21 results on '"Ramaker, Jip"'
Search Results
2. The landscape of cell-free mitochondrial DNA in liquid biopsy for cancer detection
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van der Pol, Ymke, Moldovan, Norbert, Ramaker, Jip, Bootsma, Sanne, Lenos, Kristiaan J., Vermeulen, Louis, Sandhu, Shahneen, Bahce, Idris, Pegtel, D. Michiel, Wong, Stephen Q., Dawson, Sarah-Jane, Chandrananda, Dineika, and Mouliere, Florent
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- 2023
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3. Multi-modal cell-free DNA genomic and fragmentomic patterns enhance cancer survival and recurrence analysis
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Moldovan, Norbert, van der Pol, Ymke, van den Ende, Tom, Boers, Dries, Verkuijlen, Sandra, Creemers, Aafke, Ramaker, Jip, Vu, Trang, Bootsma, Sanne, Lenos, Kristiaan J., Vermeulen, Louis, Fransen, Marieke F., Pegtel, Michiel, Bahce, Idris, van Laarhoven, Hanneke, and Mouliere, Florent
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- 2024
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4. Platelet RNA sequencing for cancer screening in patients with unprovoked venous thromboembolism: a prospective cohort study
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Mulder, Frits I., Kraaijpoel, Noémie, Carrier, Marc, Guman, Noori A., Jara-Palomares, Luis, Di Nisio, Marcello, Ageno, Walter, Beyer-Westendorf, Jan, Klok, Frederikus A., Vanassche, Thomas, Otten, Hans-Martin B., Cosmi, Benilde, Wolde, Marije ten, In ‘t Veld, Sjors G.J. G., Post, Edward, Ramaker, Jip, Zwaan, Kenn, Peters, Mike, Delluc, Aurélien, Kamphuisen, Pieter W., Sanchez-Lopez, Veronica, Porreca, Ettore, Bossuyt, Patrick M.M., Büller, Harry R., Wurdinger, Thomas, Best, Myron G., and van Es, Nick
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- 2023
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5. Towards IVDR‐compliance by implementing quality control steps in a quantitative extracellular vesicle‐miRNA liquid biopsy assay for response monitoring in patients with classic Hodgkin lymphoma.
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Drees, Esther E. E., Groenewegen, Nils J., Verkuijlen, Sandra A. W. M., van Eijndhoven, Monique A. J., Ramaker, Jip, Veenstra, Pepijn, Hussain, Mirjam, Groothuis‐Oudshoorn, Catharina G. M., de Jong, Daphne, Zijlstra, Josée M., de Rooij, Johan, and Pegtel, D. Michiel
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HODGKIN'S disease ,QUALITY control ,PATIENT monitoring ,EXTRACELLULAR vesicles ,BIOPSY - Abstract
Previously, we showed that quantification of lymphoma‐associated miRNAs miR‐155‐5p, ‐127‐3p and let‐7a‐5p levels in plasma extracellular vesicles (EVs) report treatment response in patients with classic Hodgkin lymphoma (cHL). Prior to clinical implementation, quality control (QC) steps and validation are required to meet international regulatory standards. Most published EV‐based diagnostic assays have yet to meet these requirements. In order to advance the assay towards regulatory compliance (e.g., IVDR 2017/746), we incorporated three QC steps in our experimental EV‐miRNA quantitative real‐time reverse‐transcription PCR (q‐RT‐PCR) assay in an ISO‐13485 certified quality‐management system (QMS). Liposomes encapsulated with a synthetic (nematode‐derived) miRNA spike‐in controlled for EV isolation by automated size‐exclusion chromatography (SEC). Additional miRNA spike‐ins controlled for RNA isolation and cDNA conversion efficiency. After deciding on quality criteria, in total 107 out of 120 samples from 46 patients passed QC. Generalized linear mixed‐effect modelling with bootstrapping determined the diagnostic performance of the quality‐controlled data at an area under the curve (AUC) of 0.84 (confidence interval [CI]: 0.76–0.92) compared to an AUC of 0.87 (CI: 0.80–0.94) of the experimental assay. After the inclusion of QC steps, the accuracy of the assay was determined to be 78.5% in predicting active disease status in cHL patients during treatment. We demonstrate that a quality‐controlled plasma EV‐miRNA assay is technically robust, taking EV‐miRNA as liquid biopsy assay an important step closer to clinical evaluation. [ABSTRACT FROM AUTHOR]
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- 2024
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6. Tumor-Educated Platelet RNA for the Detection and (Pseudo)progression Monitoring of Glioblastoma
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Sol, Nik, in ‘t Veld, Sjors G.J.G., Vancura, Adrienne, Tjerkstra, Maud, Leurs, Cyra, Rustenburg, François, Schellen, Pepijn, Verschueren, Heleen, Post, Edward, Zwaan, Kenn, Ramaker, Jip, Wedekind, Laurine E., Tannous, Jihane, Ylstra, Bauke, Killestein, Joep, Mateen, Farrah, Idema, Sander, de Witt Hamer, Philip C., Navis, Anna C., Leenders, William P.J., Hoeben, Ann, Moraal, Bastiaan, Noske, David P., Vandertop, W. Peter, Nilsson, R. Jonas A., Tannous, Bakhos A., Wesseling, Pieter, Reijneveld, Jaap C., Best, Myron G., and Wurdinger, Thomas
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- 2020
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7. Multi-modal cell-free DNA genomic and fragmentomic patterns enhance cancer survival and recurrence analysis
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Moldovan, Norbert, primary, van der Pol, Ymke, additional, van den Ende, Tom, additional, Boers, Dries, additional, Verkuijlen, Sandra, additional, Creemers, Aafke, additional, Ramaker, Jip, additional, Vu, Trang, additional, Bootsma, Sanne, additional, Lenos, Kristiaan J., additional, Vermeulen, Louis, additional, Fransen, Marieke F., additional, Pegtel, Michiel, additional, Bahce, Idris, additional, van Laarhoven, Hanneke, additional, and Mouliere, Florent, additional
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- 2023
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8. Tumor-educated platelet blood tests for Non-Small Cell Lung Cancer detection and management
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Antunes-Ferreira, Mafalda, D’Ambrosi, Silvia, Arkani, Mohammad, Post, Edward, in ‘t Veld, Sjors G. J. G., Ramaker, Jip, Zwaan, Kenn, Kucukguzel, Ece Demirel, Wedekind, Laurine E., Griffioen, Arjan W., Oude Egbrink, Mirjam, Kuijpers, Marijke J. E., van den Broek, Daan, Noske, David P., Hartemink, Koen J., Sabrkhany, Siamack, Bahce, Idris, Sol, Nik, Bogaard, Harm-Jan, Koppers-Lalic, Danijela, Best, Myron G., Wurdinger, Thomas, Neurosurgery, Pulmonary medicine, Medical oncology laboratory, AII - Cancer immunology, CCA - Cancer biology and immunology, CCA - Cancer Treatment and quality of life, ACS - Pulmonary hypertension & thrombosis, CCA - Imaging and biomarkers, and CCA - Cancer immunology
- Abstract
Liquid biopsy approaches offer a promising technology for early and minimally invasive cancer detection. Tumor-educated platelets (TEPs) have emerged as a promising liquid biopsy biosource for the detection of various cancer types. In this study, we processed and analyzed the TEPs collected from 466 Non-small Cell Lung Carcinoma (NSCLC) patients and 410 asymptomatic individuals (controls) using the previously established thromboSeq protocol. We developed a novel particle-swarm optimization machine learning algorithm which enabled the selection of an 881 RNA biomarker panel (AUC 0.88). Herein we propose and validate in an independent cohort of samples (n = 558) two approaches for blood samples testing: one with high sensitivity (95% NSCLC detected) and another with high specificity (94% controls detected). Our data explain how TEP-derived spliced RNAs may serve as a biomarker for minimally-invasive clinical blood tests, complement existing imaging tests, and assist the detection and management of lung cancer patients.
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- 2023
9. Discrimination Between Pre‐ and Postcapillary Pulmonary Hypertension Using Platelet RNA
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Arkani, Mohammad, primary, Kianzad, Azar, additional, Jansen, Samara, additional, Smit, Josien, additional, Post, Edward, additional, Ramaker, Jip, additional, Lagerweij, Tonny, additional, In’t Veld, Sjors G. J. G., additional, Noske, David P., additional, Vonk Noordegraaf, Anton, additional, Wurdinger, Thomas, additional, Best, Myron G., additional, and Bogaard, Harm‐Jan, additional
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- 2023
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10. Distinct Platelet Ribonucleic Acid Signatures in Patients with Pulmonary Hypertension
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Smits, A. Josien, primary, Arkani, Mohammad, additional, In ’t Veld, Sjors G.J.G., additional, Huis in ‘t Veld, Anna E., additional, Sol, Nik, additional, Groeneveldt, Joanne A., additional, Botros, Liza, additional, Braams, Natalia J., additional, Jansen, Samara M.A., additional, Ramaker, Jip, additional, Zwaan, Kenn, additional, Post, Edward, additional, Nossent, Esther J., additional, Boonstra, Anco, additional, de Man, Frances S., additional, Noordegraaf, Anton Vonk, additional, Gomez-Arroyo, Jose, additional, Best, Myron G., additional, Wurdinger, Tom, additional, and Bogaard, Harm Jan, additional
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- 2022
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11. Detection and localization of early- and late-stage cancers using platelet RNA
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In ’t Veld, Sjors G.J.G., primary, Arkani, Mohammad, additional, Post, Edward, additional, Antunes-Ferreira, Mafalda, additional, D’Ambrosi, Silvia, additional, Vessies, Daan C.L., additional, Vermunt, Lisa, additional, Vancura, Adrienne, additional, Muller, Mirte, additional, Niemeijer, Anna-Larissa N., additional, Tannous, Jihane, additional, Meijer, Laura L., additional, Le Large, Tessa Y.S., additional, Mantini, Giulia, additional, Wondergem, Niels E., additional, Heinhuis, Kimberley M., additional, van Wilpe, Sandra, additional, Smits, A. Josien, additional, Drees, Esther E.E., additional, Roos, Eva, additional, Leurs, Cyra E., additional, Tjon Kon Fat, Lee-Ann, additional, van der Lelij, Ewoud J., additional, Dwarshuis, Govert, additional, Kamphuis, Maarten J., additional, Visser, Lisanne E., additional, Harting, Romee, additional, Gregory, Annemijn, additional, Schweiger, Markus W., additional, Wedekind, Laurine E., additional, Ramaker, Jip, additional, Zwaan, Kenn, additional, Verschueren, Heleen, additional, Bahce, Idris, additional, de Langen, Adrianus J., additional, Smit, Egbert F., additional, van den Heuvel, Michel M., additional, Hartemink, Koen J., additional, Kuijpers, Marijke J.E., additional, oude Egbrink, Mirjam G.A., additional, Griffioen, Arjan W., additional, Rossel, Rafael, additional, Hiltermann, T. Jeroen N., additional, Lee-Lewandrowski, Elizabeth, additional, Lewandrowski, Kent B., additional, De Witt Hamer, Philip C., additional, Kouwenhoven, Mathilde, additional, Reijneveld, Jaap C., additional, Leenders, William P.J., additional, Hoeben, Ann, additional, Verdonck-de Leeuw, Irma M., additional, Leemans, C. René, additional, Baatenburg de Jong, Robert J., additional, Terhaard, Chris H.J., additional, Takes, Robert P., additional, Langendijk, Johannes A., additional, de Jager, Saskia C., additional, Kraaijeveld, Adriaan O., additional, Pasterkamp, Gerard, additional, Smits, Minke, additional, Schalken, Jack A., additional, Łapińska-Szumczyk, Sylwia, additional, Łojkowska, Anna, additional, Żaczek, Anna J., additional, Lokhorst, Henk, additional, van de Donk, Niels W.C.J., additional, Nijhof, Inger, additional, Prins, Henk-Jan, additional, Zijlstra, Josée M., additional, Idema, Sander, additional, Baayen, Johannes C., additional, Teunissen, Charlotte E., additional, Killestein, Joep, additional, Besselink, Marc G., additional, Brammen, Lindsay, additional, Bachleitner-Hofmann, Thomas, additional, Mateen, Farrah, additional, Plukker, John T.M., additional, Heger, Michal, additional, de Mast, Quirijn, additional, Lisman, Ton, additional, Pegtel, D. Michiel, additional, Bogaard, Harm-Jan, additional, Jassem, Jacek, additional, Supernat, Anna, additional, Mehra, Niven, additional, Gerritsen, Winald, additional, de Kroon, Cornelis D., additional, Lok, Christianne A.R., additional, Piek, Jurgen M.J., additional, Steeghs, Neeltje, additional, van Houdt, Winan J., additional, Brakenhoff, Ruud H., additional, Sonke, Gabe S., additional, Verheul, Henk M., additional, Giovannetti, Elisa, additional, Kazemier, Geert, additional, Sabrkhany, Siamack, additional, Schuuring, Ed, additional, Sistermans, Erik A., additional, Wolthuis, Rob, additional, Meijers-Heijboer, Hanne, additional, Dorsman, Josephine, additional, Oudejans, Cees, additional, Ylstra, Bauke, additional, Westerman, Bart A., additional, van den Broek, Daan, additional, Koppers-Lalic, Danijela, additional, Wesseling, Pieter, additional, Nilsson, R. Jonas A., additional, Vandertop, W. Peter, additional, Noske, David P., additional, Tannous, Bakhos A., additional, Sol, Nik, additional, Best, Myron G., additional, and Wurdinger, Thomas, additional
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- 2022
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12. Real-time analysis of the cancer genome and fragmentome from plasma and urine short and long cell-free DNA using Nanopore sequencing
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van der Pol, Ymke, primary, Tantyo, Normastuti Adhini, additional, Evander, Nils, additional, Hentschel, Anouk E., additional, Ramaker, Jip, additional, Bahce, Idris, additional, Nieuwenhuijzen, Jakko A., additional, Steenbergen, Renske D.M., additional, Pegtel, D. Michiel, additional, Moldovan, Norbert, additional, and Mouliere, Florent, additional
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- 2022
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13. Distinct Platelet RNA Signatures in Patients with Pulmonary Hypertension
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Smits, A Josien, Arkani, Mohammad, In 't Veld, Sjors G J G, Huis In 't Veld, Anna E, Sol, Nik, Groeneveldt, Joanne A, Botros, Liza, Braams, Natalia J, Jansen, Samara Ma, Ramaker, Jip, Zwaan, Kenn, Post, Edward, Nossent, Esther J, Boonstra, Anco, de Man, Frances S, Vonk Noordegraaf, Anton, Gomez-Arroyo, Jose, Best, Myron G, Wurdinger, Tom, Bogaard, Harm Jan, Pulmonology, and Neurosurgery
- Abstract
RATIONALE: Pulmonary hypertension encompasses progressive disorders leading to right ventricular dysfunction and early death. Late detection is an important cause of poor clinical outcomes. However, biomarkers that accurately predict the presence of pulmonary hypertension are currently lacking. OBJECTIVES: In this study we provide evidence that blood platelets contain a distinctive RNA profile that may be exploited for detection of pulmonary hypertension. METHODS: Blood platelet RNA was isolated prospectively from 177 prevalent patients with different subtypes of pulmonary hypertension as well as 195 controls clinically not suspected of pulmonary hypertension. Sequencing libraries were created using SMARTer cDNA amplification, and sequenced on the Illumina HiSeq platform. RNA-sequencing reads were mapped to the human reference genome, and intron-spanning spliced RNA reads were selected. Differential spliced RNA panels were calculated by ANOVA-statistics. A particle swarm optimisation (PSO)-enhanced classification algorithm was built employing a development (n=213 samples) and independent validation series (n=159 samples). RESULTS: We detected a total of 4014 different RNAs in blood platelets from pulmonary hypertension patients (n=177) and asymptomatic controls (n=195). GSEA gene ontology analysis revealed enriched RNA levels for genes related to RNA-processing, translation and mitochondrial function. A PSO-selected RNA panel of 408 distinctive differentially spliced RNAs mediated detection of pulmonary hypertension with 93% sensitivity, 62% specificity, 77% accuracy, 0.89 (95%CI 0.83-0.93) area under the curve and a negative predictive value of 91% in the independent validation series. Prediction score was independent of age, sex, smoking, pulmonary hypertension subtype, and the use of pulmonary hypertension-specific medication or anti-coagulants. CONCLUSION: A platelet RNA-panel may accurately discriminate patients with pulmonary hypertension from asymptomatic controls. In the light of current diagnostic delays, this study is the starting point for further development and evaluation of a platelet RNA-based blood test, to ultimately improve early diagnosis and clinical outcomes in patients with pulmonary hypertension.
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- 2022
14. Detection and localization of early- and late-stage cancers using platelet RNA
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In ’t Veld, Sjors G.J.G., Arkani, Mohammad, Post, Edward, Antunes-Ferreira, Mafalda, D'Ambrosi, Silvia, Vessies, Daan C.L., Vermunt, Lisa, Vancura, Adrienne, Muller, Mirte, Niemeijer, Anna Larissa N., Tannous, Jihane, Meijer, Laura L., Le Large, Tessa Y.S., Mantini, Giulia, Wondergem, Niels E., Heinhuis, Kimberley M., van Wilpe, Sandra, Smits, A. Josien, Drees, Esther E.E., Roos, Eva, Leurs, Cyra E., Tjon Kon Fat, Lee Ann, van der Lelij, Ewoud J., Dwarshuis, Govert, Kamphuis, Maarten J., Visser, Lisanne E., Harting, Romee, Gregory, Annemijn, Schweiger, Markus W., Wedekind, Laurine E., Ramaker, Jip, Zwaan, Kenn, Verschueren, Heleen, Bahce, Idris, de Langen, Adrianus J., Smit, Egbert F., van den Heuvel, Michel M., Hartemink, Koen J., Kuijpers, Marijke J.E., oude Egbrink, Mirjam G.A., Griffioen, Arjan W., Rossel, Rafael, Hiltermann, T. Jeroen N., Lee-Lewandrowski, Elizabeth, Lewandrowski, Kent B., De Witt Hamer, Philip C., Kouwenhoven, Mathilde, Reijneveld, Jaap C., Leenders, William P.J., Hoeben, Ann, Verdonck-de Leeuw, Irma M., Leemans, C. René, Baatenburg de Jong, Robert J., Terhaard, Chris H.J., Takes, Robert P., Langendijk, Johannes A., de Jager, Saskia C., Kraaijeveld, Adriaan O., Pasterkamp, Gerard, Smits, Minke, Schalken, Jack A., Łapińska-Szumczyk, Sylwia, Łojkowska, Anna, Żaczek, Anna J., Lokhorst, Henk, van de Donk, Niels W.C.J., Nijhof, Inger, Prins, Henk Jan, Zijlstra, Josée M., Idema, Sander, Baayen, Johannes C., Teunissen, Charlotte E., Killestein, Joep, Besselink, Marc G., Brammen, Lindsay, Bachleitner-Hofmann, Thomas, Mateen, Farrah, Plukker, John T.M., Heger, Michal, de Mast, Quirijn, Lisman, Ton, Pegtel, D. Michiel, Bogaard, Harm Jan, Jassem, Jacek, Supernat, Anna, Mehra, Niven, Gerritsen, Winald, de Kroon, Cornelis D., Lok, Christianne A.R., Piek, Jurgen M.J., Steeghs, Neeltje, van Houdt, Winan J., Brakenhoff, Ruud H., Sonke, Gabe S., Verheul, Henk M., Giovannetti, Elisa, Kazemier, Geert, Sabrkhany, Siamack, Schuuring, Ed, Sistermans, Erik A., Wolthuis, Rob, Meijers-Heijboer, Hanne, Dorsman, Josephine, Oudejans, Cees, Ylstra, Bauke, Westerman, Bart A., van den Broek, Daan, Koppers-Lalic, Danijela, Wesseling, Pieter, Nilsson, R. Jonas A., Vandertop, W. Peter, Noske, David P., Tannous, Bakhos A., Sol, Nik, Best, Myron G., Wurdinger, Thomas, In ’t Veld, Sjors G.J.G., Arkani, Mohammad, Post, Edward, Antunes-Ferreira, Mafalda, D'Ambrosi, Silvia, Vessies, Daan C.L., Vermunt, Lisa, Vancura, Adrienne, Muller, Mirte, Niemeijer, Anna Larissa N., Tannous, Jihane, Meijer, Laura L., Le Large, Tessa Y.S., Mantini, Giulia, Wondergem, Niels E., Heinhuis, Kimberley M., van Wilpe, Sandra, Smits, A. Josien, Drees, Esther E.E., Roos, Eva, Leurs, Cyra E., Tjon Kon Fat, Lee Ann, van der Lelij, Ewoud J., Dwarshuis, Govert, Kamphuis, Maarten J., Visser, Lisanne E., Harting, Romee, Gregory, Annemijn, Schweiger, Markus W., Wedekind, Laurine E., Ramaker, Jip, Zwaan, Kenn, Verschueren, Heleen, Bahce, Idris, de Langen, Adrianus J., Smit, Egbert F., van den Heuvel, Michel M., Hartemink, Koen J., Kuijpers, Marijke J.E., oude Egbrink, Mirjam G.A., Griffioen, Arjan W., Rossel, Rafael, Hiltermann, T. Jeroen N., Lee-Lewandrowski, Elizabeth, Lewandrowski, Kent B., De Witt Hamer, Philip C., Kouwenhoven, Mathilde, Reijneveld, Jaap C., Leenders, William P.J., Hoeben, Ann, Verdonck-de Leeuw, Irma M., Leemans, C. René, Baatenburg de Jong, Robert J., Terhaard, Chris H.J., Takes, Robert P., Langendijk, Johannes A., de Jager, Saskia C., Kraaijeveld, Adriaan O., Pasterkamp, Gerard, Smits, Minke, Schalken, Jack A., Łapińska-Szumczyk, Sylwia, Łojkowska, Anna, Żaczek, Anna J., Lokhorst, Henk, van de Donk, Niels W.C.J., Nijhof, Inger, Prins, Henk Jan, Zijlstra, Josée M., Idema, Sander, Baayen, Johannes C., Teunissen, Charlotte E., Killestein, Joep, Besselink, Marc G., Brammen, Lindsay, Bachleitner-Hofmann, Thomas, Mateen, Farrah, Plukker, John T.M., Heger, Michal, de Mast, Quirijn, Lisman, Ton, Pegtel, D. Michiel, Bogaard, Harm Jan, Jassem, Jacek, Supernat, Anna, Mehra, Niven, Gerritsen, Winald, de Kroon, Cornelis D., Lok, Christianne A.R., Piek, Jurgen M.J., Steeghs, Neeltje, van Houdt, Winan J., Brakenhoff, Ruud H., Sonke, Gabe S., Verheul, Henk M., Giovannetti, Elisa, Kazemier, Geert, Sabrkhany, Siamack, Schuuring, Ed, Sistermans, Erik A., Wolthuis, Rob, Meijers-Heijboer, Hanne, Dorsman, Josephine, Oudejans, Cees, Ylstra, Bauke, Westerman, Bart A., van den Broek, Daan, Koppers-Lalic, Danijela, Wesseling, Pieter, Nilsson, R. Jonas A., Vandertop, W. Peter, Noske, David P., Tannous, Bakhos A., Sol, Nik, Best, Myron G., and Wurdinger, Thomas
- Abstract
Cancer patients benefit from early tumor detection since treatment outcomes are more favorable for less advanced cancers. Platelets are involved in cancer progression and are considered a promising biosource for cancer detection, as they alter their RNA content upon local and systemic cues. We show that tumor-educated platelet (TEP) RNA-based blood tests enable the detection of 18 cancer types. With 99% specificity in asymptomatic controls, thromboSeq correctly detected the presence of cancer in two-thirds of 1,096 blood samples from stage I–IV cancer patients and in half of 352 stage I–III tumors. Symptomatic controls, including inflammatory and cardiovascular diseases, and benign tumors had increased false-positive test results with an average specificity of 78%. Moreover, thromboSeq determined the tumor site of origin in five different tumor types correctly in over 80% of the cancer patients. These results highlight the potential properties of TEP-derived RNA panels to supplement current approaches for blood-based cancer screening.
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- 2022
15. Detection and localization of early- and late-stage cancers using platelet RNA
- Author
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Pharmaceutics, Sub Membrane Biochemistry & Biophysics, Afd Pharmaceutics, In ’t Veld, Sjors G.J.G., Arkani, Mohammad, Post, Edward, Antunes-Ferreira, Mafalda, D'Ambrosi, Silvia, Vessies, Daan C.L., Vermunt, Lisa, Vancura, Adrienne, Muller, Mirte, Niemeijer, Anna Larissa N., Tannous, Jihane, Meijer, Laura L., Le Large, Tessa Y.S., Mantini, Giulia, Wondergem, Niels E., Heinhuis, Kimberley M., van Wilpe, Sandra, Smits, A. Josien, Drees, Esther E.E., Roos, Eva, Leurs, Cyra E., Tjon Kon Fat, Lee Ann, van der Lelij, Ewoud J., Dwarshuis, Govert, Kamphuis, Maarten J., Visser, Lisanne E., Harting, Romee, Gregory, Annemijn, Schweiger, Markus W., Wedekind, Laurine E., Ramaker, Jip, Zwaan, Kenn, Verschueren, Heleen, Bahce, Idris, de Langen, Adrianus J., Smit, Egbert F., van den Heuvel, Michel M., Hartemink, Koen J., Kuijpers, Marijke J.E., oude Egbrink, Mirjam G.A., Griffioen, Arjan W., Rossel, Rafael, Hiltermann, T. Jeroen N., Lee-Lewandrowski, Elizabeth, Lewandrowski, Kent B., De Witt Hamer, Philip C., Kouwenhoven, Mathilde, Reijneveld, Jaap C., Leenders, William P.J., Hoeben, Ann, Verdonck-de Leeuw, Irma M., Leemans, C. René, Baatenburg de Jong, Robert J., Terhaard, Chris H.J., Takes, Robert P., Langendijk, Johannes A., de Jager, Saskia C., Kraaijeveld, Adriaan O., Pasterkamp, Gerard, Smits, Minke, Schalken, Jack A., Łapińska-Szumczyk, Sylwia, Łojkowska, Anna, Żaczek, Anna J., Lokhorst, Henk, van de Donk, Niels W.C.J., Nijhof, Inger, Prins, Henk Jan, Zijlstra, Josée M., Idema, Sander, Baayen, Johannes C., Teunissen, Charlotte E., Killestein, Joep, Besselink, Marc G., Brammen, Lindsay, Bachleitner-Hofmann, Thomas, Mateen, Farrah, Plukker, John T.M., Heger, Michal, de Mast, Quirijn, Lisman, Ton, Pegtel, D. Michiel, Bogaard, Harm Jan, Jassem, Jacek, Supernat, Anna, Mehra, Niven, Gerritsen, Winald, de Kroon, Cornelis D., Lok, Christianne A.R., Piek, Jurgen M.J., Steeghs, Neeltje, van Houdt, Winan J., Brakenhoff, Ruud H., Sonke, Gabe S., Verheul, Henk M., Giovannetti, Elisa, Kazemier, Geert, Sabrkhany, Siamack, Schuuring, Ed, Sistermans, Erik A., Wolthuis, Rob, Meijers-Heijboer, Hanne, Dorsman, Josephine, Oudejans, Cees, Ylstra, Bauke, Westerman, Bart A., van den Broek, Daan, Koppers-Lalic, Danijela, Wesseling, Pieter, Nilsson, R. Jonas A., Vandertop, W. Peter, Noske, David P., Tannous, Bakhos A., Sol, Nik, Best, Myron G., Wurdinger, Thomas, Pharmaceutics, Sub Membrane Biochemistry & Biophysics, Afd Pharmaceutics, In ’t Veld, Sjors G.J.G., Arkani, Mohammad, Post, Edward, Antunes-Ferreira, Mafalda, D'Ambrosi, Silvia, Vessies, Daan C.L., Vermunt, Lisa, Vancura, Adrienne, Muller, Mirte, Niemeijer, Anna Larissa N., Tannous, Jihane, Meijer, Laura L., Le Large, Tessa Y.S., Mantini, Giulia, Wondergem, Niels E., Heinhuis, Kimberley M., van Wilpe, Sandra, Smits, A. Josien, Drees, Esther E.E., Roos, Eva, Leurs, Cyra E., Tjon Kon Fat, Lee Ann, van der Lelij, Ewoud J., Dwarshuis, Govert, Kamphuis, Maarten J., Visser, Lisanne E., Harting, Romee, Gregory, Annemijn, Schweiger, Markus W., Wedekind, Laurine E., Ramaker, Jip, Zwaan, Kenn, Verschueren, Heleen, Bahce, Idris, de Langen, Adrianus J., Smit, Egbert F., van den Heuvel, Michel M., Hartemink, Koen J., Kuijpers, Marijke J.E., oude Egbrink, Mirjam G.A., Griffioen, Arjan W., Rossel, Rafael, Hiltermann, T. Jeroen N., Lee-Lewandrowski, Elizabeth, Lewandrowski, Kent B., De Witt Hamer, Philip C., Kouwenhoven, Mathilde, Reijneveld, Jaap C., Leenders, William P.J., Hoeben, Ann, Verdonck-de Leeuw, Irma M., Leemans, C. René, Baatenburg de Jong, Robert J., Terhaard, Chris H.J., Takes, Robert P., Langendijk, Johannes A., de Jager, Saskia C., Kraaijeveld, Adriaan O., Pasterkamp, Gerard, Smits, Minke, Schalken, Jack A., Łapińska-Szumczyk, Sylwia, Łojkowska, Anna, Żaczek, Anna J., Lokhorst, Henk, van de Donk, Niels W.C.J., Nijhof, Inger, Prins, Henk Jan, Zijlstra, Josée M., Idema, Sander, Baayen, Johannes C., Teunissen, Charlotte E., Killestein, Joep, Besselink, Marc G., Brammen, Lindsay, Bachleitner-Hofmann, Thomas, Mateen, Farrah, Plukker, John T.M., Heger, Michal, de Mast, Quirijn, Lisman, Ton, Pegtel, D. Michiel, Bogaard, Harm Jan, Jassem, Jacek, Supernat, Anna, Mehra, Niven, Gerritsen, Winald, de Kroon, Cornelis D., Lok, Christianne A.R., Piek, Jurgen M.J., Steeghs, Neeltje, van Houdt, Winan J., Brakenhoff, Ruud H., Sonke, Gabe S., Verheul, Henk M., Giovannetti, Elisa, Kazemier, Geert, Sabrkhany, Siamack, Schuuring, Ed, Sistermans, Erik A., Wolthuis, Rob, Meijers-Heijboer, Hanne, Dorsman, Josephine, Oudejans, Cees, Ylstra, Bauke, Westerman, Bart A., van den Broek, Daan, Koppers-Lalic, Danijela, Wesseling, Pieter, Nilsson, R. Jonas A., Vandertop, W. Peter, Noske, David P., Tannous, Bakhos A., Sol, Nik, Best, Myron G., and Wurdinger, Thomas
- Published
- 2022
16. The Effect of Preanalytical and Physiological Variables on Cell-Free DNA Fragmentation
- Author
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van der Pol, Ymke, primary, Moldovan, Norbert, additional, Verkuijlen, Sandra, additional, Ramaker, Jip, additional, Boers, Dries, additional, Onstenk, Wendy, additional, de Rooij, Johan, additional, Bahce, Idris, additional, Pegtel, D Michiel, additional, and Mouliere, Florent, additional
- Published
- 2022
- Full Text
- View/download PDF
17. Genome-wide cell-free DNA termini in patients with cancer
- Author
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Moldovan, Norbert, primary, van der Pol, Ymke, additional, van den Ende, Tom, additional, Boers, Dries, additional, Verkuijlen, Sandra, additional, Creemers, Aafke, additional, Ramaker, Jip, additional, Vu, Trang, additional, Fransen, Marieke F., additional, Pegtel, Michiel, additional, Bahce, Idris, additional, van Laarhoven, Hanneke, additional, and Mouliere, Florent, additional
- Published
- 2021
- Full Text
- View/download PDF
18. The effect of pre-analytical and physiological variables on cell-free DNA fragmentation
- Author
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van der Pol, Ymke, primary, Moldovan, Norbert, additional, Verkuijlen, Sandra, additional, Ramaker, Jip, additional, Boers, Dries, additional, Onstenk, Wendy, additional, de Rooij, Johan, additional, Bahce, Idris, additional, Pegtel, D. Michiel, additional, and Mouliere, Florent, additional
- Published
- 2021
- Full Text
- View/download PDF
19. mRNA sequencing of educated platelets generates a diagnostic biomarker for discrimination between pre- and post-capillary pulmonary hypertension
- Author
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Arkani, Mohammad, primary, Jansen, Samara, additional, In'T Veld, Sjors, additional, Smits, Josien, additional, Post, Edward, additional, Zwaan, Kenn, additional, Ramaker, Jip, additional, De Man, Frances S., additional, Vonk Noordegraaf, Anton, additional, Best, Myron, additional, Wurdinger, Thomas, additional, and Bogaard, Harm-Jan, additional
- Published
- 2020
- Full Text
- View/download PDF
20. GENE-60. THE EPITRANSCRIPTOMIC CODE IN LGG: METABOLICALLY REPROGRAMMED IDH-MUTANT GLIOMAS ALTER tRNA MODIFICATION LANDSCAPE
- Author
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Scheepbouwer, Chantal, primary, Borland, Kayla, additional, Aparicio, Ernesto, additional, Verschueren, Heleen, additional, Wedekind, Laurine, additional, Ramaker, Jip, additional, Misovic, Branko, additional, CM Kouwenhoven, Mathilde, additional, Noske, David, additional, Vandertop, Peter, additional, Wesseling, Pieter, additional, Wurdinger, Tom, additional, Hackenberg, Michael, additional, Kellner, Stefanie, additional, and Koppers-Lalic, Danijela, additional
- Published
- 2019
- Full Text
- View/download PDF
21. Tumor-educated platelet blood tests for Non-Small Cell Lung Cancer detection and management.
- Author
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Antunes-Ferreira M, D'Ambrosi S, Arkani M, Post E, In 't Veld SGJG, Ramaker J, Zwaan K, Kucukguzel ED, Wedekind LE, Griffioen AW, Oude Egbrink M, Kuijpers MJE, van den Broek D, Noske DP, Hartemink KJ, Sabrkhany S, Bahce I, Sol N, Bogaard HJ, Koppers-Lalic D, Best MG, and Wurdinger T
- Subjects
- Humans, Biomarkers, Tumor genetics, Algorithms, RNA metabolism, Blood Platelets metabolism, Hematologic Tests, Carcinoma, Non-Small-Cell Lung genetics, Lung Neoplasms genetics
- Abstract
Liquid biopsy approaches offer a promising technology for early and minimally invasive cancer detection. Tumor-educated platelets (TEPs) have emerged as a promising liquid biopsy biosource for the detection of various cancer types. In this study, we processed and analyzed the TEPs collected from 466 Non-small Cell Lung Carcinoma (NSCLC) patients and 410 asymptomatic individuals (controls) using the previously established thromboSeq protocol. We developed a novel particle-swarm optimization machine learning algorithm which enabled the selection of an 881 RNA biomarker panel (AUC 0.88). Herein we propose and validate in an independent cohort of samples (n = 558) two approaches for blood samples testing: one with high sensitivity (95% NSCLC detected) and another with high specificity (94% controls detected). Our data explain how TEP-derived spliced RNAs may serve as a biomarker for minimally-invasive clinical blood tests, complement existing imaging tests, and assist the detection and management of lung cancer patients., (© 2023. The Author(s).)
- Published
- 2023
- Full Text
- View/download PDF
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