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1. Tumor budding and lymphovascular invasion as prognostic factors in p16-positive oropharyngeal squamous cell carcinomas: Molecular Diagnostics

Author

Stögbauer, Fabian, Wirth, Markus, Lauterbach, Maren, Wollenberg, Barbara, Schmidl, Benedikt, Hoch, Cosima C., Ourailidis, Iordanis, Hess, Jochen, Eckstein, Markus, Hartmann, Arndt, Iro, Heinrich, Gostian, Antoniu-Oreste, Balk, Matthias, Jesinghaus, Moritz, Ribbat-Idel, Julika, Sailer, Verena-Wilbeth, Perner, Sven, Bruchhage, Karl-Ludwig, Hoffmann, Markus, Lükewille, Lukas, Stuhlmann-Laeisz, Christiane Maria, Röcken, Christoph, Mogler, Carolin, Budczies, Jan, and Boxberg, Melanie

Published
2025
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4. cancerclass: An R Package for Development and Validation of Diagnostic Tests from High-Dimensional Molecular Data

Author

Budczies Jan, Daniel Kosztyla, Christian von Törne, Albrecht Stenzinger, Silvia Darb-Esfahani, Manfred Dietel, and Carsten Denkert

Subjects
Statistics, HA1-4737
Abstract

Progress in molecular high-throughput techniques has led to the opportunity of a comprehensive monitoring of biomolecules in medical samples. In the era of personalized medicine, these data form the basis for the development of diagnostic, prognostic and predictive tests for cancer. Because of the high number of features that are measured simultaneously in a relatively low number of samples, supervised learning approaches are sensitive to over?tting and performance overestimation. Bioinformatic methods were developed to cope with these problems including control of accuracy and precision. However, there is demand for easy-to-use software that integrates methods for classifier construction, performance assessment and development of diagnostic tests. To contribute to ?lling of this gap, we developed a comprehensive R package for the development and validation of diagnostic tests from high-dimensional molecular data. An important focus of the package is a careful validation of the classification results. To this end, we implemented an extended version of the multiple random validation protocol, a validation method that was introduced before. The package includes methods for continuous prediction scores. This is important in a clinical setting, because scores can be converted to probabilities and help to distinguish between clear-cut and borderline classification results. The functionality of the package is illustrated by the analysis of two cancer microarray data sets.

Published
2014
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6. Clinical Implementation of a High-Throughput Automated Comprehensive Genomic Profiling Test: TruSight Oncology 500 HT

Author

Ball, Markus, Romanovsky, Eva, Schnecko, Fabian, Kirchner, Martina, Neumann, Olaf, Brandt, Regine, Beck, Susanne, Seker-Cin, Huriye, Kluck, Klaus, Ourailidis, Iordanis, Goldschmid, Hannah, Fink, Annette, Volckmar, Anna-Lena, Menzel, Michael, Allgäuer, Michael, Schirmacher, Peter, Budczies, Jan, Stenzinger, Albrecht, and Kazdal, Daniel

Published
2025
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7. A reproducibility study on invasion in small pulmonary adenocarcinoma according to the WHO and a modified classification, supported by biomarkers

Author

Thunnissen, Erik, Blaauwgeers, Hans, Filipello, Federica, Lissenberg-Witte, Birgit, Minami, Yuko, Noguchi, Masayuki, Quesne, John Le, Papotti, Mauro Giulio, Flieder, Douglas B., Pelosi, Giuseppe, Sansano, Irene, Berezowska, Sabina, Ryška, Aleš, Brcic, Luka, Motoi, Noriko, Nakatani, Yukio, Kuempers, Christiane, Hofman, Paul, Hofman, Veronique, Dale, Vibeke Grotnes, Rossi, Giulio, Ambrosi, Francesca, Matsubara, Daisuke, Ishikawa, Yuichi, Weynand, Birgit, Calabrese, Fiorella, Pezzuto, Federica, Kern, Izidor, Nicholson, Siobhan, Mutka, Aino, Dacic, Sanja, Beasley, Mary Beth, Arrigoni, Gianluigi, Timens, Wim, Ooft, Marc, Brinkhuis, Mariel, Bulkmans, Nicole, Britstra, Rieneke, Vreuls, Willem, Jones, Kirk D., von der Thüsen, Jan H., Hager, Hendrik, Perner, Sven, Moore, David, Leonte, Diana Gabriela, Al-Janabi, Shaimaa, Schønau, Andreas, Neumann, Olaf, Kluck, Klaus, Ourailidis, Iordanis, Ball, Markus, Budczies, Jan, Kazdal, Daniel, and Stenzinger, Albrecht

Published
2025
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8. Benchmarking whole exome sequencing in the German network for personalized medicine

Author

Menzel, Michael, Martis-Thiele, Mihaela, Goldschmid, Hannah, Ott, Alexander, Romanovsky, Eva, Siemanowski-Hrach, Janna, Seillier, Lancelot, Brüchle, Nadina Ortiz, Maurer, Angela, Lehmann, Kjong-Van, Begemann, Matthias, Elbracht, Miriam, Meyer, Robert, Dintner, Sebastian, Claus, Rainer, Meier-Kolthoff, Jan P., Blanc, Eric, Möbs, Markus, Joosten, Maria, Benary, Manuela, Basitta, Patrick, Hölscher, Florian, Tischler, Verena, Groß, Thomas, Kutz, Oliver, Prause, Rebecca, William, Doreen, Horny, Kai, Goering, Wolfgang, Sivalingam, Sugirthan, Borkhardt, Arndt, Blank, Cornelia, Junk, Stefanie V., Yasin, Layal, Moskalev, Evgeny A., Carta, Maria Giulia, Ferrazzi, Fulvia, Tögel, Lars, Wolter, Steffen, Adam, Eugen, Matysiak, Uta, Rosenthal, Tessa, Dönitz, Jürgen, Lehmann, Ulrich, Schmidt, Gunnar, Bartels, Stephan, Hofmann, Winfried, Hirsch, Steffen, Dikow, Nicola, Göbel, Kirsten, Banan, Rouzbeh, Hamelmann, Stefan, Fink, Annette, Ball, Markus, Neumann, Olaf, Rehker, Jan, Kloth, Michael, Murtagh, Justin, Hartmann, Nils, Jurmeister, Phillip, Mock, Andreas, Kumbrink, Jörg, Jung, Andreas, Mayr, Eva-Maria, Jacob, Anne, Trautmann, Marcel, Kirmse, Santina, Falkenberg, Kim, Ruckert, Christian, Hirsch, Daniela, Immel, Alexander, Dietmaier, Wolfgang, Haack, Tobias, Marienfeld, Ralf, Fürstberger, Axel, Niewöhner, Jakob, Gerstenmaier, Uwe, Eberhardt, Timo, Greif, Philipp A., Appenzeller, Silke, Maurus, Katja, Doll, Julia, Jelting, Yvonne, Jonigk, Danny, Märkl, Bruno, Beule, Dieter, Horst, David, Wulf, Anna-Lena, Aust, Daniela, Werner, Martin, Reuter-Jessen, Kirsten, Ströbel, Philipp, Auber, Bernd, Sahm, Felix, Merkelbach-Bruse, Sabine, Siebolts, Udo, Roth, Wilfried, Lassmann, Silke, Klauschen, Frederick, Gaisa, Nadine T., Weichert, Wilko, Evert, Matthias, Armeanu-Ebinger, Sorin, Ossowski, Stephan, Schroeder, Christopher, Schaaf, Christian P., Malek, Nisar, Schirmacher, Peter, Kazdal, Daniel, Pfarr, Nicole, Budczies, Jan, and Stenzinger, Albrecht

Published
2024
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15. Multicentric pilot study to standardize clinical whole exome sequencing (WES) for cancer patients

Author

Menzel, Michael, Ossowski, Stephan, Kral, Sebastian, Metzger, Patrick, Horak, Peter, Marienfeld, Ralf, Boerries, Melanie, Wolter, Steffen, Ball, Markus, Neumann, Olaf, Armeanu-Ebinger, Sorin, Schroeder, Christopher, Matysiak, Uta, Goldschmid, Hannah, Schipperges, Vincent, Fürstberger, Axel, Allgäuer, Michael, Eberhardt, Timo, Niewöhner, Jakob, Blaumeiser, Andreas, Ploeger, Carolin, Haack, Tobias Bernd, Tay, Timothy Kwang Yong, Kelemen, Olga, Pauli, Thomas, Kirchner, Martina, Kluck, Klaus, Ott, Alexander, Renner, Marcus, Admard, Jakob, Gschwind, Axel, Lassmann, Silke, Kestler, Hans, Fend, Falko, Illert, Anna Lena, Werner, Martin, Möller, Peter, Seufferlein, Thomas Theodor Werner, Malek, Nisar, Schirmacher, Peter, Fröhling, Stefan, Kazdal, Daniel, Budczies, Jan, and Stenzinger, Albrecht

Published
2023
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17. Remodeling of central metabolism in invasive breast cancer compared to normal breast tissue – a GC-TOFMS based metabolomics study

Author

Budczies Jan, Denkert Carsten, Müller Berit M, Brockmöller Scarlet F, Klauschen Frederick, Györffy Balazs, Dietel Manfred, Richter-Ehrenstein Christiane, Marten Ulrike, Salek Reza M, Griffin Julian L, Hilvo Mika, Orešič Matej, Wohlgemuth Gert, and Fiehn Oliver

Subjects
Breast cancer, Metabolomics, Gas chromatography, Mass spectrometry, Cancer detection, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Changes in energy metabolism of the cells are common to many kinds of tumors and are considered a hallmark of cancer. Gas chromatography followed by time-of-flight mass spectrometry (GC-TOFMS) is a well-suited technique to investigate the small molecules in the central metabolic pathways. However, the metabolic changes between invasive carcinoma and normal breast tissues were not investigated in a large cohort of breast cancer samples so far. Results A cohort of 271 breast cancer and 98 normal tissue samples was investigated using GC-TOFMS-based metabolomics. A total number of 468 metabolite peaks could be detected; out of these 368 (79%) were significantly changed between cancer and normal tissues (p80%. Two-metabolite classifiers, constructed as ratios of the tumor and normal tissues markers, separated cancer from normal tissues with high sensitivity and specificity. Specifically, the cytidine-5-monophosphate / pentadecanoic acid metabolic ratio was the most significant discriminator between cancer and normal tissues and allowed detection of cancer with a sensitivity of 94.8% and a specificity of 93.9%. Conclusions For the first time, a comprehensive metabolic map of breast cancer was constructed by GC-TOF analysis of a large cohort of breast cancer and normal tissues. Furthermore, our results demonstrate that spectrometry-based approaches have the potential to contribute to the analysis of biopsies or clinical tissue samples complementary to histopathology.

Published
2012
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18. An intracellular targeted antibody detects EGFR as an independent prognostic factor in ovarian carcinomas

Author

Braicu Elena I, Sehouli Jalid, Buckendahl Ann-Christin, Darb-Esfahani Silvia, Weichert Wilko, Schwabe Michael, Noske Aurelia, Budczies Jan, Dietel Manfred, and Denkert Carsten

Subjects
EGFR, CRM1, COX-2, ovarian cancer, prognosis, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Abstract Background In ovarian cancer, the reported rate of EGFR expression varies between 4-70% depending on assessment method and data on patient outcome are conflicting. Methods: In this study we investigated EGFR expression and its prognostic value in a cohort of 121 invasive ovarian carcinomas, using a novel antibody against the intracellular domain of the receptor. We further evaluated an association between EGFR, the nuclear transporter CRM1 as well as COX-2. Furthermore, we evaluated EGFR expression in ten ovarian cancer cell lines and incubated cancer cells with Leptomycin B, a CRM1 specific inhibitor. Results We observed a membranous and cytoplasmic EGFR expression in 36.4% and 64% of ovarian carcinomas, respectively. Membranous EGFR was an independent prognostic factor for poor overall survival in ovarian cancer patients (HR 2.7, CI 1.1-6.4, p = 0.02) which was also found in the serous subtype (HR 4.6, CI 1.6-13.4, p = 0.004). We further observed a significant association of EGFR with COX-2 and nuclear CRM1 expression (chi-square test for trends, p = 0.006 and p = 0.013, respectively). In addition, combined membranous EGFR/COX-2 expression was significantly related to unfavorable overall survival (HR 7.2, CI 2.3-22.1, p = 0.001). In cell culture, we observed a suppression of EGFR protein levels after exposure to Leptomycin B in OVCAR-3 and SKOV-3 cells. Conclusions Our results suggest that the EGFR/COX-2/CRM1 interaction might be involved in progression of ovarian cancer and patient prognosis. Hence, it is an interesting anti-cancer target for a combination therapy. Further studies will also be needed to investigate whether EGFR is also predictive for benefit from EGFR targeted therapies.

Published
2011
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19. High Concordance of Different Assays in the Determination of Homologous Recombination Deficiency–Associated Genomic Instability in Ovarian Cancer

Author

Pfarr, Nicole, von Schwarzenberg, Karin, Zocholl, Dario, Merkelbach-Bruse, Sabine, Siemanowski, Janna, Mayr, Eva-Maria, Herold, Sylvia, Kleo, Karsten, Heukamp, Lukas C., Willing, Eva-Maria, Menzel, Michael, Lehmann, Ulrich, Bartels, Stephan, Chakraborty, Shounak, Baretton, Gustavo, Demes, Melanie C., Döring, Claudia, Kazdal, Daniel, Budczies, Jan, Rad, Roland, Wild, Peter, Christinat, Yann, McKee, Thomas, Schirmacher, Peter, Horst, David, Büttner, Reinhard, Stenzinger, Albrecht, Sehouli, Jalid, Vollbrecht, Claudia, Hummel, Michael, Braicu, Elena I., and Weichert, Wilko

Published
2024
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20. High class I HDAC activity and expression are associated with RelA/p65 activation in pancreatic cancer in vitro and in vivo

Author

Neuhaus Peter, Bahra Marcus, Müller Berit, Noske Aurelia, Darb-Esfahani Silvia, Buckendahl Ann-Christin, Budczies Jan, Denkert Carsten, Lehmann Annika, Dietel Manfred, Kristiansen Glen, and Weichert Wilko

Subjects
Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Abstract Background The strong association between aberrant HDAC activity and the occurrence of cancer has led to the development of a variety of HDAC inhibitors (HDIs), which emerge as promising new targeted anticancer therapeutics. Methods Due to the pivotal role of RelA/p65 in the tumorigenesis of pancreatic neoplasia we examined the expression of class I HDACs 1, 2 and 3 in a large cohort of human pancreatic carcinomas and correlated our findings with RelA/p65 expression status. Furthermore, we investigated the impact of the HDIs SAHA and VPA on RelA/p65 activity in pancreatic cancer cell culture models. Results Class I HDACs were strongly expressed in a subset of pancreatic adenocarcinomas and high expression was significantly correlated with increased nuclear translocation of RelA/p65 (p = 0.024). The link of HDAC activity and RelA/p65 in this tumor entity was confirmed in vitro, where RelA/p65 nuclear translocation as well as RelA/p65 DNA binding activity could be markedly diminished by HDI treatment. Conclusion The RelA/p65 inhibitory effects of SAHA and VPA in vitro and the close relationship of class I HDACs and RelA/p65 in vivo suggest that treatment with HDIs could serve as a promising approach to suppress NF-κB activity which in turn may lead to enhanced apoptosis and chemosensitization of pancreatic cancers.

Published
2009
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21. Metabolite profiling of human colon carcinoma – deregulation of TCA cycle and amino acid turnover

Author

Noske Aurelia, Niesporek Silvia, Kind Tobias, Scholz Martin, Wohlgemuth Gert, Weichert Wilko, Budczies Jan, Denkert Carsten, Buckendahl Anna, Dietel Manfred, and Fiehn Oliver

Subjects
Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Abstract Background Apart from genetic alterations, development and progression of colorectal cancer has been linked to influences from nutritional intake, hyperalimentation, and cellular metabolic changes that may be the basis for new diagnostic and therapeutic approaches. However, in contrast to genomics and proteomics, comprehensive metabolomic investigations of alterations in malignant tumors have rarely been conducted. Results In this study we investigated a set of paired samples of normal colon tissue and colorectal cancer tissue with gas-chromatography time-of-flight mass-spectrometry, which resulted in robust detection of a total of 206 metabolites. Metabolic phenotypes of colon cancer and normal tissues were different at a Bonferroni corrected significance level of p = 0.00170 and p = 0.00005 for the first two components of an unsupervised PCA analysis. Subsequent supervised analysis found 82 metabolites to be significantly different at p < 0.01. Metabolites were connected to abnormalities in metabolic pathways by a new approach that calculates the distance of each pair of metabolites in the KEGG database interaction lattice. Intermediates of the TCA cycle and lipids were found down-regulated in cancer, whereas urea cycle metabolites, purines, pyrimidines and amino acids were generally found at higher levels compared to normal colon mucosa. Conclusion This study demonstrates that metabolic profiling facilitates biochemical phenotyping of normal and neoplastic colon tissue at high significance levels and points to GC-TOF-based metabolomics as a new method for molecular pathology investigations.

Published
2008
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22. Robust detection and verification of linear relationships to generate metabolic networks using estimates of technical errors

Author

Holschneider Matthias, Budczies Jan, Kose Frank, and Fiehn Oliver

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background The size and magnitude of the metabolome, the ratio between individual metabolites and the response of metabolic networks is controlled by multiple cellular factors. A tight control over metabolite ratios will be reflected by a linear relationship of pairs of metabolite due to the flexibility of metabolic pathways. Hence, unbiased detection and validation of linear metabolic variance can be interpreted in terms of biological control. For robust analyses, criteria for rejecting or accepting linearities need to be developed despite technical measurement errors. The entirety of all pair wise linear metabolic relationships then yields insights into the network of cellular regulation. Results The Bayesian law was applied for detecting linearities that are validated by explaining the residues by the degree of technical measurement errors. Test statistics were developed and the algorithm was tested on simulated data using 3–150 samples and 0–100% technical error. Under the null hypothesis of the existence of a linear relationship, type I errors remained below 5% for data sets consisting of more than four samples, whereas the type II error rate quickly raised with increasing technical errors. Conversely, a filter was developed to balance the error rates in the opposite direction. A minimum of 20 biological replicates is recommended if technical errors remain below 20% relative standard deviation and if thresholds for false error rates are acceptable at less than 5%. The algorithm was proven to be robust against outliers, unlike Pearson's correlations. Conclusion The algorithm facilitates finding linear relationships in complex datasets, which is radically different from estimating linearity parameters from given linear relationships. Without filter, it provides high sensitivity and fair specificity. If the filter is activated, high specificity but only fair sensitivity is yielded. Total error rates are more favorable with deactivated filters, and hence, metabolomic networks should be generated without the filter. In addition, Bayesian likelihoods facilitate the detection of multiple linear dependencies between two variables. This property of the algorithm enables its use as a discovery tool and to generate novel hypotheses of the existence of otherwise hidden biological factors.

Published
2007
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25. Spatial profiling of the microenvironment reveals low intratumoral heterogeneity and STK11-associated immune evasion in therapy-naïve lung adenocarcinomas

Author

Goldschmid, Hannah, Kluck, Klaus, Ball, Markus, Kirchner, Martina, Allgäuer, Michael, Winter, Hauke, Herth, Felix, Heußel, Claus-Peter, Pullamsetti, Soni Savai, Savai, Rajkumar, Yong, Timothy Tay Kwang, Schirmacher, Peter, Peters, Solange, Thomas, Michael, Christopoulos, Petros, Budczies, Jan, Stenzinger, Albrecht, and Kazdal, Daniel

Published
2023
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26. Genomic architecture of FGFR2 fusions in cholangiocarcinoma and its implication for molecular testing

Author

Neumann, Olaf, Burn, Timothy C., Allgäuer, Michael, Ball, Markus, Kirchner, Martina, Albrecht, Thomas, Volckmar, Anna-Lena, Beck, Susanne, Endris, Volker, Goldschmid, Hannah, Lehmann, Ulrich, Seker-Cin, Huriye, Uhrig, Sebastian, Roessler, Stephanie, Budczies, Jan, Fröhling, Stefan, Longerich, Thomas, Wagner, Alex H., Vogel, Arndt, Schirmacher, Peter, Stenzinger, Albrecht, and Kazdal, Daniel

Published
2022
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27. Struktur und Inhalt der EU-IVDR: Bestandsaufnahme und Implikationen für die Pathologie

Author

Kahles, Andy, Goldschmid, Hannah, Volckmar, Anna-Lena, Plöger, Carolin, Kazdal, Daniel, Penzel, Roland, Budczies, Jan, Kempny, Gisela, Kazmierczak, Marlon, Flechtenmacher, Christa, Baretton, Gustavo, Weichert, Wilko, Horst, David, Klauschen, Frederick, Gassner, Ulrich M., Brüggemann, Monika, Vogeser, Michael, Schirmacher, Peter, and Stenzinger, Albrecht

Published
2022
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28. Towards computational fluorescence microscopy: Machine learning-based integrated prediction of morphological and molecular tumor profiles

Author

Binder, Alexander, Bockmayr, Michael, Hägele, Miriam, Wienert, Stephan, Heim, Daniel, Hellweg, Katharina, Stenzinger, Albrecht, Parlow, Laura, Budczies, Jan, Goeppert, Benjamin, Treue, Denise, Kotani, Manato, Ishii, Masaru, Dietel, Manfred, Hocke, Andreas, Denkert, Carsten, Müller, Klaus-Robert, and Klauschen, Frederick

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

Recent advances in cancer research largely rely on new developments in microscopic or molecular profiling techniques offering high level of detail with respect to either spatial or molecular features, but usually not both. Here, we present a novel machine learning-based computational approach that allows for the identification of morphological tissue features and the prediction of molecular properties from breast cancer imaging data. This integration of microanatomic information of tumors with complex molecular profiling data, including protein or gene expression, copy number variation, gene methylation and somatic mutations, provides a novel means to computationally score molecular markers with respect to their relevance to cancer and their spatial associations within the tumor microenvironment.

Published
2018

29. Prioritization of metabolic genes as novel therapeutic targets in estrogen-receptor negative breast tumors using multi-omics data and text mining

Author

Barupal, Dinesh Kumar, Gao, Bei, Budczies, Jan, Phinney, Brett S, Perroud, Bertrand, Denkert, Carsten, and Fiehn, Oliver

Subjects
Genetics, Biotechnology, Breast Cancer, Cancer, ChemRICH, candidate gene prioritization, metabolic networks, multi-omics, set-enrichment, Oncology and Carcinogenesis
Abstract

Estrogen-receptor negative (ERneg) breast cancer is an aggressive breast cancer subtype in the need for new therapeutic options. We have analyzed metabolomics, proteomics and transcriptomics data for a cohort of 276 breast tumors (MetaCancer study) and nine public transcriptomics datasets using univariate statistics, meta-analysis, Reactome pathway analysis, biochemical network mapping and text mining of metabolic genes. In the MetaCancer cohort, a total of 29% metabolites, 21% proteins and 33% transcripts were significantly different (raw p

Published
2019

30. Trailblazing precision medicine in Europe: A joint view by Genomic Medicine Sweden and the Centers for Personalized Medicine, ZPM, in Germany

Author

Lindstrand, Anna, Wedell, Anna, Gisselsson, David, Melén, Erik, Helenius, Gisela, Ehrencrona, Hans, Engstrand, Lars, Palmqvist, Lars, Levin, Lars-Åke, Lovmar, Lovisa, Landström, Maréne, Hallbeck, Martin, Wadelius, Mia, Sikora, Per, Beer, Ambros J., Illert, Anna L., Budczies, Jan, Nikolaou, Konstantin, Kohlbacher, Oliver, Horak, Peter, Kuhn, Peter, Schroeder, Christopher, Boerries, Melanie, Lassmann, Silke, Gaidzik, Verena I., Stenzinger, Albrecht, Edsjö, Anders, Ploeger, Carolin, Friedman, Mikaela, Fröhling, Stefan, Wirta, Valtteri, Seufferlein, Thomas, Botling, Johan, Duyster, Justus, Akhras, Michael, Thimme, Robert, Fioretos, Thoas, Bitzer, Michael, Cavelier, Lucia, Schirmacher, Peter, Malek, Nisar, and Rosenquist, Richard

Published
2022
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32. The impact of TP53 co-mutations and immunologic microenvironment on outcome of lung cancer with EGFR exon 20 insertions

Author

Christopoulos, Petros, Kluck, Klaus, Kirchner, Martina, Lüders, Heike, Roeper, Julia, Falkenstern-Ge, Roger-Fei, Szewczyk, Marlen, Sticht, Florian, Saalfeld, Felix C., Wesseler, Claas, Hackanson, Björn, Dintner, Sebastian, Faehling, Martin, Kuon, Jonas, Janning, Melanie, Kauffmann-Guerrero, Diego, Kazdal, Daniel, Kurz, Sylke, Eichhorn, Florian, Bozorgmehr, Farastuk, Shah, Rajiv, Tufman, Amanda, Wermke, Martin, Loges, Sonja, Brueckl, Wolfgang M., Schulz, Christian, Misch, Daniel, Frost, Nikolaj, Kollmeier, Jens, Reck, Martin, Griesinger, Frank, Grohé, Christian, Hong, Jin-Liern, Lin, Huamao M., Budczies, Jan, Stenzinger, Albrecht, and Thomas, Michael

Published
2022
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33. Machine learning–based liquid biomarker analysis from the NEONAX trial for response prediction to perioperative (PO) and adjuvant (A) gemcitabine/nab-paclitaxel in resectable PDAC (rPDAC).

Author

Seufferlein, Thomas, Lahusen, Anton, Kirchner, Martina, Jarboui, Mohamed Ali, Kluck, Klaus, Wisser, Sarah, Uhl, Waldemar, Kornmann, Marko, Algül, Hana, Friess, Helmut, Schuhbaur, Jasmin, Kleger, Alexander, Perkhofer, Lukas, Budczies, Jan, Tempero, Margaret A., Reinacher-Schick, Anke C., Stenzinger, Albrecht, Tannapfel, Andrea, Eiseler, Tim, and Ettrich, Thomas Jens

Published
2025
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34. The Different Immune Profiles of Normal Colonic Mucosa in Cancer-Free Lynch Syndrome Carriers and Lynch Syndrome Colorectal Cancer Patients

Author

Bohaumilitzky, Lena, Kluck, Klaus, Hüneburg, Robert, Gallon, Richard, Nattermann, Jacob, Kirchner, Martina, Kristiansen, Glen, Hommerding, Oliver, Pfuderer, Pauline L., Wagner, Lelia, Echterdiek, Fabian, Kösegi, Svenja, Müller, Nico, Fischer, Konstantin, Nelius, Nina, Hartog, Ben, Borthwick, Gillian, Busch, Elena, Haag, Georg Martin, Bläker, Hendrik, Möslein, Gabriela, von Knebel Doeberitz, Magnus, Seppälä, Toni T., Ahtiainen, Maarit, Mecklin, Jukka-Pekka, Bishop, D. Timothy, Burn, John, Stenzinger, Albrecht, Budczies, Jan, Kloor, Matthias, and Ahadova, Aysel

Published
2022
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35. An analysis of PIK3CA hotspot mutations and response to neoadjuvant therapy in breast cancer patients from four prospective clinical trials

Author

Jank, Paul, primary, Karn, Thomas, additional, van Mackelenbergh, Marion, additional, Lindner, Judith, additional, Treue, Denise, additional, Huober, Jens, additional, Engels, Knut, additional, Solbach, Christine, additional, Diebold, Kurt, additional, Marme, Frederik, additional, Müller, Volkmar, additional, Schneeweiss, Andreas, additional, Sinn, Hans-Peter, additional, Fehm, Tanja, additional, Schem, Christian, additional, Stickeler, Elmar, additional, Fasching, Peter A., additional, Budczies, Jan, additional, Felder, Bärbel, additional, Nekljudova, Valentina, additional, Holtschmidt, Johannes, additional, Untch, Michael, additional, Denkert, Carsten, additional, and Loibl, Sibylle, additional

Published
2024
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37. Deciphering the immunosuppressive tumor microenvironment in ALK- and EGFR-positive lung adenocarcinoma

Author

Budczies, Jan, Kirchner, Martina, Kluck, Klaus, Kazdal, Daniel, Glade, Julia, Allgäuer, Michael, Kriegsmann, Mark, Heußel, Claus-Peter, Herth, Felix J., Winter, Hauke, Meister, Michael, Muley, Thomas, Goldmann, Torsten, Fröhling, Stefan, Wermke, Martin, Waller, Cornelius F., Tufman, Amanda, Reck, Martin, Peters, Solange, Schirmacher, Peter, Thomas, Michael, Christopoulos, Petros, and Stenzinger, Albrecht

Published
2022
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38. Targeting rare and non-canonical driver variants in NSCLC – An uncharted clinical field

Author

Volckmar, Anna-Lena, Christopoulos, Petros, Kirchner, Martina, Allgäuer, Michael, Neumann, Olaf, Budczies, Jan, Rempel, Eugen, Horak, Peter, Glade, Julia, Goldschmid, Hannah, Seker-Cin, Huriye, Brandt, Regine, Kriegsmann, Mark, Leichsenring, Jonas, Winter, Hauke, Faehling, Martin, Fischer, Jürgen R., Heußel, Claus Peter, Herth, Felix, Brummer, Tilman, Fröhling, Stefan, Schirmacher, Peter, Thomas, Michael, Endris, Volker, Penzel, Roland, Kazdal, Daniel, Bochtler, Tilmann, and Stenzinger, Albrecht

Published
2021
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39. Harmonization and Standardization of Panel-Based Tumor Mutational Burden Measurement: Real-World Results and Recommendations of the Quality in Pathology Study

Author

Stenzinger, Albrecht, Endris, Volker, Budczies, Jan, Merkelbach-Bruse, Sabine, Kazdal, Daniel, Dietmaier, Wolfgang, Pfarr, Nicole, Siebolts, Udo, Hummel, Michael, Herold, Sylvia, Andreas, Johanna, Zoche, Martin, Tögel, Lars, Rempel, Eugen, Maas, Jörg, Merino, Diana, Stewart, Mark, Zaoui, Karim, Schlesner, Matthias, Glimm, Hanno, Fröhling, Stefan, Allen, Jeff, Horst, David, Baretton, Gustavo, Wickenhauser, Claudia, Tiemann, Markus, Evert, Matthias, Moch, Holger, Kirchner, Thomas, Büttner, Reinhard, Schirmacher, Peter, Jung, Andreas, Haller, Florian, Weichert, Wilko, and Dietel, Manfred

Published
2020
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44. Pre-operative cellular dissociation grading in biopsies is highly predictive of post-operative tumour stage and patient outcome in head and neck squamous cell carcinoma

Author

Jesinghaus, Moritz, Steiger, Katja, Stögbauer, Fabian, Haller, Bernhard, Kolk, Andreas, Straßen, Ulrich, Pickhard, Anja, Wirth, Markus, Silva, Miguel, Budczies, Jan, Becker von Rose, Aaron, Konukiewitz, Björn, Kuhn, Peer, Klinghammer, Konrad, Dapper, Hendrik, Münch, Stefan, Combs, Stephanie E., Weichert, Wilko, and Boxberg, Melanie

Published
2020
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46. Spatial and Temporal Heterogeneity of Panel-Based Tumor Mutational Burden in Pulmonary Adenocarcinoma: Separating Biology From Technical Artifacts

Author

Kazdal, Daniel, Endris, Volker, Allgäuer, Michael, Kriegsmann, Mark, Leichsenring, Jonas, Volckmar, Anna-Lena, Harms, Alexander, Kirchner, Martina, Kriegsmann, Katharina, Neumann, Olaf, Brandt, Regine, Talla, Suranand B., Rempel, Eugen, Ploeger, Carolin, von Winterfeld, Moritz, Christopoulos, Petros, Merino, Diana M., Stewart, Mark, Allen, Jeff, Bischoff, Helge, Meister, Michael, Muley, Thomas, Herth, Felix, Penzel, Roland, Warth, Arne, Winter, Hauke, Fröhling, Stefan, Peters, Solange, Swanton, Charles, Thomas, Michael, Schirmacher, Peter, Budczies, Jan, and Stenzinger, Albrecht

Published
2019
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48. Genomic heterogeneity at baseline is associated with T790M resistance mutations in EGFR‐mutated lung cancer treated with the first‐/second‐generation tyrosine kinase inhibitors

Author

Menzel, Michael, primary, Kirchner, Martina, additional, Kluck, Klaus, additional, Ball, Markus, additional, Beck, Susanne, additional, Allgäuer, Michael, additional, Assmann, Christin, additional, Schnorbach, Johannes, additional, Volckmar, Anna‐Lena, additional, Tay, Timothy Kwang Yong, additional, Goldschmid, Hannah, additional, Tan, Daniel SW, additional, Thomas, Michael, additional, Kazdal, Daniel, additional, Budczies, Jan, additional, Stenzinger, Albrecht, additional, and Christopoulos, Petros, additional

Published
2024
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49. Correction: Tumour budding-based grading as independent prognostic biomarker in HPV-positive and HPV-negative head and neck cancer

Author

Stögbauer, Fabian, primary, Beck, Susanne, additional, Ourailidis, Iordanis, additional, Hess, Jochen, additional, Poremba, Christopher, additional, Lauterbach, Maren, additional, Wollenberg, Barbara, additional, Buchberger, Anna Maria Stefanie, additional, Jesinghaus, Moritz, additional, Schirmacher, Peter, additional, Stenzinger, Albrecht, additional, Weichert, Wilko, additional, Boxberg, Melanie, additional, and Budczies, Jan, additional

Published
2024
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50. Dynamics of the Intratumoral Immune Response during Progression of High-Grade Serous Ovarian Cancer

Author

Stanske, Mandy, Wienert, Stephan, Castillo-Tong, Dan Cacsire, Kreuzinger, Caroline, Vergote, Ignace, Lambrechts, Sandrijne, Gabra, Hani, Gourley, Charlie, Ganapathi, Ram N., Kolaschinski, Ivonne, Budczies, Jan, Sehouli, Jalid, Ruscito, Ilary, Denkert, Carsten, Kulbe, Hagen, Schmitt, Wolfgang, Jöhrens, Korinna, Braicu, Ioana, and Darb-Esfahani, Silvia

Published
2018
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