaston, Birmingham, United Kingdom
| | - Hakan Cangul
- Wellchild Paediatric Research Centre and Department of Medical and Molecular Genetics, University of Birmingham College of Medical and Dental Sciences, Edgbaston, Birmingham, United Kingdom
- Department of Medical Genetics, Uludag University School of Medicine, Bursa, Turkey
| | - Diane Gleeson
- The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Anna Straatman-Iwanowska
- Wellchild Paediatric Research Centre and Department of Medical and Molecular Genetics, University of Birmingham College of Medical and Dental Sciences, Edgbaston, Birmingham, United Kingdom
| | - Nicholas Davies
- School of Biosciences, University of Birmingham School of Medicine, Birmingham, United Kingdom
| | - Stephen Keenan
- The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
- European Bioinformatics Institute, Cambridge, United Kingdom
| | - Shanaz Pasha
- Wellchild Paediatric Research Centre and Department of Medical and Molecular Genetics, University of Birmingham College of Medical and Dental Sciences, Edgbaston, Birmingham, United Kingdom
| | - Fatimah Rahman
- Wellchild Paediatric Research Centre and Department of Medical and Molecular Genetics, University of Birmingham College of Medical and Dental Sciences, Edgbaston, Birmingham, United Kingdom
| | - Dean Gentle
- Wellchild Paediatric Research Centre and Department of Medical and Molecular Genetics, University of Birmingham College of Medical and Dental Sciences, Edgbaston, Birmingham, United Kingdom
- Cancer Research UK Renal Molecular Oncology Group, Department of Medical and Molecular Genetics, University of Birmingham College of Medical and Dental Sciences, Edgbaston, Birmingham, United Kingdom
| | - Maaike P. G. Vreeswijk
- Department of Human Genetics, Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter Devilee
- Department of Human Genetics, Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Clinical Genetics and the Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Margaret A. Knowles
- Cancer Research UK Clinical Centre, Leeds Institute for Molecular Medicine, St James's University Hospital, Leeds, United Kingdom
| | | | - Richard C. Trembath
- Department of Medical and Molecular Genetics, King's College London School of Medicine, Guy's Hospital, London, United Kingdom
| | - Carlos Dalence
- Division of Paediatric Haematology/Oncology, St. Joseph Children's Hospital, Tampa, Florida, United States of America
| | - Erol Kismet
- Department of Pediatric Oncology, Gulhane Military Medical Academy, Ankara, Turkey
| | - Vedat Köseoğlu
- Department of Pediatric Oncology, Gulhane Military Medical Academy, Ankara, Turkey
| | - Hans-Christoph Rossbach
- Division of Paediatric Haematology/Oncology, St. Joseph Children's Hospital, Tampa, Florida, United States of America
| | - Paul Gissen
- Wellchild Paediatric Research Centre and Department of Medical and Molecular Genetics, University of Birmingham College of Medical and Dental Sciences, Edgbaston, Birmingham, United Kingdom
| | - David Tannahill
- The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
- Cranfield Health, Cranfield University, Bedford, United Kingdom
| | - Eamonn R. Maher
- Wellchild Paediatric Research Centre and Department of Medical and Molecular Genetics, University of Birmingham College of Medical and Dental Sciences, Edgbaston, Birmingham, United Kingdom
- Cancer Research UK Renal Molecular Oncology Group, Department of Medical and Molecular Genetics, University of Birmingham College of Medical and Dental Sciences, Edgbaston, Birmingham, United Kingdom
- West Midlands Region Genetics Service, Birmingham Women's Hospital, Edgbaston, United Kingdom
- * E-mail:
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Flicek P, Aken BL, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, Fernandez-Banet J, Gordon L, Gräf S, Haider S, Hammond M, Howe K, Jenkinson A, Johnson N, Kähäri A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Koscielny G, Kulesha E, Lawson D, Longden I, Massingham T, McLaren W, Megy K, Overduin B, Pritchard B, Rios D, Ruffier M, Schuster M, Slater G, Smedley D, Spudich G, Tang YA, Trevanion S, Vilella A, Vogel J, White S, Wilder SP, Zadissa A, Birney E, Cunningham F, Dunham I, Durbin R, Fernández-Suarez XM, Herrero J, Hubbard TJP, Parker A, Proctor G, Smith J, Searle SMJ. Ensembl's 10th year. Nucleic Acids Res 2009; 38:D557-62. [PMID: 19906699 PMCID: PMC2808936 DOI: 10.1093/nar/gkp972] [Citation(s) in RCA: 238] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Ensembl (http://www.ensembl.org) integrates genomic information for a comprehensive set of chordate genomes with a particular focus on resources for human, mouse, rat, zebrafish and other high-value sequenced genomes. We provide complete gene annotations for all supported species in addition to specific resources that target genome variation, function and evolution. Ensembl data is accessible in a variety of formats including via our genome browser, API and BioMart. This year marks the tenth anniversary of Ensembl and in that time the project has grown with advances in genome technology. As of release 56 (September 2009), Ensembl supports 51 species including marmoset, pig, zebra finch, lizard, gorilla and wallaby, which were added in the past year. Major additions and improvements to Ensembl since our previous report include the incorporation of the human GRCh37 assembly, enhanced visualisation and data-mining options for the Ensembl regulatory features and continued development of our software infrastructure.
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Affiliation(s)
- Paul Flicek
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
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22
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Kersey PJ, Lawson D, Birney E, Derwent PS, Haimel M, Herrero J, Keenan S, Kerhornou A, Koscielny G, Kähäri A, Kinsella RJ, Kulesha E, Maheswari U, Megy K, Nuhn M, Proctor G, Staines D, Valentin F, Vilella AJ, Yates A. Ensembl Genomes: extending Ensembl across the taxonomic space. Nucleic Acids Res 2009; 38:D563-9. [PMID: 19884133 PMCID: PMC2808935 DOI: 10.1093/nar/gkp871] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Ensembl Genomes (http://www.ensemblgenomes.org) is a new portal offering integrated access to genome-scale data from non-vertebrate species of scientific interest, developed using the Ensembl genome annotation and visualisation platform. Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. Many of the databases supporting the portal have been built in close collaboration with the scientific community, which we consider as essential for maintaining the accuracy and usefulness of the resource. A common set of user interfaces (which include a graphical genome browser, FTP, BLAST search, a query optimised data warehouse, programmatic access, and a Perl API) is provided for all domains. Data types incorporated include annotation of (protein and non-protein coding) genes, cross references to external resources, and high throughput experimental data (e.g. data from large scale studies of gene expression and polymorphism visualised in their genomic context). Additionally, extensive comparative analysis has been performed, both within defined clades and across the wider taxonomy, and sequence alignments and gene trees resulting from this can be accessed through the site.
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Affiliation(s)
- P J Kersey
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK.
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23
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Hubbard TJP, Aken BL, Ayling S, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Clarke L, Coates G, Fairley S, Fitzgerald S, Fernandez-Banet J, Gordon L, Graf S, Haider S, Hammond M, Holland R, Howe K, Jenkinson A, Johnson N, Kahari A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Kulesha E, Lawson D, Longden I, Megy K, Meidl P, Overduin B, Parker A, Pritchard B, Rios D, Schuster M, Slater G, Smedley D, Spooner W, Spudich G, Trevanion S, Vilella A, Vogel J, White S, Wilder S, Zadissa A, Birney E, Cunningham F, Curwen V, Durbin R, Fernandez-Suarez XM, Herrero J, Kasprzyk A, Proctor G, Smith J, Searle S, Flicek P. Ensembl 2009. Nucleic Acids Res 2008; 37:D690-7. [PMID: 19033362 PMCID: PMC2686571 DOI: 10.1093/nar/gkn828] [Citation(s) in RCA: 683] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The Ensembl project (http://www.ensembl.org) is a comprehensive genome information system featuring an integrated set of genome annotation, databases, and other information for chordate, selected model organism and disease vector genomes. As of release 51 (November 2008), Ensembl fully supports 45 species, and three additional species have preliminary support. New species in the past year include orangutan and six additional low coverage mammalian genomes. Major additions and improvements to Ensembl since our previous report include a major redesign of our website; generation of multiple genome alignments and ancestral sequences using the new Enredo-Pecan-Ortheus pipeline and development of our software infrastructure, particularly to support the Ensembl Genomes project (http://www.ensemblgenomes.org/).
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Affiliation(s)
- T J P Hubbard
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
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24
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Keenan S, Mavaddat N, Iddon J, Pickard JD, Sahakian BJ. Effects of methylphenidate on cognition and apathy in normal pressure hydrocephalus: a case study and review. Br J Neurosurg 2005; 19:46-50. [PMID: 16147583 DOI: 10.1080/02688690500080893] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The psychostimulant methylphenidate has been previously shown to improve cognitive performance in both normal control volunteers and patient populations. In the present case study, the effects of methylphenidate on cognitive and behavioural function were examined in a single patient with idiopathic normal pressure hydrocephalus (NPH) who had undergone ventriculoperitoneal shunting. A double-blind placebo-controlled ABBA drug design was employed, with the administration of two different doses of methylphenidate followed by neuropsychological assessment on a number of psychometric tests and cognitive tasks drawn from the Cambridge Neuropsychological Test Automated Battery (CANTAB). Methylphenidate produced a dose-dependent positive improvement in behavioural measures in the patient associated with a reduction in apathy. It also had a dose-independent enhancing effect on performance of a Spatial Recognition task. These findings require replication in a large sample of patients to determine whether methylphenidate may prove to be generally useful in enhancing cognition and reducing apathy in normal pressure hydrocephalus.
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Affiliation(s)
- S Keenan
- Department of Psychiatry, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
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25
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Ashurst JL, Chen CK, Gilbert JGR, Jekosch K, Keenan S, Meidl P, Searle SM, Stalker J, Storey R, Trevanion S, Wilming L, Hubbard T. The Vertebrate Genome Annotation (Vega) database. Nucleic Acids Res 2005; 33:D459-65. [PMID: 15608237 PMCID: PMC540089 DOI: 10.1093/nar/gki135] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The Vertebrate Genome Annotation (Vega) database (http://vega.sanger.ac.uk) has been designed to be a community resource for browsing manual annotation of finished sequences from a variety of vertebrate genomes. Its core database is based on an Ensembl-style schema, extended to incorporate curation-specific metadata. In collaboration with the genome sequencing centres, Vega attempts to present consistent high-quality annotation of the published human chromosome sequences. In addition, it is also possible to view various finished regions from other vertebrates, including mouse and zebrafish. Vega displays only manually annotated gene structures built using transcriptional evidence, which can be examined in the browser. Attempts have been made to standardize the annotation procedure across each vertebrate genome, which should aid comparative analysis of orthologues across the different finished regions.
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Affiliation(s)
- J L Ashurst
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.
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26
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Ross MT, Grafham DV, Coffey AJ, Scherer S, McLay K, Muzny D, Platzer M, Howell GR, Burrows C, Bird CP, Frankish A, Lovell FL, Howe KL, Ashurst JL, Fulton RS, Sudbrak R, Wen G, Jones MC, Hurles ME, Andrews TD, Scott CE, Searle S, Ramser J, Whittaker A, Deadman R, Carter NP, Hunt SE, Chen R, Cree A, Gunaratne P, Havlak P, Hodgson A, Metzker ML, Richards S, Scott G, Steffen D, Sodergren E, Wheeler DA, Worley KC, Ainscough R, Ambrose KD, Ansari-Lari MA, Aradhya S, Ashwell RIS, Babbage AK, Bagguley CL, Ballabio A, Banerjee R, Barker GE, Barlow KF, Barrett IP, Bates KN, Beare DM, Beasley H, Beasley O, Beck A, Bethel G, Blechschmidt K, Brady N, Bray-Allen S, Bridgeman AM, Brown AJ, Brown MJ, Bonnin D, Bruford EA, Buhay C, Burch P, Burford D, Burgess J, Burrill W, Burton J, Bye JM, Carder C, Carrel L, Chako J, Chapman JC, Chavez D, Chen E, Chen G, Chen Y, Chen Z, Chinault C, Ciccodicola A, Clark SY, Clarke G, Clee CM, Clegg S, Clerc-Blankenburg K, Clifford K, Cobley V, Cole CG, Conquer JS, Corby N, Connor RE, David R, Davies J, Davis C, Davis J, Delgado O, Deshazo D, Dhami P, Ding Y, Dinh H, Dodsworth S, Draper H, Dugan-Rocha S, Dunham A, Dunn M, Durbin KJ, Dutta I, Eades T, Ellwood M, Emery-Cohen A, Errington H, Evans KL, Faulkner L, Francis F, Frankland J, Fraser AE, Galgoczy P, Gilbert J, Gill R, Glöckner G, Gregory SG, Gribble S, Griffiths C, Grocock R, Gu Y, Gwilliam R, Hamilton C, Hart EA, Hawes A, Heath PD, Heitmann K, Hennig S, Hernandez J, Hinzmann B, Ho S, Hoffs M, Howden PJ, Huckle EJ, Hume J, Hunt PJ, Hunt AR, Isherwood J, Jacob L, Johnson D, Jones S, de Jong PJ, Joseph SS, Keenan S, Kelly S, Kershaw JK, Khan Z, Kioschis P, Klages S, Knights AJ, Kosiura A, Kovar-Smith C, Laird GK, Langford C, Lawlor S, Leversha M, Lewis L, Liu W, Lloyd C, Lloyd DM, Loulseged H, Loveland JE, Lovell JD, Lozado R, Lu J, Lyne R, Ma J, Maheshwari M, Matthews LH, McDowall J, McLaren S, McMurray A, Meidl P, Meitinger T, Milne S, Miner G, Mistry SL, Morgan M, Morris S, Müller I, Mullikin JC, Nguyen N, Nordsiek G, Nyakatura G, O'Dell CN, Okwuonu G, Palmer S, Pandian R, Parker D, Parrish J, Pasternak S, Patel D, Pearce AV, Pearson DM, Pelan SE, Perez L, Porter KM, Ramsey Y, Reichwald K, Rhodes S, Ridler KA, Schlessinger D, Schueler MG, Sehra HK, Shaw-Smith C, Shen H, Sheridan EM, Shownkeen R, Skuce CD, Smith ML, Sotheran EC, Steingruber HE, Steward CA, Storey R, Swann RM, Swarbreck D, Tabor PE, Taudien S, Taylor T, Teague B, Thomas K, Thorpe A, Timms K, Tracey A, Trevanion S, Tromans AC, d'Urso M, Verduzco D, Villasana D, Waldron L, Wall M, Wang Q, Warren J, Warry GL, Wei X, West A, Whitehead SL, Whiteley MN, Wilkinson JE, Willey DL, Williams G, Williams L, Williamson A, Williamson H, Wilming L, Woodmansey RL, Wray PW, Yen J, Zhang J, Zhou J, Zoghbi H, Zorilla S, Buck D, Reinhardt R, Poustka A, Rosenthal A, Lehrach H, Meindl A, Minx PJ, Hillier LW, Willard HF, Wilson RK, Waterston RH, Rice CM, Vaudin M, Coulson A, Nelson DL, Weinstock G, Sulston JE, Durbin R, Hubbard T, Gibbs RA, Beck S, Rogers J, Bentley DR. The DNA sequence of the human X chromosome. Nature 2005; 434:325-37. [PMID: 15772651 PMCID: PMC2665286 DOI: 10.1038/nature03440] [Citation(s) in RCA: 738] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2005] [Accepted: 02/07/2005] [Indexed: 01/19/2023]
Abstract
The human X chromosome has a unique biology that was shaped by its evolution as the sex chromosome shared by males and females. We have determined 99.3% of the euchromatic sequence of the X chromosome. Our analysis illustrates the autosomal origin of the mammalian sex chromosomes, the stepwise process that led to the progressive loss of recombination between X and Y, and the extent of subsequent degradation of the Y chromosome. LINE1 repeat elements cover one-third of the X chromosome, with a distribution that is consistent with their proposed role as way stations in the process of X-chromosome inactivation. We found 1,098 genes in the sequence, of which 99 encode proteins expressed in testis and in various tumour types. A disproportionately high number of mendelian diseases are documented for the X chromosome. Of this number, 168 have been explained by mutations in 113 X-linked genes, which in many cases were characterized with the aid of the DNA sequence.
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MESH Headings
- Animals
- Antigens, Neoplasm/genetics
- Centromere/genetics
- Chromosomes, Human, X/genetics
- Chromosomes, Human, Y/genetics
- Contig Mapping
- Crossing Over, Genetic/genetics
- Dosage Compensation, Genetic
- Evolution, Molecular
- Female
- Genetic Linkage/genetics
- Genetics, Medical
- Genomics
- Humans
- Male
- Polymorphism, Single Nucleotide/genetics
- RNA/genetics
- Repetitive Sequences, Nucleic Acid/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Testis/metabolism
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Affiliation(s)
- Mark T Ross
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
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27
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Hubbard T, Andrews D, Caccamo M, Cameron G, Chen Y, Clamp M, Clarke L, Coates G, Cox T, Cunningham F, Curwen V, Cutts T, Down T, Durbin R, Fernandez-Suarez XM, Gilbert J, Hammond M, Herrero J, Hotz H, Howe K, Iyer V, Jekosch K, Kahari A, Kasprzyk A, Keefe D, Keenan S, Kokocinsci F, London D, Longden I, McVicker G, Melsopp C, Meidl P, Potter S, Proctor G, Rae M, Rios D, Schuster M, Searle S, Severin J, Slater G, Smedley D, Smith J, Spooner W, Stabenau A, Stalker J, Storey R, Trevanion S, Ureta-Vidal A, Vogel J, White S, Woodwark C, Birney E. Ensembl 2005. Nucleic Acids Res 2005; 33:D447-53. [PMID: 15608235 PMCID: PMC540092 DOI: 10.1093/nar/gki138] [Citation(s) in RCA: 354] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2004] [Revised: 11/01/2004] [Accepted: 11/01/2004] [Indexed: 11/17/2022] Open
Abstract
The Ensembl (http://www.ensembl.org/) project provides a comprehensive and integrated source of annotation of large genome sequences. Over the last year the number of genomes available from the Ensembl site has increased by 7 to 16, with the addition of the six vertebrate genomes of chimpanzee, dog, cow, chicken, tetraodon and frog and the insect genome of honeybee. The majority have been annotated automatically using the Ensembl gene build system, showing its flexibility to reliably annotate a wide variety of genomes. With the increased number of vertebrate genomes, the comparative analysis provided to users has been greatly improved, with new website interfaces allowing annotation of different genomes to be directly compared. The Ensembl software system is being increasingly widely reused in different projects showing the benefits of a completely open approach to software development and distribution.
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Affiliation(s)
- T Hubbard
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
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Abstract
The Ensembl pipeline is an extension to the Ensembl system which allows automated annotation of genomic sequence. The software comprises two parts. First, there is a set of Perl modules ("Runnables" and "RunnableDBs") which are 'wrappers' for a variety of commonly used analysis tools. These retrieve sequence data from a relational database, run the analysis, and write the results back to the database. They inherit from a common interface, which simplifies the writing of new wrapper modules. On top of this sits a job submission system (the "RuleManager") which allows efficient and reliable submission of large numbers of jobs to a compute farm. Here we describe the fundamental software components of the pipeline, and we also highlight some features of the Sanger installation which were necessary to enable the pipeline to scale to whole-genome analysis.
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Affiliation(s)
- Simon C Potter
- The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
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Humphray SJ, Oliver K, Hunt AR, Plumb RW, Loveland JE, Howe KL, Andrews TD, Searle S, Hunt SE, Scott CE, Jones MC, Ainscough R, Almeida JP, Ambrose KD, Ashwell RIS, Babbage AK, Babbage S, Bagguley CL, Bailey J, Banerjee R, Barker DJ, Barlow KF, Bates K, Beasley H, Beasley O, Bird CP, Bray-Allen S, Brown AJ, Brown JY, Burford D, Burrill W, Burton J, Carder C, Carter NP, Chapman JC, Chen Y, Clarke G, Clark SY, Clee CM, Clegg S, Collier RE, Corby N, Crosier M, Cummings AT, Davies J, Dhami P, Dunn M, Dutta I, Dyer LW, Earthrowl ME, Faulkner L, Fleming CJ, Frankish A, Frankland JA, French L, Fricker DG, Garner P, Garnett J, Ghori J, Gilbert JGR, Glison C, Grafham DV, Gribble S, Griffiths C, Griffiths-Jones S, Grocock R, Guy J, Hall RE, Hammond S, Harley JL, Harrison ESI, Hart EA, Heath PD, Henderson CD, Hopkins BL, Howard PJ, Howden PJ, Huckle E, Johnson C, Johnson D, Joy AA, Kay M, Keenan S, Kershaw JK, Kimberley AM, King A, Knights A, Laird GK, Langford C, Lawlor S, Leongamornlert DA, Leversha M, Lloyd C, Lloyd DM, Lovell J, Martin S, Mashreghi-Mohammadi M, Matthews L, McLaren S, McLay KE, McMurray A, Milne S, Nickerson T, Nisbett J, Nordsiek G, Pearce AV, Peck AI, Porter KM, Pandian R, Pelan S, Phillimore B, Povey S, Ramsey Y, Rand V, Scharfe M, Sehra HK, Shownkeen R, Sims SK, Skuce CD, Smith M, Steward CA, Swarbreck D, Sycamore N, Tester J, Thorpe A, Tracey A, Tromans A, Thomas DW, Wall M, Wallis JM, West AP, Whitehead SL, Willey DL, Williams SA, Wilming L, Wray PW, Young L, Ashurst JL, Coulson A, Blöcker H, Durbin R, Sulston JE, Hubbard T, Jackson MJ, Bentley DR, Beck S, Rogers J, Dunham I. DNA sequence and analysis of human chromosome 9. Nature 2004; 429:369-74. [PMID: 15164053 PMCID: PMC2734081 DOI: 10.1038/nature02465] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2003] [Accepted: 03/08/2004] [Indexed: 11/09/2022]
Abstract
Chromosome 9 is highly structurally polymorphic. It contains the largest autosomal block of heterochromatin, which is heteromorphic in 6-8% of humans, whereas pericentric inversions occur in more than 1% of the population. The finished euchromatic sequence of chromosome 9 comprises 109,044,351 base pairs and represents >99.6% of the region. Analysis of the sequence reveals many intra- and interchromosomal duplications, including segmental duplications adjacent to both the centromere and the large heterochromatic block. We have annotated 1,149 genes, including genes implicated in male-to-female sex reversal, cancer and neurodegenerative disease, and 426 pseudogenes. The chromosome contains the largest interferon gene cluster in the human genome. There is also a region of exceptionally high gene and G + C content including genes paralogous to those in the major histocompatibility complex. We have also detected recently duplicated genes that exhibit different rates of sequence divergence, presumably reflecting natural selection.
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Affiliation(s)
- S J Humphray
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
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Birney E, Andrews TD, Bevan P, Caccamo M, Chen Y, Clarke L, Coates G, Cuff J, Curwen V, Cutts T, Down T, Eyras E, Fernandez-Suarez XM, Gane P, Gibbins B, Gilbert J, Hammond M, Hotz HR, Iyer V, Jekosch K, Kahari A, Kasprzyk A, Keefe D, Keenan S, Lehvaslaiho H, McVicker G, Melsopp C, Meidl P, Mongin E, Pettett R, Potter S, Proctor G, Rae M, Searle S, Slater G, Smedley D, Smith J, Spooner W, Stabenau A, Stalker J, Storey R, Ureta-Vidal A, Woodwark KC, Cameron G, Durbin R, Cox A, Hubbard T, Clamp M. An overview of Ensembl. Genome Res 2004; 14:925-8. [PMID: 15078858 PMCID: PMC479121 DOI: 10.1101/gr.1860604] [Citation(s) in RCA: 305] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Ensembl (http://www.ensembl.org/) is a bioinformatics project to organize biological information around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of individual genomes, and of the synteny and orthology relationships between them. It is also a framework for integration of any biological data that can be mapped onto features derived from the genomic sequence. Ensembl is available as an interactive Web site, a set of flat files, and as a complete, portable open source software system for handling genomes. All data are provided without restriction, and code is freely available. Ensembl's aims are to continue to "widen" this biological integration to include other model organisms relevant to understanding human biology as they become available; to "deepen" this integration to provide an ever more seamless linkage between equivalent components in different species; and to provide further classification of functional elements in the genome that have been previously elusive.
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Affiliation(s)
- Ewan Birney
- EMBL European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
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Birney E, Andrews D, Bevan P, Caccamo M, Cameron G, Chen Y, Clarke L, Coates G, Cox T, Cuff J, Curwen V, Cutts T, Down T, Durbin R, Eyras E, Fernandez-Suarez XM, Gane P, Gibbins B, Gilbert J, Hammond M, Hotz H, Iyer V, Kahari A, Jekosch K, Kasprzyk A, Keefe D, Keenan S, Lehvaslaiho H, McVicker G, Melsopp C, Meidl P, Mongin E, Pettett R, Potter S, Proctor G, Rae M, Searle S, Slater G, Smedley D, Smith J, Spooner W, Stabenau A, Stalker J, Storey R, Ureta-Vidal A, Woodwark C, Clamp M, Hubbard T. Ensembl 2004. Nucleic Acids Res 2004; 32:D468-70. [PMID: 14681459 PMCID: PMC308772 DOI: 10.1093/nar/gkh038] [Citation(s) in RCA: 143] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organize biology around the sequences of large genomes. It is a comprehensive and integrated source of annotation of large genome sequences, available via interactive website, web services or flat files. As well as being one of the leading sources of genome annotation, Ensembl is an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements. The facilities of the system range from sequence analysis to data storage and visualization and installations exist around the world both in companies and at academic sites. With a total of nine genome sequences available from Ensembl and more genomes to follow, recent developments have focused mainly on closer integration between genomes and external data.
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Affiliation(s)
- E Birney
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
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Sirén AL, Fratelli M, Brines M, Goemans C, Casagrande S, Lewczuk P, Keenan S, Gleiter C, Pasquali C, Capobianco A, Mennini T, Heumann R, Cerami A, Ehrenreich H, Ghezzi P. Erythropoietin prevents neuronal apoptosis after cerebral ischemia and metabolic stress. Proc Natl Acad Sci U S A 2001; 98:4044-9. [PMID: 11259643 PMCID: PMC31176 DOI: 10.1073/pnas.051606598] [Citation(s) in RCA: 736] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2000] [Indexed: 12/16/2022] Open
Abstract
Erythropoietin (EPO) promotes neuronal survival after hypoxia and other metabolic insults by largely unknown mechanisms. Apoptosis and necrosis have been proposed as mechanisms of cellular demise, and either could be the target of actions of EPO. This study evaluates whether antiapoptotic mechanisms can account for the neuroprotective actions of EPO. Systemic administration of EPO (5,000 units/kg of body weight, i.p.) after middle-cerebral artery occlusion in rats dramatically reduces the volume of infarction 24 h later, in concert with an almost complete reduction in the number of terminal deoxynucleotidyltransferase-mediated dUTP nick-end labeling of neurons within the ischemic penumbra. In both pure and mixed neuronal cultures, EPO (0.1--10 units/ml) also inhibits apoptosis induced by serum deprivation or kainic acid exposure. Protection requires pretreatment, consistent with the induction of a gene expression program, and is sustained for 3 days without the continued presence of EPO. EPO (0.3 units/ml) also protects hippocampal neurons against hypoxia-induced neuronal death through activation of extracellular signal-regulated kinases and protein kinase Akt-1/protein kinase B. The action of EPO is not limited to directly promoting cell survival, as EPO is trophic but not mitogenic in cultured neuronal cells. These data suggest that inhibition of neuronal apoptosis underlies short latency protective effects of EPO after cerebral ischemia and other brain injuries. The neurotrophic actions suggest there may be longer-latency effects as well. Evaluation of EPO, a compound established as clinically safe, as neuroprotective therapy in acute brain injury is further supported.
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Affiliation(s)
- A L Sirén
- Max Planck Institute for Experimental Medicine, Georg August University, 37075 Goettingen, Germany
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Brines ML, Ghezzi P, Keenan S, Agnello D, de Lanerolle NC, Cerami C, Itri LM, Cerami A. Erythropoietin crosses the blood-brain barrier to protect against experimental brain injury. Proc Natl Acad Sci U S A 2000; 97:10526-31. [PMID: 10984541 PMCID: PMC27058 DOI: 10.1073/pnas.97.19.10526] [Citation(s) in RCA: 1049] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Erythropoietin (EPO), recognized for its central role in erythropoiesis, also mediates neuroprotection when the recombinant form (r-Hu-EPO) is directly injected into ischemic rodent brain. We observed abundant expression of the EPO receptor at brain capillaries, which could provide a route for circulating EPO to enter the brain. In confirmation of this hypothesis, systemic administration of r-Hu-EPO before or up to 6 h after focal brain ischemia reduced injury by approximately 50-75%. R-Hu-EPO also ameliorates the extent of concussive brain injury, the immune damage in experimental autoimmune encephalomyelitis, and the toxicity of kainate. Given r-Hu-EPO's excellent safety profile, clinical trials evaluating systemically administered r-Hu-EPO as a general neuroprotective treatment are warranted.
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Affiliation(s)
- M L Brines
- The Kenneth S. Warren Laboratories, 765 Old Saw Mill River Road, Tarrytown, NY 10591, USA.
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Abstract
BACKGROUND Given the high costs of delivering care to critically ill patients, practitioners and policymakers are beginning to scrutinize the costs and outcomes associated with intensive care. Health economics is a discipline concerned with determining the best way of using resources to maximize the health of the community. This involves addressing questions such as which procedure, test, therapy, or program should be provided, and to whom, given available resources. PURPOSE The purpose of this article is to review general economic principles that will help intensivists to better interpret published economic evaluations. DATA SOURCES Selected articles from the health economics and critical care literature. RESULTS In this article, we use an economic evaluation that examines sedation strategies in critically ill patients. We discuss how learning to critically appraise an economic evaluation is only part of the task for end users. Determining whether and how to apply the results of economic evaluations to local settings presents bigger challenges and remains largely a matter of judgment. CONCLUSIONS Economic evaluations use analytic techniques to systematically consider all possible costs and consequences of clinical actions. Although they should never form the sole basis for clinical decisions for individual patients, economic evaluations offer potentially useful information at different levels of decision-making.
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Affiliation(s)
- D K Heyland
- Department of Medicine, Queen's University, Kingston, Ontario, Canada
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Beverley DW, Ball RJ, Smith RA, Harran MJ, Durrans GM, Keenan S, Smith J, Durack B. Planning for the future: the experience of implementing a children's day assessment unit in a district general hospital. Arch Dis Child 1997; 77:287-92; discussion 292-3. [PMID: 9389229 PMCID: PMC1717351 DOI: 10.1136/adc.77.4.287] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A paediatric day assessment unit was opened in May 1995. An audit of the first year's activity showed that, despite an increase in emergency admissions of 8.4%, the number of children admitted as an emergency overnight was reduced by 3% in paediatrics and 7.2% in surgery. In the first year, 1731 children were assessed as an emergency of whom 658 did not require admission to the inpatient ward. Midnight occupancy fell 17.7% in paediatrics and 25.4% in surgery. The nurse staffing costs fell over Pounds 32,000 in the first year. No adverse events occurred during the first year of operation; this type of facility could lead to a more efficient use of resources in any children's unit.
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Affiliation(s)
- D W Beverley
- Department of Paediatrics, York District Hospital
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Tong W, Perkins R, Strelitz R, Collantes ER, Keenan S, Welsh WJ, Branham WS, Sheehan DM. Quantitative structure-activity relationships (QSARs) for estrogen binding to the estrogen receptor: predictions across species. Environ Health Perspect 1997; 105:1116-24. [PMID: 9353176 PMCID: PMC1470374 DOI: 10.1289/ehp.971051116] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The recognition of adverse effects due to environmental endocrine disruptors in humans and wildlife has focused attention on the need for predictive tools to select the most likely estrogenic chemicals from a very large number of chemicals for subsequent screening and/or testing for potential environmental toxicity. A three-dimensional quantitative structure-activity relationship (QSAR) model using comparative molecular field analysis (CoMFA) was constructed based on relative binding affinity (RBA) data from an estrogen receptor (ER) binding assay using calf uterine cytosol. The model demonstrated significant correlation of the calculated steric and electrostatic fields with RBA and yielded predictions that agreed well with experimental values over the entire range of RBA values. Analysis of the CoMFA three-dimensional contour plots revealed a consistent picture of the structural features that are largely responsible for the observed variations in RBA. Importantly, we established a correlation between the predicted RBA values for calf ER and their actual RBA values for human ER. These findings suggest a means to begin to construct a more comprehensive estrogen knowledge base by combining RBA assay data from multiple species in 3D-QSAR based predictive models, which could then be used to screen untested chemicals for their potential to bind to the ER. Another QSAR model was developed based on classical physicochemical descriptors generated using the CODESSA (Comprehensive Descriptors for Structural and Statistical Analysis) program. The predictive ability of the CoMFA model was superior to the corresponding CODESSA model.
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Affiliation(s)
- W Tong
- R.O.W. Sciences, Jefferson, AR 72079, USA
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Douglass AB, Bornstein R, Nino-Murcia G, Keenan S, Miles L, Zarcone VP, Guilleminault C, Dement WC. The Sleep Disorders Questionnaire. I: Creation and multivariate structure of SDQ. Sleep 1994; 17:160-7. [PMID: 8036370 DOI: 10.1093/sleep/17.2.160] [Citation(s) in RCA: 347] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The development of the Sleep Disorders Questionnaire (SDQ) from the Sleep Questionnaire and Assessment of Wakefulness (SQAW) of Stanford University is described in detail. The extraction of the best question items from the SQAW and their subsequent rewording in the SDQ to insure greater completion rates are described. Two item test-retest reliability studies are reported on 71 controls and on 130 sleep-disorder patients, which confirmed adequate reliability. To create multivariate scoring scales, SDQ was then given in a multicenter study to 519 persons, 435 of whom were sleep-disorder patients with full polysomnography. Canonical Discriminant Function Analysis was employed, which resulted in four clinical-diagnostic scales: SA for sleep apnea, NAR for narcolepsy, PSY for psychiatric sleep disorder and PLM for periodic limb movement disorder. Each was adjusted for male and female responses and transformed to a percentile using the observed distribution of raw scores. Using Receiver Operating Characteristics analysis, cutoff points were determined for each scale to maximize its sensitivity and specificity. Positive and negative predictive values were also calculated. The SA and NAR scales proved to be the most discriminating.
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Affiliation(s)
- A B Douglass
- Ann Arbor VA Medical Center Psychiatry Service, Michigan
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Abstract
This study investigated inter-rater reliability for scoring periodic leg movements in sleep (PLMS) and related phenomena. Five highly experienced polysomnographic technologists each scored 24 nocturnal polysomnograms, the majority of which contained an appreciable number of PLMS. Results indicated high inter-rater reliability for some variables but more modest reliability for others. We discuss these findings in terms of efforts of standardization in polysomnographic scoring of sleep disorders.
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Affiliation(s)
- D L Bliwise
- Sleep Disorders Center, Stanford Medical School, California
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40
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Affiliation(s)
- B Byrne
- Jefferson Medical College, Philadelphia, PA 19107
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Nino-Murcia G, Bliwise DL, Keenan S, Dement W. The assessment of a new technology for evaluating respiratory abnormalities in sleep. Int J Technol Assess Health Care 1986; 3:427-45. [PMID: 10302060 DOI: 10.1017/s0266462300001240] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
This study assessed the diagnostic utility of two technologies for evaluating respiratory abnormalities in sleep. We compared conventional polysomnography with a new, ambulatory microprocessor technology. Two key features of the comparison involved: (a) the use of multiple, skilled interpreters of each system; and (b) inter-rater agreement within the systems as a crucial test for the diagnostic utility of each. Results indicated that general categories of respiratory abnormalities could be judged more reliably than more specific categories, regardless of technology. For certain categories of respiratory abnormalities, however, inter-rater agreement with the newer technology was extremely low (e.g., reliability coefficients of .12, .09, and -0.6). Factors contributing to these low diagnostic reliabilities are discussed. Our data indicate that any assessment of new technology cannot be made apart from the clinical judgments to be rendered with that new technology. This approach may be generalizable to the assessment of other diagnostic technologies.
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Carskadon MA, Dement WC, Mitler MM, Roth T, Westbrook PR, Keenan S. Guidelines for the multiple sleep latency test (MSLT): a standard measure of sleepiness. Sleep 1986; 9:519-24. [PMID: 3809866 DOI: 10.1093/sleep/9.4.519] [Citation(s) in RCA: 907] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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Welsh DK, Nino-Murcia G, Gander PH, Keenan S, Dement WC. Regular 48-hour cycling of sleep duration and mood in a 35-year-old woman: use of lithium in time isolation. Biol Psychiatry 1986; 21:527-37. [PMID: 3083878 DOI: 10.1016/0006-3223(86)90195-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Abstract
A four step synthesis of 6-(0-carboxymethyl) oximinoethynylestradiol is reported. This compound, 6-(0-carboxymethyl) oximinomestranol, the 3-(0-carboxymethyl) oximes of norethindrone and norgestrel and the 3-hemisuccinate of ethynylestradiol were synthesized and conjugated with bovine serum albumin. Rabbits were immunized at 3 dose levels of haptene (20, 66 and 200 nmoles) and eight weeks later with a booster containing 66 nmoles of haptene. The antibody titer and association constant of responding rabbits was nearly independent of dose although most antibody production occurred after the booster injection. Antibodies to mestranol crossreacted more than 100 percent with ethynylestradiol and to a small extent with norethindrone and norgestrel.
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