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1. Effective sample size: a measure of individual uncertainty in predictions

Author

Thomassen, Doranne, Cessie, Saskia le, van Houwelingen, Hans, and Steyerberg, Ewout

Subjects
Statistics - Methodology
Abstract

Clinical prediction models are estimated using a sample of limited size from the target population, leading to uncertainty in predictions, even when the model is correctly specified. Generally, not all patient profiles are observed uniformly in model development. As a result, sampling uncertainty varies between individual patients' predictions. We aimed to develop an intuitive measure of individual prediction uncertainty. The variance of a patient's prediction can be equated to the variance of the sample mean outcome in n* hypothetical patients with the same predictor values. This hypothetical sample size n* can be interpreted as the number of similar patients n_eff that the prediction is effectively based on, given that the model is correct. For generalised linear models, we derived analytical expressions for the effective sample size. In addition, we illustrated the concept in patients with acute myocardial infarction. In model development, n_eff can be used to balance accuracy versus uncertainty of predictions. In a validation sample, the distribution of n_eff indicates which patients were more and less represented in the development data, and whether predictions might be too uncertain for some to be practically meaningful. In a clinical setting, the effective sample size may facilitate communication of uncertainty about predictions. We propose the effective sample size as a clinically interpretable measure of uncertainty in individual predictions. Its implications should be explored further for the development, validation and clinical implementation of prediction models., Comment: 11 pages, 5 figures

Published
2023
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2. Setting International Standards in Analyzing Patient-Reported Outcomes and Quality of Life Endpoints in Cancer Clinical Trials-Innovative Medicines Initiative (SISAQOL-IMI): stakeholder views, objectives, and procedures

Author

Bui, Cat, Emechebe, Nnadozie, Kamalakar, Rajesh, Papadopoulos, Elektra, Sail, Kavita, Sen, Rohini, Turner, Sean C, Cocks, Kim, Reijneveld, Jaap, Gerlinger, Christoph, Keating, Karen, Su, Yun, Wolf, Birgit, Ge, Miaomiao, Ingelgaard, Anders, Peil, Barbara, Voorhaar, Maarten, Wong, Brendon, Dekanic Arbanas, Gracia, Kuljanic, Karin, Petranovic, Duska, Rede, Ivana, Arraras, Juan, Coons, Stephen Joel, Eremenco, Sonya, Murray, Lindsey, Reeve, Bryce, De Vries, Corinne, Herold, Ralf, Pignatti, Francesco, Machingura, Abigirl, Martinelli, Francesca, Musoro, Jammbe, Piccart, Martine, Barriuso, Jorge, Cherny, Nathan, Dafni, Ourania, De Vries, Elisabeth, Gyawali, Bishal, Kiesewetter, Barbara, Oosting, Sjoukje, Roitberg, Felipe, Rumpold, Gerhard, Schoepf, Felix, Tschuggnall, Michael, Black, Jennifer, Sasseville, Maxime, Soltys, Katherine, Ferrer, Montserrat, Garin, Olatz, Vilagut, Gemma, Schürmann, Christoph, Thomas, Stefanie, Wieseler, Beate, Snyder, Claire, Alonso Abad, Ariel, Bogaerts, Kris, Brackx, Febe, Molenberghs, Geert, Verbeke, Geert, Frigolett Catalan, Cristián, Choi, Jan, Thomassen, Doranne, Geissler, Jan, Sauerbrei, Willi, Gross, Franziska, Pilz, Micha Johannes, Barbachano, Yolanda, Campbell, Lisa, Rantell, Khadija, Desplanques, Gregoire, Regnault, Antoine, Morgan, Kate, Plate, Ananda, ten Seldam, Silene, Terada, Mitsumi, Mizusawa, Junki, Mitchell, Sandra, Wilder Smith, Ashley, Reksten, Tove Ragna, Schiel, Anja, Hansen Joseph, Kenth Louis, Campbell, Alicyn, Cappelleri, Joseph, de Besi, Patrizia, Russell-Smith, Alexander, Sandin, Rickard, Mamolo, Carla, Brundage, Michael, Tu, Dongsheng, Groenvold, Mogens, Petersen, Morten, Cleeland, Charlie, Williams, Lori, Shelley Wang, Xin, Ringash, Jolie, Calvert, Melanie, Cruz Rivera, Samantha, Aiyegbusi, Olalekan Lee, Goetghebeur, Els, Liu, Limin, Van Lancker, Kelly, Boele, Florien, Gilbert, Alexandra, Peacock, Rosemary, Basch, Ethan, King, Madeleine, Rutherford, Claudia, Bhatnagar, Vishal, Fiero, Mallorie, Horodniceanu, Erica, Johnson, Laura Lee, Kluetz, Paul, Rodriguez, Lisa, Pe, Madeline, Alanya, Ahu, Falk, Ragnhild Sorum, Amdal, Cecilie Delphin, Bjordal, Kristin, Chang, Jane, Cislo, Paul, Coens, Corneel, Dirven, Linda, Speck, Rebecca M, Fitzgerald, Kristina, Galinsky, Jayne, Giesinger, Johannes M, Holzner, Bernhard, Le Cessie, Saskia, O'Connor, Daniel, Oliver, Kathy, Pawar, Vivek, Quinten, Chantal, Schlichting, Michael, Ren, Jinma, Roychoudhury, Satrajit, Taphoorn, Martin J B, Velikova, Galina, Wintner, Lisa M, Griebsch, Ingolf, and Bottomley, Andrew

Published
2023
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3. Single-arm studies involving patient-reported outcome data in oncology: a literature review on current practice

Author

Aiyegbusi, Olalekan Lee, Alanya, Ahu, Barbachano, Yolanda, Basch, Ethan, Calvert, Melanie, Campbell, Alicyn, Cappelleri, Joseph, Choi, Jungyeon, Cruz Rivera, Samantha, Delphin Amdal, Cecilie, Fiero, Mallorie, Goetghebeur, Els, Kamalakar, Rajesh, Keating, Karen, Kluetz, Paul, le Cessie, Saskia, Liu, Limin, Molenberghs, Geert, Musoro, Jammbe, Ness, David, Rantell, Khadija, Regnault, Antoine, Reijneveld, Jaap, Roychoudhury, Satrajit, Rumpold, Gerhard, Russell-Smith, Alexander, Rutherford, Claudia, Sail, Kavita, Sandin, Rickard, Sasseville, Maxime, Sauerbrei, Willi, Schiel, Anja, Schlichting, Michael, Soltys, Kathy, Sorum Falk, Ragnhild, Su, Yun, ten Seldam, Silene, Thomassen, Doranne, Van Lancker, Kelly, Musoro, Jammbe Z, Amdal, Cecilie Delphin, Cappelleri, Joseph C, Falk, Ragnhild Sørum, Fiero, Mallorie H, and Reijneveld, Jaap C

Published
2023
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5. Discontinuation of Anti-Tumour Necrosis Factor Therapy in Patients with Perianal Fistulizing Crohn's Disease:Individual Participant Data Meta-Analysis of 309 Patients from 12 Studies

Author

Ten Bokkel Huinink, Sebastiaan, Thomassen, Doranne, Steyerberg, Ewout W., Pauwels, Renske W.M., Casanova, Maria J., Bouguen, Guillaume, Mak, Joyce W.Y., Molnár, Tamas, Lobo, Alan J., Seidelin, Jacob B., Amiot, Aurelien, D'Haens, Geert, Rivière, Pauline, Guidi, Luisa, Bor, Renata, Lin, Wei Chen, Peyrin-Biroulet, Laurent, Gisbert, Javier P., Janneke van der Woude, C., de Vries, Annemarie C., Ten Bokkel Huinink, Sebastiaan, Thomassen, Doranne, Steyerberg, Ewout W., Pauwels, Renske W.M., Casanova, Maria J., Bouguen, Guillaume, Mak, Joyce W.Y., Molnár, Tamas, Lobo, Alan J., Seidelin, Jacob B., Amiot, Aurelien, D'Haens, Geert, Rivière, Pauline, Guidi, Luisa, Bor, Renata, Lin, Wei Chen, Peyrin-Biroulet, Laurent, Gisbert, Javier P., Janneke van der Woude, C., and de Vries, Annemarie C.

Abstract

BACKGROUND: The risk of relapse after anti-tumour necrosis factor [TNF] therapy discontinuation in Crohn's disease patients with perianal fistulas [pCD] is unclear. We aimed to assess this risk. METHODS: A systematic literature search was conducted to identify cohort studies on the incidence of relapse following anti-TNF discontinuation in pCD patients. Individual participant data were requested from the original study cohorts. Inclusion criteria were age ≥16 years, pCD as a (co)indication for start of anti-TNF therapy, more than three doses, and remission of luminal and pCD at anti-TNF discontinuation. The primary outcome was the cumulative incidence of CD relapse using Kaplan-Meier estimates. Secondary outcomes included response to re-treatment and risk factors associated with relapse as assessed by Cox regression analysis. RESULTS: In total, 309 patients from 12 studies in ten countries were included. The median duration of anti-TNF treatment was 14 months [interquartile range 5.8-32.5]. Most patients were treated for pCD without active luminal disease [89%], received first-line anti-TNF therapy [87%], and continued immunomodulatory therapy following anti-TNF discontinuation [78%]. The overall cumulative incidence of relapse was 36% (95% confidence interval [CI] 25-48%) and 42% [95% CI 32-53%] at 1 and 2 years after anti-TNF discontinuation, respectively. Risk factors for relapse included smoking (hazard ratio [HR] 1.5 [1.0, 2.1]) and history of proctitis (HR 1.7 [1.1, 2.5]). The overall re-treatment response rate was 82%. CONCLUSIONS: This individual participant data meta-analysis, on predominantly patients with pCD without active luminal disease and first-line anti-TNF therapy, shows that over half of patients remain in remission 2 years after anti-TNF discontinuation. Therefore, anti-TNF discontinuation may be considered in this subgroup.

Published
2024

6. Validation and update of a prediction model for risk of relapse after cessation of anti-TNF treatment in Crohn’s disease

Author

ten Bokkel Huinink, Sebastiaan, de Jong, Djuna C., Nieboer, Daan, Thomassen, Doranne, Steyerberg, Ewout W., Dijkgraaf, Marcel G.W., Bodelier, Alexander G.L., West, Rachel L., Römkens, Tessa E.H., Hoentjen, Frank, Mallant, Rosalie C., van Tuyl, Bas A.C., Mares, Wout G.N., Wolfhagen, Frank H.J., Dijkstra, Gerard, Reijnders, Jurriën G.P., de Boer, Nanne K., Tan, Adriaan C.I.T.L., van Boeckel, Petra G.A., Tack, Greetje J., van Asseldonk, Dirk P., D’Haens, Geert R.A.M., van der Woude, C Janneke, Duijvestein, Marjolijn, and de Vries, Annemarie C

Published
2022
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8. Discontinuation of Anti-Tumour Necrosis Factor Therapy in Patients with Perianal Fistulizing Crohn’s Disease: Individual Participant Data Meta-Analysis of 309 Patients from 12 Studies

Author

Huinink, S ten Bokkel, primary, Thomassen, Doranne, additional, Steyerberg, Ewout W, additional, Pauwels, Renske W M, additional, Casanova, Maria J, additional, Bouguen, Guillaume, additional, Mak, Joyce W Y, additional, Molnár, Tamas, additional, Lobo, Alan J, additional, Seidelin, Jacob B, additional, Amiot, Aurelien, additional, D’Haens, Geert, additional, Rivière, Pauline, additional, Guidi, Luisa, additional, Bor, Renata, additional, Lin, Wei-Chen, additional, Peyrin-Biroulet, Laurent, additional, Gisbert, Javier P, additional, van der Woude, C Janneke, additional, and de Vries, Annemarie C, additional

Published
2023
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9. Setting International Standards in Analyzing Patient-Reported Outcomes and Quality of Life Endpoints in Cancer Clinical Trials-Innovative Medicines Initiative (SISAQOL-IMI): stakeholder views, objectives, and procedures

Author

Pe, Madeline, primary, Alanya, Ahu, additional, Falk, Ragnhild Sorum, additional, Amdal, Cecilie Delphin, additional, Bjordal, Kristin, additional, Chang, Jane, additional, Cislo, Paul, additional, Coens, Corneel, additional, Dirven, Linda, additional, Speck, Rebecca M, additional, Fitzgerald, Kristina, additional, Galinsky, Jayne, additional, Giesinger, Johannes M, additional, Holzner, Bernhard, additional, Le Cessie, Saskia, additional, O'Connor, Daniel, additional, Oliver, Kathy, additional, Pawar, Vivek, additional, Quinten, Chantal, additional, Schlichting, Michael, additional, Ren, Jinma, additional, Roychoudhury, Satrajit, additional, Taphoorn, Martin J B, additional, Velikova, Galina, additional, Wintner, Lisa M, additional, Griebsch, Ingolf, additional, Bottomley, Andrew, additional, Bui, Cat, additional, Emechebe, Nnadozie, additional, Kamalakar, Rajesh, additional, Papadopoulos, Elektra, additional, Sail, Kavita, additional, Sen, Rohini, additional, Turner, Sean C, additional, Cocks, Kim, additional, Reijneveld, Jaap, additional, Gerlinger, Christoph, additional, Keating, Karen, additional, Su, Yun, additional, Wolf, Birgit, additional, Ge, Miaomiao, additional, Ingelgaard, Anders, additional, Peil, Barbara, additional, Voorhaar, Maarten, additional, Wong, Brendon, additional, Dekanic Arbanas, Gracia, additional, Kuljanic, Karin, additional, Petranovic, Duska, additional, Rede, Ivana, additional, Arraras, Juan, additional, Coons, Stephen Joel, additional, Eremenco, Sonya, additional, Murray, Lindsey, additional, Reeve, Bryce, additional, De Vries, Corinne, additional, Herold, Ralf, additional, Pignatti, Francesco, additional, Machingura, Abigirl, additional, Martinelli, Francesca, additional, Musoro, Jammbe, additional, Piccart, Martine, additional, Barriuso, Jorge, additional, Cherny, Nathan, additional, Dafni, Ourania, additional, De Vries, Elisabeth, additional, Gyawali, Bishal, additional, Kiesewetter, Barbara, additional, Oosting, Sjoukje, additional, Roitberg, Felipe, additional, Rumpold, Gerhard, additional, Schoepf, Felix, additional, Tschuggnall, Michael, additional, Black, Jennifer, additional, Sasseville, Maxime, additional, Soltys, Katherine, additional, Ferrer, Montserrat, additional, Garin, Olatz, additional, Vilagut, Gemma, additional, Schürmann, Christoph, additional, Thomas, Stefanie, additional, Wieseler, Beate, additional, Snyder, Claire, additional, Alonso Abad, Ariel, additional, Bogaerts, Kris, additional, Brackx, Febe, additional, Molenberghs, Geert, additional, Verbeke, Geert, additional, Frigolett Catalan, Cristián, additional, Choi, Jan, additional, Thomassen, Doranne, additional, Geissler, Jan, additional, Sauerbrei, Willi, additional, Gross, Franziska, additional, Pilz, Micha Johannes, additional, Barbachano, Yolanda, additional, Campbell, Lisa, additional, Rantell, Khadija, additional, Desplanques, Gregoire, additional, Regnault, Antoine, additional, Morgan, Kate, additional, Plate, Ananda, additional, ten Seldam, Silene, additional, Terada, Mitsumi, additional, Mizusawa, Junki, additional, Mitchell, Sandra, additional, Wilder Smith, Ashley, additional, Reksten, Tove Ragna, additional, Schiel, Anja, additional, Hansen Joseph, Kenth Louis, additional, Campbell, Alicyn, additional, Cappelleri, Joseph, additional, de Besi, Patrizia, additional, Russell-Smith, Alexander, additional, Sandin, Rickard, additional, Mamolo, Carla, additional, Brundage, Michael, additional, Tu, Dongsheng, additional, Groenvold, Mogens, additional, Petersen, Morten, additional, Cleeland, Charlie, additional, Williams, Lori, additional, Shelley Wang, Xin, additional, Ringash, Jolie, additional, Calvert, Melanie, additional, Cruz Rivera, Samantha, additional, Aiyegbusi, Olalekan Lee, additional, Goetghebeur, Els, additional, Liu, Limin, additional, Van Lancker, Kelly, additional, Boele, Florien, additional, Gilbert, Alexandra, additional, Peacock, Rosemary, additional, Basch, Ethan, additional, King, Madeleine, additional, Rutherford, Claudia, additional, Bhatnagar, Vishal, additional, Fiero, Mallorie, additional, Horodniceanu, Erica, additional, Johnson, Laura Lee, additional, Kluetz, Paul, additional, and Rodriguez, Lisa, additional

Published
2023
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10. Discontinuation of Anti-Tumour Necrosis Factor Therapy in Patients with Perianal Fistulizing Crohn's Disease: Individual Participant Data Meta-Analysis of 309 Patients from 12 Studies.

Author

Huinink, Sebastiaan ten Bokkel, Thomassen, Doranne, Steyerberg, Ewout W, Pauwels, Renske W M, Casanova, Maria J, Bouguen, Guillaume, Mak, Joyce W Y, Molnár, Tamas, Lobo, Alan J, Seidelin, Jacob B, Amiot, Aurelien, D'Haens, Geert, Rivière, Pauline, Guidi, Luisa, Bor, Renata, Lin, Wei-Chen, Peyrin-Biroulet, Laurent, Gisbert, Javier P, Woude, C Janneke van der, and Vries, Annemarie C de

Abstract

Background The risk of relapse after anti-tumour necrosis factor [TNF] therapy discontinuation in Crohn's disease patients with perianal fistulas [pCD] is unclear. We aimed to assess this risk. Methods A systematic literature search was conducted to identify cohort studies on the incidence of relapse following anti-TNF discontinuation in pCD patients. Individual participant data were requested from the original study cohorts. Inclusion criteria were age ≥16 years, pCD as a (co)indication for start of anti-TNF therapy, more than three doses, and remission of luminal and pCD at anti-TNF discontinuation. The primary outcome was the cumulative incidence of CD relapse using Kaplan–Meier estimates. Secondary outcomes included response to re-treatment and risk factors associated with relapse as assessed by Cox regression analysis. Results In total, 309 patients from 12 studies in ten countries were included. The median duration of anti-TNF treatment was 14 months [interquartile range 5.8–32.5]. Most patients were treated for pCD without active luminal disease [89%], received first-line anti-TNF therapy [87%], and continued immunomodulatory therapy following anti-TNF discontinuation [78%]. The overall cumulative incidence of relapse was 36% (95% confidence interval [CI] 25–48%) and 42% [95% CI 32–53%] at 1 and 2 years after anti-TNF discontinuation, respectively. Risk factors for relapse included smoking (hazard ratio [HR] 1.5 [1.0, 2.1]) and history of proctitis (HR 1.7 [1.1, 2.5]). The overall re-treatment response rate was 82%. Conclusions This individual participant data meta-analysis, on predominantly patients with pCD without active luminal disease and first-line anti-TNF therapy, shows that over half of patients remain in remission 2 years after anti-TNF discontinuation. Therefore, anti-TNF discontinuation may be considered in this subgroup. [ABSTRACT FROM AUTHOR]

Published
2024
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11. Single-arm studies involving patient-reported outcome data in oncology: a literature review on current practice

Author

Liu, Limin, primary, Choi, Jungyeon, additional, Musoro, Jammbe Z, additional, Sauerbrei, Willi, additional, Amdal, Cecilie Delphin, additional, Alanya, Ahu, additional, Barbachano, Yolanda, additional, Cappelleri, Joseph C, additional, Falk, Ragnhild Sørum, additional, Fiero, Mallorie H, additional, Regnault, Antoine, additional, Reijneveld, Jaap C, additional, Sandin, Rickard, additional, Thomassen, Doranne, additional, Roychoudhury, Satrajit, additional, Goetghebeur, Els, additional, le Cessie, Saskia, additional, Aiyegbusi, Olalekan Lee, additional, Basch, Ethan, additional, Calvert, Melanie, additional, Campbell, Alicyn, additional, Cappelleri, Joseph, additional, Cruz Rivera, Samantha, additional, Delphin Amdal, Cecilie, additional, Fiero, Mallorie, additional, Kamalakar, Rajesh, additional, Keating, Karen, additional, Kluetz, Paul, additional, Liu, Limin, additional, Molenberghs, Geert, additional, Musoro, Jammbe, additional, Ness, David, additional, Rantell, Khadija, additional, Reijneveld, Jaap, additional, Rumpold, Gerhard, additional, Russell-Smith, Alexander, additional, Rutherford, Claudia, additional, Sail, Kavita, additional, Sasseville, Maxime, additional, Schiel, Anja, additional, Schlichting, Michael, additional, Soltys, Kathy, additional, Sorum Falk, Ragnhild, additional, Su, Yun, additional, ten Seldam, Silene, additional, and Van Lancker, Kelly, additional

Published
2023
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14. Validation and update of a prediction model for risk of relapse after cessation of anti-TNF treatment in Crohn's disease

Author

Huinink, Sebastiaan ten Bokkel, Jong, Djuna C. de, Nieboer, Daan, Thomassen, Doranne, Steyerberg, Ewout W., Dijkgraaf, Marcel G.W., Hoentjen, F., Duijvestein, Marjolijn, Vries, Annemarie C. de, Huinink, Sebastiaan ten Bokkel, Jong, Djuna C. de, Nieboer, Daan, Thomassen, Doranne, Steyerberg, Ewout W., Dijkgraaf, Marcel G.W., Hoentjen, F., Duijvestein, Marjolijn, and Vries, Annemarie C. de

Abstract

Item does not contain fulltext

Published
2022

15. Discontinuation of Anti-Tumour Necrosis Factor Therapy in Patients with Perianal Fistulizing Crohn's Disease: Individual Participant Data Meta-Analysis of 309 Patients from 12 Studies.

Author

Ten Bokkel Huinink S, Thomassen D, Steyerberg EW, Pauwels RWM, Casanova MJ, Bouguen G, Mak JWY, Molnár T, Lobo AJ, Seidelin JB, Amiot A, D'Haens G, Rivière P, Guidi L, Bor R, Lin WC, Peyrin-Biroulet L, Gisbert JP, Janneke van der Woude C, and de Vries AC

Subjects
Humans, Adolescent, Infliximab therapeutic use, Tumor Necrosis Factor-alpha, Tumor Necrosis Factor Inhibitors therapeutic use, Recurrence, Necrosis complications, Treatment Outcome, Retrospective Studies, Crohn Disease complications, Crohn Disease drug therapy, Rectal Fistula etiology, Rectal Fistula complications
Abstract

Background: The risk of relapse after anti-tumour necrosis factor [TNF] therapy discontinuation in Crohn's disease patients with perianal fistulas [pCD] is unclear. We aimed to assess this risk., Methods: A systematic literature search was conducted to identify cohort studies on the incidence of relapse following anti-TNF discontinuation in pCD patients. Individual participant data were requested from the original study cohorts. Inclusion criteria were age ≥16 years, pCD as a (co)indication for start of anti-TNF therapy, more than three doses, and remission of luminal and pCD at anti-TNF discontinuation. The primary outcome was the cumulative incidence of CD relapse using Kaplan-Meier estimates. Secondary outcomes included response to re-treatment and risk factors associated with relapse as assessed by Cox regression analysis., Results: In total, 309 patients from 12 studies in ten countries were included. The median duration of anti-TNF treatment was 14 months [interquartile range 5.8-32.5]. Most patients were treated for pCD without active luminal disease [89%], received first-line anti-TNF therapy [87%], and continued immunomodulatory therapy following anti-TNF discontinuation [78%]. The overall cumulative incidence of relapse was 36% (95% confidence interval [CI] 25-48%) and 42% [95% CI 32-53%] at 1 and 2 years after anti-TNF discontinuation, respectively. Risk factors for relapse included smoking (hazard ratio [HR] 1.5 [1.0, 2.1]) and history of proctitis (HR 1.7 [1.1, 2.5]). The overall re-treatment response rate was 82%., Conclusions: This individual participant data meta-analysis, on predominantly patients with pCD without active luminal disease and first-line anti-TNF therapy, shows that over half of patients remain in remission 2 years after anti-TNF discontinuation. Therefore, anti-TNF discontinuation may be considered in this subgroup., (© The Author(s) 2023. Published by Oxford University Press on behalf of European Crohn’s and Colitis Organisation.)

Published
2024
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