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Rieke DT, Schmalbrock LK, Ihlow J, Kleo K, von Brünneck AC, Nolte F, Keller U, Ochsenreither S. Renal Extramedullary Hematopoiesis in Mast Cell Leukemia with Bone Marrow Fibrosis. Case Rep Hematol 2024; 2024:3502887. [PMID: 38213502 PMCID: PMC10781526 DOI: 10.1155/2024/3502887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 01/13/2024] Open
Abstract
Systemic mastocytosis is defined by the clonal proliferation of abnormal mast cells. The clinical course can range from indolent forms with normal life expectancy to advanced mast cell leukemia with dismal prognosis. An association with other diseases, including myeloproliferative neoplasia, has been described. We present a case of a 75-year patient with a history of cutaneous mastocytosis who was diagnosed with mast cell leukemia more than 9 years ago and did not receive treatment. The patient presented to our clinic with acute kidney failure because of renal extramedullary hematopoiesis. Bone marrow histopathology revealed extensive fibrosis and 50% infiltration by mast cells with a c-KIT D816V mutation. No mutations supporting primary myelofibrosis were identified. Treatment with midostaurin was started, and the patient was discharged after improvement of renal function. Here, we discuss diagnostic challenges between different forms of mast cell leukemia and overlaps with other hematological malignancies.
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Affiliation(s)
- Damian T Rieke
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Hindenburgdamm 30, Berlin 12203, Germany
- Berlin Institute of Health (BIH) at Charité, Universitätsmedizin Berlin, Anna-Louisa-Karsch-Straße 2, Berlin 10178, Germany
- German Cancer Consortium (DKTK) Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Laura K Schmalbrock
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Hindenburgdamm 30, Berlin 12203, Germany
- Berlin Institute of Health (BIH) at Charité, Universitätsmedizin Berlin, Anna-Louisa-Karsch-Straße 2, Berlin 10178, Germany
- German Cancer Consortium (DKTK) Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jana Ihlow
- Berlin Institute of Health (BIH) at Charité, Universitätsmedizin Berlin, Anna-Louisa-Karsch-Straße 2, Berlin 10178, Germany
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Charitéplatz 1, Berlin 10117, Germany
| | - Karsten Kleo
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Charitéplatz 1, Berlin 10117, Germany
| | | | - Florian Nolte
- Praxis Onkologie Seestrasse, Seestrasse 64, Berlin 13347, Germany
| | - Ulrich Keller
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Hindenburgdamm 30, Berlin 12203, Germany
- Berlin Institute of Health (BIH) at Charité, Universitätsmedizin Berlin, Anna-Louisa-Karsch-Straße 2, Berlin 10178, Germany
- German Cancer Consortium (DKTK) Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sebastian Ochsenreither
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Hindenburgdamm 30, Berlin 12203, Germany
- German Cancer Consortium (DKTK) Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
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Benary M, Wang XD, Schmidt M, Soll D, Hilfenhaus G, Nassir M, Sigler C, Knödler M, Keller U, Beule D, Keilholz U, Leser U, Rieke DT. Leveraging Large Language Models for Decision Support in Personalized Oncology. JAMA Netw Open 2023; 6:e2343689. [PMID: 37976064 PMCID: PMC10656647 DOI: 10.1001/jamanetworkopen.2023.43689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/04/2023] [Indexed: 11/19/2023] Open
Abstract
Importance Clinical interpretation of complex biomarkers for precision oncology currently requires manual investigations of previous studies and databases. Conversational large language models (LLMs) might be beneficial as automated tools for assisting clinical decision-making. Objective To assess performance and define their role using 4 recent LLMs as support tools for precision oncology. Design, Setting, and Participants This diagnostic study examined 10 fictional cases of patients with advanced cancer with genetic alterations. Each case was submitted to 4 different LLMs (ChatGPT, Galactica, Perplexity, and BioMedLM) and 1 expert physician to identify personalized treatment options in 2023. Treatment options were masked and presented to a molecular tumor board (MTB), whose members rated the likelihood of a treatment option coming from an LLM on a scale from 0 to 10 (0, extremely unlikely; 10, extremely likely) and decided whether the treatment option was clinically useful. Main Outcomes and Measures Number of treatment options, precision, recall, F1 score of LLMs compared with human experts, recognizability, and usefulness of recommendations. Results For 10 fictional cancer patients (4 with lung cancer, 6 with other; median [IQR] 3.5 [3.0-4.8] molecular alterations per patient), a median (IQR) number of 4.0 (4.0-4.0) compared with 3.0 (3.0-5.0), 7.5 (4.3-9.8), 11.5 (7.8-13.0), and 13.0 (11.3-21.5) treatment options each was identified by the human expert and 4 LLMs, respectively. When considering the expert as a criterion standard, LLM-proposed treatment options reached F1 scores of 0.04, 0.17, 0.14, and 0.19 across all patients combined. Combining treatment options from different LLMs allowed a precision of 0.29 and a recall of 0.29 for an F1 score of 0.29. LLM-generated treatment options were recognized as AI-generated with a median (IQR) 7.5 (5.3-9.0) points in contrast to 2.0 (1.0-3.0) points for manually annotated cases. A crucial reason for identifying AI-generated treatment options was insufficient accompanying evidence. For each patient, at least 1 LLM generated a treatment option that was considered helpful by MTB members. Two unique useful treatment options (including 1 unique treatment strategy) were identified only by LLM. Conclusions and Relevance In this diagnostic study, treatment options of LLMs in precision oncology did not reach the quality and credibility of human experts; however, they generated helpful ideas that might have complemented established procedures. Considering technological progress, LLMs could play an increasingly important role in assisting with screening and selecting relevant biomedical literature to support evidence-based, personalized treatment decisions.
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Affiliation(s)
- Manuela Benary
- Charité Comprehensive Cancer Center, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Core Unit Bioinformatics, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Charitéplatz 1, Berlin, Germany
| | - Xing David Wang
- Knowledge Management in Bioinformatics, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Max Schmidt
- Charité Comprehensive Cancer Center, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Dominik Soll
- Charité Comprehensive Cancer Center, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Endocrinology and Metabolic Diseases, Charité Universitätsmedizin Berlin, Department of Endocrinology and Metabolic Diseases, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Georg Hilfenhaus
- Charité Comprehensive Cancer Center, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Hematology, Oncology and Cancer Immunology, Campus Charité Mitte, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Mani Nassir
- Charité Comprehensive Cancer Center, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Hematology, Oncology and Cancer Immunology, Campus Charité Mitte, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Christian Sigler
- Charité Comprehensive Cancer Center, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Maren Knödler
- Charité Comprehensive Cancer Center, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Ulrich Keller
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium and German Cancer Research Center, Partner Site Berlin, Germany
| | - Dieter Beule
- Core Unit Bioinformatics, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Charitéplatz 1, Berlin, Germany
| | - Ulrich Keilholz
- Charité Comprehensive Cancer Center, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium and German Cancer Research Center, Partner Site Berlin, Germany
| | - Ulf Leser
- Knowledge Management in Bioinformatics, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Damian T. Rieke
- Charité Comprehensive Cancer Center, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium and German Cancer Research Center, Partner Site Berlin, Germany
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de Bortoli T, Benary M, Horak P, Lamping M, Stintzing S, Tinhofer I, Leyvraz S, Schäfer R, Klauschen F, Keller U, Stenzinger A, Fröhling S, Kurzrock R, Keilholz U, Rieke DT, Jelas I. Tumour mutational burden and survival with molecularly matched therapy. Eur J Cancer 2023; 190:112925. [PMID: 37544709 DOI: 10.1016/j.ejca.2023.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/15/2023] [Accepted: 05/18/2023] [Indexed: 08/08/2023]
Abstract
BACKGROUND The impact of tumour mutational burden (TMB) on outcome with molecularly matched therapy is unknown. Higher TMB could predict resistance to molecularly matched therapy through co-occurring driver mutations. METHODS One hundred and four patients with advanced cancers underwent molecular profiling in the DKTK-MASTER program. Fifty-five patients received systemic therapy excluding immunotherapy. Patients with molecularly matched (n = 35) or non-molecularly informed therapy (n = 20) were analysed for TMB and survival. Results were validated in an independent cohort of patients receiving molecularly matched (n = 68) or non-molecularly informed therapy (n = 40). Co-occurring driver mutations and TMB were analysed in the exploratory cohort and The Cancer Genome Atlas (TCGA) datasets. RESULTS Patients were stratified by the median TMB of 1.67 mutations per Megabase (mut/Mb) of 35 patients receiving molecularly matched therapy into TMB-high or TMB-low groups. Median overall survival (4 months [95% CI, 3.3-7.6] versus 12.8 months [95% CI, 10-not reached], p < 0.001) and progression-free survival (1.8 months [95% CI, 1.1-3.7] versus 7.9 months [95% CI, 2.8-17.0], p = 0.003) were significantly shorter in the TMB-high group compared to the TMB-low group. In the validation cohort, shorter OS and PFS were identified in the TMB-high group (TMB cut-off of 4 mut/Mb) treated with molecularly matched therapy. No differences were observed in patients receiving non-molecularly informed systemic therapy. A significant correlation between co-occurring driver mutations and TMB (n = 104, r = 0.78 [95% CI, 0.68-0.85], p < 0.001) was found in the exploratory cohort as well as the majority (24/33) of TCGA studies. CONCLUSION A high TMB was associated with unfavourable outcome in patients receiving molecularly matched therapy, indicating untargeted resistance pathways. Therefore, TMB should be further investigated as a predictive biomarker in precision oncology programs.
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Affiliation(s)
- Till de Bortoli
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Manuela Benary
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany; Core Unit Bioinformatics, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Peter Horak
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Sites Berlin and Heidelberg, Germany; Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mario Lamping
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany; Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Hindenburgdamm 30, 12203 Berlin, Germany
| | - Sebastian Stintzing
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Sites Berlin and Heidelberg, Germany; Department of Hematology, Oncology and Cancer Immunology, Campus Charité Mitte, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Ingeborg Tinhofer
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Sites Berlin and Heidelberg, Germany; Department of Radiooncology and Radiotherapy, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Serge Leyvraz
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Reinhold Schäfer
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Sites Berlin and Heidelberg, Germany
| | - Frederick Klauschen
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Sites Berlin and Heidelberg, Germany; Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Ulrich Keller
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Sites Berlin and Heidelberg, Germany; Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Hindenburgdamm 30, 12203 Berlin, Germany
| | - Albrecht Stenzinger
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Sites Berlin and Heidelberg, Germany; Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan Fröhling
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Sites Berlin and Heidelberg, Germany; Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Razelle Kurzrock
- Worldwide Innovative Network (WIN) Association-WIN Consortium, Villejuif, France
| | - Ulrich Keilholz
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Sites Berlin and Heidelberg, Germany
| | - Damian T Rieke
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Sites Berlin and Heidelberg, Germany; Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Hindenburgdamm 30, 12203 Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany.
| | - Ivan Jelas
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany; Department of Hematology, Oncology and Cancer Immunology, Campus Charité Mitte, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany.
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Rieke DT, Schröder S, Schafhausen P, Blanc E, Zuljan E, von der Emde B, Beule D, Keller U, Keilholz U, Klinghammer K. Targeted treatment in a case series of AR+, HRAS/PIK3CA co-mutated salivary duct carcinoma. Front Oncol 2023; 13:1107134. [PMID: 37427101 PMCID: PMC10325704 DOI: 10.3389/fonc.2023.1107134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 05/26/2023] [Indexed: 07/11/2023] Open
Abstract
Background and purpose A subgroup of salivary duct carcinoma (SDC) harbor overexpression of the androgen receptor (AR), and co-occurring mutations in the HRAS- and PIK3CA-genes. The impact of genomic complexity on targeted treatment strategies in advanced cancer is unknown. Materials and methods We analyzed molecular and clinical data from an institutional molecular tumor board (MTB) to identify AR+, HRAS/PIK3CA co-mutated SDC. Follow-up was performed within the MTB registrational study or retrospective chart review after approval by the local ethics committee. Response was assessed by the investigator. A systematic literature search was performed in MEDLINE to identify additional clinically annotated cases. Results 4 patients with AR+ HRAS/PIK3CA co-mutated SDC and clinical follow-up data were identified from the MTB. An additional 9 patients with clinical follow-up were identified from the literature. In addition to AR overexpression and HRAS and PIK3CA-alterations, PD-L1 expression and Tumor Mutational Burden > 10 Mutations per Megabase were identified as additional potentially targetable alterations. Among evaluable patients, androgen deprivation therapy (ADT) was initiated in 7 patients (1 Partial Response (PR), 2 Stable Disease (SD), 3 Progressive Disease (PD), 2 not evaluable), tipifarnib was initiated in 6 patients (1 PR, 4 SD, 1 PD). One patient each was treated with immune checkpoint inhibition (Mixed Response) and combination therapies of tipifarnib and ADT (SD) and alpelisib and ADT (PR). Conclusion Available data further support comprehensive molecular profiling of SDC. Combination therapies, PI3K-inhibitors and immune therapy warrant further investigation, ideally in clinical trials. Future research should consider this rare subgroup of SDC.
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Affiliation(s)
- Damian T. Rieke
- Department of Hematology, Oncology and Cancer Immunology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Comprehensive Cancer Center, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health (BIH) at Charité – Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sebastian Schröder
- Department of Hematology, Oncology and Cancer Immunology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Philippe Schafhausen
- Department of Oncology, Hematology, and Bone Marrow Transplantation with Section of Pneumology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Eric Blanc
- Berlin Institute of Health (BIH) at Charité – Universitätsmedizin Berlin, Berlin, Germany
- Core Unit Bioinformatics (CUBI), Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Erika Zuljan
- Berlin Institute of Health (BIH) at Charité – Universitätsmedizin Berlin, Berlin, Germany
- Core Unit Bioinformatics (CUBI), Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Benjamin von der Emde
- Department of Hematology, Oncology and Cancer Immunology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Dieter Beule
- Berlin Institute of Health (BIH) at Charité – Universitätsmedizin Berlin, Berlin, Germany
- Core Unit Bioinformatics (CUBI), Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Ulrich Keller
- Department of Hematology, Oncology and Cancer Immunology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Ulrich Keilholz
- Comprehensive Cancer Center, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Konrad Klinghammer
- Department of Hematology, Oncology and Cancer Immunology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
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Möhrmann L, Rostock L, Oleś M, Jahn A, Arlt M, Paramasivam N, Jöhrens K, Rupp L, Schmitz M, Richter D, Uhrig S, Fröhlich M, Hutter B, Hüllein J, Wolf EE, Hanf D, Gieldon L, Kreutzfeldt S, Heilig CE, Teleanu V, Lipka DB, Mock A, Jelas I, Rieke DT, Wiesweg M, Boerries M, Illert AL, Desuki A, Kindler T, Krackhardt AM, Westphalen CB, Grosch H, Apostolidis L, Stenzinger A, Kerle IA, Heining C, Hübschmann D, Schröck E, Fröhling S, Glimm H. Abstract 926: Genomics-based personalized oncology of advanced thymic epithelial tumors. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Introduction: Thymic epithelial tumors (TETs) are very rare. Thymoma A and AB have a better prognosis than more aggressive thymoma B, thymic carcinoma (TC) and neuroendocrine tumors of the thymus (NET). While previous efforts such as TCGA have mainly characterized thymomas (Radovich et al., Cancer Cell 2018), the molecular landscape of TCs and NETs is still elusive.
Patients and Methods: Between 03/2014 and 07/2020, we enrolled 44 TET patients (27 TCs, 11 thymomas, 6 NETs) in a prospective observational study (MASTER) conducted by the National Center for Tumor Diseases (NCT) Heidelberg, NCT Dresden and the German Cancer Consortium (DKTK). MASTER applied whole genome/exome sequencing (WGS, n=22; WES, n=22), transcriptome (n=40) and germline analysis to inform therapy recommendations by a dedicated molecular tumor board (MTB). We systematically gathered follow-up data to evaluate outcome and compared progression-free survival (PFS) of the first treatment according to an MTB recommendation (PFS2) to the last prior systemic treatment (PFS1) in each patient (PFS ratio).
Results: Tumor mutational burden (TMB) was low (median=0.99 mutations/Mb, range 0.08-3.48) but higher than in TCGA (p<0.05). TMB was higher in TCs than in thymoma (p<0.05). Most frequently mutated genes were TP53 (30%), CYLD (16%), SETD2 (14%) and KIT (14%). Germline analysis revealed (likely) pathogenic germline alterations in 25% of patients (MUTYH, n=3; BRCA1, n=2; BRCA2, BAP1, CHEK2, FANCA, TP53, MEN1, n=1). A comprehensive analysis of candidate biomarkers of homologous recombination repair (HRR) defects revealed a subgroup of TET patients with a rationale for PARP inhibitor therapy. Unsupervised clustering of RNA sequencing data mainly revealed clustering that correlated with WHO classification. Additionally, TCs clustered in two subgroups that we identified as immunologically hot and cold tumors using immunohistochemistry validation. Overall survival of patients with hot tumors was significantly longer (p<0.05). The MTB recommended therapies for 42 patients (95%), which were implemented in 24 cases (57%). Five patients had a PFS2 > 6 months and a PFS ratio > 1.3. The best outcome was achieved using imatinib in a patient with a KIT mutation (p.W557R). After progression, the MTB recommended ponatinib based on a secondary KIT mutation (p.V654A). The patient was still on ponatinib when the observation period ended.
Conclusion: We demonstrate that comprehensive molecular analysis provides clinically relevant information in a subgroup of TET patients. Thymoma, TCs, and NETs present with different molecular characteristics. Distinction between immunologically hot and cold TCs may have value for risk stratification and therapeutic strategies. PARP inhibition could be a potential new treatment option in a small subgroup of TETs. Molecular testing of KIT, germline analysis and genetic counseling should be recommended for all patients with advanced TETs.
Citation Format: Lino Möhrmann, Lysann Rostock, Małgorzata Oleś, Arne Jahn, Marie Arlt, Nagarajan Paramasivam, Korinna Jöhrens, Luise Rupp, Marc Schmitz, Daniela Richter, Sebastian Uhrig, Martina Fröhlich, Barbara Hutter, Jennifer Hüllein, Elena E. Wolf, Dorothea Hanf, Laura Gieldon, Simon Kreutzfeldt, Christoph E. Heilig, Veronica Teleanu, Daniel B. Lipka, Andreas Mock, Ivan Jelas, Damian T. Rieke, Marcel Wiesweg, Melanie Boerries, Anna L. Illert, Alexander Desuki, Thomas Kindler, Angela M. Krackhardt, C. Benedikt Westphalen, Heidrun Grosch, Leonidas Apostolidis, Albrecht Stenzinger, Irina A. Kerle, Christoph Heining, Daniel Hübschmann, Evelin Schröck, Stefan Fröhling, Hanno Glimm. Genomics-based personalized oncology of advanced thymic epithelial tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 926.
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Affiliation(s)
- Lino Möhrmann
- 1National Center for Tumor Diseases (NCT), Dresden, Germany
| | - Lysann Rostock
- 1National Center for Tumor Diseases (NCT), Dresden, Germany
| | | | - Arne Jahn
- 3Institute for Clinical Genetics, Technische Universität Dresden, Dresden, Germany
| | - Marie Arlt
- 3Institute for Clinical Genetics, Technische Universität Dresden, Dresden, Germany
| | | | | | - Luise Rupp
- 5Institute of Immunology, Technische Universität Dresden, Dresden, Germany
| | - Marc Schmitz
- 5Institute of Immunology, Technische Universität Dresden, Dresden, Germany
| | | | | | | | - Barbara Hutter
- 2German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Elena E. Wolf
- 1National Center for Tumor Diseases (NCT), Dresden, Germany
| | - Dorothea Hanf
- 1National Center for Tumor Diseases (NCT), Dresden, Germany
| | - Laura Gieldon
- 6Institute of Medical Genetics, Carl von Ossietzky University, Oldenburg, Germany
| | | | | | | | - Daniel B. Lipka
- 7National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Andreas Mock
- 8Institute of Pathology, Ludwig-Maximilians-Universität München (LMU), Munich, Germany
| | - Ivan Jelas
- 9Charité Comprehensive Cancer Center, Berlin, Germany
| | | | - Marcel Wiesweg
- 10West German Cancer Center, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Melanie Boerries
- 11Medical Center - University of Freiburg, Freiburg im Breisgau, Germany
| | - Anna L. Illert
- 11Medical Center - University of Freiburg, Freiburg im Breisgau, Germany
| | - Alexander Desuki
- 12University Cancer Center, University Medical Center Mainz, Mainz, Germany
| | - Thomas Kindler
- 12University Cancer Center, University Medical Center Mainz, Mainz, Germany
| | - Angela M. Krackhardt
- 13Klinikum Rechts der Isar, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | | | - Heidrun Grosch
- 15Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany
| | | | - Albrecht Stenzinger
- 16Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Irina A. Kerle
- 1National Center for Tumor Diseases (NCT), Dresden, Germany
| | | | | | - Evelin Schröck
- 3Institute for Clinical Genetics, Technische Universität Dresden, Dresden, Germany
| | - Stefan Fröhling
- 7National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Hanno Glimm
- 1National Center for Tumor Diseases (NCT), Dresden, Germany
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6
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Rieke DT, de Bortoli T, Horak P, Lamping M, Benary M, Jelas I, Rüter G, Berger J, Zettwitz M, Kagelmann N, Kind A, Fabian F, Beule D, Glimm H, Brors B, Stenzinger A, Fröhling S, Keilholz U. Feasibility and outcome of reproducible clinical interpretation of high-dimensional molecular data: a comparison of two molecular tumor boards. BMC Med 2022; 20:367. [PMID: 36274133 PMCID: PMC9590222 DOI: 10.1186/s12916-022-02560-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 09/09/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Structured and harmonized implementation of molecular tumor boards (MTB) for the clinical interpretation of molecular data presents a current challenge for precision oncology. Heterogeneity in the interpretation of molecular data was shown for patients even with a limited number of molecular alterations. Integration of high-dimensional molecular data, including RNA- (RNA-Seq) and whole-exome sequencing (WES), is expected to further complicate clinical application. To analyze challenges for MTB harmonization based on complex molecular datasets, we retrospectively compared clinical interpretation of WES and RNA-Seq data by two independent molecular tumor boards. METHODS High-dimensional molecular cancer profiling including WES and RNA-Seq was performed for patients with advanced solid tumors, no available standard therapy, ECOG performance status of 0-1, and available fresh-frozen tissue within the DKTK-MASTER Program from 2016 to 2018. Identical molecular profiling data of 40 patients were independently discussed by two molecular tumor boards (MTB) after prior annotation by specialized physicians, following independent, but similar workflows. Identified biomarkers and resulting treatment options were compared between the MTBs and patients were followed up clinically. RESULTS A median of 309 molecular aberrations from WES and RNA-Seq (n = 38) and 82 molecular aberrations from WES only (n = 3) were considered for clinical interpretation for 40 patients (one patient sequenced twice). A median of 3 and 2 targeted treatment options were identified per patient, respectively. Most treatment options were identified for receptor tyrosine kinase, PARP, and mTOR inhibitors, as well as immunotherapy. The mean overlap coefficient between both MTB was 66%. Highest agreement rates were observed with the interpretation of single nucleotide variants, clinical evidence levels 1 and 2, and monotherapy whereas the interpretation of gene expression changes, preclinical evidence levels 3 and 4, and combination therapy yielded lower agreement rates. Patients receiving treatment following concordant MTB recommendations had significantly longer overall survival than patients receiving treatment following discrepant recommendations or physician's choice. CONCLUSIONS Reproducible clinical interpretation of high-dimensional molecular data is feasible and agreement rates are encouraging, when compared to previous reports. The interpretation of molecular aberrations beyond single nucleotide variants and preclinically validated biomarkers as well as combination therapies were identified as additional difficulties for ongoing harmonization efforts.
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Affiliation(s)
- Damian T Rieke
- Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Chariteplatz 1, 10117, Berlin, Germany. .,Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Hindenburgdamm 30, 12203, Berlin, Germany. .,Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Anna-Louisa-Karsch-Straße 2, 10178, Berlin, Germany. .,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Till de Bortoli
- Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Chariteplatz 1, 10117, Berlin, Germany
| | - Peter Horak
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mario Lamping
- Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Chariteplatz 1, 10117, Berlin, Germany.,Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Hindenburgdamm 30, 12203, Berlin, Germany
| | - Manuela Benary
- Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Chariteplatz 1, 10117, Berlin, Germany.,Core Unit Bioinformatics (CUBI), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Ivan Jelas
- Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Chariteplatz 1, 10117, Berlin, Germany
| | - Gina Rüter
- Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Chariteplatz 1, 10117, Berlin, Germany
| | - Johannes Berger
- Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Chariteplatz 1, 10117, Berlin, Germany
| | - Marit Zettwitz
- Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Chariteplatz 1, 10117, Berlin, Germany
| | - Niklas Kagelmann
- Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Chariteplatz 1, 10117, Berlin, Germany
| | - Andreas Kind
- Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Chariteplatz 1, 10117, Berlin, Germany
| | - Falk Fabian
- Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Chariteplatz 1, 10117, Berlin, Germany
| | - Dieter Beule
- Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Anna-Louisa-Karsch-Straße 2, 10178, Berlin, Germany.,Core Unit Bioinformatics (CUBI), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Hanno Glimm
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department for Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC), Dresden, Germany.,Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
| | - Benedikt Brors
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Stefan Fröhling
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ulrich Keilholz
- Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Chariteplatz 1, 10117, Berlin, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
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7
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Leyvraz S, Konietschke F, Peuker C, Schütte M, Kessler T, Ochsenreither S, Ditzhaus M, Sprünken ED, Dörpholz G, Lamping M, Rieke DT, Klinghammer K, Burock S, Ulrich C, Poch G, Schäfer R, Klauschen F, Joussen A, Yaspo ML, Keilholz U. Biomarker-driven therapies for metastatic uveal melanoma: A prospective precision oncology feasibility study. Eur J Cancer 2022; 169:146-155. [DOI: 10.1016/j.ejca.2022.04.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/30/2022] [Accepted: 04/01/2022] [Indexed: 02/07/2023]
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8
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Krysiak K, Danos AM, Kiwala S, McMichael JF, Coffman AC, Barnell EK, Sheta L, Saliba J, Grisdale CJ, Kujan L, Pema S, Lever J, Spies NC, Chiorean A, Rieke DT, Clark KA, Jani P, Takahashi H, Horak P, Ritter DI, Zhou X, Ainscough BJ, Delong S, Lamping M, Marr AR, Li BV, Lin WH, Terraf P, Salama Y, Campbell KM, Farncombe KM, Ji J, Zhao X, Xu X, Kanagal-Shamanna R, Cotto KC, Skidmore ZL, Walker JR, Zhang J, Milosavljevic A, Patel RY, Giles RH, Kim RH, Schriml LM, Mardis ER, Jones SJM, Raca G, Rao S, Madhavan S, Wagner AH, Griffith OL, Griffith M. A community approach to the cancer-variant-interpretation bottleneck. Nat Cancer 2022; 3:522-525. [PMID: 35624339 PMCID: PMC9872366 DOI: 10.1038/s43018-022-00379-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
As guidelines, therapies, and literature on cancer variants expand, the lack of consensus variant interpretations impedes clinical applications. CIViC is a public domain, crowd-sourced, and adaptable knowledgebase of evidence for the Clinical Interpretation of Variants in Cancer, designed to reduce barriers to knowledge sharing and alleviate the variant interpretation bottleneck.
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Affiliation(s)
- Kilannin Krysiak
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA.
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA.
| | - Arpad M Danos
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Susanna Kiwala
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Joshua F McMichael
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Adam C Coffman
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Erica K Barnell
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Lana Sheta
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Jason Saliba
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Cameron J Grisdale
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Lynzey Kujan
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Shahil Pema
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Jake Lever
- School of Computer Science, University of Glasgow, Glasgow, UK
| | - Nicholas C Spies
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Andreea Chiorean
- Department of Medicine, Division of Medical Oncology, University Health Network, Toronto, Ontario, Canada
| | - Damian T Rieke
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Kaitlin A Clark
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Payal Jani
- Department of Medicine, Division of Medical Oncology, University Health Network, Toronto, Ontario, Canada
| | - Hideaki Takahashi
- Department of Experimental Therapeutics/Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Peter Horak
- Department of Translational Medical Oncology, National Center for Tumor Diseases Heidelberg and German Cancer Research Center, Heidelberg, Germany
| | - Deborah I Ritter
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Cancer Center, Texas Children's Hospital, Houston, Texas, USA
| | - Xin Zhou
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Benjamin J Ainscough
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Sean Delong
- Lassonde School of Engineering, York University, Toronto, Ontario, Canada
| | - Mario Lamping
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Alex R Marr
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Brian V Li
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Panieh Terraf
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yasser Salama
- Department of Medicine, Division of Medical Oncology, University Health Network, Toronto, Ontario, Canada
| | - Katie M Campbell
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Kirsten M Farncombe
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Jianling Ji
- Children's Hospital Los Angeles, University of Southern California, Los Angeles, CA, USA
| | - Xiaonan Zhao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Xinjie Xu
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Rashmi Kanagal-Shamanna
- Department of Hematopathology and Molecular Diagnostics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kelsy C Cotto
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Zachary L Skidmore
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Jason R Walker
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Ronak Y Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Rachel H Giles
- International Kidney Cancer Coalition, Amsterdam, the Netherlands
| | - Raymond H Kim
- Fred A. Litwin Family Centre in Genetic Medicine, Familial Cancer Clinic, Princess Margaret Cancer Centre, University Health Network, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Lynn M Schriml
- University of Maryland School of Medicine, Baltimore, MD, USA
| | - Elaine R Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
- Department of Neurosurgery, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Gordana Raca
- Children's Hospital Los Angeles, University of Southern California, Los Angeles, CA, USA
| | - Shruti Rao
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC, USA
| | - Subha Madhavan
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC, USA
| | - Alex H Wagner
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
- Department of Biomedical Informatics, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Obi L Griffith
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA.
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
| | - Malachi Griffith
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA.
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
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9
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Kittner M, Lamping M, Rieke DT, Götze J, Bajwa B, Jelas I, Rüter G, Hautow H, Sänger M, Habibi M, Zettwitz M, de Bortoli T, Ostermann L, Ševa J, Starlinger J, Kohlbacher O, Malek NP, Keilholz U, Leser U. Annotation and initial evaluation of a large annotated German oncological corpus. JAMIA Open 2021; 4:ooab025. [PMID: 33898938 PMCID: PMC8054032 DOI: 10.1093/jamiaopen/ooab025] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/08/2021] [Accepted: 03/18/2021] [Indexed: 11/15/2022] Open
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.
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Affiliation(s)
- Madeleine Kittner
- Knowledge Management for Bioinformatics, Humboldt Universität zu Berlin, Berlin, Germany
| | - Mario Lamping
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Charité Comprehensive Cancer Center, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Damian T Rieke
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Charité Comprehensive Cancer Center, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Julian Götze
- Innere Medizin I, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Bariya Bajwa
- Innere Medizin I, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Ivan Jelas
- Charité Comprehensive Cancer Center, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Gina Rüter
- Charité Comprehensive Cancer Center, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Hanjo Hautow
- Knowledge Management for Bioinformatics, Humboldt Universität zu Berlin, Berlin, Germany
| | - Mario Sänger
- Knowledge Management for Bioinformatics, Humboldt Universität zu Berlin, Berlin, Germany
| | - Maryam Habibi
- Knowledge Management for Bioinformatics, Humboldt Universität zu Berlin, Berlin, Germany
| | - Marit Zettwitz
- Charité Comprehensive Cancer Center, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Till de Bortoli
- Charité Comprehensive Cancer Center, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Leonie Ostermann
- Innere Medizin I, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Jurica Ševa
- Knowledge Management for Bioinformatics, Humboldt Universität zu Berlin, Berlin, Germany
| | - Johannes Starlinger
- Knowledge Management for Bioinformatics, Humboldt Universität zu Berlin, Berlin, Germany
| | - Oliver Kohlbacher
- Institut für Translationale Bioinformatik, Universitätsklinikum Tübingen, Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
- Department of Computer Science, University of Tübingen, Tübingen, Germany
- Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Nisar P Malek
- Innere Medizin I, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Ulrich Keilholz
- Charité Comprehensive Cancer Center, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Ulf Leser
- Knowledge Management for Bioinformatics, Humboldt Universität zu Berlin, Berlin, Germany
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10
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Rieke DT, Keller U. A CD205-directed antibody drug conjugate – lymphoma precision oncology or sophisticated chemotherapy? Haematologica 2020; 105:2504-2506. [PMID: 33131240 PMCID: PMC7604558 DOI: 10.3324/haematol.2020.261073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Damian T Rieke
- Department of Hematology, Oncology and Tumor Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, 12203 Berlin; Berlin Institute of Health (BIH), 10178 Berlin
| | - Ulrich Keller
- Department of Hematology, Oncology and Tumor Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, 12203 Berlin; Max-Delbrück-Center for Molecular Medicine, 13092 Berlin, Germany.
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11
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Pitel BA, Rao S, Fitz CDV, Madhavan S, Dientsmann R, Horak P, King I, Mockus SM, Raca G, Rieke DT, Rogan P, Sonkin D, Tamborero D, Vlachos IS, Walsh B, Warner JL, Griffith M, Griffith OL, Chakravarty D, Wagner AH. 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. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-3222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Comprehensive interpretation of a patient's cancer genome is a cross-disciplinary process requiring the expertise of oncologists, molecular pathologists, genetic counselors, genomic scientists, and bioinformaticians. The Variant Interpretation for Cancer Consortium (VICC) has created a non-clinical forum for the variant interpretation process by connecting experts from multiple academic institutions and industry to create a Virtual Molecular Tumor Board (VMTB). During VICC-VMTB sessions, experts retrospectively discuss de-identified, challenging patient cases in the context of genomic interpretation guidelines to evaluate a patient's profile across several distinct components: genomic variants; disease context; therapeutic history; family history; demographic information; genomic assay information; and variant allele frequency. These components are processed through the prism of publically available knowledge and expertise of VMTB members, resulting in a broad spectrum of clinically relevant assertions about the patient's disease that may be of prognostic, diagnostic, or predictive relevance. Through these evaluations, the VICC-VMTB primarily works as a means of illuminating challenges in genomic interpretation and advancing the objectives of domain-specific VICC working groups. Examples of challenges that have been highlighted by the VICC-VMTB forum include: 1) inconsistent disease and therapy ontologies across resources are being addressed by Disease Harmonization & Drug Harmonization working groups, respectively; 2) use of machine-learning and natural language processing into clinical-grade variant interpretation are being addressed by the AI-Assisted Curation working group; 3) aggregation and harmonization of knowledgebase data into a centralized resource is being addressed by the Data Licensing and Variant Harmonization working groups; 4) inefficiencies in knowledgebase search functions are being addressed by the Search working group; 5) determination of accurate prediction of biological consequences of rare variants is being addressed by the In Silico Interpretation working group; and 6) standardization of genomic variant curation is being addressed by the Knowledge Curation and Interpretation Standards working group. These VICC working groups provide dedicated expert assemblies intended to specifically tackle these challenges, further increasing the breadth for which genomic information can be made useful in cancer variant interpretation. The VICC-VMTB has been a pertinent link between cancer genomes and clinical interpretation. We are confident VICC-VMTB will continue to be a gateway of acceleration and progress needed in the field of cancer interpretation to provide accurate and efficient answers for our patients in the future.
Citation Format: Beth A. Pitel, Shruti Rao, Catherine Del Vecchio Fitz, Subha Madhavan, Rodrigo Dientsmann, Peter Horak, Ian King, Susan M. Mockus, Gordana Raca, Damian T. Rieke, Peter Rogan, Dmitriy Sonkin, David Tamborero, Ioannis S. Vlachos, Brian Walsh, Jeremy L. Warner, Malachi Griffith, Obi L. Griffith, Debyani Chakravarty, Alex H. Wagner. 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 [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3222.
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Affiliation(s)
| | | | | | | | | | | | - Ian King
- 6University of Toronto, Toronto, Ontario, Canada
| | - Susan M. Mockus
- 7The Jackson Laboratory for Genomic Medicine, Farmington, CT
| | - Gordana Raca
- 8Children's Hospital Los Angeles, Los Angeles, CA
| | | | - Peter Rogan
- 10University of Western Ontario, London, Ontario, Canada
| | | | | | | | - Brian Walsh
- 14Oregon Health & Science University, Portland, OR
| | | | | | | | | | - Alex H. Wagner
- 16Washington University School of Medicine, St. Louis, MO
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12
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Messerschmidt C, Obermayer B, Klinghammer K, Ochsenreither S, Treue D, Stenzinger A, Glimm H, Fröhling S, Kindler T, Brandts CH, Schulze-Osthoff K, Weichert W, Tinhofer I, Klauschen F, Keilholz U, Beule D, Rieke DT. Distinct immune evasion in APOBEC-enriched, HPV-negative HNSCC. Int J Cancer 2020; 147:2293-2302. [PMID: 32468570 DOI: 10.1002/ijc.33123] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 04/06/2020] [Accepted: 05/11/2020] [Indexed: 12/20/2022]
Abstract
Immune checkpoint inhibition leads to response in some patients with head and neck squamous cell carcinoma (HNSCC). Robust biomarkers are lacking to date. We analyzed viral status, gene expression signatures, mutational load and mutational signatures in whole exome and RNA-sequencing data of the HNSCC TCGA dataset (n = 496) and a validation set (DKTK MASTER cohort, n = 10). Public single-cell gene expression data from 17 HPV-negative HNSCC were separately reanalyzed. APOBEC3-associated TCW motif mutations but not total single nucleotide variant burden were significantly associated with inflammation. This association was restricted to HPV-negative HNSCC samples. An APOBEC-enriched, HPV-negative subgroup was identified, that showed higher T-cell inflammation and immune checkpoint expression, as well as expression of APOBEC3 genes. Mutations in immune-evasion pathways were also enriched in these tumors. Analysis of single-cell sequencing data identified expression of APOBEC3B and 3C genes in malignant cells. We identified an APOBEC-enriched subgroup of HPV-negative HNSCC with a distinct immunogenic phenotype, potentially mediating response to immunotherapy.
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Affiliation(s)
- Clemens Messerschmidt
- Core Unit Bioinformatics, Berlin Institute of Health (BIH), Berlin, Germany.,Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Benedikt Obermayer
- Core Unit Bioinformatics, Berlin Institute of Health (BIH), Berlin, Germany.,Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Konrad Klinghammer
- Department of Hematology and Oncology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Hindenburgdamm 30, Berlin, 12203, Germany
| | - Sebastian Ochsenreither
- Department of Hematology and Oncology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Hindenburgdamm 30, Berlin, 12203, Germany.,Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Denise Treue
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Albrecht Stenzinger
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Hanno Glimm
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), Dresden, Germany.,University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Stefan Fröhling
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas Kindler
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Hematology, Medical Oncology & Pneumology, University Medical Center, Mainz, Germany.,University Cancer Center Mainz (UCT), Johannes Gutenberg-University, Mainz, Germany
| | - Christian H Brandts
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,University Cancer Center Frankfurt (UCT), Goethe University Frankfurt, Frankfurt, Germany.,Department of Medicine, Hematology/Oncology, Goethe University, Frankfurt, Germany
| | - Klaus Schulze-Osthoff
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Interfaculty Institute of Biochemistry, Tübingen University, Tübingen, Germany
| | - Wilko Weichert
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Pathology, Technical University Munich, Munich, Germany
| | - Ingeborg Tinhofer
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Radiooncology and Radiotherapy, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Frederick Klauschen
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Ulrich Keilholz
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dieter Beule
- Core Unit Bioinformatics, Berlin Institute of Health (BIH), Berlin, Germany.,Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Damian T Rieke
- Department of Hematology and Oncology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Hindenburgdamm 30, Berlin, 12203, Germany.,Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany
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13
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Wagner AH, Walsh B, Mayfield G, Tamborero D, Sonkin D, Krysiak K, Deu-Pons J, Duren RP, Gao J, McMurry J, Patterson S, Del Vecchio Fitz C, Pitel BA, Sezerman OU, Ellrott K, Warner JL, Rieke DT, Aittokallio T, Cerami E, Ritter DI, Schriml LM, Freimuth RR, Haendel M, Raca G, Madhavan S, Baudis M, Beckmann JS, Dienstmann R, Chakravarty D, Li XS, Mockus S, Elemento O, Schultz N, Lopez-Bigas N, Lawler M, Goecks J, Griffith M, Griffith OL, Margolin AA. A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer. Nat Genet 2020; 52:448-457. [PMID: 32246132 PMCID: PMC7127986 DOI: 10.1038/s41588-020-0603-8] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 02/26/2020] [Indexed: 12/19/2022]
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.
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Affiliation(s)
- Alex H Wagner
- Washington University School of Medicine, St. Louis, MO, USA
| | - Brian Walsh
- Oregon Health and Science University, Portland, OR, USA
| | | | - David Tamborero
- Pompeu Fabra University, Barcelona, Spain
- Karolinska Institute, Solna, Sweden
| | | | | | - Jordi Deu-Pons
- Institute for Research in Biomedicine, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies, Barcelona, Spain
| | | | - Jianjiong Gao
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Julie McMurry
- Oregon Health and Science University, Portland, OR, USA
| | - Sara Patterson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | | | | | - Kyle Ellrott
- Oregon Health and Science University, Portland, OR, USA
| | | | | | - Tero Aittokallio
- Institute for Molecular Medicine Finland, Helsinki, Finland
- University of Turku, Turku, Finland
| | | | - Deborah I Ritter
- Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX, USA
| | - Lynn M Schriml
- University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Melissa Haendel
- Oregon Health and Science University, Portland, OR, USA
- Linus Pauling Institute at Oregon State University, Corvallis, OR, USA
| | - Gordana Raca
- Children's Hospital Los Angeles, Los Angeles, CA, USA
- Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Subha Madhavan
- Georgetown University Medical Center, Washington, DC, USA
| | | | | | | | | | | | - Susan Mockus
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | | | - Nuria Lopez-Bigas
- Pompeu Fabra University, Barcelona, Spain
- Institute for Research in Biomedicine, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies, Barcelona, Spain
| | | | - Jeremy Goecks
- Oregon Health and Science University, Portland, OR, USA
| | | | - Obi L Griffith
- Washington University School of Medicine, St. Louis, MO, USA.
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14
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Lamping M, Benary M, Leyvraz S, Messerschmidt C, Blanc E, Kessler T, Schütte M, Lenze D, Jöhrens K, Burock S, Klinghammer K, Ochsenreither S, Sers C, Schäfer R, Tinhofer I, Beule D, Klauschen F, Yaspo ML, Keilholz U, Rieke DT. Support of a molecular tumour board by an evidence-based decision management system for precision oncology. Eur J Cancer 2020; 127:41-51. [PMID: 31982633 DOI: 10.1016/j.ejca.2019.12.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 12/06/2019] [Accepted: 12/10/2019] [Indexed: 12/19/2022]
Abstract
BACKGROUND Reliable and reproducible interpretation of molecular aberrations constitutes a bottleneck of precision medicine. Evidence-based decision management systems may improve rational therapy recommendations. To cope with an increasing amount of complex molecular data in the clinical care of patients with cancer, we established a workflow for the interpretation of molecular analyses. METHODS A specialized physician screened results from molecular analyses for potential biomarkers, irrespective of the diagnostic modality. Best available evidence was retrieved and categorized through establishment of an in-house database and interrogation of publicly available databases. Annotated biomarkers were ranked using predefined evidence levels and subsequently discussed at a molecular tumour board (MTB), which generated treatment recommendations. Subsequent translation into patient treatment and clinical outcomes were followed up. RESULTS One hundred patients were discussed in the MTB between January 2016 and May 2017. Molecular data were obtained for 70 of 100 patients (50 whole exome/RNA sequencing, 18 panel sequencing, 2 immunohistochemistry (IHC)/microsatellite instability analysis). The MTB generated a median of two treatment recommendations each for 63 patients. Thirty-nine patients were treated: 6 partial responses and 12 stable diseases were achieved as best responses. Genetic counselling for germline events was recommended for seven patients. CONCLUSION The development of an evidence-based workflow allowed for the clinical interpretation of complex molecular data and facilitated the translation of personalized treatment strategies into routine clinical care. The high number of treatment recommendations in patients with comprehensive genomic data and promising responses in patients treated with combination therapy warrant larger clinical studies.
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Affiliation(s)
- Mario Lamping
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany.
| | - Manuela Benary
- Department of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany; IRI Life Sciences, Humboldt-Universität zu Berlin, Philippstraße 13, 10115, Berlin, Germany
| | - Serge Leyvraz
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany
| | - Clemens Messerschmidt
- Core Unit Bioinformatics, Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Straße 2, 10178, Berlin, Germany
| | - Eric Blanc
- Core Unit Bioinformatics, Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Straße 2, 10178, Berlin, Germany
| | - Thomas Kessler
- Alacris Theranostics GmbH, Max Planck Straße 3, 12489, Berlin, Germany
| | - Moritz Schütte
- Alacris Theranostics GmbH, Max Planck Straße 3, 12489, Berlin, Germany
| | - Dido Lenze
- Department of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany
| | - Korinna Jöhrens
- Department of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany
| | - Susen Burock
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany
| | - Konrad Klinghammer
- Department of Hematology and Oncology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Hindenburgdamm 30, 12203 Berlin, Germany
| | - Sebastian Ochsenreither
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany; Department of Hematology and Oncology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Hindenburgdamm 30, 12203 Berlin, Germany
| | - Christine Sers
- Department of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany
| | - Reinhold Schäfer
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany; German Cancer Consortium (DKTK) and German Cancer Research Centre (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Ingeborg Tinhofer
- German Cancer Consortium (DKTK) and German Cancer Research Centre (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany; Department of Radiooncology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany
| | - Dieter Beule
- Core Unit Bioinformatics, Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Straße 2, 10178, Berlin, Germany
| | - Frederick Klauschen
- Department of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany
| | - Marie-Laure Yaspo
- Alacris Theranostics GmbH, Max Planck Straße 3, 12489, Berlin, Germany; Max Planck Institute for Molecular Genetics, Otto Warburg Laboratory Gene Regulation and Systems Biology of Cancer, Ihnestraße 63, 14195, Berlin, Germany
| | - Ulrich Keilholz
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany; German Cancer Consortium (DKTK) and German Cancer Research Centre (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Damian T Rieke
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany; Department of Hematology and Oncology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Hindenburgdamm 30, 12203 Berlin, Germany; Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Straße 2, 10178, Berlin, Germany.
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15
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Kreutzfeldt S, Apostolidis L, Oles M, Horak P, Heilig CE, Heining C, Hutter B, Gieldon L, Klink B, Lamping M, Rieke DT, Uhrig S, Jann H, Pape UF, Stenzinger A, Winkler EC, Wiedenmann B, Jäger D, Brors B, Schröck E, Keilholz U, Pavel M, Glimm H, Fröhling S. 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. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Therapeutic options for neuroendocrine neoplasms (NEN) are limited. Within the MASTER program, a multi-institutional registry trial for prospective stratification of younger adults with advanced-stage cancer across all histologies and patients with rare tumors conducted under the auspices of NCT Heidelberg/Dresden and the German Cancer Consortium, we apply prospective whole-exome/genome sequencing (WES/WGS) and RNA sequencing (RNA-seq) to determine therapeutic choices for individual patients who have exhausted standard therapy options. We here report the clinical and molecular characteristics of the NEN cohort within this study. Between 2013 and 2018, 108 patients (male, n=65; female, n=43) were enrolled. Histologies according to the 2017 WHO Classification were neuroendocrine tumor grade 1 (NET G1), n=8; NET G2, n=31; NET G3, n=9; neuroendocrine carcinoma, n=49; and mixed neuroendocrine/non-neuroendocrine neoplasm, n=11. Primary tumor sites were gastrointestinal tract, n=30; pancreas, n=31; thorax, n=21; genitourinary system, n=11; head and neck, n=5; and other regions, n=10. All patients had advanced-stage disease and had received a median of 2 prior lines of systemic therapy. WES, WGS, and RNA-seq were performed in 69, 40, and 87 patients, respectively. Clinical evaluation of germline and somatic molecular data (single-nucleotide variants, small insertions and deletions, copy number variations, mutational burden, mutational signatures, homologous recombination deficiency scores, gene expression patterns, etc.) from 105 patients by a dedicated molecular tumor board yielded evidence-based recommendations for clinical management in 91 cases (87%). Treatment recommendations were grouped as follows: PARP inhibition, n=35; immunotherapy, n=27; mTOR inhibition, n=22; CDK4/6 inhibition, n=15; tyrosine or serine/threonine kinase inhibition, n=57 (ALK, n=1; ERBB, n=6; FGFR, n=10; MET, n=5; RET, n=12; VEGFR, n=4, MEK, n=9; other, n=10), DNA-crosslinking chemotherapy, n=16; anti-claudin18.2 antibody, n=5; BET inhibition, n=5; and DLL3 antibody, n=5. As of November 2018, at least 18 patients had received molecularly guided treatment (PARP inhibition, immunotherapy, mTOR inhibition, tyrosine or serine/threonine kinase inhibition) of which 11 were evaluable for response (partial response, n=4; stable disease, n=2; progressive diseases, n=5). Twenty-seven patients died before therapy could be started, 16 are currently receiving other regimens, and for the remaining patients no follow-up data are available yet. In conclusion, comprehensive molecular profiling offers valuable insight into to the genomic and transcriptomic landscape of NEN and creates additional therapeutic opportunities in a subset of patients.
Citation Format: Simon Kreutzfeldt, Leonidas Apostolidis, Malgorzata Oles, Peter Horak, Christoph E. Heilig, Christoph Heining, Barbara Hutter, Laura Gieldon, Barbara Klink, Mario Lamping, Damian T. Rieke, Sebastian Uhrig, Henning Jann, Ulrich F. Pape, Albrecht Stenzinger, Eva C. Winkler, Bertram Wiedenmann, Dirk Jäger, Benedikt Brors, Evelin Schröck, Ulrich Keilholz, Marianne Pavel, Hanno Glimm, Stefan Fröhling. Clinical relevance of comprehensive genomic analysis in patients with advanced-stage neuroendocrine neoplasms: Results from the MASTER trial of the German Cancer Consortium [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 919.
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Affiliation(s)
- Simon Kreutzfeldt
- 1National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Malgorzata Oles
- 1National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Peter Horak
- 1National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christoph E. Heilig
- 1National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christoph Heining
- 3National Center for Tumor Diseases (NCT) Dresden and University Hospital Carl Gustav Carus, Dresden, Germany
| | - Barbara Hutter
- 4German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Laura Gieldon
- 5Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Barbara Klink
- 5Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Mario Lamping
- 6Charité Comprehensive Cancer Center, Charité University Medicine, Berlin, Germany
| | - Damian T. Rieke
- 6Charité Comprehensive Cancer Center, Charité University Medicine, Berlin, Germany
| | | | - Henning Jann
- 7Department of Hepatology and Gastroenterology, Charité University Medicine, Berlin, Berlin, Germany
| | - Ulrich F. Pape
- 7Department of Hepatology and Gastroenterology, Charité University Medicine, Berlin, Berlin, Germany
| | - Albrecht Stenzinger
- 8Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Eva C. Winkler
- 2National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Bertram Wiedenmann
- 7Department of Hepatology and Gastroenterology, Charité University Medicine, Berlin, Berlin, Germany
| | - Dirk Jäger
- 2National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Benedikt Brors
- 4German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Evelin Schröck
- 5Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Ulrich Keilholz
- 6Charité Comprehensive Cancer Center, Charité University Medicine, Berlin, Germany
| | - Marianne Pavel
- 9Department of Medicine, Division of Endocrinology, Friedrich Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Hanno Glimm
- 3National Center for Tumor Diseases (NCT) Dresden and University Hospital Carl Gustav Carus, Dresden, Germany
| | - Stefan Fröhling
- 1National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
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16
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Rieke DT, Lamping M, Schuh M, Le Tourneau C, Basté N, Burkard ME, Metzeler KH, Leyvraz S, Keilholz U. Comparison of Treatment Recommendations by Molecular Tumor Boards Worldwide. JCO Precis Oncol 2018; 2:1-14. [DOI: 10.1200/po.18.00098] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Purpose Precision oncology holds the promise of improving patient outcome. It is based on the idea that the testing of genomic biomarkers can lead to the recommendation of a treatment option tailored to the specific patient. To derive treatment recommendations from molecular profiles, interdisciplinary molecular tumor boards (MTBs) have been established recently in many academic institutions. The recommendation process in MTBs, however, has not been well defined, which limits applicability to larger clinical trials and patient populations. Methods We created four fictional patients on the basis of recent real cases with genomic information on mutations, fusions, copy numbers, and gene expression. We identified 29 tumor boards from nine countries worldwide and asked them to provide treatment recommendations for the sample patients. In addition, a questionnaire regarding the setup and methods used by MTBs was circulated. Results Five MTBs from four countries provided treatment recommendations and answered the questionnaire. For one patient, three tumor board treatment recommendations were identical, and two tumor boards had identical treatment strategies for the other three patients. There was heterogeneity in the interpretation of tumor and germline aberrations as well as in standards of prioritization. Conclusion Differences in the interpretation and recommendation process contribute to heterogeneity in MTB recommendations. Additional comparative analyses of recommendations could help improve rational decision making and lead to standardization.
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Affiliation(s)
- Damian T. Rieke
- Damian T. Rieke, Mario Lamping, Serge Leyvraz, and Ulrich Keilholz, Charité Comprehensive Cancer Center, Charité–Universitätsmedizin Berlin; Damian T. Rieke, Berlin Institute of Health, Berlin; Klaus H. Metzeler, University Hospital, LMU Munich, Munich, Germany; Marissa Schuh, Markey Cancer Center, University of Kentucky, Lexington, KY; Christophe Le Tourneau, Institut Curie and INSERM U900 Research Unit, Saint-Cloud; Christophe Le Tourneau, Institut Curie, Paris; Christophe Le Tourneau, Versailles-Saint
| | - Mario Lamping
- Damian T. Rieke, Mario Lamping, Serge Leyvraz, and Ulrich Keilholz, Charité Comprehensive Cancer Center, Charité–Universitätsmedizin Berlin; Damian T. Rieke, Berlin Institute of Health, Berlin; Klaus H. Metzeler, University Hospital, LMU Munich, Munich, Germany; Marissa Schuh, Markey Cancer Center, University of Kentucky, Lexington, KY; Christophe Le Tourneau, Institut Curie and INSERM U900 Research Unit, Saint-Cloud; Christophe Le Tourneau, Institut Curie, Paris; Christophe Le Tourneau, Versailles-Saint
| | - Marissa Schuh
- Damian T. Rieke, Mario Lamping, Serge Leyvraz, and Ulrich Keilholz, Charité Comprehensive Cancer Center, Charité–Universitätsmedizin Berlin; Damian T. Rieke, Berlin Institute of Health, Berlin; Klaus H. Metzeler, University Hospital, LMU Munich, Munich, Germany; Marissa Schuh, Markey Cancer Center, University of Kentucky, Lexington, KY; Christophe Le Tourneau, Institut Curie and INSERM U900 Research Unit, Saint-Cloud; Christophe Le Tourneau, Institut Curie, Paris; Christophe Le Tourneau, Versailles-Saint
| | - Christophe Le Tourneau
- Damian T. Rieke, Mario Lamping, Serge Leyvraz, and Ulrich Keilholz, Charité Comprehensive Cancer Center, Charité–Universitätsmedizin Berlin; Damian T. Rieke, Berlin Institute of Health, Berlin; Klaus H. Metzeler, University Hospital, LMU Munich, Munich, Germany; Marissa Schuh, Markey Cancer Center, University of Kentucky, Lexington, KY; Christophe Le Tourneau, Institut Curie and INSERM U900 Research Unit, Saint-Cloud; Christophe Le Tourneau, Institut Curie, Paris; Christophe Le Tourneau, Versailles-Saint
| | - Neus Basté
- Damian T. Rieke, Mario Lamping, Serge Leyvraz, and Ulrich Keilholz, Charité Comprehensive Cancer Center, Charité–Universitätsmedizin Berlin; Damian T. Rieke, Berlin Institute of Health, Berlin; Klaus H. Metzeler, University Hospital, LMU Munich, Munich, Germany; Marissa Schuh, Markey Cancer Center, University of Kentucky, Lexington, KY; Christophe Le Tourneau, Institut Curie and INSERM U900 Research Unit, Saint-Cloud; Christophe Le Tourneau, Institut Curie, Paris; Christophe Le Tourneau, Versailles-Saint
| | - Mark E. Burkard
- Damian T. Rieke, Mario Lamping, Serge Leyvraz, and Ulrich Keilholz, Charité Comprehensive Cancer Center, Charité–Universitätsmedizin Berlin; Damian T. Rieke, Berlin Institute of Health, Berlin; Klaus H. Metzeler, University Hospital, LMU Munich, Munich, Germany; Marissa Schuh, Markey Cancer Center, University of Kentucky, Lexington, KY; Christophe Le Tourneau, Institut Curie and INSERM U900 Research Unit, Saint-Cloud; Christophe Le Tourneau, Institut Curie, Paris; Christophe Le Tourneau, Versailles-Saint
| | - Klaus H. Metzeler
- Damian T. Rieke, Mario Lamping, Serge Leyvraz, and Ulrich Keilholz, Charité Comprehensive Cancer Center, Charité–Universitätsmedizin Berlin; Damian T. Rieke, Berlin Institute of Health, Berlin; Klaus H. Metzeler, University Hospital, LMU Munich, Munich, Germany; Marissa Schuh, Markey Cancer Center, University of Kentucky, Lexington, KY; Christophe Le Tourneau, Institut Curie and INSERM U900 Research Unit, Saint-Cloud; Christophe Le Tourneau, Institut Curie, Paris; Christophe Le Tourneau, Versailles-Saint
| | - Serge Leyvraz
- Damian T. Rieke, Mario Lamping, Serge Leyvraz, and Ulrich Keilholz, Charité Comprehensive Cancer Center, Charité–Universitätsmedizin Berlin; Damian T. Rieke, Berlin Institute of Health, Berlin; Klaus H. Metzeler, University Hospital, LMU Munich, Munich, Germany; Marissa Schuh, Markey Cancer Center, University of Kentucky, Lexington, KY; Christophe Le Tourneau, Institut Curie and INSERM U900 Research Unit, Saint-Cloud; Christophe Le Tourneau, Institut Curie, Paris; Christophe Le Tourneau, Versailles-Saint
| | - Ulrich Keilholz
- Damian T. Rieke, Mario Lamping, Serge Leyvraz, and Ulrich Keilholz, Charité Comprehensive Cancer Center, Charité–Universitätsmedizin Berlin; Damian T. Rieke, Berlin Institute of Health, Berlin; Klaus H. Metzeler, University Hospital, LMU Munich, Munich, Germany; Marissa Schuh, Markey Cancer Center, University of Kentucky, Lexington, KY; Christophe Le Tourneau, Institut Curie and INSERM U900 Research Unit, Saint-Cloud; Christophe Le Tourneau, Institut Curie, Paris; Christophe Le Tourneau, Versailles-Saint
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Lier A, Penzel R, Heining C, Horak P, Fröhlich M, Uhrig S, Budczies J, Kirchner M, Volckmar AL, Hutter B, Kreutzfeldt S, Endris V, Richter D, Wolf S, Pfütze K, Neumann O, Buchhalter I, Morais de Oliveira CM, Singer S, Leichsenring J, Herpel E, Klauschen F, Jost PJ, Metzeler KH, Schulze-Osthoff K, Kopp HG, Kindler T, Rieke DT, Lamping M, Brandts C, Falkenhorst J, Bauer S, Schröck E, Folprecht G, Boerries M, von Bubnoff N, Weichert W, Brors B, Lichter P, von Kalle C, Schirmacher P, Glimm H, Fröhling S, Stenzinger A. Validating Comprehensive Next-Generation Sequencing Results for Precision Oncology: The NCT/DKTK Molecularly Aided Stratification for Tumor Eradication Research Experience. JCO Precis Oncol 2018; 2:1-13. [DOI: 10.1200/po.18.00171] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Purpose Rapidly evolving genomics technologies, in particular comprehensive next-generation sequencing (NGS), have led to exponential growth in the understanding of cancer biology, shifting oncology toward personalized treatment strategies. However, comprehensive NGS approaches, such as whole-exome sequencing, have limitations that are related to the technology itself as well as to the input source. Hence, clinical implementation of comprehensive NGS in a quality-controlled diagnostic workflow requires both the standardization of sequencing procedures and continuous validation of sequencing results by orthogonal methods in an ongoing program to enable the determination of key test parameters and continuous improvement of NGS and bioinformatics pipelines. Patients and Methods We present validation data on 220 patients who were enrolled between 2013 and 2016 in a multi-institutional, genomics-guided precision oncology program (Molecularly Aided Stratification for Tumor Eradication Research) of the National Center for Tumor Diseases Heidelberg and the German Cancer Consortium. Results More than 90% of clinically actionable genomic alterations identified by combined whole-exome sequencing and transcriptome sequencing were successfully validated, with varying frequencies of discordant results across different types of alterations (fusions, 3.7%; single-nucleotide variants, 2.6%; amplifications, 1.1%; overexpression, 0.9%; deletions, 0.6%). The implementation of new computational methods for NGS data analysis led to a substantial improvement of gene fusion calling over time. Conclusion Collectively, these data demonstrate the value of a rigorous validation program that partners with comprehensive NGS to successfully implement and continuously improve cancer precision medicine in a clinical setting.
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Affiliation(s)
- Amelie Lier
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Roland Penzel
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Christoph Heining
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Peter Horak
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Martina Fröhlich
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Sebastian Uhrig
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Jan Budczies
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Martina Kirchner
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Anna-Lena Volckmar
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Barbara Hutter
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Simon Kreutzfeldt
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Volker Endris
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Daniela Richter
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Stephan Wolf
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Katrin Pfütze
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Olaf Neumann
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Ivo Buchhalter
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Cristiano M. Morais de Oliveira
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Stephan Singer
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Jonas Leichsenring
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Esther Herpel
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Frederick Klauschen
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Philipp J. Jost
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Klaus H. Metzeler
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Klaus Schulze-Osthoff
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Hans-Georg Kopp
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Thomas Kindler
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Damian T. Rieke
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Mario Lamping
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Christian Brandts
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Johanna Falkenhorst
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Sebastian Bauer
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Evelin Schröck
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Gunnar Folprecht
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Melanie Boerries
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Nikolas von Bubnoff
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Wilko Weichert
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Benedikt Brors
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Peter Lichter
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Christof von Kalle
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Peter Schirmacher
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Hanno Glimm
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Stefan Fröhling
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Albrecht Stenzinger
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
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Rieke DT, Ochsenreither S, Klinghammer K, Seiwert TY, Klauschen F, Tinhofer I, Keilholz U. Methylation of RAD51B, XRCC3 and other homologous recombination genes is associated with expression of immune checkpoints and an inflammatory signature in squamous cell carcinoma of the head and neck, lung and cervix. Oncotarget 2018; 7:75379-75393. [PMID: 27683114 PMCID: PMC5342748 DOI: 10.18632/oncotarget.12211] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 09/07/2016] [Indexed: 12/29/2022] Open
Abstract
Immune checkpoints are emerging treatment targets, but mechanisms underlying checkpoint expression are poorly understood. Since alterations in DNA repair genes have been connected to the efficacy of checkpoint inhibitors, we investigated associations between methylation of DNA repair genes and CTLA4 and CD274 (PD-L1) expression.A list of DNA repair genes (179 genes) was selected from the literature, methylation status and expression of inflammation-associated genes (The Cancer Genome Atlas data) was correlated in head and neck squamous cell carcinoma (HNSCC), cervical and lung squamous cell carcinoma.A significant positive correlation of the methylation status of 15, 3 and 2 genes with checkpoint expression was identified, respectively. RAD51B methylation was identified in all cancer subtypes. In HNSCC and cervical cancer, there was significant enrichment for homologous recombination genes. Methylation of the candidate genes was also associated with expression of other checkpoints, ligands, MHC- and T-cell associated genes as well as an interferon-inflammatory immune gene signature, predictive for the efficacy of PD-1 inhibition in HNSCC.Homologous recombination deficiency might therefore be mediated by DNA repair gene hypermethylation and linked to an immune-evasive phenotype in SCC. The methylation status of these genes could represent a new predictive biomarker for immune checkpoint inhibition.
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Affiliation(s)
- Damian T Rieke
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Sebastian Ochsenreither
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Department of Hematology and Medical Oncology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Konrad Klinghammer
- Department of Hematology and Medical Oncology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Tanguy Y Seiwert
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Frederick Klauschen
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Inge Tinhofer
- Department of Radiooncology and Radiotherapy, Charité - Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Research Center Heidelberg (DKFZ)/German Cancer Consortium (DKTK) partner site Berlin, Berlin, Germany
| | - Ulrich Keilholz
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Department of Hematology and Medical Oncology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Berlin, Germany
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Schütte M, Ogilvie LA, Rieke DT, Lange BMH, Yaspo ML, Lehrach H. Cancer Precision Medicine: Why More Is More and DNA Is Not Enough. Public Health Genomics 2017; 20:70-80. [PMID: 28595192 DOI: 10.1159/000477157] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 05/02/2017] [Indexed: 11/19/2022] Open
Abstract
Every tumour is different. They arise in patients with different genomes, from cells with different epigenetic modifications, and by random processes affecting the genome and/or epigenome of a somatic cell, allowing it to escape the usual controls on its growth. Tumours and patients therefore often respond very differently to the drugs they receive. Cancer precision medicine aims to characterise the tumour (and often also the patient) to be able to predict, with high accuracy, its response to different treatments, with options ranging from the selective characterisation of a few genomic variants considered particularly important to predict the response of the tumour to specific drugs, to deep genome analysis of both tumour and patient, combined with deep transcriptome analysis of the tumour. Here, we compare the expected results of carrying out such analyses at different levels, from different size panels to a comprehensive analysis incorporating both patient and tumour at the DNA and RNA levels. In doing so, we illustrate the additional power gained by this unusually deep analysis strategy, a potential basis for a future precision medicine first strategy in cancer drug therapy. However, this is only a step along the way of increasingly detailed molecular characterisation, which in our view will, in the future, introduce additional molecular characterisation techniques, including systematic analysis of proteins and protein modification states and different types of metabolites in the tumour, systematic analysis of circulating tumour cells and nucleic acids, the use of spatially resolved analysis techniques to address the problem of tumour heterogeneity as well as the deep analyses of the immune system of the patient to, e.g., predict the response of the patient to different types of immunotherapy. Such analyses will generate data sets of even greater complexity, requiring mechanistic modelling approaches to capture enough of the complex situation in the real patient to be able to accurately predict his/her responses to all available therapies.
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Abstract
Recurrent or metastatic head and neck cancer describes tumor deposits that arise locally, regionally, or at distant sites after treatment or distant metastases at the time of primary diagnosis. Prognosis for R/M squamous cell carcinomas of the head and neck (HNSCC) is poor and treatment options are limited in this situation. Human papillomavirus (HPV) is an important risk factor for HNSCC. About 40 % of all HNSCC have been attributed to HPV in Europe. HPV positivity at initial diagnosis is the single best prognostic factor for survival. However, data for the prognostic and predictive value of HPV in the R/M situation are still scarce. Due to the rising incidence of HPV-associated cancers, the number of R/M HPV+ carcinomas is also expected to rise. This chapter therefore aims to give an overview of the current knowledge concerning the role of HPV as a prognostic and predictive marker in recurrent or metastatic HNSCC.
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Affiliation(s)
- Damian T Rieke
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Ulrich Keilholz
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Berlin, Germany.
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Abstract
Head and neck squamous cell carcinoma (HNSCC) is one of the most common solid cancers worldwide. It is mainly caused by exposure to tobacco smoke and alcohol as well as infection with the human papilloma virus (HPV). The prognosis is poor, especially once it recurs or metastasizes. Current therapeutic options include surgery, radio- and chemotherapy. Epidermal growth factor receptor (EGFR) inhibitors are so far the only targeted agents that have been approved in head and neck cancer. Primary or secondary resistance is frequent or will eventually develop. Several driver mutations and other genomic aberrations have been described in HNSCC including EGFR overexpression and amplification. Yet, no predictive biomarkers for the application of EGFR inhibitors have been identified. Further targeted agents are in development for HNSCC, of which inhibitors of the PI3K pathway are the closest to clinical application. In recent years, the incidence of HPV-driven HNSCC has risen in Western countries. HPV-positive and -negative HNSCC are distinct molecular tumor entities, and consequences for targeted therapies have been discussed. This review looks at approved and investigational targeted treatment strategies as well as potential predictive biomarkers such as the HPV status to guide treatment.
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Affiliation(s)
- Damian T Rieke
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Berlin, Germany
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Rieke DT, Zuo Z, Endhardt K, Keck M, Khattri A, Mahmutoglu D, Leung K, Dinali ME, Braegelmann J, Seiwert TY. Abstract 2832: Fibroblast growth factors in head and neck cancer: Genetic alterations and therapeutic targeting with ponatinib. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-2832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: FGF signaling plays an important role in cancer. Little is known about its involvement in head and neck squamous cell carcinoma (HNSCC). FGFR1 focal amplification and high expression (Freier, Schwaenen et al.), expression of FG-BP (Li et al.) and FGF2 autocrine signalling loops (Marshall et al.) have been described in connection with HNSSC. We therefore examined copy number alterations for several FGFR and FGF-related Genes in 159 patient tissues and cell lines as well as expression levels in 116 patient tissues and 40 cell lines. Based upon our findings we tried a combined FGFR-inhibiton with ponatinib in 5 head and neck cancer-cell lines alone and in combination with gefitinib. Methods: Copy Number Data analysis for 144 patient tissues and cell lines (Nanostring) as well as for 20 cell lines (aCGH) of which 5 were covered by both techniques and showed comparable results. Expression data analysis for 116 tissues and 40 cell lines (Agilent). Viability for 5 cell lines treated with gefitinib and ponatinib alone and in combination. Immunoblotting was performed to deterimed PI3K-AKT and MAPK signaling. Results: Frequent copy number increase could be detected for FGF19 in tissues and cell lines. FGFR1 copy number increase could be seen in only 1 tissue sample, but appeared to be deleted in several samples. High relative expression could be detected for FGFBP1 in tissues and cell lines. Viability testing showed high efficacy in 5/5 cell lines tested for ponatinib but was not solely mediated by AKT or MAPK signaling. Combined treatment with ponatinib and gefitinib was more effective than treatment with either agent alone and synergy was present. Conclusions: FGF signaling is important in Head and Neck Cancer. FGF19 amplification is frequent. We were unable to replicate FGFR1 amplification with only one tissue showing FGFR1 copy number increase. High expression levels could be shown for FGFBP1, providing an alternative hypothesis for explaining the efficacy of FGF2 inhibition as previously shown (Marshall et. al.). Ponatinib is effective as a single agent on HNSSC cell line models and shows synergistic effect in combination with gefitinib. It is promising to evaluate FGF pathway inhibition (e.g. with ponatinib) in its ability to overcome EGFR-inhibitor resistance.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2832. doi:1538-7445.AM2012-2832
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