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Darmofal M, Suman S, Atwal G, Toomey M, Chen JF, Chang JC, Vakiani E, Varghese AM, Balakrishnan Rema A, Syed A, Schultz N, Berger MF, Morris Q. Deep-Learning Model for Tumor-Type Prediction Using Targeted Clinical Genomic Sequencing Data. Cancer Discov 2024; 14:1064-1081. [PMID: 38416134 PMCID: PMC11145170 DOI: 10.1158/2159-8290.cd-23-0996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/07/2023] [Accepted: 02/23/2024] [Indexed: 02/29/2024]
Abstract
Tumor type guides clinical treatment decisions in cancer, but histology-based diagnosis remains challenging. Genomic alterations are highly diagnostic of tumor type, and tumor-type classifiers trained on genomic features have been explored, but the most accurate methods are not clinically feasible, relying on features derived from whole-genome sequencing (WGS), or predicting across limited cancer types. We use genomic features from a data set of 39,787 solid tumors sequenced using a clinically targeted cancer gene panel to develop Genome-Derived-Diagnosis Ensemble (GDD-ENS): a hyperparameter ensemble for classifying tumor type using deep neural networks. GDD-ENS achieves 93% accuracy for high-confidence predictions across 38 cancer types, rivaling the performance of WGS-based methods. GDD-ENS can also guide diagnoses of rare type and cancers of unknown primary and incorporate patient-specific clinical information for improved predictions. Overall, integrating GDD-ENS into prospective clinical sequencing workflows could provide clinically relevant tumor-type predictions to guide treatment decisions in real time. SIGNIFICANCE We describe a highly accurate tumor-type prediction model, designed specifically for clinical implementation. Our model relies only on widely used cancer gene panel sequencing data, predicts across 38 distinct cancer types, and supports integration of patient-specific nongenomic information for enhanced decision support in challenging diagnostic situations. See related commentary by Garg, p. 906. This article is featured in Selected Articles from This Issue, p. 897.
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Affiliation(s)
- Madison Darmofal
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, New York
| | - Shalabh Suman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Gurnit Atwal
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Vector Institute, Toronto, Ontario, Canada
| | - Michael Toomey
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, New York
| | - Jie-Fu Chen
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jason C. Chang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Efsevia Vakiani
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Anna M. Varghese
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Aijazuddin Syed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nikolaus Schultz
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael F. Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Quaid Morris
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
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Mackinnon AC, Chandrashekar DS, Suster DI. Molecular pathology as basis for timely cancer diagnosis and therapy. Virchows Arch 2024; 484:155-168. [PMID: 38012424 DOI: 10.1007/s00428-023-03707-2] [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: 08/21/2023] [Revised: 10/16/2023] [Accepted: 11/08/2023] [Indexed: 11/29/2023]
Abstract
Precision and personalized therapeutics have witnessed significant advancements in technology, revolutionizing the capabilities of laboratories to generate vast amounts of genetic data. Coupled with computational resources for analysis and interpretation, and integrated with various other types of data, including genomic data, electronic medical health (EMH) data, and clinical knowledge, these advancements support optimized health decisions. Among these technologies, next-generation sequencing (NGS) stands out as a transformative tool in the field of cancer treatment, playing a crucial role in precision oncology. NGS-based workflows are employed across a range of applications, including gene panels, exome sequencing, and whole-genome sequencing, supporting comprehensive analysis of the entire cancer genome, including mutations, copy number variations, gene expression profiles, and epigenetic modifications. By utilizing the power of NGS, these workflows contribute to enhancing our understanding of disease mechanisms, diagnosis confirmation, identifying therapeutic targets, and guiding personalized treatment decisions. This manuscript explores the diverse applications of NGS in cancer treatment, highlighting its significance in guiding diagnosis and treatment decisions, identifying therapeutic targets, monitoring disease progression, and improving patient outcomes.
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Affiliation(s)
- A Craig Mackinnon
- Department of Pathology, University of Alabama at Birmingham, 619 19Th Street South, Birmingham, AL, 35249, USA.
| | | | - David I Suster
- Department of Pathology, Rutgers University New Jersey Medical School, 150 Bergen Street, Newark, NJ, 07103, USA.
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3
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Roohani S, Alberti Y, Mirwald M, Ehret F, Stromberger C, Roohani SF, Bender K, Flörcken A, Märdian S, Zips D, Kaul D. Meningeal Solitary Fibrous Tumor: A Single-Center Retrospective Cohort Study. Sarcoma 2024; 2024:8846018. [PMID: 38274845 PMCID: PMC10807944 DOI: 10.1155/2024/8846018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 12/13/2023] [Accepted: 12/28/2023] [Indexed: 01/27/2024] Open
Abstract
Background Meningeal solitary fibrous tumors (SFTs) are rare, malignant, mesenchymal tumors of the central nervous system. While surgical gross total resection is widely accepted as a positive prognostic factor for local control (LC), the role of postoperative radiotherapy (PORT) remains controversial. We sought to report our institutional experience with a particular focus on outcomes after PORT. Materials and Methods In this single-center, retrospective cohort study, 20 patients with the primary diagnosis of histopathologically confirmed meningeal SFT were analyzed. Data on patient characteristics, imaging, treatment modalities, histopathology, and oncological outcomes were collected. LC and overall survival (OS) were assessed using the Kaplan-Meier estimator. Results The median follow-up time was 95.8 months. After surgery only, 9 out of 11 patients (81.8%) developed a local recurrence while, after surgery and PORT, 3 out of 9 patients (33.33%) showed local failure. The 5- and 10-year LC rates were 50.5% and 40.4% in the surgery-only group and 80% at both time points in the surgery with the PORT group. In the surgery-only group, 4 out of 11 patients (36.4%) died, and 4 out of 9 patients (44.4%) died in the surgery and PORT group. OS rates after 5 and 10 years were 88.9% and 66.7% in the surgery-only group and 88.9% and 76.2% in the surgery with PORT group. Conclusions Our findings suggest that PORT may improve LC in patients with meningeal SFT. The low incidence of meningeal SFT impedes prospective studies and requires further international collaborative efforts to exploit retrospective datasets and molecular analysis to improve patient outcomes.
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Affiliation(s)
- Siyer Roohani
- Charité−Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Radiation Oncology, Augustenburger Platz 1, Berlin 13353, Germany
- Berlin Institute of Health at Charité−Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité Junior Clinician Scientist Program, Charitéplatz 1, Berlin 10117, Germany
- Charité−Universitätsmedizin Berlin, German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Berlin, Germany
| | - Yasemin Alberti
- Department of Radiotherapy, West German Cancer Center, University of Duisburg-Essen, University Hospital Essen, Essen, Germany
| | - Maximilian Mirwald
- Charité−Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Radiation Oncology, Augustenburger Platz 1, Berlin 13353, Germany
| | - Felix Ehret
- Charité−Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Radiation Oncology, Augustenburger Platz 1, Berlin 13353, Germany
- Charité−Universitätsmedizin Berlin, German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Berlin, Germany
| | - Carmen Stromberger
- Vivantes Klinikum Neukölln, Department of Radiooncology and Radiotherapy, Berlin, Germany
| | - Soleiman Fabris Roohani
- Charité−Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Radiation Oncology, Augustenburger Platz 1, Berlin 13353, Germany
| | - Katja Bender
- Charité−Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Radiation Oncology, Augustenburger Platz 1, Berlin 13353, Germany
| | - Anne Flörcken
- Charité−Universitätsmedizin Berlin, German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Berlin, Germany
- Charité−Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Department of Hematology, Oncology and Tumor Immunology, Augustenburger Platz 1, Berlin 13353, Germany
| | - Sven Märdian
- Charité−Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Center for Musculoskeletal Surgery, Campus Virchow-Klinikum, Augustenburger Platz 1, Berlin 13353, Germany
| | - Daniel Zips
- Charité−Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Radiation Oncology, Augustenburger Platz 1, Berlin 13353, Germany
- Charité−Universitätsmedizin Berlin, German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Berlin, Germany
| | - David Kaul
- Charité−Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Radiation Oncology, Augustenburger Platz 1, Berlin 13353, Germany
- Charité−Universitätsmedizin Berlin, German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Berlin, Germany
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Miettinen M, Abdullaev Z, Turakulov R, Quezado M, Luiña Contreras A, Curcio CA, Rys J, Chlopek M, Lasota J, Aldape KD. Assessment of The Utility of The Sarcoma DNA Methylation Classifier In Surgical Pathology. Am J Surg Pathol 2024; 48:112-122. [PMID: 37921028 PMCID: PMC10842611 DOI: 10.1097/pas.0000000000002138] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
Diagnostic classification of soft tissue tumors is based on histology, immunohistochemistry, genetic findings, and radiologic and clinical correlations. Recently, a sarcoma DNA methylation classifier was developed, covering 62 soft tissue and bone tumor entities. The classifier is based on large-scale analysis of methylation sites across the genome. It includes DNA copy number analysis and determines O 6 methylguanine DNA methyl-transferase methylation status. In this study, we evaluated 619 well-studied soft tissue and bone tumors with the sarcoma classifier. Problem cases and typical examples of different entities were included. The classifier had high sensitivity and specificity for fusion sarcomas: Ewing, synovial, CIC -rearranged, and BCOR -rearranged. It also performed well for leiomyosarcoma, malignant peripheral nerve sheath tumors (MPNST), and malignant vascular tumors. There was low sensitivity for diagnoses of desmoid fibromatosis, neurofibroma, and schwannoma. Low specificity of matches was observed for angiomatoid fibrous histiocytoma, inflammatory myofibroblastic tumor, Langerhans histiocytosis, schwannoma, undifferentiated sarcoma, and well-differentiated/dedifferentiated liposarcoma. Diagnosis of lipomatous tumors was greatly assisted by the detection of MDM2 amplification and RB1 loss in the copy plot. The classifier helped to establish diagnoses for KIT-negative gastrointestinal stromal tumors, MPNSTs with unusual immunophenotypes, and undifferentiated melanomas. O 6 methylguanine DNA methyl-transferase methylation was infrequent and most common in melanomas (35%), MPNSTs (11%), and undifferentiated sarcomas (11%). The Sarcoma Methylation Classifier will likely evolve with the addition of new entities and refinement of the present methylation classes. The classifier may also help to define new entities and give new insight into the interrelationships of sarcomas.
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Affiliation(s)
- Markku Miettinen
- Laboratory of Pathology, National Cancer Institute, NIH, Bethesda, Maryland
| | - Zied Abdullaev
- Laboratory of Pathology, National Cancer Institute, NIH, Bethesda, Maryland
| | - Rust Turakulov
- Laboratory of Pathology, National Cancer Institute, NIH, Bethesda, Maryland
| | - Martha Quezado
- Laboratory of Pathology, National Cancer Institute, NIH, Bethesda, Maryland
| | | | | | - Janusz Rys
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Cracow Branch, Krakow, Poland
| | - Malgorzata Chlopek
- Laboratory of Pathology, National Cancer Institute, NIH, Bethesda, Maryland
| | - Jerzy Lasota
- Laboratory of Pathology, National Cancer Institute, NIH, Bethesda, Maryland
| | - Kenneth D. Aldape
- Laboratory of Pathology, National Cancer Institute, NIH, Bethesda, Maryland
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Black JO, Al-Ibraheemi A, Arnold MA, Coffin CM, Davis JL, Parham DM, Rudzinski ER, Shenoy A, Surrey LF, Tan SY, Spunt SL. The Pathologic Diagnosis of Pediatric Soft Tissue Tumors in the Era of Molecular Medicine: The Sarcoma Pediatric Pathology Research Interest Group Perspective. Arch Pathol Lab Med 2024; 148:107-116. [PMID: 37196343 DOI: 10.5858/arpa.2022-0364-ra] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2023] [Indexed: 05/19/2023]
Abstract
CONTEXT.— Pediatric soft tissue tumors are one of the areas of pediatric pathology that frequently generate consult requests. Evolving classification systems, ancillary testing methods, new treatment options, research enrollment opportunities, and tissue archival processes create additional complexity in handling these unique specimens. Pathologists are at the heart of this critical decision-making, balancing responsibilities to consider expediency, accessibility, and cost-effectiveness of ancillary testing during pathologic examination and reporting. OBJECTIVE.— To provide a practical approach to handling pediatric soft tissue tumor specimens, including volume considerations, immunohistochemical staining panel recommendations, genetic and molecular testing approaches, and other processes that impact the quality and efficiency of tumor tissue triage. DATA SOURCES.— The World Health Organization Classification of Soft Tissue and Bone Tumors, 5th edition, other recent literature investigating tissue handling, and the collective clinical experience of the group are used in this manuscript. CONCLUSIONS.— Pediatric soft tissue tumors can be difficult to diagnose, and evaluation can be improved by adopting a thoughtful, algorithmic approach to maximize available tissue and minimize time to diagnosis.
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Affiliation(s)
- Jennifer O Black
- From the Department of Pathology and Laboratory Medicine, Children's Hospital of Colorado, Aurora (Black, Arnold)
| | - Alyaa Al-Ibraheemi
- the Department of Pathology, Children's Hospital Boston, Boston, Massachusetts (Al-Ibraheemi)
| | - Michael A Arnold
- From the Department of Pathology and Laboratory Medicine, Children's Hospital of Colorado, Aurora (Black, Arnold)
| | - Cheryl M Coffin
- the Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee (Coffin)
| | - Jessica L Davis
- From the Department of Pathology and Laboratory Medicine, Children's Hospital of Colorado, Aurora (Black, Arnold)
- the Department of Pathology and Laboratory Medicine, Oregon Health and Sciences University, Portland (Davis)
| | - David M Parham
- Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles (Parham)
| | - Erin R Rudzinski
- the Department of Laboratory Medicine and Pathology, Seattle Children's Hospital, Seattle, Washington (Rudzinski)
| | - Archana Shenoy
- the Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio (Shenoy)
| | - Lea F Surrey
- the Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania (Surrey)
| | - Serena Y Tan
- the Departments of Pathology (Tan) and Pediatrics (Spunt), Lucille Packard Children's Hospital, Stanford University School of Medicine, Stanford, California
| | - Sheri L Spunt
- the Departments of Pathology (Tan) and Pediatrics (Spunt), Lucille Packard Children's Hospital, Stanford University School of Medicine, Stanford, California
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Kopachev DN, Ryzhova MV, Kislyakov AN, Shaikhaev EG, Zheludkova OG, Kumirova EV, Meshcheryakov SV, Vlasov PA, Shkatova AM, Semenova ZB, Gushcha AO. [Supratentorial neuroepithelial tumor with PLAGL1 gene fusion - a new type of morphologically variable pediatric brain neoplasm defined by a distinct DNA methylation class. A case report and literature review]. ZHURNAL VOPROSY NEIROKHIRURGII IMENI N. N. BURDENKO 2024; 88:62-68. [PMID: 38549412 DOI: 10.17116/neiro20248802162] [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: 04/02/2024]
Abstract
BACKGROUND Methylation analysis has become a powerful diagnostic tool in modern neurooncology. This technique is valuable to diagnose new brain tumor types. OBJECTIVE To describe the MRI and histological pattern of neuroepithelial tumor with PLAGL1 gene fusion. MATERIAL AND METHODS We present a 6-year-old patient with small right frontal intraaxial tumor causing drug resistant epilepsy. Despite indolent preoperative clinical course and MRI features suggesting glioneuronal tumor, histological evaluation revealed characteristics of high-grade glioma, ependymoma and neuroblastoma. RESULTS Methylation analysis of tumor DNA confirmed a new type of a recently discovered neoplasm - neuroepithelial tumor with PLAGL1 fusion (NET PLAGL1). PCR confirmed fusion of PLAGL1 and EWSR1 genes. No seizures were observed throughout the follow-up period. There was no tumor relapse a year after surgery. CONCLUSION Methylation analysis in neurooncology is essential for unclear tumor morphology or divergence between histological and clinical data. In our case, this technique confirmed benign nature of tumor, and we preferred follow-up without unnecessary adjuvant treatment.
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Affiliation(s)
- D N Kopachev
- Research Institute for Emergency Pediatric Surgery and Traumatology, Moscow, Russia
- Neurology Research Center, Moscow, Russia
| | - M V Ryzhova
- Burdenko Neurosurgical Center, Moscow, Russia
| | - A N Kislyakov
- Morozov Children's Clinical Hospital, Moscow, Russia
| | | | - O G Zheludkova
- Voyno-Yasenetsky Practical Center for Specialized Medical Care for Children, Moscow, Russia
| | - E V Kumirova
- Morozov Children's Clinical Hospital, Moscow, Russia
| | - S V Meshcheryakov
- Research Institute for Emergency Pediatric Surgery and Traumatology, Moscow, Russia
| | - P A Vlasov
- Burdenko Neurosurgical Center, Moscow, Russia
| | | | - Zh B Semenova
- Research Institute for Emergency Pediatric Surgery and Traumatology, Moscow, Russia
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Difilippo V, Saba KH, Styring E, Magnusson L, Nilsson J, Nathrath M, Baumhoer D, Nord KH. Osteosarcomas With Few Chromosomal Alterations or Adult Onset Are Genetically Heterogeneous. J Transl Med 2024; 104:100283. [PMID: 37931683 DOI: 10.1016/j.labinv.2023.100283] [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: 06/22/2023] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 11/08/2023] Open
Abstract
Osteosarcoma is the most common primary bone malignancy, often detected in children and adolescents and commonly associated with TP53 alterations along with a high number of chromosomal rearrangements. However, osteosarcoma can affect patients of any age, and some tumors display less genetic complexity. Besides TP53 variants, data on key driving mutations are lacking for many osteosarcomas, particularly those affecting adults. To detect osteosarcoma-specific alterations, we screened transcriptomic and genomic sequencing and copy number data from 150 bone tumors originally diagnosed as osteosarcomas. To increase the precision in gene fusion detection, we developed a bioinformatic tool denoted as NAFuse, which extracts gene fusions that are verified at both the genomic and transcriptomic levels. Apart from the already reported genetic subgroups of osteosarcoma with TP53 structural variants, or MDM2 and/or CDK4 amplification, we did not identify any recurrent genetic driver that signifies the remaining cases. Among the plethora of mutations identified, we found genetic alterations characteristic of, or similar to, those of other bone and soft tissue tumors in 8 cases. These mutations were found in tumors with relatively few other genetic alterations or in adults. Due to the lack of clinical context and available tissue, we can question the diagnosis only on a genetic basis. However, our findings support the notion that osteosarcomas with few chromosomal alterations or adult onset seem genetically distinct from conventional osteosarcomas of children and adolescents.
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Affiliation(s)
- Valeria Difilippo
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Karim H Saba
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Emelie Styring
- Department of Orthopedics, Lund University, Skåne University Hospital, Lund, Sweden
| | - Linda Magnusson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Jenny Nilsson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Michaela Nathrath
- Children's Cancer Research Centre and Department of Pediatrics, Klinikum rechts der Isar, Technische Universität München, Munich, Germany; Department of Pediatric Oncology, Klinikum Kassel, Kassel, Germany
| | - Daniel Baumhoer
- Bone Tumour Reference Centre at the Institute of Pathology, University Hospital and University of Basel, Basel, Switzerland
| | - Karolin H Nord
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden.
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Singh J, Sahu S, Mohan T, Mahajan S, Sharma MC, Sarkar C, Suri V. Current status of DNA methylation profiling in neuro-oncology as a diagnostic support tool: A review. Neurooncol Pract 2023; 10:518-526. [PMID: 38009119 PMCID: PMC10666812 DOI: 10.1093/nop/npad040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2023] Open
Abstract
Over the last 2 decades, high throughput genome-wide molecular profiling has revealed characteristic genetic and epigenetic alterations associated with different types of central nervous system (CNS) tumors. DNA methylation profiling has emerged as an important molecular platform for CNS tumor classification with improved diagnostic accuracy and patient risk stratification in comparison to the standard of care histopathological analysis and any single molecular tests. The emergence of DNA methylation arrays have also played a crucial role in refining existing types and the discovery of new tumor types or subtypes. The adoption of methylation data into neuro-oncology has been greatly aided by the development of a freely accessible machine learning-based classifier. In this review, we discuss methylation workflow, address the utility of DNA methylation profiling in CNS tumors in a routine diagnostic setting, and provide an overview of the methylation-based tumor types and new types or subtypes identified with this platform.
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Affiliation(s)
- Jyotsna Singh
- Neuropathology Laboratory, Neurosciences Centre, All India Institute of Medical Sciences, New Delhi, India
| | - Saumya Sahu
- Neuropathology Laboratory, Neurosciences Centre, All India Institute of Medical Sciences, New Delhi, India
| | - Trishala Mohan
- Neuropathology Laboratory, Neurosciences Centre, All India Institute of Medical Sciences, New Delhi, India
| | - Swati Mahajan
- Neuropathology Laboratory, Neurosciences Centre, All India Institute of Medical Sciences, New Delhi, India
| | - Mehar C Sharma
- Neuropathology Laboratory, Neurosciences Centre, All India Institute of Medical Sciences, New Delhi, India
| | - Chitra Sarkar
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Vaishali Suri
- Neuropathology Laboratory, Neurosciences Centre, All India Institute of Medical Sciences, New Delhi, India
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9
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Yu R. Sellar Mass in 2 Patients With Acute-Onset Headache and Visual Symptoms: Not Your Usual Pituitary Adenoma. AACE Clin Case Rep 2023; 9:197-200. [PMID: 38045795 PMCID: PMC10690422 DOI: 10.1016/j.aace.2023.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/16/2023] [Accepted: 09/25/2023] [Indexed: 12/05/2023] Open
Abstract
Background/Objective Clinical diagnosis of rare aggressive sellar malignancies requires a high index of suspicion. The objective was to report 2 patients with primary sellar atypical teratoid (AT)/rhabdoid tumor (RT) who presented with acute-onset headache and visual symptoms. Case Report Patient 1 was a 45-year-old woman who presented with 3 weeks of headache and 1 week of eye pain and diplopia. Magnetic resonance imaging (MRI) identified a 2.2-cm sellar mass. Pituitary hormone testing showed elevated prolactin and suppressed luteinizing hormone, follicle-stimulating hormone, and estradiol levels. Patient 2 was a 32-year-old woman who presented with 1 month of headache and 1 week of diplopia. MRI showed a 2.1-cm sellar mass. Hormonal test results were reportedly unremarkable. Both patients did not have a significant medical history. They each underwent transsphenoidal resection. Surgical histology and molecular studies were consistent with primary sellar AT/RT. After surgery, patient 1 developed bilateral blindness and was lost to follow-up. Patient 2 developed hypopituitarism; her visual symptoms improved temporarily but recurred 2 weeks later. Pituitary MRI showed sellar recurrence. She underwent further debulking, but the tumor recurred promptly again. Despite radiation therapy, she died 4 months after the original presentation. Discussion AT/RT appears to be the most aggressive sellar malignancy. Conclusion Based on the 2 cases presented and the literature, I conclude that rapidly progressive headache with subsequent visual impairment in women with large sellar masses is almost pathognomonic of sellar AT/RT.
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Affiliation(s)
- Run Yu
- Division of Endocrinology, UCLA David Geffen School of Medicine, Los Angeles, California
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10
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Bernhardt M, Vokuhl C. [Peripheral neuroblastic tumors in childhood]. PATHOLOGIE (HEIDELBERG, GERMANY) 2023; 44:366-372. [PMID: 37819531 DOI: 10.1007/s00292-023-01227-z] [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: 08/17/2023] [Indexed: 10/13/2023]
Abstract
Peripheral neuroblastic tumors represent the fourth-largest group of malignant tumors in childhood. The majority of these tumors are neuroblastomas, which can be classified into undifferentiated, poorly differentiated, and differentiating subtypes. In addition, peripheral neuroblastic tumors include ganglioneuroblastoma, a composite tumor composed of Schwannian cell stroma and neuroblasts as well as benign ganglioneuroma. In this overview, histopathological diagnostic criteria and grading systems, as well as common molecular alterations that are of prognostic and therapeutic significance, are discussed.
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Affiliation(s)
- Marit Bernhardt
- Sektion Kinderpathologie, Institut für Pathologie, Universitätsklinikum Bonn, Venusberg-Campus 1, Gebäude 62, 53127, Bonn, Deutschland.
| | - Christian Vokuhl
- Sektion Kinderpathologie, Institut für Pathologie, Universitätsklinikum Bonn, Venusberg-Campus 1, Gebäude 62, 53127, Bonn, Deutschland
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Mock A, Teleanu MV, Kreutzfeldt S, Heilig CE, Hüllein J, Möhrmann L, Jahn A, Hanf D, Kerle IA, Singh HM, Hutter B, Uhrig S, Fröhlich M, Neumann O, Hartig A, Brückmann S, Hirsch S, Grund K, Dikow N, Lipka DB, Renner M, Bhatti IA, Apostolidis L, Schlenk RF, Schaaf CP, Stenzinger A, Schröck E, Hübschmann D, Heining C, Horak P, Glimm H, Fröhling S. NCT/DKFZ MASTER handbook of interpreting whole-genome, transcriptome, and methylome data for precision oncology. NPJ Precis Oncol 2023; 7:109. [PMID: 37884744 PMCID: PMC10603123 DOI: 10.1038/s41698-023-00458-w] [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: 04/02/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023] Open
Abstract
Analysis of selected cancer genes has become an important tool in precision oncology but cannot fully capture the molecular features and, most importantly, vulnerabilities of individual tumors. Observational and interventional studies have shown that decision-making based on comprehensive molecular characterization adds significant clinical value. However, the complexity and heterogeneity of the resulting data are major challenges for disciplines involved in interpretation and recommendations for individualized care, and limited information exists on how to approach multilayered tumor profiles in clinical routine. We report our experience with the practical use of data from whole-genome or exome and RNA sequencing and DNA methylation profiling within the MASTER (Molecularly Aided Stratification for Tumor Eradication Research) program of the National Center for Tumor Diseases (NCT) Heidelberg and Dresden and the German Cancer Research Center (DKFZ). We cover all relevant steps of an end-to-end precision oncology workflow, from sample collection, molecular analysis, and variant prioritization to assigning treatment recommendations and discussion in the molecular tumor board. To provide insight into our approach to multidimensional tumor profiles and guidance on interpreting their biological impact and diagnostic and therapeutic implications, we present case studies from the NCT/DKFZ molecular tumor board that illustrate our daily practice. This manual is intended to be useful for physicians, biologists, and bioinformaticians involved in the clinical interpretation of genome-wide molecular information.
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Affiliation(s)
- Andreas Mock
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Pathology, Ludwig-Maximilians-Universität (LMU) München, Munich, Germany
| | - Maria-Veronica Teleanu
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Hematology, Oncology and Rheumatology, Heidelberg Unversity Hospital, Heidelberg, Germany
| | - Simon Kreutzfeldt
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christoph E Heilig
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jennifer Hüllein
- Computational Oncology Group, Molecular Precision Oncology Program, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Lino Möhrmann
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases/University Cancer Center (NCT/UCC) Dresden, Dresden, Germany
- DKFZ, Heidelberg, Germany
| | - Arne Jahn
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus, Technische Universität Dresden and Hereditary Cancer Syndrome Center Dresden, Dresden, Germany
| | - Dorothea Hanf
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases/University Cancer Center (NCT/UCC) Dresden, Dresden, Germany
- DKFZ, Heidelberg, Germany
| | - Irina A Kerle
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases/University Cancer Center (NCT/UCC) Dresden, Dresden, Germany
- DKFZ, Heidelberg, Germany
| | - Hans Martin Singh
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Medical Oncology, NCT Heidelberg and Heidelberg University Hospital, Heidelberg, Germany
| | - Barbara Hutter
- Computational Oncology Group, Molecular Precision Oncology Program, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Sebastian Uhrig
- Computational Oncology Group, Molecular Precision Oncology Program, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Martina Fröhlich
- Computational Oncology Group, Molecular Precision Oncology Program, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Olaf Neumann
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Andreas Hartig
- Institute of Pathology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Sascha Brückmann
- Institute of Pathology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Steffen Hirsch
- Institute of Human Genetics, Heidelberg University Hospital, Heidelberg, Germany
| | - Kerstin Grund
- Institute of Human Genetics, Heidelberg University Hospital, Heidelberg, Germany
| | - Nicola Dikow
- Institute of Human Genetics, Heidelberg University Hospital, Heidelberg, Germany
| | - Daniel B Lipka
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Translational Cancer Epigenomics, Division of Translational Medical Oncology, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Marcus Renner
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Irfan Ahmed Bhatti
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Medical Oncology, NCT Heidelberg and Heidelberg University Hospital, Heidelberg, Germany
| | - Leonidas Apostolidis
- Department of Medical Oncology, NCT Heidelberg and Heidelberg University Hospital, Heidelberg, Germany
| | - Richard F Schlenk
- Department of Hematology, Oncology and Rheumatology, Heidelberg Unversity Hospital, Heidelberg, Germany
- Department of Medical Oncology, NCT Heidelberg and Heidelberg University Hospital, Heidelberg, Germany
- NCT Trial Center, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Christian P Schaaf
- Institute of Human Genetics, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Evelin Schröck
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus, Technische Universität Dresden and Hereditary Cancer Syndrome Center Dresden, Dresden, Germany
| | - Daniel Hübschmann
- Computational Oncology Group, Molecular Precision Oncology Program, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Christoph Heining
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases/University Cancer Center (NCT/UCC) Dresden, Dresden, Germany
- DKFZ, Heidelberg, Germany
| | - Peter Horak
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hanno Glimm
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases/University Cancer Center (NCT/UCC) Dresden, Dresden, Germany
- DKFZ, Heidelberg, Germany
| | - Stefan Fröhling
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany.
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12
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Morgacheva D, Ryzhova M, Zheludkova O, Belogurova M, Dinikina Y. DNA methylation-based diagnosis confirmation in a pediatric patient with low-grade glioma: a case report. Front Pediatr 2023; 11:1256876. [PMID: 37818165 PMCID: PMC10561295 DOI: 10.3389/fped.2023.1256876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 09/04/2023] [Indexed: 10/12/2023] Open
Abstract
Central nervous system (CNS) tumors in children comprise a highly heterogenous and complex group of diseases. Historically, diagnosis and confirmation of these tumors were routinely based on histological examination. However, recently obtained data demonstrate that such a diagnostic approach is not completely accurate and could lead to misdiagnosis. Also, in recent times, the quantity and quality of molecular diagnostic methods have greatly improved, which influences the current classification methods and treatment approach for pediatric CNS tumors. Nowadays, molecular methods, such as DNA methylation profiling, are an integral part of diagnosing brain and spinal tumors in children. In this paper, we present the case of an infant with a posterior fossa tumor who demonstrated a non-specific morphology and whose diagnosis was verified only after DNA methylation.
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Affiliation(s)
- Daria Morgacheva
- Almazov National Medical Research Centre, Saint-Petersburg, Russia
| | | | - Olga Zheludkova
- V.F. Voino-Yasenetskiy Scientific and Practical Center of Specialized Healthcare for Children, Moscow, Russia
| | | | - Yulia Dinikina
- Almazov National Medical Research Centre, Saint-Petersburg, Russia
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13
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Gómez-González S, Llano J, Garcia M, Garrido-Garcia A, Suñol M, Lemos I, Perez-Jaume S, Salvador N, Gene-Olaciregui N, Galán RA, Santa-María V, Perez-Somarriba M, Castañeda A, Hinojosa J, Winter U, Moreira FB, Lubieniecki F, Vazquez V, Mora J, Cruz O, La Madrid AM, Perera A, Lavarino C. EpiGe: A machine-learning strategy for rapid classification of medulloblastoma using PCR-based methyl-genotyping. iScience 2023; 26:107598. [PMID: 37664618 PMCID: PMC10470382 DOI: 10.1016/j.isci.2023.107598] [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: 03/31/2023] [Revised: 06/26/2023] [Accepted: 08/08/2023] [Indexed: 09/05/2023] Open
Abstract
Molecular classification of medulloblastoma is critical for the treatment of this brain tumor. Array-based DNA methylation profiling has emerged as a powerful approach for brain tumor classification. However, this technology is currently not widely available. We present a machine-learning decision support system (DSS) that enables the classification of the principal molecular groups-WNT, SHH, and non-WNT/non-SHH-directly from quantitative PCR (qPCR) data. We propose a framework where the developed DSS appears as a user-friendly web-application-EpiGe-App-that enables automated interpretation of qPCR methylation data and subsequent molecular group prediction. The basis of our classification strategy is a previously validated six-cytosine signature with subgroup-specific methylation profiles. This reduced set of markers enabled us to develop a methyl-genotyping assay capable of determining the methylation status of cytosines using qPCR instruments. This study provides a comprehensive approach for rapid classification of clinically relevant medulloblastoma groups, using readily accessible equipment and an easy-to-use web-application.t.
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Affiliation(s)
- Soledad Gómez-González
- Laboratory of Developmental Tumor Biology, Institut de Recerca Sant Joan de Déu, Pediatric Cancer Center Barcelona, Hospital Sant Joan de Déu, Barcelona, Spain
- Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Joshua Llano
- Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
- B2SLab, Departament d'Enginyeria de Sistemes, Automàtica i Informàtica Industrial, Universitat Politècnica de Catalunya, Barcelona, Spain
- Networking Biomedical Research Centre in the Subject Area of Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain
| | - Marta Garcia
- Laboratory of Developmental Tumor Biology, Institut de Recerca Sant Joan de Déu, Pediatric Cancer Center Barcelona, Hospital Sant Joan de Déu, Barcelona, Spain
- Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Alicia Garrido-Garcia
- Laboratory of Developmental Tumor Biology, Institut de Recerca Sant Joan de Déu, Pediatric Cancer Center Barcelona, Hospital Sant Joan de Déu, Barcelona, Spain
- Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Mariona Suñol
- Department of Pathology, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Isadora Lemos
- Laboratory of Molecular Oncology, Pediatric Cancer Center Barcelona, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Sara Perez-Jaume
- Laboratory of Developmental Tumor Biology, Institut de Recerca Sant Joan de Déu, Pediatric Cancer Center Barcelona, Hospital Sant Joan de Déu, Barcelona, Spain
- Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Noelia Salvador
- Laboratory of Molecular Oncology, Pediatric Cancer Center Barcelona, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Nagore Gene-Olaciregui
- Laboratory of Molecular Oncology, Pediatric Cancer Center Barcelona, Hospital Sant Joan de Déu, Barcelona, Spain
| | | | - Vicente Santa-María
- Neuro Oncology Unit, Pediatric Cancer Center Barcelona, Hospital Sant Joan de Déu, Barcelona, Spain
| | | | - Alicia Castañeda
- Pediatric Solid Tumor Unit, Pediatric Cancer Center Barcelona, Hospital Sant Joan de Déu, Barcelona, Spain
| | - José Hinojosa
- Department of Neurosurgery, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Ursula Winter
- Department of Pathology, Pediatric Hospital S.A.M.I.C. Prof. Dr. Juan P. Garrahan, Buenos Aires, Argentina
| | - Francisco Barbosa Moreira
- Department of Pathology, Pediatric Hospital S.A.M.I.C. Prof. Dr. Juan P. Garrahan, Buenos Aires, Argentina
| | - Fabiana Lubieniecki
- Department of Pathology, Pediatric Hospital S.A.M.I.C. Prof. Dr. Juan P. Garrahan, Buenos Aires, Argentina
| | - Valeria Vazquez
- Department of Pathology, Pediatric Hospital S.A.M.I.C. Prof. Dr. Juan P. Garrahan, Buenos Aires, Argentina
| | - Jaume Mora
- Laboratory of Developmental Tumor Biology, Institut de Recerca Sant Joan de Déu, Pediatric Cancer Center Barcelona, Hospital Sant Joan de Déu, Barcelona, Spain
- Pediatric Solid Tumor Unit, Pediatric Cancer Center Barcelona, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Ofelia Cruz
- Neuro Oncology Unit, Pediatric Cancer Center Barcelona, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Andrés Morales La Madrid
- Neuro Oncology Unit, Pediatric Cancer Center Barcelona, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Alexandre Perera
- Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
- B2SLab, Departament d'Enginyeria de Sistemes, Automàtica i Informàtica Industrial, Universitat Politècnica de Catalunya, Barcelona, Spain
- Networking Biomedical Research Centre in the Subject Area of Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain
| | - Cinzia Lavarino
- Laboratory of Developmental Tumor Biology, Institut de Recerca Sant Joan de Déu, Pediatric Cancer Center Barcelona, Hospital Sant Joan de Déu, Barcelona, Spain
- Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
- Laboratory of Molecular Oncology, Pediatric Cancer Center Barcelona, Hospital Sant Joan de Déu, Barcelona, Spain
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14
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Darmofal M, Suman S, Atwal G, Chen JF, Chang JC, Toomey M, Vakiani E, Varghese AM, Rema AB, Syed A, Schultz N, Berger M, Morris Q. Deep Learning Model for Tumor Type Prediction using Targeted Clinical Genomic Sequencing Data. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.08.23295131. [PMID: 37732244 PMCID: PMC10508812 DOI: 10.1101/2023.09.08.23295131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Tumor type guides clinical treatment decisions in cancer, but histology-based diagnosis remains challenging. Genomic alterations are highly diagnostic of tumor type, and tumor type classifiers trained on genomic features have been explored, but the most accurate methods are not clinically feasible, relying on features derived from whole genome sequencing (WGS), or predicting across limited cancer types. We use genomic features from a dataset of 39,787 solid tumors sequenced using a clinical targeted cancer gene panel to develop Genome-Derived-Diagnosis Ensemble (GDD-ENS): a hyperparameter ensemble for classifying tumor type using deep neural networks. GDD-ENS achieves 93% accuracy for high-confidence predictions across 38 cancer types, rivalling performance of WGS-based methods. GDD-ENS can also guide diagnoses on rare type and cancers of unknown primary, and incorporate patient-specific clinical information for improved predictions. Overall, integrating GDD-ENS into prospective clinical sequencing workflows has enabled clinically-relevant tumor type predictions to guide treatment decisions in real time.
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Affiliation(s)
- Madison Darmofal
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medicine; New York, NY 10065, USA
| | - Shalabh Suman
- Department of Pathology, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
| | - Gurnit Atwal
- Computational Biology Program, Ontario Institute for Cancer Research; Toronto, ON M5G 0A3, Canada
- Department of Molecular Genetics, University of Toronto; Toronto, ON M5S 1A8, Canada
- Vector Institute; Toronto, ON M5G 1M1, Canada
| | - Jie-Fu Chen
- Department of Pathology, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
| | - Jason C. Chang
- Department of Pathology, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
| | - Michael Toomey
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medicine; New York, NY 10065, USA
| | - Efsevia Vakiani
- Department of Pathology, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
| | - Anna M Varghese
- Department of Medicine, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
| | | | - Aijazuddin Syed
- Department of Pathology, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
| | - Nikolaus Schultz
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Michael Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
| | - Quaid Morris
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
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15
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Iluz A, Maoz M, Lavi N, Charbit H, Or O, Olshinka N, Demma JA, Adileh M, Wygoda M, Blumenfeld P, Gliner-Ron M, Azraq Y, Moss J, Peretz T, Eden A, Zick A, Lavon I. Rapid Classification of Sarcomas Using Methylation Fingerprint: A Pilot Study. Cancers (Basel) 2023; 15:4168. [PMID: 37627196 PMCID: PMC10453223 DOI: 10.3390/cancers15164168] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/14/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
Sarcoma classification is challenging and can lead to treatment delays. Previous studies used DNA aberrations and machine-learning classifiers based on methylation profiles for diagnosis. We aimed to classify sarcomas by analyzing methylation signatures obtained from low-coverage whole-genome sequencing, which also identifies copy-number alterations. DNA was extracted from 23 suspected sarcoma samples and sequenced on an Oxford Nanopore sequencer. The methylation-based classifier, applied in the nanoDx pipeline, was customized using a reference set based on processed Illumina-based methylation data. Classification analysis utilized the Random Forest algorithm and t-distributed stochastic neighbor embedding, while copy-number alterations were detected using a designated R package. Out of the 23 samples encompassing a restricted range of sarcoma types, 20 were successfully sequenced, but two did not contain tumor tissue, according to the pathologist. Among the 18 tumor samples, 14 were classified as reported in the pathology results. Four classifications were discordant with the pathological report, with one compatible and three showing discrepancies. Improving tissue handling, DNA extraction methods, and detecting point mutations and translocations could enhance accuracy. We envision that rapid, accurate, point-of-care sarcoma classification using nanopore sequencing could be achieved through additional validation in a diverse tumor cohort and the integration of methylation-based classification and other DNA aberrations.
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Affiliation(s)
- Aviel Iluz
- Leslie and Michael Gaffin Center for Neuro-Oncology, Hadassah Medical Center and Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9190501, Israel
- Agnes Ginges Center for Human Neurogenetics, Department of Neurology, Hadassah Medical Center and Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9190501, Israel
| | - Myriam Maoz
- Oncology Department, Sharett Institute of Oncology, Hadassah Medical Organization and Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9190501, Israel
| | - Nir Lavi
- Leslie and Michael Gaffin Center for Neuro-Oncology, Hadassah Medical Center and Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9190501, Israel
- Agnes Ginges Center for Human Neurogenetics, Department of Neurology, Hadassah Medical Center and Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9190501, Israel
- Department of Military Medicine and “Tzameret”, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9190501, Israel
| | - Hanna Charbit
- Leslie and Michael Gaffin Center for Neuro-Oncology, Hadassah Medical Center and Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9190501, Israel
- Agnes Ginges Center for Human Neurogenetics, Department of Neurology, Hadassah Medical Center and Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9190501, Israel
| | - Omer Or
- Orthopedic Department, Hadassah Medical Organization and Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9190501, Israel
| | - Noam Olshinka
- Orthopedic Department, Hadassah Medical Organization and Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9190501, Israel
| | - Jonathan Abraham Demma
- Surgical Department, Hadassah Medical Organization and Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9190501, Israel
| | - Mohammad Adileh
- Surgical Department, Hadassah Medical Organization and Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9190501, Israel
| | - Marc Wygoda
- Radiotherapy Institute, Sharett Institute of Oncology, Hadassah Medical Organization and Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9190501, Israel
| | - Philip Blumenfeld
- Radiotherapy Institute, Sharett Institute of Oncology, Hadassah Medical Organization and Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9190501, Israel
| | - Masha Gliner-Ron
- Radiology Department, Hadassah Medical Organization and Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9190501, Israel
| | - Yusef Azraq
- Radiology Department, Hadassah Medical Organization and Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9190501, Israel
| | - Joshua Moss
- Oncology Department, Sharett Institute of Oncology, Hadassah Medical Organization and Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9190501, Israel
| | - Tamar Peretz
- Oncology Department, Sharett Institute of Oncology, Hadassah Medical Organization and Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9190501, Israel
| | - Amir Eden
- Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 9190501, Israel
| | - Aviad Zick
- Oncology Department, Sharett Institute of Oncology, Hadassah Medical Organization and Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9190501, Israel
| | - Iris Lavon
- Leslie and Michael Gaffin Center for Neuro-Oncology, Hadassah Medical Center and Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9190501, Israel
- Agnes Ginges Center for Human Neurogenetics, Department of Neurology, Hadassah Medical Center and Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9190501, Israel
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16
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Roohani S, Ehret F, Perez E, Capper D, Jarosch A, Flörcken A, Märdian S, Zips D, Kaul D. Sarcoma classification by DNA methylation profiling in clinical everyday life: the Charité experience. Clin Epigenetics 2022; 14:149. [PMID: 36380356 PMCID: PMC9667620 DOI: 10.1186/s13148-022-01365-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 10/25/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Sarcomas are a heterogeneous group of rare malignant tumors with more than 100 subtypes. Accurate diagnosis remains challenging due to a lack of characteristic molecular or histomorphological hallmarks. A DNA methylation-based tumor profiling classifier for sarcomas (known as sarcoma classifier) from the German Cancer Research Center (Deutsches Krebsforschungszentrum) is now employed in selected cases to guide tumor classification and treatment decisions at our institution. Data on the usage of the classifier in daily clinical routine are lacking. METHODS In this single-center experience, we describe the clinical course of five sarcoma cases undergoing thorough pathological and reference pathological examination as well as DNA methylation-based profiling and their impact on subsequent treatment decisions. We collected data on the clinical course, DNA methylation analysis, histopathology, radiological imaging, and next-generation sequencing. RESULTS Five clinical cases involving DNA methylation-based profiling in 2021 at our institution were included. All patients' DNA methylation profiles were successfully matched to a methylation profile cluster of the sarcoma classifier's dataset. In three patients, the classifier reassured diagnosis or aided in finding the correct diagnosis in light of contradictory data and differential diagnoses. In two patients with intracranial tumors, the classifier changed the diagnosis to a novel diagnostic tumor group. CONCLUSIONS The sarcoma classifier is a valuable diagnostic tool that should be used after comprehensive clinical and histopathological evaluation. It may help to reassure the histopathological diagnosis or indicate the need for thorough reassessment in cases where it contradicts previous findings. However, certain limitations (non-classifiable cases, misclassifications, unclear degree of sample purity for analysis and others) currently preclude wide clinical application. The current sarcoma classifier is therefore not yet ready for a broad clinical routine. With further refinements, this promising tool may be implemented in daily clinical practice in selected cases.
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Affiliation(s)
- Siyer Roohani
- grid.6363.00000 0001 2218 4662Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Radiation Oncology, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Felix Ehret
- grid.6363.00000 0001 2218 4662Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Radiation Oncology, Augustenburger Platz 1, 13353 Berlin, Germany ,grid.484013.a0000 0004 6879 971XBerlin Institute of Health at Charité – Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany ,grid.7497.d0000 0004 0492 0584Charité - Universitätsmedizin Berlin, Berlin, German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Eilís Perez
- grid.6363.00000 0001 2218 4662Department of Neuropathology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt‑Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - David Capper
- grid.7497.d0000 0004 0492 0584Charité - Universitätsmedizin Berlin, Berlin, German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany ,grid.6363.00000 0001 2218 4662Department of Neuropathology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt‑Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Armin Jarosch
- grid.6363.00000 0001 2218 4662Institute of Pathology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Anne Flörcken
- grid.7497.d0000 0004 0492 0584Charité - Universitätsmedizin Berlin, Berlin, German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany ,grid.6363.00000 0001 2218 4662Department of Hematology, Oncology and Tumor Immunology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Sven Märdian
- grid.6363.00000 0001 2218 4662Centre for Musculoskeletal Surgery, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Daniel Zips
- grid.6363.00000 0001 2218 4662Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Radiation Oncology, Augustenburger Platz 1, 13353 Berlin, Germany ,grid.7497.d0000 0004 0492 0584Charité - Universitätsmedizin Berlin, Berlin, German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - David Kaul
- grid.6363.00000 0001 2218 4662Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Radiation Oncology, Augustenburger Platz 1, 13353 Berlin, Germany ,grid.7497.d0000 0004 0492 0584Charité - Universitätsmedizin Berlin, Berlin, German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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