1
|
Identification of Copy Number Alterations from Next-Generation Sequencing Data. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1361:55-74. [DOI: 10.1007/978-3-030-91836-1_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
2
|
Borchert F, Mock A, Tomczak A, Hügel J, Alkarkoukly S, Knurr A, Volckmar AL, Stenzinger A, Schirmacher P, Debus J, Jäger D, Longerich T, Fröhling S, Eils R, Bougatf N, Sax U, Schapranow MP. Knowledge bases and software support for variant interpretation in precision oncology. Brief Bioinform 2021; 22:bbab134. [PMID: 33971666 PMCID: PMC8574624 DOI: 10.1093/bib/bbab134] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 03/10/2021] [Accepted: 03/30/2021] [Indexed: 12/12/2022] Open
Abstract
Precision oncology is a rapidly evolving interdisciplinary medical specialty. Comprehensive cancer panels are becoming increasingly available at pathology departments worldwide, creating the urgent need for scalable cancer variant annotation and molecularly informed treatment recommendations. A wealth of mainly academia-driven knowledge bases calls for software tools supporting the multi-step diagnostic process. We derive a comprehensive list of knowledge bases relevant for variant interpretation by a review of existing literature followed by a survey among medical experts from university hospitals in Germany. In addition, we review cancer variant interpretation tools, which integrate multiple knowledge bases. We categorize the knowledge bases along the diagnostic process in precision oncology and analyze programmatic access options as well as the integration of knowledge bases into software tools. The most commonly used knowledge bases provide good programmatic access options and have been integrated into a range of software tools. For the wider set of knowledge bases, access options vary across different parts of the diagnostic process. Programmatic access is limited for information regarding clinical classifications of variants and for therapy recommendations. The main issue for databases used for biological classification of pathogenic variants and pathway context information is the lack of standardized interfaces. There is no single cancer variant interpretation tool that integrates all identified knowledge bases. Specialized tools are available and need to be further developed for different steps in the diagnostic process.
Collapse
Affiliation(s)
- Florian Borchert
- Digital Health Center, Hasso Plattner Institute (HPI), University of Potsdam, Prof.-Dr.-Helmert-Str. 2-3, 14482 Potsdam, Germany
| | - Andreas Mock
- Department of Translational Medical Oncology (TMO), National Center for Tumor Diseases (NCT) Heidelberg, German Cancer Research Center (DKFZ) Heidelberg, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - Aurelie Tomczak
- Institute of Pathology Heidelberg, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany
- Liver Cancer Center Heidelberg, Heidelberg University Hospital, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - Jonas Hügel
- Department of Medical Informatics, University Medical Center Göttingen, Von-Siebold-Str. 3, 37099 Göttingen, Germany
- Campus Institute Data Science, Göttingen, Germany
| | - Samer Alkarkoukly
- CECAD, Faculty of Medicine and University Hospital Cologne, University of Cologne, Joseph-Stelzmann-Straße 26, 50931 Cologne
| | - Alexander Knurr
- Division of Medical Informatics for Translational Oncology, German Cancer Research Center (DKFZ) Heidelberg, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Anna-Lena Volckmar
- Institute of Pathology Heidelberg, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany
| | - Albrecht Stenzinger
- Institute of Pathology Heidelberg, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany
| | - Peter Schirmacher
- Institute of Pathology Heidelberg, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany
- Liver Cancer Center Heidelberg, Heidelberg University Hospital, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - Jürgen Debus
- Department of Radiation Oncology, Heidelberg University Hospital, Im Neuenheimer Feld 400, 69120 Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg University Hospital, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
- Clinical Cooperation Unit Radiation Oncology, German Cancer Research Center (DKFZ) Heidelberg, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
- Heidelberg Ion-Beam Therapy Center (HIT), Department of Radiation Oncology, Heidelberg University Hospital, Im Neuenheimer Feld 450, 69120 Heidelberg, Germany
- Heidelberg Institute of Radiation Oncology (HIRO), Heidelberg University Hospital, Im Neuenheimer Feld 400, 69120 Heidelberg, Germany
| | - Dirk Jäger
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
- Clinical Coorporation Unit Applied Tumor-Immunity, German Cancer Research Center (DKFZ) Heidelberg, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Thomas Longerich
- Institute of Pathology Heidelberg, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany
- Liver Cancer Center Heidelberg, Heidelberg University Hospital, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - Stefan Fröhling
- Department of Translational Medical Oncology (TMO), National Center for Tumor Diseases (NCT) Heidelberg, German Cancer Research Center (DKFZ) Heidelberg, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Roland Eils
- Health Data Science Unit, Heidelberg University Hospital, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
- Center for Digital Health, Berlin Institute of Health and Charité Universitötsmedizin Berlin, Kapelle-Ufer 2, 10117 Berlin, Germany
| | - Nina Bougatf
- Department of Radiation Oncology, Heidelberg University Hospital, Im Neuenheimer Feld 400, 69120 Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg University Hospital, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
- Clinical Cooperation Unit Radiation Oncology, German Cancer Research Center (DKFZ) Heidelberg, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
- Heidelberg Ion-Beam Therapy Center (HIT), Department of Radiation Oncology, Heidelberg University Hospital, Im Neuenheimer Feld 450, 69120 Heidelberg, Germany
- Heidelberg Institute of Radiation Oncology (HIRO), Heidelberg University Hospital, Im Neuenheimer Feld 400, 69120 Heidelberg, Germany
| | - Ulrich Sax
- Department of Medical Informatics, University Medical Center Göttingen, Von-Siebold-Str. 3, 37099 Göttingen, Germany
- Campus Institute Data Science, Göttingen, Germany
| | - Matthieu-P Schapranow
- Digital Health Center, Hasso Plattner Institute (HPI), University of Potsdam, Prof.-Dr.-Helmert-Str. 2-3, 14482 Potsdam, Germany
| |
Collapse
|
3
|
Vesteghem C, Brøndum RF, Sønderkær M, Sommer M, Schmitz A, Bødker JS, Dybkær K, El-Galaly TC, Bøgsted M. Implementing the FAIR Data Principles in precision oncology: review of supporting initiatives. Brief Bioinform 2021; 21:936-945. [PMID: 31263868 PMCID: PMC7299292 DOI: 10.1093/bib/bbz044] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/13/2019] [Accepted: 03/21/2019] [Indexed: 12/26/2022] Open
Abstract
Compelling research has recently shown that cancer is so heterogeneous that single research centres cannot produce enough data to fit prognostic and predictive models of sufficient accuracy. Data sharing in precision oncology is therefore of utmost importance. The Findable, Accessible, Interoperable and Reusable (FAIR) Data Principles have been developed to define good practices in data sharing. Motivated by the ambition of applying the FAIR Data Principles to our own clinical precision oncology implementations and research, we have performed a systematic literature review of potentially relevant initiatives. For clinical data, we suggest using the Genomic Data Commons model as a reference as it provides a field-tested and well-documented solution. Regarding classification of diagnosis, morphology and topography and drugs, we chose to follow the World Health Organization standards, i.e. ICD10, ICD-O-3 and Anatomical Therapeutic Chemical classifications, respectively. For the bioinformatics pipeline, the Genome Analysis ToolKit Best Practices using Docker containers offer a coherent solution and have therefore been selected. Regarding the naming of variants, we follow the Human Genome Variation Society's standard. For the IT infrastructure, we have built a centralized solution to participate in data sharing through federated solutions such as the Beacon Networks.
Collapse
Affiliation(s)
- Charles Vesteghem
- Department of Clinical Medicine, Aalborg University, Denmark.,Department of Haematology, Aalborg University Hospital, Denmark
| | | | - Mads Sønderkær
- Department of Haematology, Aalborg University Hospital, Denmark
| | - Mia Sommer
- Department of Clinical Medicine, Aalborg University, Denmark.,Department of Haematology, Aalborg University Hospital, Denmark
| | | | | | - Karen Dybkær
- Department of Clinical Medicine, Aalborg University, Denmark.,Department of Haematology, Aalborg University Hospital, Denmark.,Clinical Cancer Research Center, Aalborg University Hospital, Denmark
| | - Tarec Christoffer El-Galaly
- Department of Clinical Medicine, Aalborg University, Denmark.,Department of Haematology, Aalborg University Hospital, Denmark.,Clinical Cancer Research Center, Aalborg University Hospital, Denmark
| | - Martin Bøgsted
- Department of Clinical Medicine, Aalborg University, Denmark.,Department of Haematology, Aalborg University Hospital, Denmark.,Clinical Cancer Research Center, Aalborg University Hospital, Denmark
| |
Collapse
|
4
|
Crowley F, Park W, O'Reilly EM. Targeting DNA damage repair pathways in pancreas cancer. Cancer Metastasis Rev 2021; 40:891-908. [PMID: 34403012 DOI: 10.1007/s10555-021-09983-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 07/30/2021] [Indexed: 02/07/2023]
Abstract
Pancreas ductal adenocarcinoma (PDAC) is the third most common cause of cancer death in the USA. While other cancers with historically poor prognoses have benefited from new immunotherapies and targeted agents, the 5-year survival rate for PDAC patients has remained static. The accessibility to genomic testing has improved in recent years, and it is now clear that PDAC is a heterogenous disease, with a subset of patients harboring actionable mutations. There are several targeted therapies approved by the Food and Drug administration (FDA) in PDAC: EGFR inhibitor erlotinib (combined with gemcitabine) in unselected patients, TRK inhibitors larotrectinib and entrectinib for patients with NTRK fusion mutation, the PD-1 inhibitor pembrolizumab for mismatch repair-deficient patients, and the poly-ADP-ribose polymerase (PARP) inhibitor olaparib in patients with germline BRCA mutation as a maintenance therapy. DNA damage repair (DDR) is paramount to genomic integrity and cell survival. The defective repair of DNA damage is one of the hallmarks of cancer, and abnormalities in DDR pathways are closely linked with the development of malignancies and upregulation of these pathways linked with resistance to treatment. The prevalence of somatic and germline mutations in DDR pathways in metastatic PDAC is reported to be approximately 15-25%. Patients with DDR gene alterations benefit from a personalized approach to treatment. Recently, the POLO trial demonstrated a progression-free survival (PFS) benefit in metastatic PDAC patients with a germline BRCA1/2 mutation treated with maintenance olaparib following platinum-based induction chemotherapy. This was the first phase 3 randomized trial to establish a biomarker-driven approach in the treatment of PDAC and establishes a precedent for maintenance therapy in PDAC. The review herein aims to outline the current treatment landscape for PDAC patients with DDR gene-mutated tumors, highlight novel therapeutic approaches focused on surmounting tumor resistance, and explore new strategies which may lead to an expansion in the number of patients who benefit from these targeted treatments.
Collapse
Affiliation(s)
- Fionnuala Crowley
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 300 East 66th Street, Office 1021, New York, NY, USA.,Internal Medicine, Mount Sinai Morningside West Hospital Center, New York, NY, USA.,Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Wungki Park
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 300 East 66th Street, Office 1021, New York, NY, USA.,David M. Rubenstein Center for Pancreas Research, New York, NY, USA.,Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.,Weill Cornell Medical College, New York, NY, USA
| | - Eileen M O'Reilly
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 300 East 66th Street, Office 1021, New York, NY, USA. .,David M. Rubenstein Center for Pancreas Research, New York, NY, USA. .,Weill Cornell Medical College, New York, NY, USA.
| |
Collapse
|
5
|
O'Leary MF. Leveraging Pathology Informatics Concepts to Achieve Discrete Lab Data for Clinical Use and Translational Research. Methods Mol Biol 2021; 2194:21-33. [PMID: 32926359 DOI: 10.1007/978-1-0716-0849-4_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Clinical practice is most efficient when physicians have the right information, including pathology and laboratory results, at the point of contact with the patient. In downstream workflows, subsequent groups using lab data want to have it available in a format that is easy to manipulate. With the complexity of electronic medical records, hospital information systems, and the need to accommodate data from outside systems, this is not easy to accomplish. By utilizing a group of concepts from clinical and pathology informatics, system implementations may be improved to achieve relevant laboratory data in a format that is usable by healthcare entities to improve patient care and forward endeavors in precision medicine.
Collapse
Affiliation(s)
- Mandy Flannery O'Leary
- Pathology Informatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA. .,Department of Clinical Pathology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA. .,Department of Oncologic Sciences, University of South Florida, Tampa, FL, USA.
| |
Collapse
|
6
|
Banck H, Dugas M, MÜller-Tidow C, Sandmann S. Comparison of Open-access Databases for Clinical Variant Interpretation in Cancer: A Case Study of MDS/AML. Cancer Genomics Proteomics 2021; 18:157-166. [PMID: 33608312 DOI: 10.21873/cgp.20250] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/23/2021] [Accepted: 01/29/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recently, guidelines for variant interpretation in cancer have been established. However, these guidelines do not mention which databases are most suited to performing this task. MATERIALS AND METHODS We give an overview of existing databases and evaluate their benefit in practical application. We compared three meta-databases and 12 databases for a dataset of patients with myelodysplastic syndrome or acute myeloid leukemia. RESULTS Clinical implications were found for 13% of all variants. One-third of variants with therapeutic implications were uniquely contained in one database. The VICC meta-database was the most extensive source of information, featuring 92% of variants with a drug association. However, a comparison of meta-databases and original sources indicated that some variants are missing in those meta-databases. CONCLUSION Public databases provide decision support for interpreting variants but there is still need for manual curation. Meta-databases facilitate the use of multiple resources but should be interpreted with caution.
Collapse
Affiliation(s)
- Henrik Banck
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Martin Dugas
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Carsten MÜller-Tidow
- Medizinische Klinik, Abteilung Innere Medizin V, University Hospital Heidelberg, Heidelberg, Germany
| | - Sarah Sandmann
- Institute of Medical Informatics, University of Münster, Münster, Germany;
| |
Collapse
|
7
|
Zhang Q, Fu Q, Bai X, Liang T. Molecular Profiling-Based Precision Medicine in Cancer: A Review of Current Evidence and Challenges. Front Oncol 2020; 10:532403. [PMID: 33194591 PMCID: PMC7652987 DOI: 10.3389/fonc.2020.532403] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 08/26/2020] [Indexed: 12/16/2022] Open
Abstract
Matched therapy based on next-generation sequencing is now a part of routine care to guide the treatment of patients with advanced solid tumors. However, whether and to what extent patients can benefit from this strategy on a large scale remains uncertain. In the past decade, several clinical studies were performed in this field, among which only one was a randomized trial. We reviewed the literature on this topic and summarize the existing data about the efficacy of this treatment strategy. Currently, the evidence is promising but not solid. Multiple ongoing trials are also summarized. We also discuss the limitations of this treatment strategy and certain unsolved important problems, including how to select the sample and target level, how to interpret the results, and the problem of drug accessibility. All these issues should receive more attention in future clinical trial design and the application of target therapy in cancer treatment.
Collapse
Affiliation(s)
- Qi Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- The Key Laboratory of Pancreatic Diseases of Zhejiang Province, Hangzhou, China
- The Innovation Center for the Study of Pancreatic Diseases of Zhejiang Province, Hangzhou, China
- Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, China
| | - Qihan Fu
- The Key Laboratory of Pancreatic Diseases of Zhejiang Province, Hangzhou, China
- The Innovation Center for the Study of Pancreatic Diseases of Zhejiang Province, Hangzhou, China
- Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, China
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xueli Bai
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- The Key Laboratory of Pancreatic Diseases of Zhejiang Province, Hangzhou, China
- The Innovation Center for the Study of Pancreatic Diseases of Zhejiang Province, Hangzhou, China
- Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, China
| | - Tingbo Liang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- The Key Laboratory of Pancreatic Diseases of Zhejiang Province, Hangzhou, China
- The Innovation Center for the Study of Pancreatic Diseases of Zhejiang Province, Hangzhou, China
- Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, China
| |
Collapse
|
8
|
Swift SL, Duffy S, Lang SH. Impact of tumor heterogeneity and tissue sampling for genetic mutation testing: a systematic review and post hoc analysis. J Clin Epidemiol 2020; 126:45-55. [PMID: 32540382 DOI: 10.1016/j.jclinepi.2020.06.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 06/10/2020] [Indexed: 02/07/2023]
Abstract
OBJECTIVE The objective of the study was to identify guidelines to assist systematic reviewers or clinical researchers in identifying sampling bias due to tumor heterogeneity (TH) in solid cancers assayed for somatic mutations. We also assessed current reporting standards to determine the impact of TH on sample bias. STUDY DESIGN AND SETTING We conducted a systematic review searching 13 databases (to January 2019) to identify guidelines. A post hoc analysis was performed using 12 prostate tumor somatic mutation data sets from a previous systematic review to assess reporting on TH. RESULTS Searches identified 2,085 records. No formal guidelines were identified. Forty publications contained incidental recommendations across five major themes: using multiple tumor samples (n = 29), sample purity thresholds (n = 14), using specific sequencing methods (n = 8), using liquid biopsies (n = 4), and microdissection (n = 4). In post hoc analyses, 50% (6 of 12) clearly reported pathology methods. Forty-two percent (5 of 12) did not report pathology results. Forty-two percent (5 of 12) confirmed the pathology of the sample by direct diagnosis rather than inference. Forty-two percent (5 of 12) used multiple samples per patient. Fifty-eight percent (7 of 12) reported on tumor purity (reported ranges 10% to 100%). CONCLUSIONS As precision medicine progresses to the clinic, guidelines are required to help evidence-based decision makers understand how TH may impact sample bias. Authors need to clearly report pathology methods and results and tumor purity methods and results.
Collapse
Affiliation(s)
| | - Steve Duffy
- Kleijnen Systematic Reviews Ltd, Escrick, York YO19 6FD, UK
| | - Shona H Lang
- Kleijnen Systematic Reviews Ltd, Escrick, York YO19 6FD, UK.
| |
Collapse
|
9
|
Malone ER, Oliva M, Sabatini PJB, Stockley TL, Siu LL. Molecular profiling for precision cancer therapies. Genome Med 2020; 12:8. [PMID: 31937368 PMCID: PMC6961404 DOI: 10.1186/s13073-019-0703-1] [Citation(s) in RCA: 442] [Impact Index Per Article: 110.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 12/04/2019] [Indexed: 02/07/2023] Open
Abstract
The number of druggable tumor-specific molecular aberrations has grown substantially in the past decade, with a significant survival benefit obtained from biomarker matching therapies in several cancer types. Molecular pathology has therefore become fundamental not only to inform on tumor diagnosis and prognosis but also to drive therapeutic decisions in daily practice. The introduction of next-generation sequencing technologies and the rising number of large-scale tumor molecular profiling programs across institutions worldwide have revolutionized the field of precision oncology. As comprehensive genomic analyses become increasingly available in both clinical and research settings, healthcare professionals are faced with the complex tasks of result interpretation and translation. This review summarizes the current and upcoming approaches to implement precision cancer medicine, highlighting the challenges and potential solutions to facilitate the interpretation and to maximize the clinical utility of molecular profiling results. We describe novel molecular characterization strategies beyond tumor DNA sequencing, such as transcriptomics, immunophenotyping, epigenetic profiling, and single-cell analyses. We also review current and potential applications of liquid biopsies to evaluate blood-based biomarkers, such as circulating tumor cells and circulating nucleic acids. Last, lessons learned from the existing limitations of genotype-derived therapies provide insights into ways to expand precision medicine beyond genomics.
Collapse
Affiliation(s)
- Eoghan R Malone
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Department of Medicine, University Avenue, University of Toronto, Toronto, Ontario, M5G 1Z5, Canada
| | - Marc Oliva
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Department of Medicine, University Avenue, University of Toronto, Toronto, Ontario, M5G 1Z5, Canada
| | - Peter J B Sabatini
- Department of Clinical Laboratory Genetics, University Health Network, and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Tracy L Stockley
- Department of Clinical Laboratory Genetics, University Health Network, and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Lillian L Siu
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Department of Medicine, University Avenue, University of Toronto, Toronto, Ontario, M5G 1Z5, Canada.
| |
Collapse
|
10
|
Thorogood A, Touré SB, Ordish J, Hall A, Knoppers B. Genetic database software as medical devices. Hum Mutat 2019; 39:1702-1712. [PMID: 30311376 PMCID: PMC6221175 DOI: 10.1002/humu.23621] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 08/21/2018] [Accepted: 08/22/2018] [Indexed: 12/16/2022]
Abstract
This article provides a primer on medical device regulations in the United States, Europe, and Canada. Software tools are being developed and shared globally to enhance the accessibility and usefulness of genomic databases. Interactive software tools, such as email or mobile alert systems providing variant classification updates, are opportunities to democratize access to genomic data beyond laboratories and clinicians. Uncertainty over the reliability of outputs, however, raises concerns about potential harms to patients, especially where software is accessible to lay users. Developers may also need to contend with unfamiliar medical device regulations. The application of regulatory controls to genomic software could improve patient and user safety, but could also stifle innovation. Legal uncertainty for developers is compounded where software applications are made available globally (implicating multiple regulatory frameworks), and directly to lay users. Moreover, there is considerable uncertainty over the application of (evolving) medical device regulations in the context of both software and genetics. In this article, criteria and examples are provided to inform determinations of software as medical devices, as well as risk classification. We conclude with strategies for using genomic communication and interpretation software to maximize the availability and usefulness of genetic information, while mitigating the risk of harm to users. This article provides a primer on medical device regulation of software that interprets and exchanges genomic data. We compare tests for determining if software qualifies as a medical device across the United States, Europe, and Canada, as well as risk classifications and regulatory controls. Medical device regulation of both software and genetic tools remains uncertain, raising competing concerns: insufficient regulation allows low quality outputs to undermine patient care, while excessive regulation stifles development of innovative tools delivering precision medicine.
Collapse
Affiliation(s)
- Adrian Thorogood
- Centre of Genomics and Policy, McGill University, Montreal, Canada
| | - Seydina B Touré
- Centre of Genomics and Policy, McGill University, Montreal, Canada
| | - Johan Ordish
- PHG Foundation, University of Cambridge, Cambridge, UK
| | - Alison Hall
- PHG Foundation, University of Cambridge, Cambridge, UK
| | - Bartha Knoppers
- Centre of Genomics and Policy, McGill University, Montreal, Canada
| |
Collapse
|
11
|
Abstract
With rapid advances in genetics and genomics, the commercialization and access to new applications has become more widespread and omnipresent throughout biomedical research. Thus, increasingly, more patients will have personal genomic information they may share with primary care providers (PCPs) to better understand the clinical significance of the data. To be able to respond to patient inquiries about genomic data, variant interpretation, disease risk, and other issues, PCPs will need to be able to increase or refresh their awareness about genetics and genomics, and identify reliable resources to use or refer patients. While provider educational efforts have increased, with the rapid advances in the field, ongoing efforts will be needed to prepare PCPs to manage patient needs, integrate results into care, and refer as indicated.
Collapse
Affiliation(s)
- Susanne B Haga
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, 27708, USA.
| |
Collapse
|
12
|
Gao P, Zhang R, Li Z, Ding J, Xie J, Li J. Challenges of Providing Concordant Interpretation of Somatic Variants in Non-Small Cell Lung Cancer: A Multicenter Study. J Cancer 2019; 10:1814-1824. [PMID: 31205538 PMCID: PMC6547979 DOI: 10.7150/jca.29535] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 02/21/2019] [Indexed: 12/13/2022] Open
Abstract
Background: Success of multiple-gene mutation tests by next-generation sequencing (NGS), associated with molecular targeting therapies for cancers, depending on the accuracy and consistency of interpreting variants. Here, we summarized reports from clinical laboratories for cases with non-small cell lung cancer (NSCLC) and discussed conflicting interpretations of somatic variants. Methods: Three mimetic DNA samples, containing six somatic mutations, were prepared based on three clinical case reports of NSCLC. Clinical reports and genetic testing questionnaires were collected from 67 laboratories enrolled in this investigation. Results: Thirty-four laboratories with correct variant results identified two variants, based on FDA approval of targeted drugs for the same tumor, consistently, with strong clinical significance, whereas the other variants were classified with conflicting interpretations. Discordant interpretations were reported for ERBB2 with three different classifications, including strong clinical significance (53.0%, 18/34), potential clinical significance (38.2%, 13/34), and unknown significance (8.8%, 3/34). In the variant therapeutic drug recommendation section, 32.4% of the laboratories (11/34) did not recommend all the available therapeutic drugs designated by the National Comprehensive Cancer Network (NCCN). In the remaining group of 33 laboratories with incorrect variant results, less correct classifications were acquired for the variants with strong clinical significance. Conclusions: Owing to numerous reasons, the interpretation of variants differed greatly, which might in turn lead to the inappropriate clinical care of patients with NSCLC. By analyzing the limitations of different databases used by laboratories, we integrated various types of databases with different levels of evidence to form a comprehensive and detailed variant interpretation pipeline, aiming to standardize the variant classification and provide accurate and sufficient therapeutic drug recommendation to clinicians for minimal-inappropriate therapeutic options.
Collapse
Affiliation(s)
- Peng Gao
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Ziyang Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Jiansheng Ding
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Jiehong Xie
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| |
Collapse
|
13
|
Abstract
Genomic information is increasingly being incorporated into clinical cancer care. Large-scale sequencing efforts have deepened our understanding of the genomic landscape of cancer and contributed to the expanding catalog of alterations being leveraged to aid in cancer diagnosis, prognosis, and treatment. Genomic profiling can provide clinically relevant information regarding somatic point mutations, copy number alterations, translocations, and gene fusions. Genomic features, such as mutational burden, can also be measured by more comprehensive sequencing strategies and have shown value in informing potential treatment options. Ongoing clinical trials are evaluating the use of molecularly targeted agents in genomically defined subsets of cancers within and across tumor histologies. Continued advancements in clinical genomics promise to further expand the application of genomics-enabled medicine to a broader spectrum of oncology patients.
Collapse
Affiliation(s)
- Alison Roos
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Sara A Byron
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA.
| |
Collapse
|
14
|
Polverini PJ, D'Silva NJ, Lei YL. Precision Therapy of Head and Neck Squamous Cell Carcinoma. J Dent Res 2018; 97:614-621. [PMID: 29649374 DOI: 10.1177/0022034518769645] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Precision medicine is an approach to disease prevention and treatment that takes into account genetic variability and environmental and lifestyle influences that are unique to each patient. It facilitates stratification of patient populations that vary in their susceptibility to disease and response to therapy. Shared databases and the implementation of new technology systems designed to advance the integration of this information will enable health care providers to more accurately predict and customize prevention and treatment strategies for patients. Although precision medicine has had a limited impact in most areas of medicine, it has been shown to be an increasingly successful approach to cancer therapy. Despite early promising results targeting aberrant signaling pathways or inhibitors designed to block tumor-driven processes such as angiogenesis, limited success emphasizes the need to discover new biomarkers and treatment targets that are more reliable in predicting response to therapy and result in better health outcomes. Recent successes in the use of immunity-inducing antibodies have stimulated increased interest in the use of precision immunotherapy of head and neck squamous cell carcinoma. Using next-generation sequencing, the precise profiling of tumor-infiltrating lymphocytes has great promise to identify hypoimmunogenic cancer that would benefit from a rationally designed combinatorial approach. Continued interrogation of tumors will reveal new actionable targets with increasing therapeutic efficacy and fulfill the promise of precision therapy of head and neck cancer.
Collapse
Affiliation(s)
- P J Polverini
- 1 Department of Periodontics and Oral Medicine, Division of Oral Medicine, Pathology, and Radiology, University of Michigan School of Dentistry, Ann Arbor, MI, USA.,2 Department of Pathology, University of Michigan Health System, Ann Arbor, MI, USA.,3 Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - N J D'Silva
- 1 Department of Periodontics and Oral Medicine, Division of Oral Medicine, Pathology, and Radiology, University of Michigan School of Dentistry, Ann Arbor, MI, USA.,2 Department of Pathology, University of Michigan Health System, Ann Arbor, MI, USA.,3 Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Y L Lei
- 1 Department of Periodontics and Oral Medicine, Division of Oral Medicine, Pathology, and Radiology, University of Michigan School of Dentistry, Ann Arbor, MI, USA.,3 Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.,4 Department of Otolaryngology-Head and Neck Surgery, University of Michigan Health System, Ann Arbor, MI, USA
| |
Collapse
|
15
|
Lee G, Park H, Sohn I, Lee SH, Song SH, Kim H, Lee KS, Shim YM, Lee HY. Comprehensive Computed Tomography Radiomics Analysis of Lung Adenocarcinoma for Prognostication. Oncologist 2018; 23:806-813. [PMID: 29622699 DOI: 10.1634/theoncologist.2017-0538] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 02/09/2018] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND In this era of personalized medicine, there is an expanded demand for advanced imaging biomarkers that reflect the biology of the whole tumor. Therefore, we investigated a large number of computed tomography-derived radiomics features along with demographics and pathology-related variables in patients with lung adenocarcinoma, correlating them with overall survival. MATERIALS AND METHODS Three hundred thirty-nine patients who underwent operation for lung adenocarcinoma were included. Analysis was performed using 161 radiomics features, demographic, and pathologic variables and correlated each with patient survival. Prognostic performance for survival was compared among three models: (a) using only clinicopathological data; (b) using only selected radiomics features; and (c) using both clinicopathological data and selected radiomics features. RESULTS At multivariate analysis, age, pN, tumor size, type of operation, histologic grade, maximum value of the outer 1/3 of the tumor, and size zone variance were statistically significant variables. In particular, maximum value of outer 1/3 of the tumor reflected tumor microenvironment, and size zone variance represented intratumor heterogeneity. Integration of 31 selected radiomics features with clinicopathological variables led to better discrimination performance. CONCLUSION Radiomics approach in lung adenocarcinoma enables utilization of the full potential of medical imaging and has potential to improve prognosis assessment in clinical oncology. IMPLICATIONS FOR PRACTICE Two radiomics features were prognostic for lung cancer survival at multivariate analysis: (a) maximum value of the outer one third of the tumor reflects the tumor microenvironment and (b) size zone variance represents the intratumor heterogeneity. Therefore, a radiomics approach in lung adenocarcinoma enables utilization of the full potential of medical imaging and could play a larger role in clinical oncology.
Collapse
Affiliation(s)
- Geewon Lee
- Department of Radiology and Center for Imaging Science, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
- Department of Radiology and Medical Research Institute, Pusan National University Hospital, Pusan National University School of Medicine, Busan, Korea
| | - Hyunjin Park
- School of Electronic and Electrical Engineering, Sungkyunkwan University, Suwon, Korea
- Center for Neuroscience Imaging Research, Institute for Basic Science, Suwon, Korea
| | - Insuk Sohn
- Biostatistics and Clinical Epidemiology Center, Samsung Biomedical Research Institute, Seoul, Korea
| | - Seung-Hak Lee
- Department of Electronic Electrical and Computer Engineering, Sungkyunkwan University, Suwon, Korea
| | - So Hee Song
- Department of Radiology and Center for Imaging Science, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hyeseung Kim
- Biostatistics and Clinical Epidemiology Center, Samsung Biomedical Research Institute, Seoul, Korea
| | - Kyung Soo Lee
- Department of Radiology and Center for Imaging Science, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Young Mog Shim
- Department of Thoracic and Cardiovascular Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Ho Yun Lee
- Department of Radiology and Center for Imaging Science, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| |
Collapse
|
16
|
Tsang H, Addepalli K, Davis SR. Resources for Interpreting Variants in Precision Genomic Oncology Applications. Front Oncol 2017; 7:214. [PMID: 28975082 PMCID: PMC5610688 DOI: 10.3389/fonc.2017.00214] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 08/29/2017] [Indexed: 01/08/2023] Open
Abstract
Precision genomic oncology-applying high throughput sequencing (HTS) at the point-of-care to inform clinical decisions-is a developing precision medicine paradigm that is seeing increasing adoption. Simultaneously, new developments in targeted agents and immunotherapy, when informed by rich genomic characterization, offer potential benefit to a growing subset of patients. Multiple previous studies have commented on methods for identifying both germline and somatic variants. However, interpreting individual variants remains a significant challenge, relying in large part on the integration of observed variants with biological knowledge. A number of data and software resources have been developed to assist in interpreting observed variants, determining their potential clinical actionability, and augmenting them with ancillary information that can inform clinical decisions and even generate new hypotheses for exploration in the laboratory. Here, we review available variant catalogs, variant and functional annotation software and tools, and databases of clinically actionable variants that can be used in an ad hoc approach with research samples or incorporated into a data platform for interpreting and formally reporting clinical results.
Collapse
Affiliation(s)
- Hsinyi Tsang
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, National Institutes of Health, Gaithersburg, MD, United States
- Attain, LLC, McLean, VA, United States
| | - KanakaDurga Addepalli
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, National Institutes of Health, Gaithersburg, MD, United States
- Attain, LLC, McLean, VA, United States
| | - Sean R. Davis
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| |
Collapse
|