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106 results on '"Thormann, Anja"'

3. EyeG2P: an automated variant filtering approach improves efficiency of diagnostic genomic testing for inherited ophthalmic disorders.

Author

Lenassi, Eva, Carvalho, Ana, Thormann, Anja, Abrahams, Liam, Arno, Gavin, Fletcher, Tracy, Hardcastle, Claire, Lopez, Javier, Hunt, Sarah E., Short, Patrick, Sergouniotis, Panagiotis I., Michaelides, Michel, Webster, Andrew, Cunningham, Fiona, Ramsden, Simon C., Kasperaviciute, Dalia, Fitzpatrick, David R., Black, Graeme C., and Ellingford, Jamie M.

Abstract

Background Genomic variant prioritisation is one of the most significant bottlenecks to mainstream genomic testing in healthcare. Tools to improve precision while ensuring high recall are critical to successful mainstream clinical genomic testing, in particular for whole genome sequencing where millions of variants must be considered for each patient. Methods We developed EyeG2P, a publicly available database and web application using the Ensembl Variant Effect Predictor. EyeG2P is tailored for efficient variant prioritisation for individuals with inherited ophthalmic conditions. We assessed the sensitivity of EyeG2P in 1234 individuals with a broad range of eye conditions who had previously received a confirmed molecular diagnosis through routine genomic diagnostic approaches. For a prospective cohort of 83 individuals, we assessed the precision of EyeG2P in comparison with routine diagnostic approaches. For 10 additional individuals, we assessed the utility of EyeG2P for whole genome analysis. Results EyeG2P had 99.5% sensitivity for genomic variants previously identified as clinically relevant through routine diagnostic analysis (n=1234 individuals). Prospectively, EyeG2P enabled a significant increase in precision (35% on average) in comparison with routine testing strategies (p<0.001). We demonstrate that incorporation of EyeG2P into whole genome sequencing analysis strategies can reduce the number of variants for analysis to six variants, on average, while maintaining high diagnostic yield. Conclusion Automated filtering of genomic variants through EyeG2P can increase the efficiency of diagnostic testing for individuals with a broad range of inherited ophthalmic disorders. [ABSTRACT FROM AUTHOR]

Published
2023
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6. Annotating and prioritizing genomic variants using the Ensembl Variant Effect Predictor—A tutorial

Author

Hunt, Sarah E., primary, Moore, Benjamin, additional, Amode, Ridwan M., additional, Armean, Irina M., additional, Lemos, Diana, additional, Mushtaq, Aleena, additional, Parton, Andrew, additional, Schuilenburg, Helen, additional, Szpak, Michał, additional, Thormann, Anja, additional, Perry, Emily, additional, Trevanion, Stephen J., additional, Flicek, Paul, additional, Yates, Andrew D., additional, and Cunningham, Fiona, additional

Published
2021
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7. Ensembl 2022

Author

Cunningham, Fiona, primary, Allen, James E, additional, Allen, Jamie, additional, Alvarez-Jarreta, Jorge, additional, Amode, M Ridwan, additional, Armean, Irina M, additional, Austine-Orimoloye, Olanrewaju, additional, Azov, Andrey G, additional, Barnes, If, additional, Bennett, Ruth, additional, Berry, Andrew, additional, Bhai, Jyothish, additional, Bignell, Alexandra, additional, Billis, Konstantinos, additional, Boddu, Sanjay, additional, Brooks, Lucy, additional, Charkhchi, Mehrnaz, additional, Cummins, Carla, additional, Da Rin Fioretto, Luca, additional, Davidson, Claire, additional, Dodiya, Kamalkumar, additional, Donaldson, Sarah, additional, El Houdaigui, Bilal, additional, El Naboulsi, Tamara, additional, Fatima, Reham, additional, Giron, Carlos Garcia, additional, Genez, Thiago, additional, Martinez, Jose Gonzalez, additional, Guijarro-Clarke, Cristina, additional, Gymer, Arthur, additional, Hardy, Matthew, additional, Hollis, Zoe, additional, Hourlier, Thibaut, additional, Hunt, Toby, additional, Juettemann, Thomas, additional, Kaikala, Vinay, additional, Kay, Mike, additional, Lavidas, Ilias, additional, Le, Tuan, additional, Lemos, Diana, additional, Marugán, José Carlos, additional, Mohanan, Shamika, additional, Mushtaq, Aleena, additional, Naven, Marc, additional, Ogeh, Denye N, additional, Parker, Anne, additional, Parton, Andrew, additional, Perry, Malcolm, additional, Piližota, Ivana, additional, Prosovetskaia, Irina, additional, Sakthivel, Manoj Pandian, additional, Salam, Ahamed Imran Abdul, additional, Schmitt, Bianca M, additional, Schuilenburg, Helen, additional, Sheppard, Dan, additional, Pérez-Silva, José G, additional, Stark, William, additional, Steed, Emily, additional, Sutinen, Kyösti, additional, Sukumaran, Ranjit, additional, Sumathipala, Dulika, additional, Suner, Marie-Marthe, additional, Szpak, Michal, additional, Thormann, Anja, additional, Tricomi, Francesca Floriana, additional, Urbina-Gómez, David, additional, Veidenberg, Andres, additional, Walsh, Thomas A, additional, Walts, Brandon, additional, Willhoft, Natalie, additional, Winterbottom, Andrea, additional, Wass, Elizabeth, additional, Chakiachvili, Marc, additional, Flint, Bethany, additional, Frankish, Adam, additional, Giorgetti, Stefano, additional, Haggerty, Leanne, additional, Hunt, Sarah E, additional, IIsley, Garth R, additional, Loveland, Jane E, additional, Martin, Fergal J, additional, Moore, Benjamin, additional, Mudge, Jonathan M, additional, Muffato, Matthieu, additional, Perry, Emily, additional, Ruffier, Magali, additional, Tate, John, additional, Thybert, David, additional, Trevanion, Stephen J, additional, Dyer, Sarah, additional, Harrison, Peter W, additional, Howe, Kevin L, additional, Yates, Andrew D, additional, Zerbino, Daniel R, additional, and Flicek, Paul, additional

Published
2021
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8. The Ensembl COVID-19 resource: ongoing integration of public SARS-CoV-2 data

Author

De Silva, Nishadi H, primary, Bhai, Jyothish, additional, Chakiachvili, Marc, additional, Contreras-Moreira, Bruno, additional, Cummins, Carla, additional, Frankish, Adam, additional, Gall, Astrid, additional, Genez, Thiago, additional, Howe, Kevin L, additional, Hunt, Sarah E, additional, Martin, Fergal J, additional, Moore, Benjamin, additional, Ogeh, Denye, additional, Parker, Anne, additional, Parton, Andrew, additional, Ruffier, Magali, additional, Sakthivel, Manoj Pandian, additional, Sheppard, Dan, additional, Tate, John, additional, Thormann, Anja, additional, Thybert, David, additional, Trevanion, Stephen J, additional, Winterbottom, Andrea, additional, Zerbino, Daniel R, additional, Finn, Robert D, additional, Flicek, Paul, additional, and Yates, Andrew D, additional

Published
2021
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9. A global reference for human genetic variation

Author

Altshuler, David M., (Co-Chair), Durbin, Richard M., (Co-Chair, Principal Investigator), Donnelly, Peter, Green, Eric D., Nickerson, Deborah A., Boerwinkle, Eric, Doddapaneni, Harsha, Han, Yi, Korchina, Viktoriya, Kovar, Christie, Lee, Sandra, Muzny, Donna, Reid, Jeffrey G., Zhu, Yiming, Wang, Jun, (Principal Investigator), Chang, Yuqi, Feng, Qiang, Fang, Xiaodong, Guo, Xiaosen, Jian, Min, Jiang, Hui, Jin, Xin, Lan, Tianming, Li, Guoqing, Li, Jingxiang, Li, Yingrui, Liu, Shengmao, Liu, Xiao, Lu, Yao, Ma, Xuedi, Tang, Meifang, Wang, Bo, Wang, Guangbiao, Wu, Honglong, Wu, Renhua, Xu, Xun, Yin, Ye, Zhang, Dandan, Zhang, Wenwei, Zhao, Jiao, Zhao, Meiru, Zheng, Xiaole, Lander, Eric S., (Principal Investigator), Gabriel, Stacey B., (Co-Chair), Gupta, Namrata, Gharani, Neda, Toji, Lorraine H., Gerry, Norman P., Resch, Alissa M., Barker, Jonathan, Gil, Laurent, Hunt, Sarah E., Kelman, Gavin, Kulesha, Eugene, Leinonen, Rasko, McLaren, William M., Radhakrishnan, Rajesh, Roa, Asier, Smirnov, Dmitriy, Smith, Richard E., Streeter, Ian, Thormann, Anja, Toneva, Iliana, Vaughan, Brendan, Zheng-Bradley, Xiangqun, Bentley, David R., (Principal Investigator), Grocock, Russell, Humphray, Sean, James, Terena, Kingsbury, Zoya, Lehrach, Hans, (Principal Investigator), Sudbrak, Ralf, (Project Leader), Albrecht, Marcus W., Amstislavskiy, Vyacheslav S., Borodina, Tatiana A., Lienhard, Matthias, Mertes, Florian, Sultan, Marc, Timmermann, Bernd, Yaspo, Marie-Laure, Mardis, Elaine R., (Co-Principal Investigator) (Co-Chair), Wilson, Richard K., (Co-Principal Investigator), Fulton, Lucinda, Fulton, Robert, Ananiev, Victor, Belaia, Zinaida, Beloslyudtsev, Dimitriy, Bouk, Nathan, Chen, Chao, Church, Deanna, Cohen, Robert, Cook, Charles, Garner, John, Hefferon, Timothy, Kimelman, Mikhail, Liu, Chunlei, Lopez, John, Meric, Peter, O’Sullivan, Chris, Ostapchuk, Yuri, Phan, Lon, Ponomarov, Sergiy, Schneider, Valerie, Shekhtman, Eugene, Sirotkin, Karl, Slotta, Douglas, Zhang, Hua, Balasubramaniam, Senduran, Burton, John, Danecek, Petr, Keane, Thomas M., Kolb-Kokocinski, Anja, McCarthy, Shane, Stalker, James, Quail, Michael, Schmidt, Jeanette P., (Principal Investigator), Davies, Christopher J., Gollub, Jeremy, Webster, Teresa, Wong, Brant, Zhan, Yiping, Auton, Adam, (Principal Investigator), Campbell, Christopher L., Kong, Yu, Marcketta, Anthony, Yu, Fuli, (Project Leader), Antunes, Lilian, Bainbridge, Matthew, Sabo, Aniko, Huang, Zhuoyi, Coin, Lachlan J. M., Fang, Lin, Li, Qibin, Li, Zhenyu, Lin, Haoxiang, Liu, Binghang, Luo, Ruibang, Shao, Haojing, Xie, Yinlong, Ye, Chen, Yu, Chang, Zhang, Fan, Zheng, Hancheng, Zhu, Hongmei, Alkan, Can, Dal, Elif, Kahveci, Fatma, Garrison, Erik P., (Project Lead), Kural, Deniz, Lee, Wan-Ping, Leong, Wen Fung, Stromberg, Michael, Ward, Alistair N., Wu, Jiantao, Zhang, Mengyao, Daly, Mark J., (Principal Investigator), DePristo, Mark A., (Project Leader), Handsaker, Robert E., (Project Leader), Banks, Eric, Bhatia, Gaurav, del Angel, Guillermo, Genovese, Giulio, Li, Heng, Kashin, Seva, Nemesh, James C., Poplin, Ryan E., Yoon, Seungtai C., (Principal Investigator), Lihm, Jayon, Makarov, Vladimir, Clark, Andrew G., (Principal Investigator), Gottipati, Srikanth, Keinan, Alon, Rodriguez-Flores, Juan L., Rausch, Tobias, (Project Leader), Fritz, Markus H., Stütz, Adrian M., Beal, Kathryn, Datta, Avik, Herrero, Javier, Ritchie, Graham R. S., Zerbino, Daniel, Sabeti, Pardis C., (Principal Investigator), Shlyakhter, Ilya, Schaffner, Stephen F., Vitti, Joseph, Cooper, David N., (Principal Investigator), Ball, Edward V., Stenson, Peter D., Barnes, Bret, Bauer, Markus, Cheetham, Keira R., Cox, Anthony, Eberle, Michael, Kahn, Scott, Murray, Lisa, Peden, John, Shaw, Richard, Kenny, Eimear E., (Principal Investigator), Batzer, Mark A., (Principal Investigator), Konkel, Miriam K., Walker, Jerilyn A., MacArthur, Daniel G., (Principal Investigator), Lek, Monkol, Herwig, Ralf, Koboldt, Daniel C., Larson, David, Ye, Kai, Gravel, Simon, Swaroop, Anand, Chew, Emily, Lappalainen, Tuuli, (Principal Investigator), Erlich, Yaniv, (Principal Investigator), Gymrek, Melissa, Willems, Thomas Frederick, Simpson, Jared T., Shriver, Mark D., (Principal Investigator), Rosenfeld, Jeffrey A., (Principal Investigator), Montgomery, Stephen B., (Principal Investigator), De La Vega, Francisco M., (Principal Investigator), Byrnes, Jake K., Carroll, Andrew W., DeGorter, Marianne K., Lacroute, Phil, Maples, Brian K., Martin, Alicia R., Moreno-Estrada, Andres, Shringarpure, Suyash S., Zakharia, Fouad, Halperin, Eran, (Principal Investigator), Baran, Yael, Cerveira, Eliza, Hwang, Jaeho, Malhotra, Ankit, (Co-Project Lead), Plewczynski, Dariusz, Radew, Kamen, Romanovitch, Mallory, Zhang, Chengsheng, (Co-Project Lead), Hyland, Fiona C. L., Craig, David W., (Principal Investigator), Christoforides, Alexis, Homer, Nils, Izatt, Tyler, Kurdoglu, Ahmet A., Sinari, Shripad A., Squire, Kevin, Xiao, Chunlin, Sebat, Jonathan, (Principal Investigator), Antaki, Danny, Gujral, Madhusudan, Noor, Amina, Ye, Kenny, Burchard, Esteban G., (Principal Investigator), Hernandez, Ryan D., (Principal Investigator), Gignoux, Christopher R., Haussler, David, (Principal Investigator), Katzman, Sol J., Kent, James W., Howie, Bryan, Ruiz-Linares, Andres, (Principal Investigator), Dermitzakis, Emmanouil T., (Principal Investigator), Devine, Scott E., (Principal Investigator), Abecasis, Gonçalo R., (Principal Investigator) (Co-Chair), Kang, Hyun Min, (Project Leader), Kidd, Jeffrey M., (Principal Investigator), Blackwell, Tom, Caron, Sean, Chen, Wei, Emery, Sarah, Fritsche, Lars, Fuchsberger, Christian, Jun, Goo, Li, Bingshan, Lyons, Robert, Scheller, Chris, Sidore, Carlo, Song, Shiya, Sliwerska, Elzbieta, Taliun, Daniel, Tan, Adrian, Welch, Ryan, Wing, Mary Kate, Zhan, Xiaowei, Awadalla, Philip, (Principal Investigator), Hodgkinson, Alan, Li, Yun, Shi, Xinghua, (Principal Investigator), Quitadamo, Andrew, Lunter, Gerton, (Principal Investigator), McVean, Gil A., (Principal Investigator) (Co-Chair), Marchini, Jonathan L., (Principal Investigator), Myers, Simon, (Principal Investigator), Churchhouse, Claire, Delaneau, Olivier, Gupta-Hinch, Anjali, Kretzschmar, Warren, Iqbal, Zamin, Mathieson, Iain, Menelaou, Androniki, Rimmer, Andy, Xifara, Dionysia K., Oleksyk, Taras K., (Principal Investigator), Fu, Yunxin, (Principal Investigator), Liu, Xiaoming, Xiong, Momiao, Jorde, Lynn, (Principal Investigator), Witherspoon, David, Xing, Jinchuan, Browning, Brian L., (Principal Investigator), Browning, Sharon R., (Principal Investigator), Hormozdiari, Fereydoun, Sudmant, Peter H., Khurana, Ekta, (Principal Investigator), Hurles, Matthew E., (Principal Investigator), Albers, Cornelis A., Ayub, Qasim, Chen, Yuan, Colonna, Vincenza, Jostins, Luke, Walter, Klaudia, Xue, Yali, Abyzov, Alexej, Balasubramanian, Suganthi, Chen, Jieming, Clarke, Declan, Fu, Yao, Harmanci, Arif O., Jin, Mike, Lee, Donghoon, Liu, Jeremy, Mu, Xinmeng Jasmine, Zhang, Jing, Zhang, Yan, McCarroll, Steven A., (Principal Investigator), Hartl, Chris, Shakir, Khalid, Degenhardt, Jeremiah, Korbel, Jan O., (Principal Investigator) (Co-Chair), Meiers, Sascha, Raeder, Benjamin, Casale, Francesco Paolo, Stegle, Oliver, Lameijer, Eric-Wubbo, Ding, Li, (Principal Investigator), Hall, Ira, Lee, Charles, (Principal Investigator) (Co-Chair), Bafna, Vineet, Michaelson, Jacob, Gardner, Eugene J., (Project Leader), Mills, Ryan E., (Principal Investigator), Dayama, Gargi, Chen, Ken, (Principle Investigator), Fan, Xian, Chong, Zechen, Chen, Tenghui, Eichler, Evan E., (Principal Investigator) (Co-Chair), Chaisson, Mark J., Huddleston, John, Malig, Maika, Nelson, Bradley J., Parrish, Nicholas F., Blackburne, Ben, Lindsay, Sarah J., Ning, Zemin, Zhang, Yujun, Lam, Hugo, Sisu, Cristina, Gibbs, Richard A., (Principal Investigator) (Co-Chair), Challis, Danny, Evani, Uday S., Lu, James, Nagaswamy, Uma, Yu, Jin, Li, Wangshen, Marth, Gabor T., (Principal Investigator) (Co-Chair), Habegger, Lukas, Yu, Haiyuan, (Principal Investigator), Cunningham, Fiona, Dunham, Ian, Lage, Kasper, (Principal Investigator), Jespersen, Jakob Berg, Horn, Heiko, Tyler-Smith, Chris, (Principal Investigator) (Co-Chair), Gerstein, Mark B., (Principal Investigator) (Co-Chair), Kim, Donghoon, Desalle, Rob, Narechania, Apurva, Wilson Sayres, Melissa A., Bustamante, Carlos D., (Principal Investigator) (Co-Chair), Mendez, Fernando L., Poznik, David G., Underhill, Peter A., Coin, Lachlan, (Principal Investigator), Mittelman, David, Banerjee, Ruby, Cerezo, Maria, Fitzgerald, Thomas W., Louzada, Sandra, Massaia, Andrea, Ritchie, Graham R., Yang, Fengtang, Kalra, Divya, Hale, Walker, Dan, Xu, Flicek, Paul, (Principal Investigator) (Co-Chair), Clarke, Laura, (Project Lead), Sherry, Stephen T., (Principal Investigator) (Co-Chair), Chakravarti, Aravinda, (Co-Chair), Knoppers, Bartha M., (Co-Chair), Barnes, Kathleen C., Beiswanger, Christine, Cai, Hongyu, Cao, Hongzhi, Henn, Brenna, Jones, Danielle, Kaye, Jane S., Kent, Alastair, Kerasidou, Angeliki, Mathias, Rasika, Ossorio, Pilar N., Parker, Michael, Rotimi, Charles N., Royal, Charmaine D., Sandoval, Karla, Su, Yeyang, Tian, Zhongming, Tishkoff, Sarah, Via, Marc, Wang, Yuhong, Yang, Ling, Zhu, Jiayong, Bodmer, Walter, Bedoya, Gabriel, Cai, Zhiming, Gao, Yang, Chu, Jiayou, Peltonen, Leena, Garcia-Montero, Andres, Orfao, Alberto, Dutil, Julie, Martinez-Cruzado, Juan C., Mathias, Rasika A., Hennis, Anselm, Watson, Harold, McKenzie, Colin, Qadri, Firdausi, LaRocque, Regina, Deng, Xiaoyan, Asogun, Danny, Folarin, Onikepe, Happi, Christian, Omoniwa, Omonwunmi, Stremlau, Matt, Tariyal, Ridhi, Jallow, Muminatou, Joof, Fatoumatta Sisay, Corrah, Tumani, Rockett, Kirk, Kwiatkowski, Dominic, Kooner, Jaspal, Hiê`n, Trâ`n Tinh, Dunstan, Sarah J., Hang, Nguyen Thuy, Fonnie, Richard, Garry, Robert, Kanneh, Lansana, Moses, Lina, Schieffelin, John, Grant, Donald S., Gallo, Carla, Poletti, Giovanni, Saleheen, Danish, Rasheed, Asif, Brooks, Lisa D., Felsenfeld, Adam L., McEwen, Jean E., Vaydylevich, Yekaterina, Duncanson, Audrey, Dunn, Michael, Schloss, Jeffery A., and Yang, Huanming

Published
2015
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10. Ensembl 2015

Author

Cunningham, Fiona, Amode, Ridwan M., Barrell, Daniel, Beal, Kathryn, Billis, Konstantinos, Brent, Simon, Carvalho-Silva, Denise, Clapham, Peter, Coates, Guy, Fitzgerald, Stephen, Gil, Laurent, Girón, Carlos García, Gordon, Leo, Hourlier, Thibaut, Hunt, Sarah E., Janacek, Sophie H., Johnson, Nathan, Juettemann, Thomas, Kähäri, Andreas K., Keenan, Stephen, Martin, Fergal J., Maurel, Thomas, McLaren, William, Murphy, Daniel N., Nag, Rishi, Overduin, Bert, Parker, Anne, Patricio, Mateus, Perry, Emily, Pignatelli, Miguel, Riat, Harpreet Singh, Sheppard, Daniel, Taylor, Kieron, Thormann, Anja, Vullo, Alessandro, Wilder, Steven P., Zadissa, Amonida, Aken, Bronwen L., Birney, Ewan, Harrow, Jennifer, Kinsella, Rhoda, Muffato, Matthieu, Ruffier, Magali, Searle, Stephen M.J., Spudich, Giulietta, Trevanion, Stephen J., Yates, Andy, Zerbino, Daniel R., and Flicek, Paul

Published
2015
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11. EyeG2P: an automated variant filtering approach improves efficiency of diagnostic genomic testing for inherited ophthalmic disorders

Author

Lenassi, Eva, primary, Carvalho, Ana, additional, Thormann, Anja, additional, Fletcher, Tracy, additional, Hardcastle, Claire, additional, Hunt, Sarah E, additional, Sergouniotis, Panagiotis I, additional, Michaelides, Michel, additional, Webster, Andrew R, additional, Cunningham, F, additional, Ramsden, Simon, additional, FitzPatrick, David R, additional, Black, Graeme CM, additional, and Ellingford, Jamie M, additional

Published
2021
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12. Ensembl 2014

Author

Flicek, Paul, Amode, Ridwan M., Barrell, Daniel, Beal, Kathryn, Billis, Konstantinos, Brent, Simon, Carvalho-Silva, Denise, Clapham, Peter, Coates, Guy, Fitzgerald, Stephen, Gil, Laurent, Girón, Carlos García, Gordon, Leo, Hourlier, Thibaut, Hunt, Sarah, Johnson, Nathan, Juettemann, Thomas, Kähäri, Andreas K., Keenan, Stephen, Kulesha, Eugene, Martin, Fergal J., Maurel, Thomas, McLaren, William M., Murphy, Daniel N., Nag, Rishi, Overduin, Bert, Pignatelli, Miguel, Pritchard, Bethan, Pritchard, Emily, Riat, Harpreet S., Ruffier, Magali, Sheppard, Daniel, Taylor, Kieron, Thormann, Anja, Trevanion, Stephen J., Vullo, Alessandro, Wilder, Steven P., Wilson, Mark, Zadissa, Amonida, Aken, Bronwen L., Birney, Ewan, Cunningham, Fiona, Harrow, Jennifer, Herrero, Javier, Hubbard, Tim J.P., Kinsella, Rhoda, Muffato, Matthieu, Parker, Anne, Spudich, Giulietta, Yates, Andy, Zerbino, Daniel R., and Searle, Stephen M.J.

Published
2014
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13. Annotating and prioritising genomic variants using the Ensembl Variant Effect Predictor - a tutorial

Author

Hunt, Sarah, primary, Moore, Benjamin, additional, Amode, M., additional, Armean, Irina, additional, Lemos, Diana, additional, Mushtaq, Aleena, additional, Parton, Andrew, additional, Schuilenburg, Helen, additional, Szpak, Michał, additional, Thormann, Anja, additional, Perry, Emily, additional, Trevanion, Stephen, additional, Flicek, Paul, additional, Cunningham, Fiona, additional, and Yates, Andrew, additional

Published
2021
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14. Annotating and prioritizing genomic variants using the Ensembl Variant Effect Predictor—A tutorial.

Author

Hunt, Sarah E., Moore, Benjamin, Amode, Ridwan M., Armean, Irina M., Lemos, Diana, Mushtaq, Aleena, Parton, Andrew, Schuilenburg, Helen, Szpak, Michał, Thormann, Anja, Perry, Emily, Trevanion, Stephen J., Flicek, Paul, Yates, Andrew D., and Cunningham, Fiona

Abstract

The Ensembl Variant Effect Predictor (VEP) is a freely available, open‐source tool for the annotation and filtering of genomic variants. It predicts variant molecular consequences using the Ensembl/GENCODE or RefSeq gene sets. It also reports phenotype associations from databases such as ClinVar, allele frequencies from studies including gnomAD, and predictions of deleteriousness from tools such as Sorting Intolerant From Tolerant and Combined Annotation Dependent Depletion. Ensembl VEP includes filtering options to customize variant prioritization. It is well supported and updated roughly quarterly to incorporate the latest gene, variant, and phenotype association information. Ensembl VEP analysis can be performed using a highly configurable, extensible command‐line tool, a Representational State Transfer application programming interface, and a user‐friendly web interface. These access methods are designed to suit different levels of bioinformatics experience and meet different needs in terms of data size, visualization, and flexibility. In this tutorial, we will describe performing variant annotation using the Ensembl VEP web tool, which enables sophisticated analysis through a simple interface. [ABSTRACT FROM AUTHOR]

Published
2022
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15. Additional file 2 of Meta-analysis of heterogeneous Down Syndrome data reveals consistent genome-wide dosage effects related to neurological processes

Author

Vilardell, Mireia, Rasche, Axel, Thormann, Anja, Maschke-Dutz, Elisabeth, Pérez-Jurado, Luis A, Lehrach, Hans, and Herwig, Ralf

Subjects
genetic structures
Abstract

Additional file 2: Figure S1. Enrichment of GO categories for organ, tissue and cell development with respect to the significant HSA21 genes (red bars), the significant non-HSA21 genes (green bars) and the non-significant genes (blue bars). (PDF 4 KB)

Published
2020
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16. Impact of tumour necrosis factor inhibitor treatment on radiographic progression in rheumatoid arthritis patients in clinical practice: results from the nationwide Danish DANBIO registry

Author

Ørnbjerg, Lykke Midtbøll, Østergaard, Mikkel, Bøyesen, Pernille, Krogh, Niels Steen, Thormann, Anja, Tarp, Ulrik, Poulsen, Uta Engling, Espesen, Jakob, Ringsdal, Vibeke Stevenius, Graudal, Niels, Kollerup, Gina, Jensen, Dorte Vendelbo, Madsen, Ole Rintek, Glintborg, Bente, Christensen, Torben, Lindegaard, Hanne, Dencker, Ditte, Hansen, Annette, Andersen, Anne Rødgaard, and Hetland, Merete Lund

Published
2013
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17. Ensembl 2013

Author

Flicek, Paul, Ahmed, Ikhlak, Amode, Ridwan M., Barrell, Daniel, Beal, Kathryn, Brent, Simon, Carvalho-Silva, Denise, Clapham, Peter, Coates, Guy, Fairley, Susan, Fitzgerald, Stephen, Gil, Laurent, García-Girón, Carlos, Gordon, Leo, Hourlier, Thibaut, Hunt, Sarah, Juettemann, Thomas, Kähäri, Andreas K., Keenan, Stephen, Komorowska, Monika, Kulesha, Eugene, Longden, Ian, Maurel, Thomas, McLaren, William M., Muffato, Matthieu, Nag, Rishi, Overduin, Bert, Pignatelli, Miguel, Pritchard, Bethan, Pritchard, Emily, Riat, Harpreet Singh, Ritchie, Graham R. S., Ruffier, Magali, Schuster, Michael, Sheppard, Daniel, Sobral, Daniel, Taylor, Kieron, Thormann, Anja, Trevanion, Stephen, White, Simon, Wilder, Steven P., Aken, Bronwen L., Birney, Ewan, Cunningham, Fiona, Dunham, Ian, Harrow, Jennifer, Herrero, Javier, Hubbard, Tim J. P., Johnson, Nathan, Kinsella, Rhoda, Parker, Anne, Spudich, Giulietta, Yates, Andy, Zadissa, Amonida, and Searle, Stephen M. J.

Published
2013
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19. The Ensembl COVID-19 resource: Ongoing integration of public SARS-CoV-2 data

Author

De Silva, Nishadi H., primary, Bhai, Jyothish, additional, Chakiachvili, Marc, additional, Contreras-Moreira, Bruno, additional, Cummins, Carla, additional, Frankish, Adam, additional, Gall, Astrid, additional, Genez, Thiago, additional, Howe, Kevin L., additional, Hunt, Sarah E., additional, Martin, Fergal J., additional, Moore, Benjamin, additional, Ogeh, Denye, additional, Parker, Anne, additional, Parton, Andrew, additional, Ruffier, Magali, additional, Sakthivel, Manoj Pandian, additional, Sheppard, Dan, additional, Tate, John, additional, Thormann, Anja, additional, Thybert, David, additional, Trevanion, Stephen J., additional, Winterbottom, Andrea, additional, Zerbino, Daniel R., additional, Finn, Robert D., additional, Flicek, Paul, additional, and Yates, Andrew D., additional

Published
2020
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20. Ensembl 2021

Author

Howe, Kevin L, primary, Achuthan, Premanand, additional, Allen, James, additional, Allen, Jamie, additional, Alvarez-Jarreta, Jorge, additional, Amode, M Ridwan, additional, Armean, Irina M, additional, Azov, Andrey G, additional, Bennett, Ruth, additional, Bhai, Jyothish, additional, Billis, Konstantinos, additional, Boddu, Sanjay, additional, Charkhchi, Mehrnaz, additional, Cummins, Carla, additional, Da Rin Fioretto, Luca, additional, Davidson, Claire, additional, Dodiya, Kamalkumar, additional, El Houdaigui, Bilal, additional, Fatima, Reham, additional, Gall, Astrid, additional, Garcia Giron, Carlos, additional, Grego, Tiago, additional, Guijarro-Clarke, Cristina, additional, Haggerty, Leanne, additional, Hemrom, Anmol, additional, Hourlier, Thibaut, additional, Izuogu, Osagie G, additional, Juettemann, Thomas, additional, Kaikala, Vinay, additional, Kay, Mike, additional, Lavidas, Ilias, additional, Le, Tuan, additional, Lemos, Diana, additional, Gonzalez Martinez, Jose, additional, Marugán, José Carlos, additional, Maurel, Thomas, additional, McMahon, Aoife C, additional, Mohanan, Shamika, additional, Moore, Benjamin, additional, Muffato, Matthieu, additional, Oheh, Denye N, additional, Paraschas, Dimitrios, additional, Parker, Anne, additional, Parton, Andrew, additional, Prosovetskaia, Irina, additional, Sakthivel, Manoj P, additional, Salam, Ahamed I Abdul, additional, Schmitt, Bianca M, additional, Schuilenburg, Helen, additional, Sheppard, Dan, additional, Steed, Emily, additional, Szpak, Michal, additional, Szuba, Marek, additional, Taylor, Kieron, additional, Thormann, Anja, additional, Threadgold, Glen, additional, Walts, Brandon, additional, Winterbottom, Andrea, additional, Chakiachvili, Marc, additional, Chaubal, Ameya, additional, De Silva, Nishadi, additional, Flint, Bethany, additional, Frankish, Adam, additional, Hunt, Sarah E, additional, IIsley, Garth R, additional, Langridge, Nick, additional, Loveland, Jane E, additional, Martin, Fergal J, additional, Mudge, Jonathan M, additional, Morales, Joanella, additional, Perry, Emily, additional, Ruffier, Magali, additional, Tate, John, additional, Thybert, David, additional, Trevanion, Stephen J, additional, Cunningham, Fiona, additional, Yates, Andrew D, additional, Zerbino, Daniel R, additional, and Flicek, Paul, additional

Published
2020
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21. Ensembl COVID-19 resource: ongoing integration of public SARS-CoV-2 data.

Author

De Silva, Nishadi H, Bhai, Jyothish, Chakiachvili, Marc, Contreras-Moreira, Bruno, Cummins, Carla, Frankish, Adam, Gall, Astrid, Genez, Thiago, Howe, Kevin L, Hunt, Sarah E, Martin, Fergal J, Moore, Benjamin, Ogeh, Denye, Parker, Anne, Parton, Andrew, Ruffier, Magali, Sakthivel, Manoj Pandian, Sheppard, Dan, Tate, John, and Thormann, Anja

Published
2022
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23. Ensembl 2020

Author

Yates, Andrew D, primary, Achuthan, Premanand, additional, Akanni, Wasiu, additional, Allen, James, additional, Allen, Jamie, additional, Alvarez-Jarreta, Jorge, additional, Amode, M Ridwan, additional, Armean, Irina M, additional, Azov, Andrey G, additional, Bennett, Ruth, additional, Bhai, Jyothish, additional, Billis, Konstantinos, additional, Boddu, Sanjay, additional, Marugán, José Carlos, additional, Cummins, Carla, additional, Davidson, Claire, additional, Dodiya, Kamalkumar, additional, Fatima, Reham, additional, Gall, Astrid, additional, Giron, Carlos Garcia, additional, Gil, Laurent, additional, Grego, Tiago, additional, Haggerty, Leanne, additional, Haskell, Erin, additional, Hourlier, Thibaut, additional, Izuogu, Osagie G, additional, Janacek, Sophie H, additional, Juettemann, Thomas, additional, Kay, Mike, additional, Lavidas, Ilias, additional, Le, Tuan, additional, Lemos, Diana, additional, Martinez, Jose Gonzalez, additional, Maurel, Thomas, additional, McDowall, Mark, additional, McMahon, Aoife, additional, Mohanan, Shamika, additional, Moore, Benjamin, additional, Nuhn, Michael, additional, Oheh, Denye N, additional, Parker, Anne, additional, Parton, Andrew, additional, Patricio, Mateus, additional, Sakthivel, Manoj Pandian, additional, Abdul Salam, Ahamed Imran, additional, Schmitt, Bianca M, additional, Schuilenburg, Helen, additional, Sheppard, Dan, additional, Sycheva, Mira, additional, Szuba, Marek, additional, Taylor, Kieron, additional, Thormann, Anja, additional, Threadgold, Glen, additional, Vullo, Alessandro, additional, Walts, Brandon, additional, Winterbottom, Andrea, additional, Zadissa, Amonida, additional, Chakiachvili, Marc, additional, Flint, Bethany, additional, Frankish, Adam, additional, Hunt, Sarah E, additional, IIsley, Garth, additional, Kostadima, Myrto, additional, Langridge, Nick, additional, Loveland, Jane E, additional, Martin, Fergal J, additional, Morales, Joannella, additional, Mudge, Jonathan M, additional, Muffato, Matthieu, additional, Perry, Emily, additional, Ruffier, Magali, additional, Trevanion, Stephen J, additional, Cunningham, Fiona, additional, Howe, Kevin L, additional, Zerbino, Daniel R, additional, and Flicek, Paul, additional

Published
2019
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24. Meta-analysis of heterogeneous Down Syndrome data reveals consistent genome-wide dosage effects related to neurological processes

Author

Pérez-Jurado Luis A, Maschke-Dutz Elisabeth, Thormann Anja, Rasche Axel, Vilardell Mireia, Lehrach Hans, and Herwig Ralf

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Down syndrome (DS; trisomy 21) is the most common genetic cause of mental retardation in the human population and key molecular networks dysregulated in DS are still unknown. Many different experimental techniques have been applied to analyse the effects of dosage imbalance at the molecular and phenotypical level, however, currently no integrative approach exists that attempts to extract the common information. Results We have performed a statistical meta-analysis from 45 heterogeneous publicly available DS data sets in order to identify consistent dosage effects from these studies. We identified 324 genes with significant genome-wide dosage effects, including well investigated genes like SOD1, APP, RUNX1 and DYRK1A as well as a large proportion of novel genes (N = 62). Furthermore, we characterized these genes using gene ontology, molecular interactions and promoter sequence analysis. In order to judge relevance of the 324 genes for more general cerebral pathologies we used independent publicly available microarry data from brain studies not related with DS and identified a subset of 79 genes with potential impact for neurocognitive processes. All results have been made available through a web server under http://ds-geneminer.molgen.mpg.de/. Conclusions Our study represents a comprehensive integrative analysis of heterogeneous data including genome-wide transcript levels in the domain of trisomy 21. The detected dosage effects build a resource for further studies of DS pathology and the development of new therapies.

Published
2011
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25. Ensembl 2019

Author

Cunningham, Fiona, primary, Achuthan, Premanand, additional, Akanni, Wasiu, additional, Allen, James, additional, Amode, M Ridwan, additional, Armean, Irina M, additional, Bennett, Ruth, additional, Bhai, Jyothish, additional, Billis, Konstantinos, additional, Boddu, Sanjay, additional, Cummins, Carla, additional, Davidson, Claire, additional, Dodiya, Kamalkumar Jayantilal, additional, Gall, Astrid, additional, Girón, Carlos García, additional, Gil, Laurent, additional, Grego, Tiago, additional, Haggerty, Leanne, additional, Haskell, Erin, additional, Hourlier, Thibaut, additional, Izuogu, Osagie G, additional, Janacek, Sophie H, additional, Juettemann, Thomas, additional, Kay, Mike, additional, Laird, Matthew R, additional, Lavidas, Ilias, additional, Liu, Zhicheng, additional, Loveland, Jane E, additional, Marugán, José C, additional, Maurel, Thomas, additional, McMahon, Aoife C, additional, Moore, Benjamin, additional, Morales, Joannella, additional, Mudge, Jonathan M, additional, Nuhn, Michael, additional, Ogeh, Denye, additional, Parker, Anne, additional, Parton, Andrew, additional, Patricio, Mateus, additional, Abdul Salam, Ahamed Imran, additional, Schmitt, Bianca M, additional, Schuilenburg, Helen, additional, Sheppard, Dan, additional, Sparrow, Helen, additional, Stapleton, Eloise, additional, Szuba, Marek, additional, Taylor, Kieron, additional, Threadgold, Glen, additional, Thormann, Anja, additional, Vullo, Alessandro, additional, Walts, Brandon, additional, Winterbottom, Andrea, additional, Zadissa, Amonida, additional, Chakiachvili, Marc, additional, Frankish, Adam, additional, Hunt, Sarah E, additional, Kostadima, Myrto, additional, Langridge, Nick, additional, Martin, Fergal J, additional, Muffato, Matthieu, additional, Perry, Emily, additional, Ruffier, Magali, additional, Staines, Daniel M, additional, Trevanion, Stephen J, additional, Aken, Bronwen L, additional, Yates, Andrew D, additional, Zerbino, Daniel R, additional, and Flicek, Paul, additional

Published
2018
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26. VEP-G2P: A Tool for Efficient, Flexible and Scalable Diagnostic Filtering of Genomic Variants

Author

Thormann, Anja, primary, Halachev, Mihail, additional, McLaren, William, additional, Moore, David J, additional, Svinti, Victoria, additional, Campbell, Archie, additional, Kerr, Shona M, additional, Hunt, Sarah, additional, Dunlop, Malcolm G, additional, Hurles, Matthew E, additional, Wright, Caroline F, additional, Firth, Helen V, additional, Cunningham, Fiona, additional, and FitzPatrick, David R, additional

Published
2018
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28. Ensembl variation resources

Author

Hunt, Sarah E, primary, McLaren, William, additional, Gil, Laurent, additional, Thormann, Anja, additional, Schuilenburg, Helen, additional, Sheppard, Dan, additional, Parton, Andrew, additional, Armean, Irina M, additional, Trevanion, Stephen J, additional, Flicek, Paul, additional, and Cunningham, Fiona, additional

Published
2018
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29. Additional file 1: of Establishment of age- and sex-adjusted reference data for hand bone mass and investigation of hand bone loss in patients with rheumatoid arthritis treated in clinical practice: an observational study from the DANBIO registry and the Copenhagen Osteoarthritis Study

Author

Ørnbjerg, Lykke, Østergaard, Mikkel, Jensen, Trine, Hyldstrup, Lars, Bach-Mortensen, Pernille, Bøyesen, Pernille, Thormann, Anja, Tarp, Ulrik, Bøhme, Wolfgang, Lindegaard, Hanne, Poulsen, Uta, Schlemmer, Anette, Graudal, Niels, Rødgaard, Anne, Espesen, Jakob, Kollerup, Gina, Glintborg, Bente, Madsen, Ole, Jensen, Dorte, and Hetland, Merete

Abstract

Estimated mean annual change in DXR-BMD (i.e. normal HBL/year) in 2541 Danish women and 1485 Danish men. A Table of the estimated mean annual changes in DXR-BMD (i.e. normal HBL/year) in men and women derived from the final models for each year of age from 18 to 89 years in the reference cohort. (DOCX 31 kb)

Published
2016
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30. Ensembl 2018

Author

Zerbino, Daniel R, primary, Achuthan, Premanand, additional, Akanni, Wasiu, additional, Amode, M Ridwan, additional, Barrell, Daniel, additional, Bhai, Jyothish, additional, Billis, Konstantinos, additional, Cummins, Carla, additional, Gall, Astrid, additional, Girón, Carlos García, additional, Gil, Laurent, additional, Gordon, Leo, additional, Haggerty, Leanne, additional, Haskell, Erin, additional, Hourlier, Thibaut, additional, Izuogu, Osagie G, additional, Janacek, Sophie H, additional, Juettemann, Thomas, additional, To, Jimmy Kiang, additional, Laird, Matthew R, additional, Lavidas, Ilias, additional, Liu, Zhicheng, additional, Loveland, Jane E, additional, Maurel, Thomas, additional, McLaren, William, additional, Moore, Benjamin, additional, Mudge, Jonathan, additional, Murphy, Daniel N, additional, Newman, Victoria, additional, Nuhn, Michael, additional, Ogeh, Denye, additional, Ong, Chuang Kee, additional, Parker, Anne, additional, Patricio, Mateus, additional, Riat, Harpreet Singh, additional, Schuilenburg, Helen, additional, Sheppard, Dan, additional, Sparrow, Helen, additional, Taylor, Kieron, additional, Thormann, Anja, additional, Vullo, Alessandro, additional, Walts, Brandon, additional, Zadissa, Amonida, additional, Frankish, Adam, additional, Hunt, Sarah E, additional, Kostadima, Myrto, additional, Langridge, Nicholas, additional, Martin, Fergal J, additional, Muffato, Matthieu, additional, Perry, Emily, additional, Ruffier, Magali, additional, Staines, Dan M, additional, Trevanion, Stephen J, additional, Aken, Bronwen L, additional, Cunningham, Fiona, additional, Yates, Andrew, additional, and Flicek, Paul, additional

Published
2017
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33. Vascular comorbidities in multiple sclerosis:a nationwide study from Denmark

Author

Thormann, Anja, Magyari, Melinda, Koch-Henriksen, Nils, Laursen, Bjarne, Sørensen, Per Soelberg, Thormann, Anja, Magyari, Melinda, Koch-Henriksen, Nils, Laursen, Bjarne, and Sørensen, Per Soelberg

Abstract

To investigate the occurrence of vascular comorbidities before and after the clinical onset of multiple sclerosis. In this combined case–control and cohort study, all Danish born citizens with onset of multiple sclerosis 1980–2005 were identified from the Danish Multiple Sclerosis Registry and randomly matched with controls regarding year of birth, gender, and municipality on January 1st in the year of multiple sclerosis (MS) onset (index date). Individual-level information on comorbidities was obtained from several independent nationwide registries and linked to the study population by unique personal identification numbers. To assess the presence of vascular comorbidities before and after MS onset, cases and controls were followed from January 1977 to the index date, and from the index date through December 2012. We used logistic regression to calculate odds ratios (ORs) and Cox regression to calculate hazard ratios (HRs). Before the index date, MS cases had a decreased probability for cerebrovascular comorbidity [OR 0.69 (95 % CI 0.48–0.99, p = 0.043)], and a numerically but not statistically significant decreased probability for cardiovascular comorbidity [OR 0.87 (95 % CI 0.71–1.07, p = 0.188)]. After the index date, MS cases had an increased risk for cerebrovascular comorbidity [HR 1.84 (95 % CI 1.69–2.00, p < 0.0005)], and for cardiovascular comorbidity [HR 1.08 (95 % CI 1.02–1.15, p = 0.013)]. The lower occurrence of cerebrovascular comorbidities in cases prior to MS onset could be due to protective immune mechanisms, while the higher occurrence of vascular comorbidities in cases after MS onset could be because of converging causal pathways of the coexisting diseases. These findings deserve to be studied closer in a broader spectrum of comorbidities in MS.

Published
2016

34. Inverse comorbidity in multiple sclerosis:Findings in a complete nationwide cohort

Author

Thormann, Anja, Koch-Henriksen, Nils, Laursen, Bjarne, Sørensen, Per Soelberg, Magyari, Melinda, Thormann, Anja, Koch-Henriksen, Nils, Laursen, Bjarne, Sørensen, Per Soelberg, and Magyari, Melinda

Abstract

Background Inverse comorbidity is disease occurring at lower rates than expected among persons with a given index disease. The objective was to identify inverse comorbidity in MS. Methods We performed a combined case-control and cohort study in a total nationwide cohort of cases with clinical onset of MS 1980–2005. We randomly matched each MS-case with five population controls. Comorbidity data were obtained from multiple, independent nationwide registries. Cases and controls were followed from January 1977 to the index date, and from the index date through December 2012. We controlled for false discovery rate and investigated each of eight pre-specified comorbidity categories: psychiatric, cerebrovascular, cardiovascular, lung, and autoimmune comorbidities, diabetes, cancer, and Parkinson's disease. Results A total of 8947 MS-cases and 44,735 controls were eligible for inclusion. We found no inverse associations with MS before the index date. After the index date, we found a decreased occurrence of chronic lung disease (asthma and chronic obstructive pulmonary disease) (HR 0.80 (95% CI 0.75–0.86, p<0.00025)) and overall cancer (HR 0.88 (95% CI 0.81–0.95, p=0.0005)) among MS-cases. Conclusion This study showed a decreased risk of cancers and pulmonary diseases after onset of MS. Identification of inverse comorbidity and of its underlying mechanisms may provide important new entry points into the understanding of MS.

Published
2016

35. Establishment of age- and sex-adjusted reference data for hand bone mass and investigation of hand bone loss in patients with rheumatoid arthritis treated in clinical practice:an observational study from the DANBIO registry and the Copenhagen Osteoarthritis Study

Author

Ørnbjerg, Lykke Midtbøll, Østergaard, Mikkel, Jensen, Trine, Hyldstrup, Lars, Bach-Mortensen, Pernille, Bøyesen, Pernille, Thormann, Anja, Tarp, Ulrik, Bøhme, Wolfgang Peter, Lindegaard, Hanne, Poulsen, Uta Engling, Schlemmer, Anette, Graudal, Niels, Rødgaard, Anne, Espesen, Jakob, Kollerup, Gina Birgitte, Glintborg, Bente, Madsen, Ole Rintek, Jensen, Dorte Vendelbo, Hetland, Merete Lund, Ørnbjerg, Lykke Midtbøll, Østergaard, Mikkel, Jensen, Trine, Hyldstrup, Lars, Bach-Mortensen, Pernille, Bøyesen, Pernille, Thormann, Anja, Tarp, Ulrik, Bøhme, Wolfgang Peter, Lindegaard, Hanne, Poulsen, Uta Engling, Schlemmer, Anette, Graudal, Niels, Rødgaard, Anne, Espesen, Jakob, Kollerup, Gina Birgitte, Glintborg, Bente, Madsen, Ole Rintek, Jensen, Dorte Vendelbo, and Hetland, Merete Lund

Abstract

BACKGROUND: Rheumatoid arthritis is characterised by progressive joint destruction and loss of periarticular bone mass. Hand bone loss (HBL) has therefore been proposed as an outcome measure for treatment efficacy. A definition of increased HBL adjusted for age- and sex-related bone loss is lacking. In this study, we aimed to: 1) establish reference values for normal hand bone mass (bone mineral density measured by digital x-ray radiogrammetry (DXR-BMD)); and 2) examine whether HBL is normalised in rheumatoid arthritis patients during treatment with tumour necrosis factor alpha inhibitors (TNFI).METHODS: DXR-BMD was measured from hand x-rays in a reference cohort (1485 men/2541 women) without arthritis randomly selected from an urban Danish population. Sex- and age-related HBL/year was estimated. DXR-BMD was measured in rheumatoid arthritis patients (n = 350: at start of TNFI, and ~2 years after TNFI start), of which 135 patients had three x-rays (~2 years prior to TNFI, at start of TNFI, and ~2 years after TNFI start). Individual HBL/year prior to and during TNFI was calculated and compared to reference values.RESULTS: Estimated HBL/year varied strongly with age and sex. Compared to the reference values, 75 % of 135 patients had increased HBL prior to TNFI treatment and 59 % had increased HBL during TNFI treatment (p = 0.17, Chi-squared). In 38 % (38/101) of patients with increased HBL, HBL was normalised during TNFI treatment, whereas 47 % (16/34) of patients with normal HBL prior to TNFI had increased HBL during TNFI treatment. In the 350 patients, increased HBL during TNFI was associated with time-averaged 28-joint disease activity score (odds ratio 1.69 (95 % Confidence Interval 1.34-2.15)/unit increase, p < 0.001), and patients in time-averaged remission had lower HBL than patients without remission (0.0032 vs. 0.0058 g/cm(2)/year; p < 0.001, Mann-Whitney).CONCLUSIONS: We established age- and sex-specific reference values for DXR

Published
2016

36. Ensembl 2017

Author

Aken, Bronwen L., primary, Achuthan, Premanand, additional, Akanni, Wasiu, additional, Amode, M. Ridwan, additional, Bernsdorff, Friederike, additional, Bhai, Jyothish, additional, Billis, Konstantinos, additional, Carvalho-Silva, Denise, additional, Cummins, Carla, additional, Clapham, Peter, additional, Gil, Laurent, additional, Girón, Carlos García, additional, Gordon, Leo, additional, Hourlier, Thibaut, additional, Hunt, Sarah E., additional, Janacek, Sophie H., additional, Juettemann, Thomas, additional, Keenan, Stephen, additional, Laird, Matthew R., additional, Lavidas, Ilias, additional, Maurel, Thomas, additional, McLaren, William, additional, Moore, Benjamin, additional, Murphy, Daniel N., additional, Nag, Rishi, additional, Newman, Victoria, additional, Nuhn, Michael, additional, Ong, Chuang Kee, additional, Parker, Anne, additional, Patricio, Mateus, additional, Riat, Harpreet Singh, additional, Sheppard, Daniel, additional, Sparrow, Helen, additional, Taylor, Kieron, additional, Thormann, Anja, additional, Vullo, Alessandro, additional, Walts, Brandon, additional, Wilder, Steven P., additional, Zadissa, Amonida, additional, Kostadima, Myrto, additional, Martin, Fergal J., additional, Muffato, Matthieu, additional, Perry, Emily, additional, Ruffier, Magali, additional, Staines, Daniel M., additional, Trevanion, Stephen J., additional, Cunningham, Fiona, additional, Yates, Andrew, additional, Zerbino, Daniel R., additional, and Flicek, Paul, additional

Published
2016
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37. The Ensembl Variant Effect Predictor

Author

McLaren, William, primary, Gil, Laurent, additional, Hunt, Sarah E., additional, Riat, Harpreet Singh, additional, Ritchie, Graham R. S., additional, Thormann, Anja, additional, Flicek, Paul, additional, and Cunningham, Fiona, additional

Published
2016
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39. Establishment of age- and sex-adjusted reference data for hand bone mass and investigation of hand bone loss in patients with rheumatoid arthritis treated in clinical practice: an observational study from the DANBIO registry and the Copenhagen Osteoarthritis Study

Author

Ørnbjerg, Lykke Midtbøll, primary, Østergaard, Mikkel, additional, Jensen, Trine, additional, Hyldstrup, Lars, additional, Bach-Mortensen, Pernille, additional, Bøyesen, Pernille, additional, Thormann, Anja, additional, Tarp, Ulrik, additional, Bøhme, Wolfgang Peter, additional, Lindegaard, Hanne, additional, Poulsen, Uta Engling, additional, Schlemmer, Anette, additional, Graudal, Niels, additional, Rødgaard, Anne, additional, Espesen, Jakob, additional, Kollerup, Gina Birgitte, additional, Glintborg, Bente, additional, Madsen, Ole Rintek, additional, Jensen, Dorte Vendelbo, additional, and Hetland, Merete Lund, additional

Published
2016
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41. Ensembl 2016

Author

Yates, Andrew, primary, Akanni, Wasiu, additional, Amode, M. Ridwan, additional, Barrell, Daniel, additional, Billis, Konstantinos, additional, Carvalho-Silva, Denise, additional, Cummins, Carla, additional, Clapham, Peter, additional, Fitzgerald, Stephen, additional, Gil, Laurent, additional, Girón, Carlos García, additional, Gordon, Leo, additional, Hourlier, Thibaut, additional, Hunt, Sarah E., additional, Janacek, Sophie H., additional, Johnson, Nathan, additional, Juettemann, Thomas, additional, Keenan, Stephen, additional, Lavidas, Ilias, additional, Martin, Fergal J., additional, Maurel, Thomas, additional, McLaren, William, additional, Murphy, Daniel N., additional, Nag, Rishi, additional, Nuhn, Michael, additional, Parker, Anne, additional, Patricio, Mateus, additional, Pignatelli, Miguel, additional, Rahtz, Matthew, additional, Riat, Harpreet Singh, additional, Sheppard, Daniel, additional, Taylor, Kieron, additional, Thormann, Anja, additional, Vullo, Alessandro, additional, Wilder, Steven P., additional, Zadissa, Amonida, additional, Birney, Ewan, additional, Harrow, Jennifer, additional, Muffato, Matthieu, additional, Perry, Emily, additional, Ruffier, Magali, additional, Spudich, Giulietta, additional, Trevanion, Stephen J., additional, Cunningham, Fiona, additional, Aken, Bronwen L., additional, Zerbino, Daniel R., additional, and Flicek, Paul, additional

Published
2015
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42. Which factors influence radiographic progression during treatment with tumor necrosis factor inhibitors in clinical practice?:Results from 930 patients with rheumatoid arthritis in the nationwide Danish DANBIO registry

Author

Ørnbjerg, Lykke Midtbøll, Østergaard, Mikkel, Bøyesen, Pernille, Krogh, Niels Steen, Thormann, Anja, Tarp, Ulrik, Poulsen, Uta Engling, Espesen, Jakob, Schlemmer, Annette, Graudal, Niels, Kollerup, Gina, Jensen, Dorte Vendelbo, Madsen, Ole Rintek, Glintborg, Bente, Christensen, Torben, Lindegaard, Hanne, Bøhme, Wolfgang, Hansen, Annette, Andersen, Anne Rødgaard, Hetland, Merete Lund, Ørnbjerg, Lykke Midtbøll, Østergaard, Mikkel, Bøyesen, Pernille, Krogh, Niels Steen, Thormann, Anja, Tarp, Ulrik, Poulsen, Uta Engling, Espesen, Jakob, Schlemmer, Annette, Graudal, Niels, Kollerup, Gina, Jensen, Dorte Vendelbo, Madsen, Ole Rintek, Glintborg, Bente, Christensen, Torben, Lindegaard, Hanne, Bøhme, Wolfgang, Hansen, Annette, Andersen, Anne Rødgaard, and Hetland, Merete Lund

Abstract

OBJECTIVE: To investigate baseline characteristics associated with radiographic progression and the effect of disease activity, drug, switching, and withdrawal on radiographic progression in tumor necrosis factor (TNF) inhibitor-naive patients with rheumatoid arthritis (RA) followed for about 2 years after anti-TNF initiation in clinical practice.METHODS: DANBIO-registered patients with RA who had available radiographs (anti-TNF initiation and ∼2 yrs followup) were included. Radiographs were scored, blinded to chronology with the Sharp/van der Heijde method and linked with DANBIO data. Baseline characteristics were investigated with univariate regression and significant variables included in a multivariable logistic regression analysis with ± radiographic progression [Δ total Sharp score (TSS) > 0] as dependent variable. Effect of time-averaged C-reactive protein (CRP), 28-joint Disease Activity Score with CRP (DAS28-CRP), and treatment status at followup were investigated with univariate regression analysis.RESULTS: The study included 930 patients. They were 75% women, 79% positive for IgM-rheumatoid factor (IgM-RF), median age was 57 yrs (range 19-88), disease duration 9 yrs (1-59), DAS28-CRP 5.0 (1.4-7.8), TSS median 15 [3-45 interquartile range (IQR)] and mean 31 (SD 40). Patients started treatment with infliximab (59%), etanercept (18%), or adalimumab (23%). At followup (median 526 days, IQR 392-735), 61% were treated with the initial anti-TNF, 29% had switched TNF inhibitor, and 10% had withdrawn. Twenty-seven percent of patients had progressed radiographically. ΔTSS was median 0.0 [0.0-0.5 IQR/mean 0.6 (SD 2.4)] units/year. Higher TSS, older age, positive IgM-RF, and concomitant prednisolone at baseline were associated with radiographic progression. Time-averaged DAS28-CRP and time-averaged CRP, but not type of TNF inhibitor, were associated with radiographic progression. Patients who stopped/switched during followup progressed more than p

Published
2014

43. Ensembl 2015

Author

Cunningham, Fiona, primary, Amode, M. Ridwan, additional, Barrell, Daniel, additional, Beal, Kathryn, additional, Billis, Konstantinos, additional, Brent, Simon, additional, Carvalho-Silva, Denise, additional, Clapham, Peter, additional, Coates, Guy, additional, Fitzgerald, Stephen, additional, Gil, Laurent, additional, Girón, Carlos García, additional, Gordon, Leo, additional, Hourlier, Thibaut, additional, Hunt, Sarah E., additional, Janacek, Sophie H., additional, Johnson, Nathan, additional, Juettemann, Thomas, additional, Kähäri, Andreas K., additional, Keenan, Stephen, additional, Martin, Fergal J., additional, Maurel, Thomas, additional, McLaren, William, additional, Murphy, Daniel N., additional, Nag, Rishi, additional, Overduin, Bert, additional, Parker, Anne, additional, Patricio, Mateus, additional, Perry, Emily, additional, Pignatelli, Miguel, additional, Riat, Harpreet Singh, additional, Sheppard, Daniel, additional, Taylor, Kieron, additional, Thormann, Anja, additional, Vullo, Alessandro, additional, Wilder, Steven P., additional, Zadissa, Amonida, additional, Aken, Bronwen L., additional, Birney, Ewan, additional, Harrow, Jennifer, additional, Kinsella, Rhoda, additional, Muffato, Matthieu, additional, Ruffier, Magali, additional, Searle, Stephen M.J., additional, Spudich, Giulietta, additional, Trevanion, Stephen J., additional, Yates, Andy, additional, Zerbino, Daniel R., additional, and Flicek, Paul, additional

Published
2014
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44. Which Factors Influence Radiographic Progression During Treatment with Tumor Necrosis Factor Inhibitors in Clinical Practice? Results from 930 Patients with Rheumatoid Arthritis in the Nationwide Danish DANBIO Registry

Author

Ørnbjerg, Lykke Midtbøll, primary, Østergaard, Mikkel, additional, Bøyesen, Pernille, additional, Krogh, Niels Steen, additional, Thormann, Anja, additional, Tarp, Ulrik, additional, Poulsen, Uta Engling, additional, Espesen, Jakob, additional, Schlemmer, Annette, additional, Graudal, Niels, additional, Kollerup, Gina, additional, Jensen, Dorte Vendelbo, additional, Madsen, Ole Rintek, additional, Glintborg, Bente, additional, Christensen, Torben, additional, Lindegaard, Hanne, additional, Bøhme, Wolfgang, additional, Hansen, Annette, additional, Andersen, Anne Rødgaard, additional, and Hetland, Merete Lund, additional

Published
2014
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47. Discontinuation of TNF-inhibitor treatment in clinical practice has a negative impact on radiographic progression 2 years after initiation of therapy. Results from the nationwide Danish DANBIO registry.

Author

Ørnbjerg, Lykke Midtbøll, Østergaard, Mikkel, Bøyesen, Pernille, Thormann, Anja, Tarp, Ulrik, Böhme, Wolfgang, Dencker, Ditte, Lindegaard, Hanne, Poulsen, Uta, Hansen, Annette, Ringsdal, Vibeke Stevenius, Schlemmer, Annette, Graudal, Niels Albert, Andersen, Anne, Espesen, Jakob, Kollerup, Gina, Christensen, Torben G., Randi, Pelck, Glintborg, Bente, Madsen, Ole Rintek, Jensen, Dorte V., Majgaard, Ole, Hetland, Merete Lund, Ørnbjerg, Lykke Midtbøll, Østergaard, Mikkel, Bøyesen, Pernille, Thormann, Anja, Tarp, Ulrik, Böhme, Wolfgang, Dencker, Ditte, Lindegaard, Hanne, Poulsen, Uta, Hansen, Annette, Ringsdal, Vibeke Stevenius, Schlemmer, Annette, Graudal, Niels Albert, Andersen, Anne, Espesen, Jakob, Kollerup, Gina, Christensen, Torben G., Randi, Pelck, Glintborg, Bente, Madsen, Ole Rintek, Jensen, Dorte V., Majgaard, Ole, and Hetland, Merete Lund

Published
2010

48. Treatment with TNF-inhibitor reduces radiographic joint destruction in rheumatoid arthritis patients treated in clinical practice.

Author

Ørnbjerg, Lykke Midtbøll, Østergaard, Mikkel, Bøyesen, Pernille, Thormann, Anja, Tarp, Ulrik, Böhme, Wolfgang, Dencker, Ditte, Lindegaard, Hanne, Poulsen, Uta, Hansen, Annette, Ringsdal, Vibeke Stevenius, Schlemmer, Annette, Graudal, Niels Albert, Andersen, Anne, Espesen, Jakob, Kollerup, Gina, Christensen, Torben G., Pelck, Randi, Glintborg, Bente, Madsen, Ole Rintek, Jensen, Dorte V., Majgaard, Ole, Hetland, Merete Lund, Ørnbjerg, Lykke Midtbøll, Østergaard, Mikkel, Bøyesen, Pernille, Thormann, Anja, Tarp, Ulrik, Böhme, Wolfgang, Dencker, Ditte, Lindegaard, Hanne, Poulsen, Uta, Hansen, Annette, Ringsdal, Vibeke Stevenius, Schlemmer, Annette, Graudal, Niels Albert, Andersen, Anne, Espesen, Jakob, Kollerup, Gina, Christensen, Torben G., Pelck, Randi, Glintborg, Bente, Madsen, Ole Rintek, Jensen, Dorte V., Majgaard, Ole, and Hetland, Merete Lund

Published
2010

49. Ensembl 2013

Author

Flicek, Paul, primary, Ahmed, Ikhlak, additional, Amode, M. Ridwan, additional, Barrell, Daniel, additional, Beal, Kathryn, additional, Brent, Simon, additional, Carvalho-Silva, Denise, additional, Clapham, Peter, additional, Coates, Guy, additional, Fairley, Susan, additional, Fitzgerald, Stephen, additional, Gil, Laurent, additional, García-Girón, Carlos, additional, Gordon, Leo, additional, Hourlier, Thibaut, additional, Hunt, Sarah, additional, Juettemann, Thomas, additional, Kähäri, Andreas K., additional, Keenan, Stephen, additional, Komorowska, Monika, additional, Kulesha, Eugene, additional, Longden, Ian, additional, Maurel, Thomas, additional, McLaren, William M., additional, Muffato, Matthieu, additional, Nag, Rishi, additional, Overduin, Bert, additional, Pignatelli, Miguel, additional, Pritchard, Bethan, additional, Pritchard, Emily, additional, Riat, Harpreet Singh, additional, Ritchie, Graham R. S., additional, Ruffier, Magali, additional, Schuster, Michael, additional, Sheppard, Daniel, additional, Sobral, Daniel, additional, Taylor, Kieron, additional, Thormann, Anja, additional, Trevanion, Stephen, additional, White, Simon, additional, Wilder, Steven P., additional, Aken, Bronwen L., additional, Birney, Ewan, additional, Cunningham, Fiona, additional, Dunham, Ian, additional, Harrow, Jennifer, additional, Herrero, Javier, additional, Hubbard, Tim J. P., additional, Johnson, Nathan, additional, Kinsella, Rhoda, additional, Parker, Anne, additional, Spudich, Giulietta, additional, Yates, Andy, additional, Zadissa, Amonida, additional, and Searle, Stephen M. J., additional

Published
2012
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50. Impact of tumour necrosis factor inhibitor treatment on radiographic progression in rheumatoid arthritis patients in clinical practice: results from the nationwide Danish DANBIO registry

Author

Ørnbjerg, Lykke Midtbøll, primary, Østergaard, Mikkel, additional, Bøyesen, Pernille, additional, Krogh, Niels Steen, additional, Thormann, Anja, additional, Tarp, Ulrik, additional, Poulsen, Uta Engling, additional, Espesen, Jakob, additional, Ringsdal, Vibeke Stevenius, additional, Graudal, Niels, additional, Kollerup, Gina, additional, Jensen, Dorte Vendelbo, additional, Madsen, Ole Rintek, additional, Glintborg, Bente, additional, Christensen, Torben, additional, Lindegaard, Hanne, additional, Dencker, Ditte, additional, Hansen, Annette, additional, Andersen, Anne Rødgaard, additional, and Hetland, Merete Lund, additional

Published
2012
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