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Edsjö A, Russnes HG, Lehtiö J, Tamborero D, Hovig E, Stenzinger A, Rosenquist R. High-throughput molecular assays for inclusion in personalised oncology trials - State-of-the-art and beyond. J Intern Med 2024; 295:785-803. [PMID: 38698538 DOI: 10.1111/joim.13785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
In the last decades, the development of high-throughput molecular assays has revolutionised cancer diagnostics, paving the way for the concept of personalised cancer medicine. This progress has been driven by the introduction of such technologies through biomarker-driven oncology trials. In this review, strengths and limitations of various state-of-the-art sequencing technologies, including gene panel sequencing (DNA and RNA), whole-exome/whole-genome sequencing and whole-transcriptome sequencing, are explored, focusing on their ability to identify clinically relevant biomarkers with diagnostic, prognostic and/or predictive impact. This includes the need to assess complex biomarkers, for example microsatellite instability, tumour mutation burden and homologous recombination deficiency, to identify patients suitable for specific therapies, including immunotherapy. Furthermore, the crucial role of biomarker analysis and multidisciplinary molecular tumour boards in selecting patients for trial inclusion is discussed in relation to various trial concepts, including drug repurposing. Recognising that today's exploratory techniques will evolve into tomorrow's routine diagnostics and clinical study inclusion assays, the importance of emerging technologies for multimodal diagnostics, such as proteomics and in vivo drug sensitivity testing, is also discussed. In addition, key regulatory aspects and the importance of patient engagement in all phases of a clinical trial are described. Finally, we propose a set of recommendations for consideration when planning a new precision cancer medicine trial.
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Affiliation(s)
- Anders Edsjö
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
- Division of Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Hege G Russnes
- Department of Pathology, Oslo University Hospital, Oslo, Norway
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Janne Lehtiö
- Department of Oncology and Pathology, Karolinska Institutet, Science for Life Laboratory, Stockholm, Sweden
- Cancer genomics and proteomics, Karolinska University Hospital, Solna, Sweden
| | - David Tamborero
- Department of Oncology and Pathology, Karolinska Institutet, Science for Life Laboratory, Stockholm, Sweden
| | - Eivind Hovig
- Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Albrecht Stenzinger
- Institute of Pathology, Division of Molecular Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Solna, Sweden
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Walker M, Mayr EM, Koppermann ML, Terron A, Wagner Y, Kling C, Pfarr N. [Molecular pathological analysis through the ages]. PATHOLOGIE (HEIDELBERG, GERMANY) 2024; 45:173-179. [PMID: 38619582 PMCID: PMC11045621 DOI: 10.1007/s00292-024-01326-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/18/2024] [Indexed: 04/16/2024]
Abstract
BACKGROUND Molecular pathological examinations of tumor samples encompass a wide range of diagnostic analyses. Especially in recent years, numerous new biomarkers have come to the forefront-the analysis of which is crucial for therapy decisions. OBJECTIVES Within the field of molecular pathology, the demands of next generation sequencing (NGS)-based requirements have experienced massive growth in recent years. To meet this demand, methods are constantly being adapted and further developed. The following sections aim to illuminate how this trend arises and which analyses are gaining importance. METHODS The article provides an overview of the essential nucleic acid-based analysis techniques in the field of massive parallel sequencing. Terms such as DNA- and RNA-based techniques, as well as the associated analysis methods, are described, particularly with regard to their use in routine molecular pathological diagnostics. RESULTS The breadth of genomic sequencing has been steadily growing in recent years, particularly due to the increasing relevance of personalized medicine, along with the rising approvals of targeted therapeutics. This necessitates, among other things, the analysis of new biomarkers. The diagnostics as part of interdisciplinary molecular tumor boards (MTB) are now based on large gene panels (> 1 megabase). Furthermore, through the "Modellvorhaben Genomsequenzierung" § 64e, whole exome or whole genome sequencing has been made available for oncological patients. Given these developments, it is evident that future analyses will require the integration of additional omics fields, such as whole transcriptome analysis, epigenomics, and proteomics. CONCLUSION The challenges of personalized medicine along with the necessity of simultaneously assessing numerous new biomarkers require the implementation and execution of new techniques in molecular pathology whose complexity is steadily increasing.
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Affiliation(s)
- Maria Walker
- Institut für Pathologie, Technische Universität München, Trogerstr. 18, 81675, München, Deutschland
| | - Eva-Maria Mayr
- Institut für Pathologie, Technische Universität München, Trogerstr. 18, 81675, München, Deutschland
| | - Mai-Lan Koppermann
- Institut für Pathologie, Technische Universität München, Trogerstr. 18, 81675, München, Deutschland
| | - Ana Terron
- Institut für Pathologie, Technische Universität München, Trogerstr. 18, 81675, München, Deutschland
| | - Yoko Wagner
- Institut für Pathologie, Technische Universität München, Trogerstr. 18, 81675, München, Deutschland
| | - Charlotte Kling
- Institut für Pathologie, Technische Universität München, Trogerstr. 18, 81675, München, Deutschland
- Deutsches Konsortium für Translationale Krebsforschung (DKTK), Heidelberg, Deutschland
| | - Nicole Pfarr
- Institut für Pathologie, Technische Universität München, Trogerstr. 18, 81675, München, Deutschland.
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Dreikhausen L, Klupsch A, Wiest I, Xiao Q, Schulte N, Betge J, Boch T, Brochhausen C, Gaiser T, Hofheinz RD, Ebert M, Zhan T. Clinical impact of panel gene sequencing on therapy of advanced cancers of the digestive system: a retrospective, single center study. BMC Cancer 2024; 24:526. [PMID: 38664720 PMCID: PMC11046933 DOI: 10.1186/s12885-024-12261-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Panel gene sequencing is an established diagnostic tool for precision oncology of solid tumors, but its utility for the treatment of cancers of the digestive system in clinical routine is less well documented. METHODS We retrospectively identified patients with advanced or metastatic gastrointestinal, pancreaticobiliary or hepatic cancers who received panel gene sequencing at a tertiary university hospital from 2015 to 2022. For these cases, we determined the spectrum of genetic alterations, clinicopathological parameters and treatment courses. Assessment of actionability of genetic alterations was based on the OncoKB database, cancer-specific ESMO treatment guidelines, and recommendations of the local molecular tumor board. RESULTS In total, 155 patients received panel gene sequencing using either the Oncomine Focus (62 cases), Comprehensive (91 cases) or Childhood Cancer Research Assay (2 cases). The mean age of patients was 61 years (range 24-90) and 37% were female. Most patients suffered from either colorectal cancer (53%) or cholangiocellular carcinoma (19%). 327 genetic alterations were discovered in 123 tumor samples, with an average number of 2.1 alterations per tumor. The most frequently altered genes were TP53, KRAS and PIK3CA. Actionable gene alterations were detected in 13.5-56.8% of tumors, according to ESMO guidelines or the OncoKB database, respectively. Thirteen patients were treated with targeted therapies based on identified molecular alterations, with a median progression-free survival of 8.8 months. CONCLUSIONS Actionable genetic alterations are frequently detected by panel gene sequencing in patients with advanced cancers of the digestive tract, providing clinical benefit in selected cases. However, for the majority of identified actionable alterations, sufficient clinical evidence for targeted treatments is still lacking.
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Affiliation(s)
- Lena Dreikhausen
- Department of Medicine II, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Anna Klupsch
- Department of Medicine II, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Isabella Wiest
- Department of Medicine II, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Qiyun Xiao
- Department of Medicine II, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Nadine Schulte
- Department of Medicine II, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Johannes Betge
- Department of Medicine II, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Junior Clinical Cooperation Unit Translational Gastrointestinal Oncology and Preclinical Models, German Cancer Research Center, Heidelberg, Germany
- Mannheim Cancer Center, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Medical Faculty Mannheim, DKFZ-Hector Cancer Institute, Heidelberg University, Mannheim, Germany
| | - Tobias Boch
- Department of Medicine III, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Medical Faculty Mannheim, DKFZ-Hector Cancer Institute, Heidelberg University, Mannheim, Germany
| | - Christoph Brochhausen
- Institute of Pathology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Timo Gaiser
- Institute of Pathology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Ralf-Dieter Hofheinz
- Mannheim Cancer Center, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Department of Medicine III, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Matthias Ebert
- Department of Medicine II, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Mannheim Cancer Center, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Medical Faculty Mannheim, DKFZ-Hector Cancer Institute, Heidelberg University, Mannheim, Germany
| | - Tianzuo Zhan
- Department of Medicine II, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.
- Mannheim Cancer Center, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.
- Medical Faculty Mannheim, DKFZ-Hector Cancer Institute, Heidelberg University, Mannheim, Germany.
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King AD, Deirawan H, Klein PA, Dasgeb B, Dumur CI, Mehregan DR. Next-generation sequencing in dermatology. Front Med (Lausanne) 2023; 10:1218404. [PMID: 37841001 PMCID: PMC10570430 DOI: 10.3389/fmed.2023.1218404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 09/04/2023] [Indexed: 10/17/2023] Open
Abstract
Over the past decade, Next-Generation Sequencing (NGS) has advanced our understanding, diagnosis, and management of several areas within dermatology. NGS has emerged as a powerful tool for diagnosing genetic diseases of the skin, improving upon traditional PCR-based techniques limited by significant genetic heterogeneity associated with these disorders. Epidermolysis bullosa and ichthyosis are two of the most extensively studied genetic diseases of the skin, with a well-characterized spectrum of genetic changes occurring in these conditions. NGS has also played a critical role in expanding the mutational landscape of cutaneous squamous cell carcinoma, enhancing our understanding of its molecular pathogenesis. Similarly, genetic testing has greatly benefited melanoma diagnosis and treatment, primarily due to the high prevalence of BRAF hot spot mutations and other well-characterized genetic alterations. Additionally, NGS provides a valuable tool for measuring tumor mutational burden, which can aid in management of melanoma. Lastly, NGS demonstrates promise in improving the sensitivity of diagnosing cutaneous T-cell lymphoma. This article provides a comprehensive summary of NGS applications in the diagnosis and management of genodermatoses, cutaneous squamous cell carcinoma, melanoma, and cutaneous T-cell lymphoma, highlighting the impact of NGS on the field of dermatology.
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Affiliation(s)
- Andrew D. King
- Department of Dermatology, Wayne State University School of Medicine, Detroit, MI, United States
| | - Hany Deirawan
- Department of Dermatology, Wayne State University School of Medicine, Detroit, MI, United States
| | | | - Bahar Dasgeb
- Department of Surgical Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, United States
| | - Catherine I. Dumur
- Bernhardt Laboratories, Sonic Healthcare Anatomic Pathology Division, Jacksonville, FL, United States
| | - Darius R. Mehregan
- Department of Dermatology, Wayne State University School of Medicine, Detroit, MI, United States
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Gurav M, Epari S, Gogte P, Pai T, Deshpande G, Karnik N, Shetty O, Desai S. Targeted molecular profiling of solid tumours-Indian tertiary cancer centre experience. J Cancer Res Clin Oncol 2023; 149:7413-7425. [PMID: 36935431 DOI: 10.1007/s00432-023-04693-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/12/2023] [Indexed: 03/21/2023]
Abstract
PURPOSE Molecular Profiling of solid tumours is extensively used for prognostic, theranostic, and risk prediction. Next generation sequencing (NGS) has emerged as powerful method for molecular profiling. The present study was performed to identify molecular alterations present in solid tumours in Indian tertiary cancer centre. METHODS Study included 1140 formalin Fixed paraffin embedded samples. NGS was performed using two targeted gene panels viz. Ampliseq Focus panel and Sophia Solid Tumor Plus Solution. Data was analyzed using Illumina's Local Run Manager and SOPHiA DDM software. Variant interpretation and annotations were done as per AMP/ACMG guidelines. RESULTS Total 896 cases were subjected to NGS after excluding cases with suboptimal nucleic acid quality/quantity. DNA alterations were detected in 64.9% and RNA fusions in 6.9% cases. Among detected variants, 86.7% were clinically relevant aberrations. Mutation frequency among different solid tumours was 70.8%, 67.4%, 64.4% in non-small cell lung (NSCLC), lung squamous cell carcinomas and head neck tumours respectively. EGFR, KRAS, BRAF, ALK and ROS1were commonly altered in NSCLC. Gastrointestinal tumours showed mutations in 63.6% with predominant alterations in pancreatic (88.2%), GIST (87.5%), colorectal (78.7%), cholangiocarcinoma (52.9%), neuroendocrine (45.5%), gall bladder (36.7%) and gastric adenocarcinomas (16.7%). The key genes affected were KRAS, NRAS, BRAF and PIK3CA. NGS evaluation identified co-occurring alterations in 37.7% cases otherwise missed by conventional assays. Resistance mutations were detected in progressive lung tumours (39.5%) against EGFR TKIs and ALK/ROS inhibitors. CONCLUSION This is the largest Indian study on molecular profiling of solid tumours providing extensive information about mutational signatures using NGS.
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Affiliation(s)
- Mamta Gurav
- Molecular Pathology laboratory, Department of Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Sridhar Epari
- Department of Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Prachi Gogte
- Molecular Pathology laboratory, Department of Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Trupti Pai
- Department of Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Gauri Deshpande
- Department of Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Nupur Karnik
- Department of Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Omshree Shetty
- Molecular Pathology laboratory, Department of Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India.
| | - Sangeeta Desai
- Department of Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
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Unraveling the Structural Variations of Early-Stage Mycosis Fungoides—CD3 Based Purification and Third Generation Sequencing as Novel Tools for the Genomic Landscape in CTCL. Cancers (Basel) 2022; 14:cancers14184466. [PMID: 36139626 PMCID: PMC9497107 DOI: 10.3390/cancers14184466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/08/2022] [Accepted: 09/12/2022] [Indexed: 11/16/2022] Open
Abstract
Mycosis fungoides (MF) is the most common cutaneous T-cell lymphoma (CTCL). At present, knowledge of genetic changes in early-stage MF is insufficient. Additionally, low tumor cell fraction renders calling of copy-number variations as the predominant mutations in MF challenging, thereby impeding further investigations. We show that enrichment of T cells from a biopsy of a stage I MF patient greatly increases tumor fraction. This improvement enables accurate calling of recurrent MF copy-number variants such as ARID1A and CDKN2A deletion and STAT5 amplification, undetected in the unprocessed biopsy. Furthermore, we demonstrate that application of long-read nanopore sequencing is especially useful for the structural variant rich CTCL. We detect the structural variants underlying recurrent MF copy-number variants and show phasing of multiple breakpoints into complex structural variant haplotypes. Additionally, we record multiple occurrences of templated insertion structural variants in this sample. Taken together, this study suggests a workflow to make the early stages of MF accessible for genetic analysis, and indicates long-read sequencing as a major tool for genetic analysis for MF.
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Mack M, Broche J, George S, Hajjari Z, Janke F, Ranganathan L, Ashouri M, Bleul S, Desuki A, Engels C, Fliedner SM, Hartmann N, Hummel M, Janning M, Kiel A, Köhler T, Koschade S, Lablans M, Lambarki M, Loges S, Lueong S, Meyer S, Ossowski S, Scherer F, Schroeder C, Skowronek P, Thiede C, Uhl B, Vehreschild JJ, von Bubnoff N, Wagner S, Werner TV, Westphalen CB, Fresser P, Sültmann H, Tinhofer I, Winter C. The DKTK EXLIQUID consortium – exploiting liquid biopsies to advance cancer precision medicine for molecular tumor board patients. J LAB MED 2022. [DOI: 10.1515/labmed-2022-0071] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023] Open
Abstract
Abstract
Testing for genetic alterations in tumor tissue allows clinicians to identify patients who most likely will benefit from molecular targeted treatment. EXLIQUID – exploiting liquid biopsies to advance cancer precision medicine – investigates the potential of additional non-invasive tools for guiding therapy decisions and monitoring of advanced cancer patients. The term “liquid biopsy” (LB) refers to non-invasive analysis of tumor-derived circulating material such as cell-free DNA in blood samples from cancer patients. Although recent technological advances allow sensitive and specific detection of LB biomarkers, only few LB assays have entered clinical routine to date. EXLIQUID is a German Cancer Consortium (DKTK)-wide joint funding project that aims at establishing LBs as a minimally-invasive tool to analyze molecular changes in circulating tumor DNA (ctDNA). Here, we present the structure, clinical aim, and methodical approach of the new DKTK EXLIQUID consortium. Within EXLIQUID, we will set up a multicenter repository of high-quality LB samples from patients participating in DKTK MASTER and local molecular tumor boards, which use molecular profiles of tumor tissues to guide targeted therapies. We will develop LB assays for monitoring of therapy efficacy by the analysis of tumor mutant variants and tumor-specific DNA methylation patterns in ctDNA from these patients. By bringing together LB experts from all DKTK partner sites and exploiting the diversity of their particular expertise, complementary skills and technologies, the EXLIQUID consortium addresses the challenges of translating LBs into the clinic. The DKTK structure provides EXLIQUID a unique position for the identification of liquid biomarkers even in less common tumor types, thereby extending the group of patients benefitting from non-invasive LB testing. Besides its scientific aims, EXLIQUID is building a valuable precision oncology cohort and LB platform which will be available for future collaborative research studies within the DKTK and beyond.
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Affiliation(s)
- Matthias Mack
- School of Medicine , Institute of Clinical Chemistry and Pathobiochemistry, Technical University of Munich , Munich , Germany
- German Cancer Consortium (DKTK), Partner Site Munich , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Julian Broche
- Institute of Medical Genetics and Applied Genomics, University of Tübingen , Tübingen , Germany
- German Cancer Consortium (DKTK), Partner Site Tübingen , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Stephen George
- Department of Radiooncology and Radiotherapy , Charité University Hospital Berlin , Berlin , Germany
- German Cancer Consortium (DKTK), Partner Site Berlin , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Zahra Hajjari
- West German Cancer Center , Bridge Institute of Experimental Tumor Therapy, University Hospital Essen , Essen , Germany
- German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Florian Janke
- Division of Cancer Genome Research , German Cancer Research Center (DKFZ) , Heidelberg , Germany
- German Cancer Consortium (DKTK) , Heidelberg , Germay
| | - Lavanya Ranganathan
- Department of Medicine I , Medical Center – University of Freiburg , Freiburg , Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Mohammadreza Ashouri
- School of Medicine , Institute of Clinical Chemistry and Pathobiochemistry, Technical University of Munich , Munich , Germany
- German Cancer Consortium (DKTK), Partner Site Munich , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Sabine Bleul
- Department of Medicine I , Medical Center – University of Freiburg , Freiburg , Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Alexander Desuki
- University Cancer Center (UCT), University Medical Center of the Johannes Gutenberg-University Mainz , Mainz , Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Cecilia Engels
- Charité University Hospital Berlin , Berlin , Germany
- German Cancer Consortium (DKTK), Partner Site Berlin , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Stephanie M.J. Fliedner
- University Cancer Center Schleswig-Holstein, University Medical Center Schleswig-Holstein , Kiel/Lübeck , Germany
| | - Nils Hartmann
- Institute of Pathology, University Medical Center JGU Mainz , Mainz , Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Michael Hummel
- Charité University Hospital Berlin , Berlin , Germany
- German Cancer Consortium (DKTK), Partner Site Berlin , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Melanie Janning
- DKFZ-Hector Cancer Institute at the University Medical Center Mannheim , Mannheim , Germany
- Division of Personalized Medical Oncology (A420) , German Cancer Research Center (DKFZ) , Heidelberg , Germany
- Department of Personalized Oncology, Medical Faculty Mannheim , University Hospital Mannheim, University of Heidelberg , Mannheim , Germany
| | - Alexander Kiel
- Complex Data Processing in Medical Informatics , University Medical Center Mannheim , Mannheim , Germany
- German Cancer Consortium (DKTK); and Federated Information Systems , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Thomas Köhler
- Complex Data Processing in Medical Informatics , University Medical Center Mannheim , Mannheim , Germany
- German Cancer Consortium (DKTK); and Federated Information Systems , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Sebastian Koschade
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz , German Cancer Research Center (DKFZ) , Heidelberg , Germany
- Department of Medicine, Hematology/Oncology , Goethe University , Frankfurt , Germany
| | - Martin Lablans
- Complex Data Processing in Medical Informatics , University Medical Center Mannheim , Mannheim , Germany
- German Cancer Consortium (DKTK); and Federated Information Systems , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Mohamed Lambarki
- Complex Data Processing in Medical Informatics , University Medical Center Mannheim , Mannheim , Germany
- German Cancer Consortium (DKTK); and Federated Information Systems , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Sonja Loges
- DKFZ-Hector Cancer Institute at the University Medical Center Mannheim , Mannheim , Germany
- Division of Personalized Medical Oncology (A420) , German Cancer Research Center (DKFZ) , Heidelberg , Germany
- Department of Personalized Oncology, Medical Faculty Mannheim , University Hospital Mannheim, University of Heidelberg , Mannheim , Germany
| | - Smiths Lueong
- West German Cancer Center , Bridge Institute of Experimental Tumor Therapy, University Hospital Essen , Essen , Germany
- German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Sandra Meyer
- University Hospital Frankfurt , Frankfurt , Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University of Tübingen , Tübingen , Germany
- German Cancer Consortium (DKTK), Partner Site Tübingen , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Florian Scherer
- Department of Medicine I , Medical Center – University of Freiburg , Freiburg , Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Christopher Schroeder
- Institute of Medical Genetics and Applied Genomics, University of Tübingen , Tübingen , Germany
- German Cancer Consortium (DKTK), Partner Site Tübingen , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Patrick Skowronek
- Complex Data Processing in Medical Informatics , University Medical Center Mannheim , Mannheim , Germany
- German Cancer Consortium (DKTK); and Federated Information Systems , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Christian Thiede
- Department of Medicine I , University Hospital Carl Gustav Carus , Dresden , Germany
- German Cancer Consortium (DKTK), Partner Site Dresden , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Barbara Uhl
- University Hospital Frankfurt , Frankfurt , Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Jörg Janne Vehreschild
- University Hospital Frankfurt , Frankfurt , Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Nikolas von Bubnoff
- University Cancer Center Schleswig-Holstein, University Medical Center Schleswig-Holstein , Kiel/Lübeck , Germany
| | - Sebastian Wagner
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz , German Cancer Research Center (DKFZ) , Heidelberg , Germany
- Department of Medicine, Hematology/Oncology , Goethe University , Frankfurt , Germany
| | - Tamara V. Werner
- Medical Center, Medical Faculty , Institute for Surgical Pathology, University of Freiburg , Freiburg , Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - C. Benedikt Westphalen
- Comprehensive Cancer Center Munich & Department of Medicine III , Ludwig Maximilian University of Munich , Munich , Germany
- German Cancer Consortium (DKTK), Partner Site Munich , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Patrizia Fresser
- School of Medicine , Institute of Clinical Chemistry and Pathobiochemistry, Technical University of Munich , Munich , Germany
- German Cancer Consortium (DKTK), Partner Site Munich , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Holger Sültmann
- Division of Cancer Genome Research , German Cancer Research Center (DKFZ) , Heidelberg , Germany
- German Cancer Consortium (DKTK) , Heidelberg , Germay
| | - Ingeborg Tinhofer
- Department of Radiooncology and Radiotherapy , Charité University Hospital Berlin , Berlin , Germany
- German Cancer Consortium (DKTK), Partner Site Berlin , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Christof Winter
- School of Medicine , Institute of Clinical Chemistry and Pathobiochemistry, Technical University of Munich , Munich , Germany
- German Cancer Consortium (DKTK), Partner Site Munich , German Cancer Research Center (DKFZ) , Heidelberg , Germany
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Comprehensive cancer predisposition testing within the prospective MASTER trial identifies hereditary cancer patients and supports treatment decisions for rare cancers. Ann Oncol 2022; 33:1186-1199. [PMID: 35988656 DOI: 10.1016/j.annonc.2022.07.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 07/04/2022] [Accepted: 07/18/2022] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Germline variant evaluation in precision oncology opens new paths towards the identification of patients with genetic tumor risk syndromes and the exploration of therapeutic relevance. Here, we present the results of germline variant analysis and their clinical implications in a precision oncology study for patients with predominantly rare cancers. PATIENTS AND METHODS Matched tumor and control genome/exome and RNA sequencing was performed for 1,485 patients with rare cancers (79%) and/or young adults (77% younger than 51 years) in the NCT/DKTK MASTER trial, a German multicenter, prospective observational precision oncology study. Clinical and therapeutic relevance of prospective pathogenic germline variant (PGV) evaluation was analyzed and compared to other precision oncology studies. RESULTS Ten percent of patients (n=157) harbored PGVs in 35 genes associated with autosomal dominant cancer predisposition, whereof up to 75% were unknown before study participation. Another five percent of patients (n=75) were heterozygous carriers for recessive genetic tumor risk syndromes. Particularly high PGV yields were found in patients with gastrointestinal stromal tumors (GISTs) (28%, 11/40), and more specific in wild-type GISTS (50%, n=10/20), leiomyosarcomas (21%, n=19/89), and hepatopancreaticobiliary cancers (16%, n=16/97). Forty-five percent of PGVs (n=100/221) supported treatment recommendations, and its implementation led to a clinical benefit in 40% of patients (n=10/25). A comparison of different precision oncology studies revealed variable PGV yields and considerable differences in germline variant analysis workflows. We therefore propose a detailed workflow for germline variant evaluation. CONCLUSIONS Genetic germline testing in patients with rare cancers can identify the very first patient in a hereditary cancer family and can lead to clinical benefit in a broad range of entities. Its routine implementation in precision oncology accompanied by the harmonization of germline variant evaluation workflows will increase clinical benefit and boost research.
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9
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Comprehensive genomic and epigenomic analysis in cancer of unknown primary guides molecularly-informed therapies despite heterogeneity. Nat Commun 2022; 13:4485. [PMID: 35918329 PMCID: PMC9346116 DOI: 10.1038/s41467-022-31866-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 07/06/2022] [Indexed: 11/09/2022] Open
Abstract
The benefit of molecularly-informed therapies in cancer of unknown primary (CUP) is unclear. Here, we use comprehensive molecular characterization by whole genome/exome, transcriptome and methylome analysis in 70 CUP patients to reveal substantial mutational heterogeneity with TP53, MUC16, KRAS, LRP1B and CSMD3 being the most frequently mutated known cancer-related genes. The most common fusion partner is FGFR2, the most common focal homozygous deletion affects CDKN2A. 56/70 (80%) patients receive genomics-based treatment recommendations which are applied in 20/56 (36%) cases. Transcriptome and methylome data provide evidence for the underlying entity in 62/70 (89%) cases. Germline analysis reveals five (likely) pathogenic mutations in five patients. Recommended off-label therapies translate into a mean PFS ratio of 3.6 with a median PFS1 of 2.9 months (17 patients) and a median PFS2 of 7.8 months (20 patients). Our data emphasize the clinical value of molecular analysis and underline the need for innovative, mechanism-based clinical trials. The identification of molecular biomarkers in cancer of unknown primary site (CUP) cases may enable the improvement of prognosis in these patients. Here, the authors integrate whole genome/exome, transcriptome and methylome data in 70 CUP patients, recommend therapies based on their analysis and report clinical outcome data.
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10
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Mateo J, Steuten L, Aftimos P, André F, Davies M, Garralda E, Geissler J, Husereau D, Martinez-Lopez I, Normanno N, Reis-Filho JS, Stefani S, Thomas DM, Westphalen CB, Voest E. Delivering precision oncology to patients with cancer. Nat Med 2022; 28:658-665. [PMID: 35440717 DOI: 10.1038/s41591-022-01717-2] [Citation(s) in RCA: 109] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 01/26/2022] [Indexed: 12/15/2022]
Abstract
With the increasing use of genomic profiling for diagnosis and therapy guidance in many tumor types, precision oncology is rapidly reshaping cancer care. However, the current trajectory of drug development in oncology results in a paradox: if patients cannot access advanced diagnostics, we may be developing drugs that will reach few patients. In this Perspective, we outline the major challenges to the implementation of precision oncology and discuss critical steps toward resolving these, including facilitation of equal access to genomics tests, ensuring that clinical studies provide robust evidence for new drugs and technologies, enabling physicians to interpret genomics data, and empowering patients toward shared decision-making. A multi-stakeholder approach to evidence generation, value assessment, and healthcare delivery is necessary to translate advances in precision oncology into benefits for patients with cancer globally.
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Affiliation(s)
- Joaquin Mateo
- Vall d'Hebron Institute of Oncology (VHIO) and Vall d'Hebron University Hospital, Barcelona, Spain
| | - Lotte Steuten
- Office of Health Economics, London, UK
- City University of London, London, UK
| | - Philippe Aftimos
- Institut Jules Bordet - Université Libre de Bruxelles, Brussels, Belgium
| | - Fabrice André
- Institut Gustave Roussy, INSERM U981, Université Paris Saclay, Villejuif, France
| | | | - Elena Garralda
- Vall d'Hebron Institute of Oncology (VHIO) and Vall d'Hebron University Hospital, Barcelona, Spain
| | | | | | - Iciar Martinez-Lopez
- Unit of Genetics and Genomics of the Balearic Islands, Son Espases University Hospital, Illes, Balears, Spain
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS 'Fondazione G. Pascale', Naples, Italy
| | | | | | - David M Thomas
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - C Benedikt Westphalen
- Comprehensive Cancer Center Munich & Department of Medicine III, Ludwig Maximilian University of Munich, Munich, Germany
- German Cancer Consortium (DKTK partner site Munich), Heidelberg, Germany
| | - Emile Voest
- Netherlands Cancer Institute, Amsterdam, the Netherlands.
- Oncode Institute, Utrecht, the Netherlands.
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11
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Striefler JK, Schmiester M, Brandes F, Dörr A, Pahl S, Kaul D, Rau D, Dobrindt EM, Koulaxouzidis G, Bullinger L, Märdian S, Flörcken A. Comorbidities rather than older age define outcome in adult patients with tumors of the Ewing sarcoma family. Cancer Med 2022; 11:3213-3225. [PMID: 35297222 PMCID: PMC9468425 DOI: 10.1002/cam4.4688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 03/03/2022] [Accepted: 03/09/2022] [Indexed: 11/13/2022] Open
Abstract
Background Ewing family of tumors (EFT) is rarely diagnosed in patients (pts) over the age of 18 years (years), and data on the clinical course and the outcome of adult EFT pts is sparse. Methods In this retrospective analysis, we summarize our experience with adult EFT pts. From 2002 to 2020, we identified 71 pts of whom 58 were evaluable for the final analysis. Results Median age was 31 years (18–90 years). Pts presented with skeletal (n = 26), and extra‐skeletal primary disease (n =32). Tumor size was ≥8 cm in 20 pts and 19 pts were metastasized at first diagnosis. Between the age groups (≤25 vs. 26–40 vs. ≥41 years) we observed differences of Charlson comorbidity index (CCI), tumor origin, as well as type and number of therapy cycles. Overall, median overall survival (OS) was 79 months (95% confidence interval, CI; 28.5–131.4 months), and median progression‐free survival (PFS) 34 months (95% CI; 21.4–45.8 months). We observed a poorer outcome (OS, PFS) in older pts. This could be in part due to differences in treatment intensity and the CCI (<3 vs. ≥3; hazard ratio, HR 0.334, 95% CI 0.15–0.72, p = 0.006). In addition, tumor stage had a significant impact on PFS (localized vs. metastasized stage: HR 0.403, 95% CI 0.18–0.87, p = 0.021). Conclusions Our data confirms the feasibility of intensive treatment regimens in adult EFT pts. While in our cohort outcome was influenced by age, due to differences in treatment intensity, CCI, and tumor stage, larger studies are warranted to further explore optimized treatment protocols in adult EFT pts.
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Affiliation(s)
- Jana Käthe Striefler
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany.,Department of Hematology, Oncology, and Tumor Immunology, Berlin Institute of Health, Berlin, Germany
| | - Maren Schmiester
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany.,Department of Hematology, Oncology, and Tumor Immunology, Berlin Institute of Health, Berlin, Germany
| | - Franziska Brandes
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany.,Department of Hematology, Oncology, and Tumor Immunology, Berlin Institute of Health, Berlin, Germany
| | - Anne Dörr
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany.,Department of Hematology, Oncology, and Tumor Immunology, Berlin Institute of Health, Berlin, Germany
| | - Stefan Pahl
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany.,Institute of Pathology, Campus Mitte, Berlin Institute of Health, Berlin, Germany
| | - David Kaul
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany.,Department of Radiation Oncology, Campus Virchow-Klinikum, Berlin Institute of Health, Berlin, Germany
| | - Daniel Rau
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany.,Centre for Musculoskeletal Surgery, Campus Virchow-Klinikum, Berlin Institute of Health, Berlin, Germany
| | - Eva-Maria Dobrindt
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany.,Department of Surgery, Campus Virchow-Klinikum, Berlin Institute of Health, Berlin, Germany
| | - Georgios Koulaxouzidis
- Department of Plastic, Aesthetic and Reconstructive Surgery, Congregational Hospital Linz, Sisters of Mercy, Linz, Austria
| | - Lars Bullinger
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany.,Department of Hematology, Oncology, and Tumor Immunology, Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sven Märdian
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany.,Centre for Musculoskeletal Surgery, Campus Virchow-Klinikum, Berlin Institute of Health, Berlin, Germany
| | - Anne Flörcken
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany.,Department of Hematology, Oncology, and Tumor Immunology, Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
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12
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Yan YH, Chen SX, Cheng LY, Rodriguez AY, Tang R, Cabrera K, Zhang DY. Confirming putative variants at ≤ 5% allele frequency using allele enrichment and Sanger sequencing. Sci Rep 2021; 11:11640. [PMID: 34079006 PMCID: PMC8172533 DOI: 10.1038/s41598-021-91142-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 05/21/2021] [Indexed: 12/19/2022] Open
Abstract
Whole exome sequencing (WES) is used to identify mutations in a patient's tumor DNA that are predictive of tumor behavior, including the likelihood of response or resistance to cancer therapy. WES has a mutation limit of detection (LoD) at variant allele frequencies (VAF) of 5%. Putative mutations called at ≤ 5% VAF are frequently due to sequencing errors, therefore reporting these subclonal mutations incurs risk of significant false positives. Here we performed ~ 1000 × WES on fresh-frozen and formalin-fixed paraffin-embedded (FFPE) tissue biopsy samples from a non-small cell lung cancer patient, and identified 226 putative mutations at between 0.5 and 5% VAF. Each variant was then tested using NuProbe NGSure, to confirm the original WES calls. NGSure utilizes Blocker Displacement Amplification to first enrich the allelic fraction of the mutation and then uses Sanger sequencing to determine mutation identity. Results showed that 52% of the 226 (117) putative variants were disconfirmed, among which 2% (5) putative variants were found to be misidentified in WES. In the 66 cancer-related variants, the disconfirmed rate was 82% (54/66). This data demonstrates Blocker Displacement Amplification allelic enrichment coupled with Sanger sequencing can be used to confirm putative mutations ≤ 5% VAF. By implementing this method, next-generation sequencing can reliably report low-level variants at a high sensitivity, without the cost of high sequencing depth.
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Affiliation(s)
| | - Sherry X Chen
- Department of Bioengineering, Rice University, 6500 Main St, Houston, TX, 77030, USA
| | - Lauren Y Cheng
- Department of Bioengineering, Rice University, 6500 Main St, Houston, TX, 77030, USA
| | | | - Rui Tang
- NuProbe USA, Inc., Houston, TX, USA
| | | | - David Yu Zhang
- Department of Bioengineering, Rice University, 6500 Main St, Houston, TX, 77030, USA.
- Systems, Synthetic, and Physical Biology, Rice University, 6500 Main St, Houston, TX, 77030, USA.
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13
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Uhrig S, Ellermann J, Walther T, Burkhardt P, Fröhlich M, Hutter B, Toprak UH, Neumann O, Stenzinger A, Scholl C, Fröhling S, Brors B. Accurate and efficient detection of gene fusions from RNA sequencing data. Genome Res 2021; 31:448-460. [PMID: 33441414 PMCID: PMC7919457 DOI: 10.1101/gr.257246.119] [Citation(s) in RCA: 192] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 12/30/2020] [Indexed: 12/17/2022]
Abstract
The identification of gene fusions from RNA sequencing data is a routine task in cancer research and precision oncology. However, despite the availability of many computational tools, fusion detection remains challenging. Existing methods suffer from poor prediction accuracy and are computationally demanding. We developed Arriba, a novel fusion detection algorithm with high sensitivity and short runtime. When applied to a large collection of published pancreatic cancer samples (n = 803), Arriba identified a variety of driver fusions, many of which affected druggable proteins, including ALK, BRAF, FGFR2, NRG1, NTRK1, NTRK3, RET, and ROS1. The fusions were significantly associated with KRAS wild-type tumors and involved proteins stimulating the MAPK signaling pathway, suggesting that they substitute for activating mutations in KRAS In addition, we confirmed the transforming potential of two novel fusions, RRBP1-RAF1 and RASGRP1-ATP1A1, in cellular assays. These results show Arriba's utility in both basic cancer research and clinical translation.
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Affiliation(s)
- Sebastian Uhrig
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT) Heidelberg, 69120 Heidelberg, Germany
- Computational Oncology Group, Molecular Diagnostics Program at the NCT and DKFZ, 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Julia Ellermann
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
- Division of Translational Medical Oncology, NCT Heidelberg and DKFZ, 69120 Heidelberg, Germany
| | - Tatjana Walther
- Division of Translational Medical Oncology, NCT Heidelberg and DKFZ, 69120 Heidelberg, Germany
| | - Pauline Burkhardt
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT) Heidelberg, 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Martina Fröhlich
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT) Heidelberg, 69120 Heidelberg, Germany
- Computational Oncology Group, Molecular Diagnostics Program at the NCT and DKFZ, 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Barbara Hutter
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT) Heidelberg, 69120 Heidelberg, Germany
- Computational Oncology Group, Molecular Diagnostics Program at the NCT and DKFZ, 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Umut H Toprak
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- Division of Neuroblastoma Genomics, DKFZ, 69120 Heidelberg, Germany
| | - Olaf Neumann
- Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Albrecht Stenzinger
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- German Center for Lung Research (DZL), Heidelberg site, 69120 Heidelberg, Germany
| | - Claudia Scholl
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- Division of Applied Functional Genomics, DKFZ and NCT Heidelberg, 69120 Heidelberg, Germany
| | - Stefan Fröhling
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- Division of Translational Medical Oncology, NCT Heidelberg and DKFZ, 69120 Heidelberg, Germany
- NCT Molecular Diagnostics Program, NCT Heidelberg and DKFZ, 69120 Heidelberg, Germany
| | - Benedikt Brors
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT) Heidelberg, 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- NCT Molecular Diagnostics Program, NCT Heidelberg and DKFZ, 69120 Heidelberg, Germany
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14
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Schäfer R. [RAS mutations at the molecular tumor conference]. DER PATHOLOGE 2019; 40:355-359. [PMID: 31754788 DOI: 10.1007/s00292-019-00702-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Members of the rat sarcoma (RAS) gene family belong to the most frequently mutated genes that drive pathogenesis and therapy response. As the discovery of their malignant potential dates back more than three decades, cellular mutated RAS genes and their products belong to the best characterized cancer genes. Despite urgent clinical needs, RAS therapies are still elusive and limited to preclinical studies. However, very recently, novel and promising approaches have become a reality in clinical applications and trials. In the near future, interesting therapeutic options will emerge that are capable of targeting "undruggable" RAS. This will be even more important as the detection of RAS mutations has already been an integral part of routine molecular diagnostics for many years.
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Affiliation(s)
- R Schäfer
- Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Deutschland.
- Deutsches Krebsforschungszentrum Heidelberg, Deutsches Konsortium für Translationale Krebsforschung (DKTK), Heidelberg, Deutschland.
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15
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Leichsenring J, Kazdal D, Ploeger C, Allgäuer M, Endris V, Volckmar AL, Neumann O, Kirchner M, Penzel R, Rempel E, Budczies J, Schirmacher P, Fröhling S, Stenzinger A. [From panel diagnostics to comprehensive genomic analysis : Infobesity or empowerment?]. DER PATHOLOGE 2019; 40:235-242. [PMID: 31089797 DOI: 10.1007/s00292-019-0608-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Precision oncology is obtaining a central role in the therapy of malignant diseases. The indication for targeted therapy is based on the identification of molecular targets for which next-generation sequencing (NGS) is commonly used nowadays. All approved predictive biomarkers and molecular targets, including gene fusions and copy number alterations, can be identified depending on panel design and method applied. Some clinical scenarios, however, may require more holistic genomic approaches, such as whole-genome/whole-exome and transcriptome analysis, which must be embedded in a clinical trial. Here, key aspects and applications of each method are summarized and discussed.
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Affiliation(s)
- J Leichsenring
- Pathologisches Institut, Molekularpathologisches Zentrum, Universitätsklinikum Heidelberg, Heidelberg, Deutschland
| | - D Kazdal
- Pathologisches Institut, Molekularpathologisches Zentrum, Universitätsklinikum Heidelberg, Heidelberg, Deutschland
| | - C Ploeger
- Pathologisches Institut, Molekularpathologisches Zentrum, Universitätsklinikum Heidelberg, Heidelberg, Deutschland
| | - M Allgäuer
- Pathologisches Institut, Molekularpathologisches Zentrum, Universitätsklinikum Heidelberg, Heidelberg, Deutschland
| | - V Endris
- Pathologisches Institut, Molekularpathologisches Zentrum, Universitätsklinikum Heidelberg, Heidelberg, Deutschland
| | - A-L Volckmar
- Pathologisches Institut, Molekularpathologisches Zentrum, Universitätsklinikum Heidelberg, Heidelberg, Deutschland
| | - O Neumann
- Pathologisches Institut, Molekularpathologisches Zentrum, Universitätsklinikum Heidelberg, Heidelberg, Deutschland
| | - M Kirchner
- Pathologisches Institut, Molekularpathologisches Zentrum, Universitätsklinikum Heidelberg, Heidelberg, Deutschland
| | - R Penzel
- Pathologisches Institut, Molekularpathologisches Zentrum, Universitätsklinikum Heidelberg, Heidelberg, Deutschland
| | - E Rempel
- Pathologisches Institut, Molekularpathologisches Zentrum, Universitätsklinikum Heidelberg, Heidelberg, Deutschland
| | - J Budczies
- Pathologisches Institut, Molekularpathologisches Zentrum, Universitätsklinikum Heidelberg, Heidelberg, Deutschland
| | - P Schirmacher
- Pathologisches Institut, Molekularpathologisches Zentrum, Universitätsklinikum Heidelberg, Heidelberg, Deutschland
| | - S Fröhling
- Abteilung Translationale Medizinische Onkologie, Nationales Centrum für Tumorerkrankungen (NCT) Heidelberg und Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Deutschland
| | - A Stenzinger
- Pathologisches Institut, Molekularpathologisches Zentrum, Universitätsklinikum Heidelberg, Heidelberg, Deutschland.
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