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2. A community approach to the cancer-variant-interpretation bottleneck

Author

Krysiak, Kilannin, Danos, Arpad M., Kiwala, Susanna, McMichael, Joshua F., Coffman, Adam C., Barnell, Erica K., Sheta, Lana, Saliba, Jason, Grisdale, Cameron J., Kujan, Lynzey, Pema, Shahil, Lever, Jake, Spies, Nicholas C., Chiorean, Andreea, Rieke, Damian T., Clark, Kaitlin A., Jani, Payal, Takahashi, Hideaki, Horak, Peter, Ritter, Deborah I., Zhou, Xin, Ainscough, Benjamin J., Delong, Sean, Lamping, Mario, Marr, Alex R., Li, Brian V., Lin, Wan-Hsin, Terraf, Panieh, Salama, Yasser, Campbell, Katie M., Farncombe, Kirsten M., Ji, Jianling, Zhao, Xiaonan, Xu, Xinjie, Kanagal-Shamanna, Rashmi, Cotto, Kelsy C., Skidmore, Zachary L., Walker, Jason R., Zhang, Jinghui, Milosavljevic, Aleksandar, Patel, Ronak Y., Giles, Rachel H., Kim, Raymond H., Schriml, Lynn M., Mardis, Elaine R., Jones, Steven J. M., Raca, Gordana, Rao, Shruti, Madhavan, Subha, Wagner, Alex H., Griffith, Obi L., and Griffith, Malachi

Published
2022
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6. Leveraging Large Language Models for Decision Support in Personalized Oncology

Author

Benary, Manuela, primary, Wang, Xing David, additional, Schmidt, Max, additional, Soll, Dominik, additional, Hilfenhaus, Georg, additional, Nassir, Mani, additional, Sigler, Christian, additional, Knödler, Maren, additional, Keller, Ulrich, additional, Beule, Dieter, additional, Keilholz, Ulrich, additional, Leser, Ulf, additional, and Rieke, Damian T., additional

Published
2023
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8. Contributors

Author

Albrecht, Urs-Vito, primary, Berger, Frank M., additional, Buckley, Brendan M., additional, Byrom, Bill, additional, Clark, Tim, additional, Day, Simon, additional, Hawking, Melissa, additional, Hyveled, Liselotte, additional, Kolominsky-Rabas, Peter L., additional, Kubick, Wayne, additional, Lehrach, Hans, additional, Maier, William C., additional, Mehlem, Fareed, additional, Milborrow, Gareth, additional, Nakskov, Henrik, additional, Ogilvie, Lesley A., additional, Orri, Miguel, additional, Reites, John, additional, Renz, Wolfgang, additional, Rieke, Damian T., additional, and Schüler, Peter, additional

Published
2021
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12. Abstract 926: Genomics-based personalized oncology of advanced thymic epithelial tumors

Author

Möhrmann, Lino, primary, Rostock, Lysann, additional, Oleś, Małgorzata, additional, Jahn, Arne, additional, Arlt, Marie, additional, Paramasivam, Nagarajan, additional, Jöhrens, Korinna, additional, Rupp, Luise, additional, Schmitz, Marc, additional, Richter, Daniela, additional, Uhrig, Sebastian, additional, Fröhlich, Martina, additional, Hutter, Barbara, additional, Hüllein, Jennifer, additional, Wolf, Elena E., additional, Hanf, Dorothea, additional, Gieldon, Laura, additional, Kreutzfeldt, Simon, additional, Heilig, Christoph E., additional, Teleanu, Veronica, additional, Lipka, Daniel B., additional, Mock, Andreas, additional, Jelas, Ivan, additional, Rieke, Damian T., additional, Wiesweg, Marcel, additional, Boerries, Melanie, additional, Illert, Anna L., additional, Desuki, Alexander, additional, Kindler, Thomas, additional, Krackhardt, Angela M., additional, Westphalen, C. Benedikt, additional, Grosch, Heidrun, additional, Apostolidis, Leonidas, additional, Stenzinger, Albrecht, additional, Kerle, Irina A., additional, Heining, Christoph, additional, Hübschmann, Daniel, additional, Schröck, Evelin, additional, Fröhling, Stefan, additional, and Glimm, Hanno, additional

Published
2023
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13. CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase

Author

Krysiak, Kilannin, primary, Danos, Arpad M, additional, Saliba, Jason, additional, McMichael, Joshua F, additional, Coffman, Adam C, additional, Kiwala, Susanna, additional, Barnell, Erica K, additional, Sheta, Lana, additional, Grisdale, Cameron J, additional, Kujan, Lynzey, additional, Pema, Shahil, additional, Lever, Jake, additional, Ridd, Sarah, additional, Spies, Nicholas C, additional, Andric, Veronica, additional, Chiorean, Andreea, additional, Rieke, Damian T, additional, Clark, Kaitlin A, additional, Reisle, Caralyn, additional, Venigalla, Ajay C, additional, Evans, Mark, additional, Jani, Payal, additional, Takahashi, Hideaki, additional, Suda, Avila, additional, Horak, Peter, additional, Ritter, Deborah I, additional, Zhou, Xin, additional, Ainscough, Benjamin J, additional, Delong, Sean, additional, Kesserwan, Chimene, additional, Lamping, Mario, additional, Shen, Haolin, additional, Marr, Alex R, additional, Hoang, My H, additional, Singhal, Kartik, additional, Khanfar, Mariam, additional, Li, Brian V, additional, Lin, Wan-Hsin, additional, Terraf, Panieh, additional, Corson, Laura B, additional, Salama, Yasser, additional, Campbell, Katie M, additional, Farncombe, Kirsten M, additional, Ji, Jianling, additional, Zhao, Xiaonan, additional, Xu, Xinjie, additional, Kanagal-Shamanna, Rashmi, additional, King, Ian, additional, Cotto, Kelsy C, additional, Skidmore, Zachary L, additional, Walker, Jason R, additional, Zhang, Jinghui, additional, Milosavljevic, Aleksandar, additional, Patel, Ronak Y, additional, Giles, Rachel H, additional, Kim, Raymond H, additional, Schriml, Lynn M, additional, Mardis, Elaine R, additional, Jones, Steven J M, additional, Raca, Gordana, additional, Rao, Shruti, additional, Madhavan, Subha, additional, Wagner, Alex H, additional, Griffith, Malachi, additional, and Griffith, Obi L, additional

Published
2022
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14. Biomarker-driven therapies for metastatic uveal melanoma: A prospective precision oncology feasibility study

Author

Leyvraz, Serge, primary, Konietschke, Frank, additional, Peuker, Caroline, additional, Schütte, Moritz, additional, Kessler, Thomas, additional, Ochsenreither, Sebastian, additional, Ditzhaus, Marc, additional, Sprünken, Erin D., additional, Dörpholz, Gina, additional, Lamping, Mario, additional, Rieke, Damian T., additional, Klinghammer, Konrad, additional, Burock, Susen, additional, Ulrich, Claas, additional, Poch, Gabriela, additional, Schäfer, Reinhold, additional, Klauschen, Frederick, additional, Joussen, Antonia, additional, Yaspo, Marie-Laure, additional, and Keilholz, Ulrich, additional

Published
2022
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16. Additional file 1 of Feasibility and outcome of reproducible clinical interpretation of high-dimensional molecular data: a comparison of two molecular tumor boards

Author

Rieke, Damian T., de Bortoli, Till, Horak, Peter, Lamping, Mario, Benary, Manuela, Jelas, Ivan, Rüter, Gina, Berger, Johannes, Zettwitz, Marit, Kagelmann, Niklas, Kind, Andreas, Fabian, Falk, Beule, Dieter, Glimm, Hanno, Brors, Benedikt, Stenzinger, Albrecht, Fröhling, Stefan, and Keilholz, Ulrich

Abstract

Additional file 1: Figure S1. Shows the respective molecular tumor board workflows of Heidelberg (HDB) and Berlin (BLN). Corresponding steps are indicated by their respective colors.

Published
2022
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19. Evolution of the open-access CIViC knowledgebase is driven by the needs of the cancer variant interpretation community

Author

Krysiak, Kilannin, primary, Danos, Arpad M, additional, Kiwala, Susanna, additional, McMichael, Joshua F, additional, Coffman, Adam C, additional, Barnell, Erica K, additional, Sheta, Lana, additional, Saliba, Jason, additional, Grisdale, Cameron J, additional, Kujan, Lynzey, additional, Pema, Shahil, additional, Lever, Jake, additional, Spies, Nicholas C, additional, Chiorean, Andreea, additional, Rieke, Damian T, additional, Clark, Kaitlin A, additional, Jani, Payal, additional, Takahashi, Hideaki, additional, Horak, Peter, additional, Ritter, Deborah I, additional, Zhou, Xin, additional, Ainscough, Benjamin J, additional, Delong, Sean, additional, Lamping, Mario, additional, Marr, Alex R, additional, Li, Brian V, additional, Lin, Wan-Hsin, additional, Terraf, Panieh, additional, Salama, Yasser, additional, Campbell, Katie, additional, Farncombe, Kirsten M, additional, Ji, Jianling, additional, Zhao, Xiaonan, additional, Xu, Xinjie, additional, Kanagal-Shamanna, Rashmi, additional, Cotto, Kelsy C, additional, Skidmore, Zachary L, additional, Walker, Jason R, additional, Zhang, Jinghui, additional, Milosavljevic, Aleksandar, additional, Patel, Ronak Y, additional, Giles, Rachel H, additional, Kim, Raymond H, additional, Schriml, Lynn M, additional, Mardis, Elaine R, additional, Jones, Steven JM, additional, Raca, Gordana, additional, Rao, Shruti, additional, Madhavan, Subha, additional, Wagner, Alex H, additional, Griffith, Obi L, additional, and Griffith, Malachi, additional

Published
2021
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20. Annotation and initial evaluation of a large annotated German oncological corpus

Author

Kittner, Madeleine, Lamping, Mario, Rieke, Damian T., Götze, Julian, Bajwa, Bariya, Jelas, Ivan, Rüter, Gina, Hautow, Hanjo, Sänger, Mario, Habibi, Maryam, Zettwitz, Marit, Bortoli, Till de, Ostermann, Leonie, Ševa, Jurica, Starlinger, Johannes, Kohlbacher, Oliver, Malek, Nisar P., Keilholz, Ulrich, Leser, Ulf, Kittner, Madeleine, Lamping, Mario, Rieke, Damian T., Götze, Julian, Bajwa, Bariya, Jelas, Ivan, Rüter, Gina, Hautow, Hanjo, Sänger, Mario, Habibi, Maryam, Zettwitz, Marit, Bortoli, Till de, Ostermann, Leonie, Ševa, Jurica, Starlinger, Johannes, Kohlbacher, Oliver, Malek, Nisar P., Keilholz, Ulrich, and Leser, Ulf

Abstract

Objective We present the Berlin-Tübingen-Oncology corpus (BRONCO), a large and freely available corpus of shuffled sentences from German oncological discharge summaries annotated with diagnosis, treatments, medications, and further attributes including negation and speculation. The aim of BRONCO is to foster reproducible and openly available research on Information Extraction from German medical texts. Materials and Methods BRONCO consists of 200 manually deidentified discharge summaries of cancer patients. Annotation followed a structured and quality-controlled process involving 2 groups of medical experts to ensure consistency, comprehensiveness, and high quality of annotations. We present results of several state-of-the-art techniques for different IE tasks as baselines for subsequent research. Results The annotated corpus consists of 11 434 sentences and 89 942 tokens, annotated with 11 124 annotations for medical entities and 3118 annotations of related attributes. We publish 75% of the corpus as a set of shuffled sentences, and keep 25% as held-out data set for unbiased evaluation of future IE tools. On this held-out dataset, our baselines reach depending on the specific entity types F1-scores of 0.72–0.90 for named entity recognition, 0.10–0.68 for entity normalization, 0.55 for negation detection, and 0.33 for speculation detection. Discussion Medical corpus annotation is a complex and time-consuming task. This makes sharing of such resources even more important. Conclusion To our knowledge, BRONCO is the first sizable and freely available German medical corpus. Our baseline results show that more research efforts are necessary to lift the quality of information extraction in German medical texts to the level already possible for English., Peer Reviewed

Published
2021

21. Annotation and initial evaluation of a large annotated German oncological corpus

Author

Kittner, Madeleine, primary, Lamping, Mario, additional, Rieke, Damian T, additional, Götze, Julian, additional, Bajwa, Bariya, additional, Jelas, Ivan, additional, Rüter, Gina, additional, Hautow, Hanjo, additional, Sänger, Mario, additional, Habibi, Maryam, additional, Zettwitz, Marit, additional, Bortoli, Till de, additional, Ostermann, Leonie, additional, Ševa, Jurica, additional, Starlinger, Johannes, additional, Kohlbacher, Oliver, additional, Malek, Nisar P, additional, Keilholz, Ulrich, additional, and Leser, Ulf, additional

Published
2021
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23. Abstract 3222: The Virtual Molecular Tumor Board of the Variant Interpretation for Cancer Consortium: A systematic gateway connecting cancer genome interpretation and progress in genomic knowledgebases in cancer

Author

Pitel, Beth A., primary, Rao, Shruti, additional, Fitz, Catherine Del Vecchio, additional, Madhavan, Subha, additional, Dientsmann, Rodrigo, additional, Horak, Peter, additional, King, Ian, additional, Mockus, Susan M., additional, Raca, Gordana, additional, Rieke, Damian T., additional, Rogan, Peter, additional, Sonkin, Dmitriy, additional, Tamborero, David, additional, Vlachos, Ioannis S., additional, Walsh, Brian, additional, Warner, Jeremy L., additional, Griffith, Malachi, additional, Griffith, Obi L., additional, Chakravarty, Debyani, additional, and Wagner, Alex H., additional

Published
2020
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24. Distinct immune evasion in APOBEC ‐enriched, HPV ‐negative HNSCC

Author

Messerschmidt, Clemens, primary, Obermayer, Benedikt, additional, Klinghammer, Konrad, additional, Ochsenreither, Sebastian, additional, Treue, Denise, additional, Stenzinger, Albrecht, additional, Glimm, Hanno, additional, Fröhling, Stefan, additional, Kindler, Thomas, additional, Brandts, Christian H., additional, Schulze‐Osthoff, Klaus, additional, Weichert, Wilko, additional, Tinhofer, Ingeborg, additional, Klauschen, Frederick, additional, Keilholz, Ulrich, additional, Beule, Dieter, additional, and Rieke, Damian T., additional

Published
2020
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25. Support of a molecular tumour board by an evidence-based decision management system for precision oncology

Author

Lamping, Mario, primary, Benary, Manuela, additional, Leyvraz, Serge, additional, Messerschmidt, Clemens, additional, Blanc, Eric, additional, Kessler, Thomas, additional, Schütte, Moritz, additional, Lenze, Dido, additional, Jöhrens, Korinna, additional, Burock, Susen, additional, Klinghammer, Konrad, additional, Ochsenreither, Sebastian, additional, Sers, Christine, additional, Schäfer, Reinhold, additional, Tinhofer, Ingeborg, additional, Beule, Dieter, additional, Klauschen, Frederick, additional, Yaspo, Marie-Laure, additional, Keilholz, Ulrich, additional, and Rieke, Damian T., additional

Published
2020
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26. A harmonized meta-knowledgebase of clinical interpretations of cancer genomic variants

Author

Wagner, Alex H, Walsh, Brian, Mayfield, Georgia, Tamborero, David, Sonkin, Dmitriy, Krysiak, Kilannin, Pons, Jordi Deu, Duren, Ryan P, Gao, Jianjiong, McMurry, Julie, Patterson, Sara, Del Vecchio Fitz, Catherine, Sezerman, Ozman U, Warner, Jeremy L, Rieke, Damian T, Aittokallio, Tero, Cerami, Ethan, Ritter, Deborah, Schriml, Lynn M, Freimuth, Robert R, Haendel, Melissa, Raca, Gordana, Madhavan, Subha, Baudis, Michael, Beckmann, Jacques S, Dienstmann, Rodrigo, Chakravarty, Debyani, Li, Xuan Shirley, Mockus, Susan, Elemento, Olivier, Schultz, Nikolaus, Lopez-Bigas, Nuria, Lawler, Mark, Goecks, Jeremy, Griffith, Malachi, Griffith, Obi L, and Margolin, Adam A

Subjects
Structure (mathematical logic), 0303 health sciences, Matching (statistics), Interpretation (philosophy), Cancer, Genomics, Computational biology, Biology, medicine.disease, 3. Good health, 03 medical and health sciences, 0302 clinical medicine, Precision oncology, 030220 oncology & carcinogenesis, medicine, Relevance (information retrieval), 030304 developmental biology
Abstract

Precision oncology relies on the accurate discovery and interpretation of genomic variants to enable individualized diagnosis, prognosis, and therapy selection. We found that knowledgebases containing clinical interpretations of somatic cancer variants are highly disparate in interpretation content, structure, and supporting primary literature, impeding consensus when evaluating variants and their relevance in a clinical setting. With the cooperation of experts of the Global Alliance for Genomics and Health (GA4GH) and six prominent cancer variant knowledgebases, we developed a framework for aggregating and harmonizing variant interpretations to produce a meta-knowledgebase of 12,856 aggregate interpretations covering 3,437 unique variants in 415 genes, 357 diseases, and 791 drugs. We demonstrated large gains in overlap between resources across variants, diseases, and drugs as a result of this harmonization. We subsequently demonstrated improved matching between a patient cohort and harmonized interpretations of potential clinical significance, observing an increase from an average of 33% per individual knowledgebase to 56% in aggregate. Our analyses illuminate the need for open, interoperable sharing of variant interpretation data. We also provide an open and freely available web interface (search.cancervariants.org) for exploring the harmonized interpretations from these six knowledgebases.

Published
2018
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27. Abstract 919: Clinical relevance of comprehensive genomic analysis in patients with advanced-stage neuroendocrine neoplasms: Results from the MASTER trial of the German Cancer Consortium

Author

Kreutzfeldt, Simon, primary, Apostolidis, Leonidas, additional, Oles, Malgorzata, additional, Horak, Peter, additional, Heilig, Christoph E., additional, Heining, Christoph, additional, Hutter, Barbara, additional, Gieldon, Laura, additional, Klink, Barbara, additional, Lamping, Mario, additional, Rieke, Damian T., additional, Uhrig, Sebastian, additional, Jann, Henning, additional, Pape, Ulrich F., additional, Stenzinger, Albrecht, additional, Winkler, Eva C., additional, Wiedenmann, Bertram, additional, Jäger, Dirk, additional, Brors, Benedikt, additional, Schröck, Evelin, additional, Keilholz, Ulrich, additional, Pavel, Marianne, additional, Glimm, Hanno, additional, and Fröhling, Stefan, additional

Published
2019
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28. Distinct immune evasion in APOBEC-enriched, HPV-negative HNSCC

Author

Messerschmidt, Clemens, primary, Obermayer, Benedikt, additional, Klinghammer, Konrad, additional, Ochsenreither, Sebastian, additional, Treue, Denise, additional, Stenzinger, Albrecht, additional, Glimm, Hanno, additional, Fröhling, Stefan, additional, Kindler, Thomas, additional, Brandts, Christian H., additional, Schulze-Osthoff, Klaus, additional, Weichert, Wilko, additional, Tinhofer, Ingeborg, additional, Klauschen, Frederick, additional, Keilholz, Ulrich, additional, Beule, Dieter, additional, and Rieke, Damian T., additional

Published
2019
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30. Validating Comprehensive Next-Generation Sequencing Results for Precision Oncology: The NCT/DKTK Molecularly Aided Stratification for Tumor Eradication Research Experience

Author

Lier, Amelie, primary, Penzel, Roland, additional, Heining, Christoph, additional, Horak, Peter, additional, Fröhlich, Martina, additional, Uhrig, Sebastian, additional, Budczies, Jan, additional, Kirchner, Martina, additional, Volckmar, Anna-Lena, additional, Hutter, Barbara, additional, Kreutzfeldt, Simon, additional, Endris, Volker, additional, Richter, Daniela, additional, Wolf, Stephan, additional, Pfütze, Katrin, additional, Neumann, Olaf, additional, Buchhalter, Ivo, additional, Morais de Oliveira, Cristiano M., additional, Singer, Stephan, additional, Leichsenring, Jonas, additional, Herpel, Esther, additional, Klauschen, Frederick, additional, Jost, Philipp J., additional, Metzeler, Klaus H., additional, Schulze-Osthoff, Klaus, additional, Kopp, Hans-Georg, additional, Kindler, Thomas, additional, Rieke, Damian T., additional, Lamping, Mario, additional, Brandts, Christian, additional, Falkenhorst, Johanna, additional, Bauer, Sebastian, additional, Schröck, Evelin, additional, Folprecht, Gunnar, additional, Boerries, Melanie, additional, von Bubnoff, Nikolas, additional, Weichert, Wilko, additional, Brors, Benedikt, additional, Lichter, Peter, additional, von Kalle, Christof, additional, Schirmacher, Peter, additional, Glimm, Hanno, additional, Fröhling, Stefan, additional, and Stenzinger, Albrecht, additional

Published
2018
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31. CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer

Author

Griffith, Malachi, primary, Spies, Nicholas C, additional, Krysiak, Kilannin, additional, McMichael, Joshua F, additional, Coffman, Adam C, additional, Danos, Arpad M, additional, Ainscough, Benjamin J, additional, Ramirez, Cody A, additional, Rieke, Damian T, additional, Kujan, Lynzey, additional, Barnell, Erica K, additional, Wagner, Alex H, additional, Skidmore, Zachary L, additional, Wollam, Amber, additional, Liu, Connor J, additional, Jones, Martin R, additional, Bilski, Rachel L, additional, Lesurf, Robert, additional, Feng, Yan-Yang, additional, Shah, Nakul M, additional, Bonakdar, Melika, additional, Trani, Lee, additional, Matlock, Matthew, additional, Ramu, Avinash, additional, Campbell, Katie M, additional, Spies, Gregory C, additional, Graubert, Aaron P, additional, Gangavarapu, Karthik, additional, Eldred, James M, additional, Larson, David E, additional, Walker, Jason R, additional, Good, Benjamin M, additional, Wu, Chunlei, additional, Su, Andrew I, additional, Dienstmann, Rodrigo, additional, Margolin, Adam A, additional, Tamborero, David, additional, Lopez-Bigas, Nuria, additional, Jones, Steven J M, additional, Bose, Ron, additional, Spencer, David H, additional, Wartman, Lukas D, additional, Wilson, Richard K, additional, Mardis, Elaine R, additional, and Griffith, Obi L, additional

Published
2017
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32. A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer

Author

Wagner, Alex H., Walsh, Brian, Mayfield, Georgia, Tamborero, David, Sonkin, Dmitriy, Krysiak, Kilannin, Deu-Pons, Jordi, Duren, Ryan P., Gao, Jianjiong, McMurry, Julie, Patterson, Sara, del Vecchio Fitz, Catherine, Pitel, Beth A., Sezerman, Ozman U., Ellrott, Kyle, Warner, Jeremy L., Rieke, Damian T., Aittokallio, Tero, Cerami, Ethan, Ritter, Deborah I., Schriml, Lynn M., Freimuth, Robert R., Haendel, Melissa, Raca, Gordana, Madhavan, Subha, Baudis, Michael, Beckmann, Jacques S., Dienstmann, Rodrigo, Chakravarty, Debyani, Li, Xuan Shirley, Mockus, Susan, Elemento, Olivier, Schultz, Nikolaus, Lopez-Bigas, Nuria, Lawler, Mark, Goecks, Jeremy, Griffith, Malachi, Griffith, Obi L., and Margolin, Adam A.

Abstract

Precision oncology relies on accurate discovery and interpretation of genomic variants, enabling individualized diagnosis, prognosis and therapy selection. We found that six prominent somatic cancer variant knowledgebases were highly disparate in content, structure and supporting primary literature, impeding consensus when evaluating variants and their relevance in a clinical setting. We developed a framework for harmonizing variant interpretations to produce a meta-knowledgebase of 12,856 aggregate interpretations. We demonstrated large gains in overlap between resources across variants, diseases and drugs as a result of this harmonization. We subsequently demonstrated improved matching between a patient cohort and harmonized interpretations of potential clinical significance, observing an increase from an average of 33% per individual knowledgebase to 57% in aggregate. Our analyses illuminate the need for open, interoperable sharing of variant interpretation data. We also provide a freely available web interface (search.cancervariants.org) for exploring the harmonized interpretations from these six knowledgebases.

Published
2020
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34. CIViC: A knowledgebase for expert-crowdsourcing the clinical interpretation of variants in cancer

Author

Griffith, Malachi, primary, Spies, Nicholas C, additional, Krysiak, Kilannin, additional, Coffman, Adam C, additional, McMichael, Joshua F, additional, Ainscough, Benjamin J, additional, Rieke, Damian T, additional, Danos, Arpad M, additional, Kujan, Lynzey, additional, Ramirez, Cody A, additional, Wagner, Alex H, additional, Skidmore, Zachary L, additional, Liu, Connor J, additional, Jones, Martin R, additional, Bilski, Rachel L, additional, Lesurf, Robert, additional, Barnell, Erica K, additional, Shah, Nakul M, additional, Bonakdar, Melika, additional, Trani, Lee, additional, Matlock, Matthew, additional, Ramu, Avinash, additional, Campbell, Katie M, additional, Spies, Gregory C, additional, Graubert, Aaron P, additional, Gangavarapu, Karthik, additional, Eldred, James M, additional, Larson, David E, additional, Walker, Jason R, additional, Good, Benjamin M, additional, Wu, Chunlei, additional, Su, Andrew I, additional, Dienstmann, Rodrigo, additional, Jones, Steven JM, additional, Bose, Ron, additional, Spencer, David H, additional, Wartman, Lukas D, additional, Wilson, Richard K, additional, Mardis, Elaine R, additional, and Griffith, Obi L, additional

Published
2016
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37. A diagnostic challenge of KIT p.V559D and BRAF p.G469A mutations in a paragastric mass.

Author

Habringer S, Ihlow J, Kleo K, Klostermann A, Schmidt M, Chai L, Knödler M, Leyvraz S, Sigler C, Sinn B, Maschmeyer G, Jegodka Y, Benary M, Ott CE, Tinhofer I, Schäfer R, Möbs M, Keller U, Keilholz U, and Rieke DT

Abstract

A patient with gastrointestinal stroma tumor (GIST) and KIT p.V559D and BRAF p.G469A alterations was referred to our institutional molecular tumor board (MTB) to discuss therapeutic implications. The patient had been diagnosed with B-cell chronic lymphocytic leukemia (CLL) years prior to the MTB presentation. GIST had been diagnosed 1 month earlier. After structured clinical annotation of the molecular alterations and interdisciplinary discussion, we considered BRAF/KIT co-mutation unlikely in a treatment-naïve GIST. Discordant variant allele frequencies furthermore suggested a second malignancy. NGS of a CLL sample revealed the identical class 2 BRAF alteration, thus supporting admixture of CLL cells in the paragastric mass, leading to the detection of 2 alterations. Following the MTB recommendation, the patient received imatinib and had a radiographic response. Structured annotation and interdisciplinary discussion in specialized tumor boards facilitate the clinical management of complex molecular findings. Coexisting malignancies and clonal hematopoiesis warrant consideration in case of complex and uncommon molecular findings., (© The Author(s) 2024. Published by Oxford University Press.)

Published
2024
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