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2. Next generation sequencing of high-grade adult-type diffuse glioma in the Netherlands: interlaboratory variation in the primary diagnostic and recurrent setting

Author

van Opijnen, Mark P., Broekman, Marike L. D., Cuppen, Edwin, Dubbink, Hendrikus J., ter Elst, Arja, van Eijk, Ronald, Mühlebner, Angelika, Jansen, Casper, van der Geize, Robert, Speel, Ernst-Jan M., Groenen, Patricia J. T. A., de Vos, Filip Y. F., Wesseling, Pieter, de Leng, Wendy W. J., and Maas, Sybren L. N.

Published
2024
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3. ROS1 fusions in resected stage I-III adenocarcinoma: Results from the European Thoracic Oncology Platform Lungscape project

Author

Speel, Ernst-Jan M., Dafni, Urania, Thunnissen, Erik, Hendrik Rüschoff, Jan, O'Brien, Cathal, Kowalski, Jacek, Kerr, Keith M., Bubendorf, Lukas, Sansano, Irene, Joseph, Leena, Kriegsmann, Mark, Navarro, Atilio, Monkhorst, Kim, Bille Madsen, Line, Hernandez Losa, Javier, Biernat, Wojciech, Stenzinger, Albrecht, Rüland, Andrea, Hillen, Lisa M., Marti, Nesa, Molina-Vila, Miguel A., Dellaporta, Tereza, Kammler, Roswitha, Peters, Solange, Stahel, Rolf A., Finn, Stephen P., and Radonic, Teodora

Published
2024
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4. Identification of Defined Molecular Subgroups on the Basis of Immunohistochemical Analyses and Potential Therapeutic Vulnerabilities of Pulmonary Carcinoids

Author

Leunissen, Daphne J.G., Moonen, Laura, von der Thüsen, Jan H., den Bakker, Michael A., Hillen, Lisa M., van Weert, Tijmen J.J., zur Hausen, Axel, van den Bosch, Thierry P.P., Lap, Lisa M.V., Damhuis, Ronald A., Reynaert, Niki L., van den Broek, Esther C., Fernandez-Cuesta, Lynnette, Foll, Matthieu, Alcala, Nicolas, Sexton-Oates, Alexandra, Dingemans, Anne-Marie C., Speel, Ernst-Jan M., and Derks, Jules L.

Published
2024
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5. Long-term survival in patients with gastroenteropancreatic neuroendocrine neoplasms: A population-based study

Author

Poleé, Iris N., Hermans, Bregtje C.M., van der Zwan, Jan Maarten, Bouwense, Stefan A.W., Dercksen, Marcus W., Eskens, Ferry A.L.M., Havekes, Bastiaan, Hofland, Johannes, Kerkhofs, Thomas M.A., Klümpen, Heinz-Josef, Latten-Jansen, Loes M., Speel, Ernst-Jan M., Verburg, Frederik A., Walenkamp, Annemiek M.E., Geurts, Sandra M.E., and de Vos-Geelen, Judith

Published
2022
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6. The impact of a pathologist’s personality on the interobserver variability and diagnostic accuracy of predictive PD-L1 immunohistochemistry in lung cancer

Author

Butter, Rogier, Hondelink, Liesbeth M., van Elswijk, Lisette, Blaauwgeers, Johannes L.G., Bloemena, Elisabeth, Britstra, Rieneke, Bulkmans, Nicole, van Gulik, Anna Lena, Monkhorst, Kim, de Rooij, Mathilda J., Slavujevic-Letic, Ivana, Smit, Vincent T.H.B.M., Speel, Ernst-Jan M., Thunnissen, Erik, von der Thüsen, Jan H., Timens, Wim, van de Vijver, Marc J., Yick, David C.Y., Zwinderman, Aeilko H., Cohen, Danielle, 't Hart, Nils A., and Radonic, Teodora

Published
2022
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7. Disease relapse in relation to lymph node sampling in lung carcinoid patients

Author

Moonen, Laura, primary, Derks, Jules, additional, Hillen, Lisa M, additional, van Suylen, Robert Jan, additional, den Bakker, Michael, additional, Thusen, Jan Von Der, additional, Damhuis, Ronald, additional, Buikhuisen, Wienecke, additional, van den Broek, Esther C, additional, Maessen, Jos, additional, Maat, Alexander, additional, van Schil, Paul, additional, Speel, Ernst-Jan M., additional, and Dingemans, Anne-Marie C, additional

Published
2024
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9. Prognostic Impact of KRAS G12C Mutation in Patients With NSCLC: Results From the European Thoracic Oncology Platform Lungscape Project

Author

Finn, Stephen P., Addeo, Alfredo, Dafni, Urania, Thunnissen, Erik, Bubendorf, Lukas, Madsen, Line Bille, Biernat, Wojciech, Verbeken, Eric, Hernandez-Losa, Javier, Marchetti, Antonio, Cheney, Richard, Warth, Arne, Speel, Ernst-Jan M., Quinn, Anne Marie, Monkhorst, Kim, Jantus-Lewintre, Eloisa, Tischler, Verena, Marti, Nesa, Dimopoulou, Georgia, Molina-Vila, Miguel A., Kammler, Roswitha, Kerr, Keith M., Peters, Solange, and Stahel, Rolf A.

Published
2021
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10. RET Fluorescence In Situ Hybridization Analysis Is a Sensitive but Highly Unspecific Screening Method for RET Fusions in Lung Cancer

Author

Radonic, Teodora, Geurts-Giele, W.R.R., Samsom, Kris G., Roemen, Guido M.J. M., von der Thüsen, Jan H., Thunnissen, Erik, Meijssen, Isabelle C., Sleddens, Hein F.B. M., Dinjens, Winand N.M., Boelens, Mirjam C., Weijers, Karin, Speel, Ernst Jan M., Finn, Stephen P., O’Brien, Cathal, van Wezel, Tom, Cohen, Danielle, Monkhorst, Kim, Roepman, Paul, and Dubbink, H.J.

Published
2021
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13. Programmed death-ligand 1 expression influenced by tissue sample size. Scoring based on tissue microarrays' and cross-validation with resections, in patients with, stage I–III, non-small cell lung carcinoma of the European Thoracic Oncology Platform Lungscape cohort

Author

Thunnissen, Erik, Kerr, Keith M., Dafni, Urania, Bubendorf, Lukas, Finn, Stephen P., Soltermann, Alex, Biernat, Wojciech, Cheney, Richard, Verbeken, Erik, Warth, Arne, Marchetti, Antonio, Speel, Ernst-Jan M., Pokharel, Saraswati, Quinn, Anne Marie, Monkhorst, Kim, Navarro, Atilio, Madsen, Line Bille, Tsourti, Zoi, Geiger, Thomas, Kammler, Roswitha, Peters, Solange, Stahel, Rolf A., Rosell, Rafael, Blackhall, Fiona, Molina, Miguel Angel, Weder, Walter, Finn, Stephen, Hiltbrunner, Anita, Marti, Nesa, Polydoropoulou, Varvara, Zygoura, Panagiota, Nicolson, Marianne, Stevenson, David A.J, Mathieson, William, Smit, Egbert, Radonic, Teodora, Rulle, Undine, Curioni, Alessandra, Gray, Steven G., Gately, Kathy, Barr, Martin, Meldgaard, Peter, Madsen, Line B., Savic, Spasenija, Lardinois, Didier, Nackaerts, Kristiaan, Dooms, Christophe, Wauters, Els, Van Der Borght, Sara, Wrona, Ania, Rzyman, Witold, Jassem, Jacek, Dienemann, Hendrik, Muley, Thomas, De Luca, Graziano, di Lorito, Alessia, Dingemans, Anne-Marie, Ruland, Andrea, Ferenczy, Philip, Franklin, Lynsey, Baas, Paul, van de Wiel, Bart, Camps, Carlos, and Martorell, Miguel

Published
2020
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14. External Quality Assessment on Molecular Tumor Profiling with Circulating Tumor DNA-Based Methodologies Routinely Used in Clinical Pathology within the COIN Consortium

Author

van der Leest, Paul, primary, Rozendal, Pim, additional, Hinrichs, John, additional, van Noesel, Carel J M, additional, Zwaenepoel, Karen, additional, Deiman, Birgit, additional, Huijsmans, Cornelis J J, additional, van Eijk, Ronald, additional, Speel, Ernst Jan M, additional, van Haastert, Rick J, additional, Ligtenberg, Marjolijn J L, additional, van Schaik, Ron H N, additional, Jansen, Maurice P H M, additional, Dubbink, Hendrikus J, additional, de Leng, Wendy W, additional, Leers, Mathie P G, additional, Tamminga, Menno, additional, van den Broek, Daan, additional, van Kempen, Léon C, additional, and Schuuring, Ed, additional

Published
2024
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16. External Quality Assessment on Molecular Tumor Profiling with Circulating Tumor DNA-Based Methodologies Routinely Used in Clinical Pathology within the COIN Consortium

Author

Pathologie Pathologen staf, Cancer, van der Leest, Paul, Rozendal, Pim, Hinrichs, John, van Noesel, Carel J M, Zwaenepoel, Karen, Deiman, Birgit, Huijsmans, Cornelis J J, van Eijk, Ronald, Speel, Ernst Jan M, van Haastert, Rick J, Ligtenberg, Marjolijn J L, van Schaik, Ron H N, Jansen, Maurice P H M, Dubbink, Hendrikus J, de Leng, Wendy W, Leers, Mathie P G, Tamminga, Menno, van den Broek, Daan, van Kempen, Léon C, Schuuring, Ed, Pathologie Pathologen staf, Cancer, van der Leest, Paul, Rozendal, Pim, Hinrichs, John, van Noesel, Carel J M, Zwaenepoel, Karen, Deiman, Birgit, Huijsmans, Cornelis J J, van Eijk, Ronald, Speel, Ernst Jan M, van Haastert, Rick J, Ligtenberg, Marjolijn J L, van Schaik, Ron H N, Jansen, Maurice P H M, Dubbink, Hendrikus J, de Leng, Wendy W, Leers, Mathie P G, Tamminga, Menno, van den Broek, Daan, van Kempen, Léon C, and Schuuring, Ed

Published
2024

17. Proximity ligation-based sequencing for the identification of human papillomavirus genomic integration sites in formalin-fixed paraffin embedded oropharyngeal squamous cell carcinomas

Author

Demers, Imke, Balaji, Harini, Feitsma, Harma, Stelloo, Ellen, Swennenhuis, Joost, Sergeeva, Irina, Wuerdemann, Nora, van den Hout, Mari F.C.M., Wagner, Steffen, Kremer, Bernd, Klussmann, Jens P., Huebbers, Christian U., Speel, Ernst Jan M., Demers, Imke, Balaji, Harini, Feitsma, Harma, Stelloo, Ellen, Swennenhuis, Joost, Sergeeva, Irina, Wuerdemann, Nora, van den Hout, Mari F.C.M., Wagner, Steffen, Kremer, Bernd, Klussmann, Jens P., Huebbers, Christian U., and Speel, Ernst Jan M.

Abstract

Human papillomavirus (HPV) infections are an increasing cause of oropharyngeal squamous cell carcinomas (OPSCC). Integration of the viral genome into the host genome is suggested to affect carcinogenesis, however, the correlation with OPSCC patient prognosis is still unclear. Research on HPV integration is hampered by current integration detection technologies and their unsuitability for formalin-fixed paraffin-embedded (FFPE) tissues. This study aims to develop and validate a novel targeted proximity-ligation based sequencing method (targeted locus amplification/capture [TLA/TLC]) for HPV integration detection in cell lines and FFPE OPSCCs. For the identification of HPV integrations, TLA/TLC was applied to 7 cell lines and 27 FFPE OPSCCs. Following preprocessing steps, a polymerase chain reaction (PCR)-based HPV enrichment was performed on the cell lines and a capture-based HPV enrichment was performed on the FFPE tissues before paired-end sequencing. TLA was able to sequence up to hundreds of kb around the target, detecting exact HPV integration loci, structural variants, and chromosomal rearrangements. In all cell lines, one or more integration sites were identified, in accordance with detection of integrated papillomavirus sequences PCR data and the literature. TLC detected integrated HPV in 15/27 FFPE OPSCCs and identified simple and complex integration patterns. In general, TLA/TLC confirmed PCR data and detected additional integration sites. In conclusion TLA/TLC reliably and robustly detects HPV integration in cell lines and FFPE OPSCCs, enabling large, population-based studies on the clinical relevance of HPV integration. Furthermore, this approach might be valuable for clonality assessment of HPV-related tumors in clinical diagnostics.

Published
2024

18. Next generation sequencing of high-grade adult-type diffuse glioma in the Netherlands:interlaboratory variation in the primary diagnostic and recurrent setting

Author

van Opijnen, Mark P., Broekman, Marike L.D., Cuppen, Edwin, Dubbink, Hendrikus J., ter Elst, Arja, van Eijk, Ronald, Mühlebner, Angelika, Jansen, Casper, van der Geize, Robert, Speel, Ernst Jan M., Groenen, Patricia J.T.A., de Vos, Filip Y.F., Wesseling, Pieter, de Leng, Wendy W.J., Maas, Sybren L.N., van Opijnen, Mark P., Broekman, Marike L.D., Cuppen, Edwin, Dubbink, Hendrikus J., ter Elst, Arja, van Eijk, Ronald, Mühlebner, Angelika, Jansen, Casper, van der Geize, Robert, Speel, Ernst Jan M., Groenen, Patricia J.T.A., de Vos, Filip Y.F., Wesseling, Pieter, de Leng, Wendy W.J., and Maas, Sybren L.N.

Abstract

Purpose: Next generation sequencing (NGS) is an important tool used in clinical practice to obtain the required molecular information for accurate diagnostics of high-grade adult-type diffuse glioma (HGG). Since individual centers use either in-house produced or standardized panels, interlaboratory variation could play a role in the practice of HGG diagnosis and treatment. This study aimed to investigate the current practice in NGS application for both primary and recurrent HGG. Methods: This nationwide Dutch survey used the expertise of (neuro)pathologists and clinical scientists in molecular pathology (CSMPs) by sending online questionnaires on clinical and technical aspects. Primary outcome was an overview of panel composition in the different centers for diagnostic practice of HGG. Secondary outcomes included practice for recurrent HGG and future perspectives. Results: Out of twelve neuro-oncology centers, the survey was filled out by eleven (neuro)pathologists and seven CSMPs. The composition of the diagnostic NGS panels differed in each center with numbers of genes ranging from 12 to 523. Differences are more pronounced when tests are performed to find therapeutic targets in the case of recurrent disease: about half of the centers test for gene fusions (60%) and tumor mutational burden (40%). Conclusion: Current notable interlaboratory variations as illustrated in this study should be reduced in order to refine diagnostics and improve precision oncology. In-house developed tests, standardized panels and routine application of broad gene panels all have their own advantages and disadvantages. Future research would be of interest to study the clinical impact of variation in diagnostic approaches.

Published
2024

19. Next generation sequencing of high-grade adult-type diffuse glioma in the Netherlands: interlaboratory variation in the primary diagnostic and recurrent setting

Author

CMM Groep Van Mil, Pathologie Pathologen staf, Brain, Cancer, MS Medische Oncologie, Pathologie Groep Van Diest, van Opijnen, Mark P, Broekman, Marike L D, Cuppen, Edwin, Dubbink, Hendrikus J, Ter Elst, Arja, van Eijk, Ronald, Mühlebner, Angelika, Jansen, Casper, van der Geize, Robert, Speel, Ernst-Jan M, Groenen, Patricia J T A, de Vos, Filip Y F, Wesseling, Pieter, de Leng, Wendy W J, Maas, Sybren L N, CMM Groep Van Mil, Pathologie Pathologen staf, Brain, Cancer, MS Medische Oncologie, Pathologie Groep Van Diest, van Opijnen, Mark P, Broekman, Marike L D, Cuppen, Edwin, Dubbink, Hendrikus J, Ter Elst, Arja, van Eijk, Ronald, Mühlebner, Angelika, Jansen, Casper, van der Geize, Robert, Speel, Ernst-Jan M, Groenen, Patricia J T A, de Vos, Filip Y F, Wesseling, Pieter, de Leng, Wendy W J, and Maas, Sybren L N

Published
2024

20. External Quality Assessment on Molecular Tumor Profiling with Circulating Tumor DNA-Based Methodologies Routinely Used in Clinical Pathology within the COIN Consortium

Author

van der Leest, Paul, Rozendal, Pim, Hinrichs, John, van Noesel, Carel J.M., Zwaenepoel, Karen, Deiman, Birgit, Huijsmans, Cornelis J.J., van Eijk, Ronald, Speel, Ernst Jan M., van Haastert, Rick J., Ligtenberg, Marjolijn J.L., van Schaik, Ron H.N., Jansen, Maurice P.H.M., Dubbink, Hendrikus J., de Leng, Wendy W., Leers, Mathie P.G., Tamminga, Menno, van den Broek, Daan, van Kempen, Leon C., Schuuring, Ed, van der Leest, Paul, Rozendal, Pim, Hinrichs, John, van Noesel, Carel J.M., Zwaenepoel, Karen, Deiman, Birgit, Huijsmans, Cornelis J.J., van Eijk, Ronald, Speel, Ernst Jan M., van Haastert, Rick J., Ligtenberg, Marjolijn J.L., van Schaik, Ron H.N., Jansen, Maurice P.H.M., Dubbink, Hendrikus J., de Leng, Wendy W., Leers, Mathie P.G., Tamminga, Menno, van den Broek, Daan, van Kempen, Leon C., and Schuuring, Ed

Abstract

Background: Identification of tumor-derived variants in circulating tumor DNA (ctDNA) has potential as a sensitive and reliable surrogate for tumor tissue-based routine diagnostic testing. However, variations in pre(analytical) procedures affect the efficiency of ctDNA recovery. Here, an external quality assessment (EQA) was performed to determine the performance of ctDNA mutation detection work flows that are used in current diagnostic settings across laboratories within the Dutch COIN consortium (ctDNA on the road to implementation in The Netherlands). Methods: Aliquots of 3 high-volume diagnostic leukapheresis (DLA) plasma samples and 3 artificial reference plasma samples with predetermined mutations were distributed among 16 Dutch laboratories. Participating laboratories were requested to perform ctDNA analysis for BRAF exon 15, EGFR exon 18-21, and KRAS exon 2-3 using their regular circulating cell-free DNA (ccfDNA) analysis work flow. Laboratories were assessed based on adherence to the study protocol, overall detection rate, and overall genotyping performance. Results: A broad range of preanalytical conditions (e.g., plasma volume, elution volume, and extraction methods) and analytical methodologies (e.g., droplet digital PCR [ddPCR], small-panel PCR assays, and next-generation sequencing [NGS]) were used. Six laboratories (38%) had a performance score of >0.90; all other laboratories scored between 0.26 and 0.80. Although 13 laboratories (81%) reached a 100% overall detection rate, the therapeutically relevant EGFR p.(S752_I759del) (69%), EGFR p.(N771_H773dup) (50%), and KRAS p.(G12C) (48%) mutations were frequently not genotyped accurately. Conclusions: Divergent (pre)analytical protocols could lead to discrepant clinical outcomes when using the same plasma samples. Standardization of (pre)analytical work flows can facilitate the implementation of reproducible liquid biopsy testing in the clinical routine.

Published
2024

24. A retrospective cohort study of PD-L1 prevalence, molecular associations and clinical outcomes in patients with NSCLC: Results from the European Thoracic Oncology Platform (ETOP) Lungscape Project

Author

Kerr, Keith M., Thunnissen, Erik, Dafni, Urania, Finn, Stephen P., Bubendorf, Lukas, Soltermann, Alex, Verbeken, Eric, Biernat, Wojciech, Warth, Arne, Marchetti, Antonio, Speel, Ernst-Jan M., Pokharel, Sarawati, Quinn, Anne Marie, Monkhorst, Kim, Navarro, Atilio, Madsen, Line Bille, Radonic, Teodora, Wilson, Joan, De Luca, Graziano, Gray, Steven G., Cheney, Richard, Savic, Spasenija, Martorell, Miguel, Muley, Thomas, Baas, Paul, Meldgaard, Peter, Blackhall, Fiona, Dingemans, Anne-Marie, Dziadziuszko, Rafal, Vansteenkiste, Johan, Weder, Walter, Polydoropoulou, Varvara, Geiger, Thomas, Kammler, Roswitha, Peters, Solange, and Stahel, Rolf

Published
2019
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26. Mapping of Human Polyomavirus in Renal Cell Carcinoma Tissues.

Author

Mobaraki, Ghalib, Shi, Shuai, Liu, Dan, Smits, Kim M., Severens, Kim, Lommen, Kim, Rennspiess, Dorit, Speel, Ernst-Jan M., Winnepenninckx, Véronique, Klufah, Faisal, Samarska, Iryna, and Hausen, Axel zur

Subjects
RENAL cell carcinoma, MERKEL cells, DNA viruses, GENE expression, POLYOMAVIRUSES
Abstract

Worldwide, the incidence of renal cell carcinoma (RCC) is rising, accounting for approximately 2% of all cancer diagnoses and deaths. The etiology of RCC is still obscure. Here, we assessed the presence of HPyVs in paraffin-embedded tissue (FFPE) resected tissue from patients with RCC by using different molecular techniques. Fifty-five FFPE tissues from 11 RCC patients were included in this study. Consensus and HPyV-specific primers were used to screen for HPyVs. Both PCR approaches revealed that HPyV is frequently detected in the tissues of RCC kidney resections. A total of 78% (43/55) of the tissues tested were positive for at least one HPyV (i.e., MCPyV, HPyV6, HPyV7, BKPyV, JCPyV, or WUyV). Additionally, 25 tissues (45%) were positive for only one HPyV, 14 (25%) for two HPyVs, 3 (5%) for three HPyVs, and 1 one (1%) tissue specimen was positive for four HPyVs. Eleven (20%) RCC specimens were completely devoid of HPyV sequences. MCPyV was found in 24/55 RCC tissues, HPyV7 in 19, and HPyV6 in 8. The presence of MCPyV and HPyV6 was confirmed by specific FISH or RNA-ISH. In addition, we aimed to confirm HPyV gene expression by IHC. Our results strongly indicate that these HPyVs infect RCC and nontumor tissues, possibly indicating that kidney tissues serve as a reservoir for HPyV latency. Whether HPyVs possibly contribute to the etiopathogenesis of RCC remains to be elucidated. [ABSTRACT FROM AUTHOR]

Published
2024
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29. Evaluation of NGS and RT-PCR Methods for ALK Rearrangement in European NSCLC Patients: Results from the European Thoracic Oncology Platform Lungscape Project

Author

Stahel, Rolf A., Rosell, Rafael, Blackhall, Fiona, Dafni, Urania, Kerr, Keith M., Molina, Miguel Ángel, Bubendorf, Lukas, Weder, Walter, Thunnissen, Erik, Peters, Solange, Finn, Stephen, Hiltbrunner, Anita, Kammler, Roswitha, Geiger, Thomas, Marti, Nesa, Tsourti, Zoi, Polydoropoulou, Varvara, Zygoura, Panagiota, Smyth, Paul, O’Brien, Cathal, Gray, Steven, Soltermann, Alex, Opitz, Isabelle, Curioni, Alessandra, Savic, Spasenija, Lardinois, Didier, Dingemans, Anne-Marie, Speel, Ernst-Jan M., Ruland, Andrea, Marchetti, Antonio, Di Lorito, Alessia, De Luca, Graziano, Malatesta, Sara, Nonaka, Daisuke, Quinn, Anne Marie, Franklin, Lynsey, Biernat, Wojciech, Wrona, Ania, Rzyman, Witold, Jassem, Jacek, Meldgaard, Peter, Hager, Henrik, Madsen, Line B., Camps, Carlos, Martorell, Miguel, Jantus-Lewintre, Eloisa, Guijarro, Ricardo, Nicolson, Marianne, Stevenson, David A.J., Mathieson, William, Baas, Paul, de Jong, Jeroen, Monkhorst, Kim, Smit, Egbert, van Setten, Coralien, de Langen, Joop, Felip, Enriqueta, Hernandez-Losa, Javier, Sansano, Irene, Cheney, Richard, Pine, Mary Beth, Reid, Mary, Taylor, Elizabeth, Nackaerts, Kristiaan, Dooms, Christophe, Wauters, Els, Van Der Borght, Sara, Dienemann, Hendrik, Muley, Thomas, Warth, Arne, Letovanec, Igor, Speel, Ernst-Jan, Sejda, Aleksandra, Verbeken, Eric, Navarro, Atilio, Dziadziuszko, Rafal, Vansteenkiste, Johan, O'Brien, Cathal, Sherlock, Jon, Schageman, Jeoffrey, Kerr, Keith, and Stahel, Rolf

Published
2018
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30. Recommendations for the clinical interpretation and reporting of copy number gains using gene panel NGS analysis in routine diagnostics

Author

Eijkelenboom, Astrid, Tops, Bastiaan B. J., van den Berg, Anke, van den Brule, Adrianus J. C., Dinjens, Winand N. M., Dubbink, Hendrikus J., ter Elst, Arja, Geurts-Giele, Willemina R. R., Groenen, Patricia J. T. A., Groenendijk, Floris H., Heideman, Daniëlle A. M., Huibers, Manon M. H., Huijsmans, Cornelis J. J., Jeuken, Judith W. M., van Kempen, Léon C., Korpershoek, Esther, Kroeze, Leonie I., de Leng, Wendy W. J., van Noesel, Carel J. M., Speel, Ernst-Jan M., Vogel, Maartje J., van Wezel, Tom, Nederlof, Petra M., Schuuring, Ed, and Ligtenberg, Marjolijn J. L.

Published
2019
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34. Prevalence and clinical association of MET gene overexpression and amplification in patients with NSCLC: Results from the European Thoracic Oncology Platform (ETOP) Lungscape project

Author

Bubendorf, Lukas, Dafni, Urania, Schöbel, Martin, Finn, Stephen P., Tischler, Verena, Sejda, Aleksandra, Marchetti, Antonio, Thunnissen, Erik, Verbeken, Eric K., Warth, Arne, Sansano, Irene, Cheney, Richard, Speel, Ernst Jan M., Nonaka, Daisuke, Monkhorst, Kim, Hager, Henrik, Martorell, Miguel, Savic, Spasenija, Kerr, Keith M., Tan, Qiang, Tsourti, Zoi, Geiger, Thomas R., Kammler, Roswitha, Schulze, Katja, Das-Gupta, Ashis, Shames, David, Peters, Solange, and Stahel, Rolf A.

Published
2017
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36. Abdominal inflammatory myofibroblastic tumour: Clinicopathological and molecular analysis of 20 cases, highlighting potential therapeutic targets.

Author

Vernemmen, Astrid I P, Samarska, Iryna V, Speel, Ernst‐Jan M, Riedl, Robert G, Goudkade, Danny, de Bruïne, Adriaan P, Wouda, Siep, van Marion, Arienne M, Verlinden, Ivana V, van Lijnschoten, Ineke, Friederich, Pieter, Winnepenninckx, Véronique J L, zur Hausen, Axel, Sciot, Raf M E, and van den Hout, Mari F C M

Subjects
DRUG target, ANAPLASTIC lymphoma kinase, DNA analysis, GENE fusion, RNA analysis, PROTEIN-tyrosine kinases
Abstract

Aims: Inflammatory myofibroblastic tumour (IMT) is a rare mesenchymal neoplasm of intermediate malignant potential, occurring at any age and at multiple sites. Epithelioid inflammatory myofibroblastic sarcoma (EIMS) is an aggressive subtype of IMT, typically involving the abdomen. Most IMTs harbour kinase gene fusions, especially involving ALK and ROS1, but 20–30% of IMTs show no detectable translocations. The aim of this study is to further delineate clinicopathological and molecular characteristics of abdominal IMT and discover potential new therapeutic targets. Methods and results: In 20 IMTs, including four EIMS, RNA fusion analysis was performed, followed by multiplex DNA analysis if no ALK or ROS1 fusion was detected. Fourteen IMTs (70.0%) had an ALK translocation and the fusion partner was identified in 11, including a RRBP1::ALK fusion, not previously described in classical (non‐EIMS) IMT. RANBP2::ALK fusion was demonstrated in all EIMS. One IMT had a ROS1 fusion. In all ALK/ROS1 translocation‐negative IMTs mutations or fusions – as yet unreported in primary IMT – were found in genes related to the receptor tyrosine kinase (RTK)/PI3K/AKT pathway. Three of four patients with EIMS died of disease [mean survival 8 months (4–15 months)], whereas only one of 14 classical IMT patients succumbed to disease [mean follow‐up time 52 months (2–204 months); P < 0.01]. Conclusion: This study shows the wide clinical spectrum of abdominal IMTs and affirms the poor prognosis of EIMS, raising discussion about its status as IMT subtype. Furthermore, the newly detected alterations of the RTK/PI3K/AKT pathway expand the molecular landscape of IMTs and provide potential therapeutic targets. [ABSTRACT FROM AUTHOR]

Published
2024
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37. Predictive Genetic Biomarkers for the Development of Peritoneal Metastases in Colorectal Cancer

Author

Heuvelings, Danique J. I., primary, Wintjens, Anne G. W. E., additional, Moonen, Laura, additional, Engelen, Sanne M. E., additional, de Hingh, Ignace H. J. T., additional, Valkenburg-van Iersel, Liselot B., additional, den Dulk, Marcel, additional, Beckervordersandforth, Jan, additional, Thijssen, Sharon G. M., additional, Leunissen, Daphne J. G., additional, Stassen, Laurents P. S., additional, Keszthelyi, Daniel, additional, Mujagic, Zlatan, additional, Speel, Ernst-Jan M., additional, and Bouvy, Nicole D., additional

Published
2023
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38. Predictive genetic biomarkers for the development of peritoneal metastases in colorectal cancer

Author

Heuvelings, Danique J.I., primary, Wintjens, Anne G.W.E, additional, Moonen, Laura, additional, Engelen, Sanne M.E., additional, Iersel, Liselot B. Valkenburg - van, additional, Dulk, Marcel Den, additional, Beckervordersandforth, Jan, additional, Thijssen, Sharon G.M., additional, Leunissen, Daphne J.G., additional, Stassen, Laurents P.S., additional, Keszthelyi, Daniel, additional, de Hingh, Ignace H.J.T., additional, Mujagic, Zlatan, additional, Speel, Ernst-Jan M., additional, and Bouvy, Nicole D., additional

Published
2023
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39. Association of RANKL and EGFR gene expression with bone metastases in patients with metastatic non-small cell lung cancer

Author

Brouns, Anita J.W.M., Hendriks, Lizza E.L., Robbesom-van den Berge, Iris J., Driessen, Annemariek J.H.M., Roemen, Guido M.J.M., van Herpen, Britt L.J., Dekkers, Zoë, Heitzer, Bas, Leunissen, Daphne J.G., Moonen, Laura, Lunde, Ragnar, Westenend, Marcel, van Driel, Marjolein, Speel, Ernst Jan M., Dingemans, Anne Marie C., Brouns, Anita J.W.M., Hendriks, Lizza E.L., Robbesom-van den Berge, Iris J., Driessen, Annemariek J.H.M., Roemen, Guido M.J.M., van Herpen, Britt L.J., Dekkers, Zoë, Heitzer, Bas, Leunissen, Daphne J.G., Moonen, Laura, Lunde, Ragnar, Westenend, Marcel, van Driel, Marjolein, Speel, Ernst Jan M., and Dingemans, Anne Marie C.

Published
2023

40. Molecular mechanism of extracutaneous tumours in patients with basal cell nevus syndrome

Author

Verkouteren, Babette Ja, Roemen, Guido Mjm, Schuurs-Hoeijmakers, Janneke Hm, Abdul Hamid, Myrurgia, van Geel, Michel, Speel, Ernst-Jan M, Mosterd, Klara, Verkouteren, Babette Ja, Roemen, Guido Mjm, Schuurs-Hoeijmakers, Janneke Hm, Abdul Hamid, Myrurgia, van Geel, Michel, Speel, Ernst-Jan M, and Mosterd, Klara

Abstract

Basal cell nevus syndrome (BCNS) is a rare genetic disorder accompanied by a broad variety of tumours, of which basal cell carcinomas and odontogenic keratocysts are the most common. BCNS is caused by a germline or postzygotic mutation in either PTCH1 or SUFU As BCNS is a rare disease, it is difficult to establish whether less frequently occurring tumours are actually part of the syndrome. In this study, the molecular mechanism behind four extracutaneous tumours in patients with BCNS was elucidated. A leiomyoma of the testis and meningioma were confirmed to be associated with BCNS in two patients by presence of a second mutation or loss of heterozygosity in PTCH1 In a meningioma of a patient with a mosaic postzygotic PTCH1 mutation an association could not be conclusively confirmed. SUFU was probably not involved in the development of a thyroid carcinoma in a patient with a germline SUFU mutation. Hence, we have proven that meningioma and leiomyoma of the testis are rare extracutaneous tumours that are part of BCNS.

Published
2023

41. Association of RANKL and EGFR gene expression with bone metastases in patients with metastatic non-small cell lung cancer

Author

Brouns, Anita J.W.M., primary, Hendriks, Lizza E.L., additional, Robbesom-van den Berge, Iris J., additional, Driessen, Annemariek J.H.M., additional, Roemen, Guido M.J.M., additional, van Herpen, Britt L.J., additional, Dekkers, Zoë, additional, Heitzer, Bas, additional, Leunissen, Daphne J.G., additional, Moonen, Laura, additional, Lunde, Ragnar, additional, Westenend, Marcel, additional, van Driel, Marjolein, additional, Speel, Ernst-Jan M., additional, and Dingemans, Anne-Marie C., additional

Published
2023
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42. Figure S1 from Molecular Subtypes of Pulmonary Large-cell Neuroendocrine Carcinoma Predict Chemotherapy Treatment Outcome

Author

Derks, Jules L., primary, Leblay, Noémie, primary, Thunnissen, Erik, primary, van Suylen, Robert Jan, primary, den Bakker, Michael, primary, Groen, Harry J.M., primary, Smit, Egbert F., primary, Damhuis, Ronald, primary, van den Broek, Esther C., primary, Charbrier, Amélie, primary, Foll, Matthieu, primary, McKay, James D., primary, Fernandez-Cuesta, Lynnette, primary, Speel, Ernst-Jan M., primary, and Dingemans, Anne-Marie C., primary

Published
2023
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43. Supplementary Figure Legends from CD44 and OTP Are Strong Prognostic Markers for Pulmonary Carcinoids

Author

Swarts, Dorian R.A., primary, Henfling, Mieke E.R., primary, Van Neste, Leander, primary, van Suylen, Robert-Jan, primary, Dingemans, Anne-Marie C., primary, Dinjens, Winand N.M., primary, Haesevoets, Annick, primary, Rudelius, Martina, primary, Thunnissen, Erik, primary, Volante, Marco, primary, Van Criekinge, Wim, primary, van Engeland, Manon, primary, Ramaekers, Frans C.S., primary, and Speel, Ernst-Jan M., primary

Published
2023
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44. Supplementary Methods from CD44 and OTP Are Strong Prognostic Markers for Pulmonary Carcinoids

Author

Swarts, Dorian R.A., primary, Henfling, Mieke E.R., primary, Van Neste, Leander, primary, van Suylen, Robert-Jan, primary, Dingemans, Anne-Marie C., primary, Dinjens, Winand N.M., primary, Haesevoets, Annick, primary, Rudelius, Martina, primary, Thunnissen, Erik, primary, Volante, Marco, primary, Van Criekinge, Wim, primary, van Engeland, Manon, primary, Ramaekers, Frans C.S., primary, and Speel, Ernst-Jan M., primary

Published
2023
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45. Supplementary Figure 2 from CD44 and OTP Are Strong Prognostic Markers for Pulmonary Carcinoids

Author

Swarts, Dorian R.A., primary, Henfling, Mieke E.R., primary, Van Neste, Leander, primary, van Suylen, Robert-Jan, primary, Dingemans, Anne-Marie C., primary, Dinjens, Winand N.M., primary, Haesevoets, Annick, primary, Rudelius, Martina, primary, Thunnissen, Erik, primary, Volante, Marco, primary, Van Criekinge, Wim, primary, van Engeland, Manon, primary, Ramaekers, Frans C.S., primary, and Speel, Ernst-Jan M., primary

Published
2023
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46. Table S1 from Molecular Subtypes of Pulmonary Large-cell Neuroendocrine Carcinoma Predict Chemotherapy Treatment Outcome

Author

Derks, Jules L., primary, Leblay, Noémie, primary, Thunnissen, Erik, primary, van Suylen, Robert Jan, primary, den Bakker, Michael, primary, Groen, Harry J.M., primary, Smit, Egbert F., primary, Damhuis, Ronald, primary, van den Broek, Esther C., primary, Charbrier, Amélie, primary, Foll, Matthieu, primary, McKay, James D., primary, Fernandez-Cuesta, Lynnette, primary, Speel, Ernst-Jan M., primary, and Dingemans, Anne-Marie C., primary

Published
2023
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47. Supplementary Figure 1 from CD44 and OTP Are Strong Prognostic Markers for Pulmonary Carcinoids

Author

Swarts, Dorian R.A., primary, Henfling, Mieke E.R., primary, Van Neste, Leander, primary, van Suylen, Robert-Jan, primary, Dingemans, Anne-Marie C., primary, Dinjens, Winand N.M., primary, Haesevoets, Annick, primary, Rudelius, Martina, primary, Thunnissen, Erik, primary, Volante, Marco, primary, Van Criekinge, Wim, primary, van Engeland, Manon, primary, Ramaekers, Frans C.S., primary, and Speel, Ernst-Jan M., primary

Published
2023
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48. Supplementary Figure 3 from CD44 and OTP Are Strong Prognostic Markers for Pulmonary Carcinoids

Author

Swarts, Dorian R.A., primary, Henfling, Mieke E.R., primary, Van Neste, Leander, primary, van Suylen, Robert-Jan, primary, Dingemans, Anne-Marie C., primary, Dinjens, Winand N.M., primary, Haesevoets, Annick, primary, Rudelius, Martina, primary, Thunnissen, Erik, primary, Volante, Marco, primary, Van Criekinge, Wim, primary, van Engeland, Manon, primary, Ramaekers, Frans C.S., primary, and Speel, Ernst-Jan M., primary

Published
2023
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49. Supplementary data file from Molecular Subtypes of Pulmonary Large-cell Neuroendocrine Carcinoma Predict Chemotherapy Treatment Outcome

Author

Derks, Jules L., primary, Leblay, Noémie, primary, Thunnissen, Erik, primary, van Suylen, Robert Jan, primary, den Bakker, Michael, primary, Groen, Harry J.M., primary, Smit, Egbert F., primary, Damhuis, Ronald, primary, van den Broek, Esther C., primary, Charbrier, Amélie, primary, Foll, Matthieu, primary, McKay, James D., primary, Fernandez-Cuesta, Lynnette, primary, Speel, Ernst-Jan M., primary, and Dingemans, Anne-Marie C., primary

Published
2023
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50. Supplemental legend from Molecular Subtypes of Pulmonary Large-cell Neuroendocrine Carcinoma Predict Chemotherapy Treatment Outcome

Author

Derks, Jules L., primary, Leblay, Noémie, primary, Thunnissen, Erik, primary, van Suylen, Robert Jan, primary, den Bakker, Michael, primary, Groen, Harry J.M., primary, Smit, Egbert F., primary, Damhuis, Ronald, primary, van den Broek, Esther C., primary, Charbrier, Amélie, primary, Foll, Matthieu, primary, McKay, James D., primary, Fernandez-Cuesta, Lynnette, primary, Speel, Ernst-Jan M., primary, and Dingemans, Anne-Marie C., primary

Published
2023
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