1
|
Van Der Schueren C, Decruyenaere P, Avila Cobos F, Bult J, Deleu J, Dipalo LL, Helsmoortel HH, Hulstaert E, Morlion A, Ramos Varas E, Schoofs K, Trypsteen W, Vanden Eynde E, Van Droogenbroeck H, Verniers K, Vandesompele J, Decock A. Subpar reporting of pre-analytical variables in RNA-focused blood plasma studies. Mol Oncol 2024. [PMID: 38564603 DOI: 10.1002/1878-0261.13647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 02/13/2024] [Accepted: 03/22/2024] [Indexed: 04/04/2024] Open
Abstract
Extracellular RNA (cell-free RNA; exRNA) from blood-derived liquid biopsies is an appealing, minimally invasive source of disease biomarkers. As pre-analytical variables strongly influence exRNA measurements, their reporting is essential for meaningful interpretation and replication of results. The aim of this review was to chart to what extent pre-analytical variables are documented, to pinpoint shortcomings and to improve future reporting. In total, 200 blood plasma exRNA studies published in 2018 or 2023 were reviewed for annotation of 22 variables associated with blood collection, plasma preparation, and RNA purification. Our results show that pre-analytical variables are poorly documented, with only three out of 22 variables described in over half of the publications. The percentage of variables reported ranged from 4.6% to 54.6% (mean 24.84%) in 2023 and from 4.6% to 57.1% (mean 28.60%) in 2018. Recommendations and guidelines (i.e., BRISQ, ASCO-CAP, BloodPAC, PPMPT, and CEN standards) have currently not resulted in improved reporting. In conclusion, our results highlight the lack of reporting pre-analytical variables in exRNA studies and advocate for a consistent use of available standards, endorsed by funders and journals.
Collapse
Affiliation(s)
| | - Philippe Decruyenaere
- Department of Biomolecular Medicine, Ghent University, Belgium
- Department of Hematology, Ghent University Hospital, Belgium
| | - Francisco Avila Cobos
- Department of Biomolecular Medicine, Ghent University, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Belgium
| | - Johanna Bult
- Department of Biomolecular Medicine, Ghent University, Belgium
- Department of Hematology, University Medical Center Groningen, The Netherlands
| | - Jill Deleu
- Department of Biomolecular Medicine, Ghent University, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Belgium
| | - Laudonia Lidia Dipalo
- Department of Biomolecular Medicine, Ghent University, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Belgium
| | - Hetty Hilde Helsmoortel
- Department of Biomolecular Medicine, Ghent University, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Belgium
| | - Eva Hulstaert
- Department of Biomolecular Medicine, Ghent University, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Belgium
- Department of Dermatology, AZ Sint-Blasius, Belgium
| | - Annelien Morlion
- Department of Biomolecular Medicine, Ghent University, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Belgium
| | - Elena Ramos Varas
- Department of Biomolecular Medicine, Ghent University, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Belgium
| | - Kathleen Schoofs
- Department of Biomolecular Medicine, Ghent University, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Belgium
- Translational Oncogenomics and Bioinformatics Lab, Cancer Research Institute Ghent (CRIG), Belgium
- Center for Medical Biotechnology, VIB-UGent, Belgium
| | - Wim Trypsteen
- Department of Biomolecular Medicine, Ghent University, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Belgium
| | - Eveline Vanden Eynde
- Department of Biomolecular Medicine, Ghent University, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Belgium
| | - Hanne Van Droogenbroeck
- Department of Biomolecular Medicine, Ghent University, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Belgium
| | - Kimberly Verniers
- Department of Biomolecular Medicine, Ghent University, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Belgium
| | - Jo Vandesompele
- Department of Biomolecular Medicine, Ghent University, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Belgium
- CellCarta, Belgium
| | - Anneleen Decock
- Department of Biomolecular Medicine, Ghent University, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Belgium
| |
Collapse
|
2
|
Nault R, Cave MC, Ludewig G, Moseley HN, Pennell KG, Zacharewski T. A Case for Accelerating Standards to Achieve the FAIR Principles of Environmental Health Research Experimental Data. ENVIRONMENTAL HEALTH PERSPECTIVES 2023; 131:65001. [PMID: 37352010 PMCID: PMC10289218 DOI: 10.1289/ehp11484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/25/2023]
Abstract
BACKGROUND Funding agencies, publishers, and other stakeholders are pushing environmental health science investigators to improve data sharing; to promote the findable, accessible, interoperable, and reusable (FAIR) principles; and to increase the rigor and reproducibility of the data collected. Accomplishing these goals will require significant cultural shifts surrounding data management and strategies to develop robust and reliable resources that bridge the technical challenges and gaps in expertise. OBJECTIVE In this commentary, we examine the current state of managing data and metadata-referred to collectively as (meta)data-in the experimental environmental health sciences. We introduce new tools and resources based on in vivo experiments to serve as examples for the broader field. METHODS We discuss previous and ongoing efforts to improve (meta)data collection and curation. These include global efforts by the Functional Genomics Data Society to develop metadata collection tools such as the Investigation, Study, Assay (ISA) framework, and the Center for Expanded Data Annotation and Retrieval. We also conduct a case study of in vivo data deposited in the Gene Expression Omnibus that demonstrates the current state of in vivo environmental health data and highlights the value of using the tools we propose to support data deposition. DISCUSSION The environmental health science community has played a key role in efforts to achieve the goals of the FAIR guiding principles and is well positioned to advance them further. We present a proposed framework to further promote these objectives and minimize the obstacles between data producers and data scientists to maximize the return on research investments. https://doi.org/10.1289/EHP11484.
Collapse
Affiliation(s)
- Rance Nault
- Biochemistry & Molecular Biology Department, Institute for Integrative Toxicology, Michigan State University, East Lansing, Michigan, USA
| | - Matthew C. Cave
- Division of Gastroenterology, Hepatology, and Nutrition, University of Louisville, Louisville, Kentucky, USA
| | - Gabriele Ludewig
- Department of Occupational and Environmental Health, University of Iowa, Iowa City, Iowa, USA
| | - Hunter N.B. Moseley
- Molecular and Cellular Biochemistry Department, University of Kentucky, Lexington, Kentucky, USA
| | - Kelly G. Pennell
- Department of Civil Engineering, University of Kentucky, Lexington, Kentucky, USA
| | - Tim Zacharewski
- Biochemistry & Molecular Biology Department, Institute for Integrative Toxicology, Michigan State University, East Lansing, Michigan, USA
| |
Collapse
|
3
|
Dameri M, Cirmena G, Ravera F, Ferrando L, Cuccarolo P, Stabile M, Fanelli GN, Nuzzo PV, Calabrese M, Tagliafico A, Ballestrero A, Zoppoli G. Standard Operating Procedures (SOPs) for non-invasive multiple biomarkers detection in an academic setting: a critical review of the literature for the RENOVATE study protocol. Crit Rev Oncol Hematol 2023; 185:103963. [PMID: 36931614 DOI: 10.1016/j.critrevonc.2023.103963] [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: 12/01/2022] [Revised: 02/06/2023] [Accepted: 02/13/2023] [Indexed: 03/17/2023] Open
Abstract
Liquid biopsy has the potential to drastically change clinical practice, paving the way to a novel non-invasive approach for cancer diagnosis and treatment. One of the limitations for the implementation of liquid biopsy in clinical practice is the lack of shared and reproducible standard operating procedures (SOPs) for sample collection, processing and storage. Here, we present a critical review of the literature focusing on the available SOPs to guide liquid biopsy management in research settings and describe SOPs that our laboratory developed and employed in the context of a prospective clinical-translational trial (RENOVATE, NCT04781062). The main aim of this manuscript is to address common issues, towards the implementation of interlaboratory shared protocols for optimized preanalytical handling of blood and urine samples. To our knowledge, this work is one of the few up-to-date, freely available comprehensive reports on trial-level procedures for the handling of liquid biopsy.
Collapse
Affiliation(s)
- Martina Dameri
- Department of Internal Medicine and Medical Specialties DiMI, University of Genoa, 16132, Genoa, Italy
| | | | - Francesco Ravera
- Department of Internal Medicine and Medical Specialties DiMI, University of Genoa, 16132, Genoa, Italy; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, 10044, New York, NY, USA
| | | | - Paola Cuccarolo
- Department of Internal Medicine and Medical Specialties DiMI, University of Genoa, 16132, Genoa, Italy
| | - Mario Stabile
- Department of Internal Medicine and Medical Specialties DiMI, University of Genoa, 16132, Genoa, Italy
| | - Giuseppe Nicolò Fanelli
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 10021, New York, NY, USA; First Division of Pathology, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy
| | - Pier Vitale Nuzzo
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, 10044, New York, NY, USA
| | | | - Alberto Tagliafico
- IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy; Department of Health Sciences DISSAL, University of Genoa, 16132, Genoa, Italy
| | - Alberto Ballestrero
- Department of Internal Medicine and Medical Specialties DiMI, University of Genoa, 16132, Genoa, Italy; IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - Gabriele Zoppoli
- Department of Internal Medicine and Medical Specialties DiMI, University of Genoa, 16132, Genoa, Italy; IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy.
| |
Collapse
|
4
|
Hernandez KM, Bramlett KS, Agius P, Baden J, Cao R, Clement O, Corner AS, Craft J, Dean DA, Dry JR, Grigaityte K, Grossman RL, Hicks J, Higa N, Holzer TR, Jensen J, Johann DJ, Katz S, Kolatkar A, Keynton JL, Lee JSH, Maar D, Martini JF, Meyer CG, Roberts PC, Ryder M, Salvatore L, Schageman JJ, Somiari S, Stetson D, Stern M, Xu L, Leiman LC. Contrived Materials and a Data Set for the Evaluation of Liquid Biopsy Tests: A Blood Profiling Atlas in Cancer (BLOODPAC) Community Study. J Mol Diagn 2023; 25:143-155. [PMID: 36828596 DOI: 10.1016/j.jmoldx.2022.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 10/21/2022] [Accepted: 12/02/2022] [Indexed: 02/24/2023] Open
Abstract
The Blood Profiling Atlas in Cancer (BLOODPAC) Consortium is a collaborative effort involving stakeholders from the public, industry, academia, and regulatory agencies focused on developing shared best practices on liquid biopsy. This report describes the results from the JFDI (Just Freaking Do It) study, a BLOODPAC initiative to develop standards on the use of contrived materials mimicking cell-free circulating tumor DNA, to comparatively evaluate clinical laboratory testing procedures. Nine independent laboratories tested the concordance, sensitivity, and specificity of commercially available contrived materials with known variant-allele frequencies (VAFs) ranging from 0.1% to 5.0%. Each participating laboratory utilized its own proprietary evaluation procedures. The results demonstrated high levels of concordance and sensitivity at VAFs of >0.1%, but reduced concordance and sensitivity at a VAF of 0.1%; these findings were similar to those from previous studies, suggesting that commercially available contrived materials can support the evaluation of testing procedures across multiple technologies. Such materials may enable more objective comparisons of results on materials formulated in-house at each center in multicenter trials. A unique goal of the collaborative effort was to develop a data resource, the BLOODPAC Data Commons, now available to the liquid-biopsy community for further study. This resource can be used to support independent evaluations of results, data extension through data integration and new studies, and retrospective evaluation of data collection.
Collapse
Affiliation(s)
- Kyle M Hernandez
- Department of Medicine, University of Chicago, Chicago, Illinois; Center for Translational Data Science, University of Chicago, Chicago, Illinois
| | | | | | | | - Ru Cao
- Thermo Fisher Scientific, Austin, Texas
| | | | - Adam S Corner
- Digital Biology Group, Bio-Rad Laboratories Inc., Pleasanton, California
| | | | | | | | | | - Robert L Grossman
- Department of Medicine, University of Chicago, Chicago, Illinois; Open Commons Consortium, Chicago, Illinois; Pfizer, San Diego, California
| | - James Hicks
- Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA
| | - Nikki Higa
- Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA
| | | | | | - Donald J Johann
- Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | | | - Anand Kolatkar
- Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA
| | | | - Jerry S H Lee
- Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA; Lawrence J. Ellison Institute for Transformative Medicine, Los Angeles, California
| | - Dianna Maar
- Digital Biology Group, Bio-Rad Laboratories Inc., Pleasanton, California
| | | | - Christopher G Meyer
- Center for Translational Data Science, University of Chicago, Chicago, Illinois
| | | | | | | | | | | | | | - Mark Stern
- Bristol Myers Squibb, Newton, New Jersey
| | - Liya Xu
- Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA
| | | |
Collapse
|
5
|
Clarke CA, Lang K, Putcha G, Beer JP, Champagne M, Ferris A, Godsey JH, Grossman RL, Hoyos JM, Johann DJ, Krunic N, Kuhn P, Lee J, Maddala T, Mata M, McDole J, Perez O, Scher H, Stewart MD, Bhan SS, Zhang Q, Leiman LC. BLOODPAC: Collaborating to chart a path towards blood-based screening for early cancer detection. Clin Transl Sci 2022; 16:5-9. [PMID: 36251491 PMCID: PMC9841293 DOI: 10.1111/cts.13427] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 02/04/2023] Open
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Donald J. Johann
- University of Arkansas for Medical SciencesLittle RockArkansasUSA
| | | | - Peter Kuhn
- University of Southern CaliforniaLos AngelesCaliforniaUSA
| | | | | | | | - Jeremiah McDole
- Bio‐Rad Laboratories IncDigital Biology GroupPleasantonCaliforniaUSA
| | | | - Howard Scher
- Memorial Sloan Kettering Cancer CenterNew YorkNew YorkUSA
| | | | | | - Qu Zhang
- GlaxoSmithKlineCollegevillePennsylvaniaUSA
| | | |
Collapse
|
6
|
Leiman LC, Baden J, D'Auria K, Lin CJ, Meier K. Creating Standards for Liquid Biopsies: The BLOODPAC Experience. Expert Rev Mol Diagn 2022; 22:677-679. [PMID: 35979936 DOI: 10.1080/14737159.2022.2113059] [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: 11/04/2022]
Abstract
Since the first Food and Drug Administration (FDA) approval in 2013, liquid biopsy-based platforms have transformed the precision management of patients with advanced cancer. Liquid biopsy holds a demonstrated role in precision medicine that historically focused on targeted therapy selection. Yet, continued innovation in this area is expected to drive growing utility for liquid biopsy-based tests in other areas of clinical need, including minimal (or molecular) residual disease monitoring and early-stage.
Collapse
Affiliation(s)
| | - Jonathan Baden
- Bristol-Myers Squibb, Princeton, New Jersey, United States
| | - Kevin D'Auria
- Guardant Health, Redwood City, California, United States
| | - C Jimmy Lin
- Freenome, South San Francisco, United States
| | | |
Collapse
|
7
|
Chang L, Li J, Zhang R. Liquid biopsy for early diagnosis of non-small cell lung carcinoma: recent research and detection technologies. Biochim Biophys Acta Rev Cancer 2022; 1877:188729. [DOI: 10.1016/j.bbcan.2022.188729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 03/14/2022] [Accepted: 04/10/2022] [Indexed: 02/07/2023]
|
8
|
Circulating Tumor Cell Kinetics and Morphology from the Liquid Biopsy Predict Disease Progression in Patients with Metastatic Colorectal Cancer Following Resection. Cancers (Basel) 2022; 14:cancers14030642. [PMID: 35158910 PMCID: PMC8833610 DOI: 10.3390/cancers14030642] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/05/2022] [Accepted: 01/11/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary As a minimally invasive procedure, the liquid biopsy enables the longitudinal evaluation of a patient’s disease and response to treatment. Current clinical practice stratifies patient status based on a uniform threshold for circulating tumor cell (CTC) positivity, overlooking various cell subtypes and timepoints of sample collection. In a disease known for its tumor heterogeneity, we investigated colorectal cancer patients’ peripheral blood samples to determine whether the prevalence of morphologically distinct CTC subtypes and time-points of sample collection correlate with clinical disease hallmarks and survival data. Our results highlight nuances between the CTC subtypes’ clinical and survival significance. Furthermore, we found that time-point-conscious cell enumeration is critical, both for determining CTC positivity and the change in cell populations over time. To improve its clinical utility moving forward, we suggest that liquid biopsy analysis integrates morphology and time-based analysis alongside standard CTC enumeration at various stages of a patient’s treatment. Abstract The liquid biopsy has the potential to improve current clinical practice in oncology by providing real-time personalized information about a patient’s disease status and response to treatment. In this study, we evaluated 161 peripheral blood (PB) samples that were collected around surgical resection from 47 metastatic colorectal cancer (mCRC) patients using the High-Definition Single Cell Assay (HDSCA) workflow. In conjunction with the standard circulating tumor cell (CTC) enumeration, cellular morphology and kinetics between time-points of collection were considered in the survival analysis. CTCs, CTC-Apoptotic, and CTC clusters were found to indicate poor survival with an increase in cell count from pre-resection to post-resection. This study demonstrates that CTC subcategorization based on morphological differences leads to nuanced results between the subtypes, emphasizing the heterogeneity within the CTC classification. Furthermore, we show that factoring in the time-point of each blood collection is critical, both for its static enumeration and for the change in cell populations between draws. By integrating morphology and time-based analysis alongside standard CTC enumeration, liquid biopsy platforms can provide greater insight into the pathophysiology of mCRC by highlighting the complexity of the disease across a patient’s treatment.
Collapse
|
9
|
Hulstaert E, Decock A, Morlion A, Everaert C, Verniers K, Nuytens J, Nijs N, Schroth GP, Kuersten S, Gross SM, Mestdagh P, Vandesompele J. Messenger RNA capture sequencing of extracellular RNA from human biofluids using a comprehensive set of spike-in controls. STAR Protoc 2021; 2:100475. [PMID: 33937877 PMCID: PMC8076706 DOI: 10.1016/j.xpro.2021.100475] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Comprehensive transcriptome analysis of extracellular RNA (exRNA) purified from human biofluids is challenging because of the low RNA concentration and compromised RNA integrity. Here, we describe an optimized workflow to (1) isolate exRNA from different types of biofluids and (2) to prepare messenger RNA (mRNA)-enriched sequencing libraries using complementary hybridization probes. Importantly, the workflow includes 2 sets of synthetic spike-in RNA molecules as processing controls for RNA purification and sequencing library preparation and as an alternative data normalization strategy. For complete details on the use and execution of this protocol, please refer to Hulstaert et al. (2020). Extracellular RNA from biofluids has a low concentration and a compromised integrity An optimized workflow for mRNA capture sequencing of human biofluids is provided Synthetic spike-in RNA molecules serve as processing controls Spike-in RNAs allow for data normalization and calculation of mRNA concentration
Collapse
Affiliation(s)
- Eva Hulstaert
- Center for Medical Genetics, Department of Biomolecular Medicine, OncoRNALab, Ghent University, C. Heymanslaan 10, 9000 Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, C. Heymanslaan 10, 9000 Ghent, Belgium.,Department of Dermatology, Ghent University Hospital, C. Heymanslaan 10, 9000 Ghent, Belgium
| | - Anneleen Decock
- Center for Medical Genetics, Department of Biomolecular Medicine, OncoRNALab, Ghent University, C. Heymanslaan 10, 9000 Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, C. Heymanslaan 10, 9000 Ghent, Belgium
| | - Annelien Morlion
- Center for Medical Genetics, Department of Biomolecular Medicine, OncoRNALab, Ghent University, C. Heymanslaan 10, 9000 Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, C. Heymanslaan 10, 9000 Ghent, Belgium
| | - Celine Everaert
- Center for Medical Genetics, Department of Biomolecular Medicine, OncoRNALab, Ghent University, C. Heymanslaan 10, 9000 Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, C. Heymanslaan 10, 9000 Ghent, Belgium
| | - Kimberly Verniers
- Center for Medical Genetics, Department of Biomolecular Medicine, OncoRNALab, Ghent University, C. Heymanslaan 10, 9000 Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, C. Heymanslaan 10, 9000 Ghent, Belgium
| | - Justine Nuytens
- Center for Medical Genetics, Department of Biomolecular Medicine, OncoRNALab, Ghent University, C. Heymanslaan 10, 9000 Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, C. Heymanslaan 10, 9000 Ghent, Belgium
| | - Nele Nijs
- Biogazelle, Technologiepark 82, 9052 Zwijnaarde, Belgium
| | | | | | | | - Pieter Mestdagh
- Center for Medical Genetics, Department of Biomolecular Medicine, OncoRNALab, Ghent University, C. Heymanslaan 10, 9000 Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, C. Heymanslaan 10, 9000 Ghent, Belgium.,Biogazelle, Technologiepark 82, 9052 Zwijnaarde, Belgium
| | - Jo Vandesompele
- Center for Medical Genetics, Department of Biomolecular Medicine, OncoRNALab, Ghent University, C. Heymanslaan 10, 9000 Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, C. Heymanslaan 10, 9000 Ghent, Belgium.,Biogazelle, Technologiepark 82, 9052 Zwijnaarde, Belgium
| |
Collapse
|
10
|
Grossman RL, Dry JR, Hanlon SE, Johann DJ, Kolatkar A, Lee JSH, Meyer C, Salvatore L, Wells W, Leiman L. BloodPAC Data Commons for Liquid Biopsy Data. JCO Clin Cancer Inform 2021; 5:479-486. [PMID: 33929890 PMCID: PMC8140805 DOI: 10.1200/cci.20.00179] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/16/2021] [Accepted: 03/16/2021] [Indexed: 01/22/2023] Open
Abstract
PURPOSE The Blood Profiling Atlas in Cancer (BloodPAC) Data Commons (BPDC) is being developed and is operated by the public-private BloodPAC Consortium to support the liquid biopsy community. It is an interoperable data commons with the ultimate aim of serving as a recognized source of valid scientific evidence for liquid biopsy assays for industry, academia, and standards and regulatory stakeholders. METHODS The BPDC is implemented using the open source Gen3 data commons platform (https://gen3.org). In particular, the BPDC Data Exploration Portal, BPDC Data Submission Portal, the BPDC Workspace Hub, and the BloodPAC application programming interface (API) were all automatically generated from the BloodPAC Data Model using the Gen3 data commons platform. BPDC uses Gen3's implementation of the data commons framework services so that it can interoperate through secure, compliant APIs with other data commons using data commons framework service, such as National Cancer Institute's Cancer Research Data Commons. RESULTS The BPDC contains 57 studies and projects spanning more than 4,100 cases. This amounts to 5,700 aliquots (blood plasma, serum, or a contrived sample) that have been subjected to a liquid biopsy assay, quantified, and then contributed by members of the BloodPAC Consortium. In all, there are more than 31,000 files in the commons as of December 2020. We describe the BPDC, the data it manages, the process that the BloodPAC Consortium used to develop it, and some of the applications that have been developed using its API. CONCLUSION The BPDC has been the data platform used by BloodPAC during the past 4 years to manage the data for the consortium and to provide workspaces for its working groups.
Collapse
Affiliation(s)
- Robert L. Grossman
- Center for Translational Data Science, University of Chicago, Chicago, IL
- Open Commons Consortium, Chicago, IL
| | | | | | | | - Anand Kolatkar
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA
| | - Jerry S. H. Lee
- Lawrence J. Ellison Institute for Transformative Medicine, University of Southern California, Los Angeles, CA
| | - Christopher Meyer
- Center for Translational Data Science, University of Chicago, Chicago, IL
| | | | - Walt Wells
- Center for Translational Data Science, University of Chicago, Chicago, IL
- Progressive Insurance, Cleveland, OH
| | | |
Collapse
|
11
|
Fiste O, Liontos M, Koutsoukos K, Terpos E, Dimopoulos MA, Zagouri F. Circulating tumor DNA-based predictive biomarkers in breast cancer clinical trials: a narrative review. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1603. [PMID: 33437802 PMCID: PMC7791253 DOI: 10.21037/atm-20-1175] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Breast carcinoma is the most frequent and the second leading cause of cancer mortality in women worldwide. Current treatment decisions are based on tumor profiling of the initial tissue biopsy. Cancer though evolves both spatially and temporarily in a significant percentage of patients during treatment. However, sequential biopsies from the primary tumor or its metastatic sites are not either convenient or feasible in the majority of cases. In the era of precision medicine, analysis of circulating blood-based biomarkers in the field of liquid biopsies provides an insight into the dynamic molecular profiling of the primary tumor and its metastases, in a relatively non-invasive way. The latter permits not only patient stratification but also longitudinal evaluation of treatment response, when incorporated into clinical trials. This review summarizes the results from recent and ongoing circulating tumor DNA (ctDNA)-based biomarker-driven clinical trials, with respect to ctDNA analysis’ predictive role, both in adjuvant, neo-adjuvant, and metastatic setting. Furthermore, current challenges in ctDNA analysis applications are critically discussed, including pre-analytical and analytical issues, and future perspectives in this field, through the conduct of well-designed, multicenter, randomized, large-scale, biomarker-stratified trials, with robust statistical methods. Despite in its infancy, ctDNA analysis holds great promise as a minimally invasive tool regarding tailored, personalized treatment guidance for breast cancer patients.
Collapse
Affiliation(s)
- Oraianthi Fiste
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Michael Liontos
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Konstantinos Koutsoukos
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Evangelos Terpos
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Meletios A Dimopoulos
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Flora Zagouri
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| |
Collapse
|
12
|
Godsey JH, Silvestro A, Barrett JC, Bramlett K, Chudova D, Deras I, Dickey J, Hicks J, Johann DJ, Leary R, Lee JSH, McMullen J, McShane L, Nakamura K, Richardson AO, Ryder M, Simmons J, Tanzella K, Yee L, Leiman LC. Generic Protocols for the Analytical Validation of Next-Generation Sequencing-Based ctDNA Assays: A Joint Consensus Recommendation of the BloodPAC's Analytical Variables Working Group. Clin Chem 2020; 66:1156-1166. [PMID: 32870995 PMCID: PMC7462123 DOI: 10.1093/clinchem/hvaa164] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 07/07/2020] [Indexed: 12/12/2022]
Abstract
Liquid biopsy, particularly the analysis of circulating tumor DNA (ctDNA), has demonstrated considerable promise for numerous clinical intended uses. Successful validation and commercialization of novel ctDNA tests have the potential to improve the outcomes of patients with cancer. The goal of the Blood Profiling Atlas Consortium (BloodPAC) is to accelerate the development and validation of liquid biopsy assays that will be introduced into the clinic. To accomplish this goal, the BloodPAC conducts research in the following areas: Data Collection and Analysis within the BloodPAC Data Commons; Preanalytical Variables; Analytical Variables; Patient Context Variables; and Reimbursement. In this document, the BloodPAC's Analytical Variables Working Group (AV WG) attempts to define a set of generic analytical validation protocols tailored for ctDNA-based Next-Generation Sequencing (NGS) assays. Analytical validation of ctDNA assays poses several unique challenges that primarily arise from the fact that very few tumor-derived DNA molecules may be present in circulation relative to the amount of nontumor-derived cell-free DNA (cfDNA). These challenges include the exquisite level of sensitivity and specificity needed to detect ctDNA, the potential for false negatives in detecting these rare molecules, and the increased reliance on contrived samples to attain sufficient ctDNA for analytical validation. By addressing these unique challenges, the BloodPAC hopes to expedite sponsors' presubmission discussions with the Food and Drug Administration (FDA) with the protocols presented herein. By sharing best practices with the broader community, this work may also save the time and capacity of FDA reviewers through increased efficiency.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - James Hicks
- University of Southern California, Los Angeles, CA
| | | | | | | | | | - Lisa McShane
- National Cancer Institute at the National Institutes of Health (NIH/NCI), Rockville, MD
| | | | | | | | | | | | - Laura Yee
- National Cancer Institute at the National Institutes of Health (NIH/NCI), Rockville, MD
| | | |
Collapse
|
13
|
Shishido SN, Welter L, Rodriguez-Lee M, Kolatkar A, Xu L, Ruiz C, Gerdtsson AS, Restrepo-Vassalli S, Carlsson A, Larsen J, Greenspan EJ, Hwang ES, Waitman KR, Nieva J, Bethel K, Hicks J, Kuhn P. Preanalytical Variables for the Genomic Assessment of the Cellular and Acellular Fractions of the Liquid Biopsy in a Cohort of Breast Cancer Patients. J Mol Diagn 2020; 22:319-337. [PMID: 31978562 PMCID: PMC7103765 DOI: 10.1016/j.jmoldx.2019.11.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 08/19/2019] [Accepted: 11/18/2019] [Indexed: 01/02/2023] Open
Abstract
Liquid biopsy allows assessment of multiple analytes, providing temporal information with potential for improving understanding of cancer evolution and clinical management of patients. Although liquid biopsies are intensely investigated for prediction and response monitoring, preanalytic variables are of primary concern for clinical implementation, including categories of collection method and sample storage. Herein, an integrated high-density single-cell assay workflow for morphometric and genomic analysis of the liquid biopsy is used to characterize the effects of preanalytical variation and reproducibility of data from a breast cancer cohort. Following prior work quantifying performance of commonly used blood collection tubes, this study completes the analysis of four time points to assay (24, 48, 72, and 96 hours), demonstrating precision up to 48 hours after collection for assay sensitivity, highly reproducible rare cell enumeration, morphometric characterization, and high efficiency and capacity for single-cell genomic analysis. For the cell-free analysis, both freezing and use of fresh plasma produced similar quality and quantity of cell-free DNA for sequencing. The genomic analysis (copy number variation and single-nucleotide variation) described herein is broadly applicable to liquid biopsy platforms capable of isolating cell-free and cell-based DNA. Morphometric parameters and genomic signatures of individual circulating tumor cells were evaluated in relation to patient clinical response, providing preliminary evidence of clinical validity as a potential biomarker aiding clinical diagnostics or monitoring progression.
Collapse
Affiliation(s)
- Stephanie N Shishido
- Department of Biological Sciences, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California
| | - Lisa Welter
- Department of Biological Sciences, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California
| | - Mariam Rodriguez-Lee
- Department of Biological Sciences, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California
| | - Anand Kolatkar
- Department of Biological Sciences, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California
| | - Liya Xu
- Department of Biological Sciences, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California
| | - Carmen Ruiz
- Department of Biological Sciences, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California
| | - Anna S Gerdtsson
- Department of Biological Sciences, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California
| | - Sara Restrepo-Vassalli
- Department of Biological Sciences, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California
| | - Anders Carlsson
- Department of Biological Sciences, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California
| | - Joe Larsen
- Department of Biological Sciences, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California
| | - Emily J Greenspan
- Center for Strategic Scientific Initiatives, National Cancer Institute, Bethesda, Maryland
| | - E Shelley Hwang
- Department of Surgery, Duke University Hospital, Durham, North Carolina
| | | | - Jorge Nieva
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Kelly Bethel
- Department of Pathology, Scripps Clinic Medical Group, La Jolla, California
| | - James Hicks
- Department of Biological Sciences, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California
| | - Peter Kuhn
- Department of Biological Sciences, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California.
| |
Collapse
|
14
|
Febbo PG, Martin AM, Scher HI, Barrett JC, Beaver JA, Beresford PJ, Blumenthal GM, Bramlett K, Compton C, Dittamore R, Eberhard DA, Edelstein D, Godsey J, Gruen A, Hanlon SE, Hicks J, Hovelson D, Hullings M, Johann D, Johnson J, Kolatkar A, Kuhn P, Levine R, Martini JF, Miller DP, Moore C, Moy B, Pathak A, Philip R, Reese D, Royalty W, Ryder M, Sakul H, Salvatore LM, Schade A, Silvestro A, Simmons JK, Simons J, Singh Bhan S, Smalley MD, Somiari SB, Talasaz A, Tewari M, Tseng HR, Vinson J, Wells W, Welsh A, Grossman RL, Lee JSH, Leiman LC. Minimum Technical Data Elements for Liquid Biopsy Data Submitted to Public Databases. Clin Pharmacol Ther 2020; 107:730-734. [PMID: 32017048 PMCID: PMC7158216 DOI: 10.1002/cpt.1747] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 11/26/2019] [Indexed: 12/24/2022]
Affiliation(s)
| | | | - Howard I Scher
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | | | - Julia A Beaver
- Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Springs, Maryland, USA
| | | | | | | | | | | | | | | | | | - Andrew Gruen
- Seven Bridges Genomics, Boston, Massachusetts, USA
| | - Sean E Hanlon
- Office of the Director, National Cancer Institute, Bethesda, Maryland, USA
| | - James Hicks
- University of Southern California, Los Angeles, California, USA
| | | | | | | | | | - Anand Kolatkar
- University of Southern California, Los Angeles, California, USA
| | - Peter Kuhn
- University of Southern California, Los Angeles, California, USA
| | - Rebecca Levine
- Prostate Cancer Foundation, Los Angeles, California, USA
| | | | - Daniel P Miller
- Center for Translational Data Science, University of Chicago, Chicago, Illinois, USA
| | | | - Bryan Moy
- Seven Bridges Genomics, Boston, Massachusetts, USA
| | - Anand Pathak
- Center for Device and Radiological Health, US Food and Drug Administration, Silver Springs, Maryland, USA
| | - Reena Philip
- Center for Device and Radiological Health, US Food and Drug Administration, Silver Springs, Maryland, USA
| | - David Reese
- Provista Diagnostics Inc, New York, New York, USA
| | | | | | | | | | | | | | | | | | | | | | - Stella B Somiari
- CSSIMMW (Windber Research Institute), Windber, Pennsylvania, USA
| | | | | | | | - Jake Vinson
- Prostate Cancer Clinical Trials Consortium, New York, New York, USA
| | - Walt Wells
- Open Commons Consortium, Chicago, Illinois, USA
| | | | - Robert L Grossman
- Center for Translational Data Science, University of Chicago, Chicago, Illinois, USA
| | - Jerry S H Lee
- University of Southern California, Los Angeles, California, USA
| | | |
Collapse
|
15
|
Preoperative detection of KRAS G12D mutation in ctDNA is a powerful predictor for early recurrence of resectable PDAC patients. Br J Cancer 2020; 122:857-867. [PMID: 31969677 PMCID: PMC7078253 DOI: 10.1038/s41416-019-0704-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 10/30/2019] [Accepted: 12/10/2019] [Indexed: 02/07/2023] Open
Abstract
Background About 25–37% of resectable pancreatic ductal adenocarcinoma (PDAC) had a great chance of early recurrence after radical resection, which is mainly due to preoperative micrometastasis. We herein demonstrated the profiles of ctDNA in resectable PDAC and use of ctDNA to identify patients with potential micrometastasis. Methods A total of 113 and 44 resectable PDACs were enrolled in discovery and validation cohorts, separately. A panel containing 50 genes was used to screen ctDNA by an NGS-based assessment with high specificity. Results In the discovery cohort, the overall detection rate was 38.05% (43/113). Among positive ctDNA, KRAS mutation had the highest detection rate (23.01%, 26/113), while the others were <5%. Survival analysis showed that plasma KRAS mutations, especially KRAS G12D mutation, had significant association with OS and RFS of resectable PDAC. Plasma KRAS G12D mutation showed a strong correlation with early distant metastasis. In the validation cohort, survival analysis showed similar association between plasma KRAS G12D mutation and poor outcomes. Conclusions This study demonstrated that plasma KRAS mutations, especially KRAS G12D mutation, served as a useful predictive biomarker for prognosis of resectable PDAC. More importantly, due to high correlation with micrometastasis, preoperative detection of plasma KRAS G12D mutation helps in optimising surgical selection of resectable PDAC.
Collapse
|
16
|
Hartshorn CM, Russell LM, Grodzinski P. National Cancer Institute Alliance for nanotechnology in cancer-Catalyzing research and translation toward novel cancer diagnostics and therapeutics. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2019; 11:e1570. [PMID: 31257722 PMCID: PMC6788937 DOI: 10.1002/wnan.1570] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 05/23/2019] [Indexed: 12/22/2022]
Abstract
Nanotechnology has been a burgeoning research field, which is finding compelling applications in several practical areas of everyday life. It has provided novel, paradigm shifting solutions to medical problems and particularly to cancer. In order to accelerate integration of nanotechnology into cancer research and oncology, the National Cancer Institute (NCI) of the National Institutes of Health (NIH) established the NCI Alliance for Nanotechnology in Cancer program in 2005. This effort brought together scientists representing physical sciences, chemistry, and engineering working at the nanoscale with biologists and clinicians working on cancer to form a uniquely multidisciplinary cancer nanotechnology research community. The last 14 years of the program have produced a remarkable body of scientific discovery and demonstrated its utility to the development of practical cancer interventions. This paper takes stock of how the Alliance program influenced melding of disparate research disciplines into the field of nanomedicine and cancer nanotechnology, has been highly productive in the scientific arena, and produced a mechanism of seamless transfer of novel technologies developed in academia to the clinical and commercial space. This article is categorized under: Toxicology and Regulatory Issues in Nanomedicine > Regulatory and Policy Issues in Nanomedicine Therapeutic Approaches and Drug Discovery > Nanomedicine for Oncologic Disease Diagnostic Tools > in vivo Nanodiagnostics and Imaging.
Collapse
Affiliation(s)
- Christopher M. Hartshorn
- Nanodelivery Systems and Devices Branch, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, MD 20850, USA
| | - Luisa M. Russell
- Nanodelivery Systems and Devices Branch, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, MD 20850, USA
| | - Piotr Grodzinski
- Nanodelivery Systems and Devices Branch, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, MD 20850, USA
| |
Collapse
|
17
|
Do N, Grossman R, Feldman T, Fillmore N, Elbers D, Tuck D, Dhond R, Selva L, Meng F, Fitzsimons M, Ajjarapu S, Ayandeh S, Hall R, Do S, Brophy M. The Veterans Precision Oncology Data Commons: Transforming VA data into a national resource for research in precision oncology. Semin Oncol 2019; 46:314-320. [PMID: 31629530 DOI: 10.1053/j.seminoncol.2019.09.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 09/17/2019] [Indexed: 01/14/2023]
Abstract
The Department of Veterans Affairs (VA) has a strong track record providing high-quality, evidence-based care to cancer patients. In order to accelerate discoveries that will further improve care for Veterans with cancer, the VA has partnered with the Center for Translational Data Science at the University of Chicago and the Open Commons Consortium to establish a data sharing platform, the Veterans Precision Oncology Data Commons (VPODC). The VPODC makes clinical, genomic, and imaging data from the VA available to the research community at large. In this paper, we detail our motivation for data sharing, describe the VPODC, and outline our collaboration model. By transforming VA data into a national resource for research in precision oncology, the VPODC seeks to foster innovation through collaboration and resource sharing that will ultimately lead to improved care for Veterans with cancer.
Collapse
Affiliation(s)
- Nhan Do
- VA Boston Healthcare System, Boston University School of Medicine, Boston, Massachusetts.
| | | | - Theodore Feldman
- VA Boston Healthcare System, Harvard Medical School, Boston, Massachusetts
| | - Nathanael Fillmore
- VA Boston Healthcare System, Harvard Medical School, Boston, Massachusetts
| | - Danne Elbers
- VA Boston Healthcare System, University of Vermont, Burlington, Vermont
| | - David Tuck
- VA Boston Healthcare System, Boston University School of Medicine, Boston, Massachusetts
| | - Rupali Dhond
- VA Boston Healthcare System, Boston, Massachusetts
| | - Luis Selva
- VA Boston Healthcare System, Boston University School of Medicine, Boston, Massachusetts
| | - Frank Meng
- VA Boston Healthcare System, Boston University School of Medicine, Boston, Massachusetts
| | | | - Samuel Ajjarapu
- VA Boston Healthcare System, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Robert Hall
- VA Boston Healthcare System, Boston, Massachusetts
| | - Stephanie Do
- VA Boston Healthcare System, College of William and Mary, Williamsburg, Virginia
| | - Mary Brophy
- VA Boston Healthcare System, Boston University School of Medicine, Boston, Massachusetts
| |
Collapse
|
18
|
Heitzer E, Haque IS, Roberts CES, Speicher MR. Current and future perspectives of liquid biopsies in genomics-driven oncology. Nat Rev Genet 2019; 20:71-88. [PMID: 30410101 DOI: 10.1038/s41576-018-0071-5] [Citation(s) in RCA: 782] [Impact Index Per Article: 156.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Precision oncology seeks to leverage molecular information about cancer to improve patient outcomes. Tissue biopsy samples are widely used to characterize tumours but are limited by constraints on sampling frequency and their incomplete representation of the entire tumour bulk. Now, attention is turning to minimally invasive liquid biopsies, which enable analysis of tumour components (including circulating tumour cells and circulating tumour DNA) in bodily fluids such as blood. The potential of liquid biopsies is highlighted by studies that show they can track the evolutionary dynamics and heterogeneity of tumours and can detect very early emergence of therapy resistance, residual disease and recurrence. However, the analytical validity and clinical utility of liquid biopsies must be rigorously demonstrated before this potential can be realized.
Collapse
Affiliation(s)
- Ellen Heitzer
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria. .,BioTechMed-Graz, Graz, Austria. .,Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Graz, Austria.
| | | | | | - Michael R Speicher
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria.,BioTechMed-Graz, Graz, Austria
| |
Collapse
|
19
|
Abstract
Data commons have emerged as the best current method for enabling data aggregation across multiple projects and multiple data sources. Good data harmonization techniques are critical to maintain quality of data within a data commons, as well as to allow future meta-analysis across different data commons. We present some of the current best practices for data harmonization.
Collapse
|
20
|
Abstract
One of the recommendations of the Cancer Moonshot Blue Ribbon Panel report from 2016 was the creation of a national cancer data ecosystem. We review some of the approaches for building cancer data ecosystems and some of the progress that has been made. A data commons is the colocation of data with cloud computing infrastructure and commonly used software services, tools, and applications for managing, integrating, analyzing, and sharing data to create an interoperable resource for the research community. We discuss data commons and their potential role in cancer data ecosystems and, in particular, how multiple data commons can interoperate to form part of the foundation for a cancer data ecosystem.
Collapse
|
21
|
The cornerstone of integrating circulating tumor DNA into cancer management. Biochim Biophys Acta Rev Cancer 2018; 1871:1-11. [PMID: 30419316 DOI: 10.1016/j.bbcan.2018.11.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 08/23/2018] [Accepted: 11/07/2018] [Indexed: 12/26/2022]
Abstract
Recent circulating tumor DNA (ctDNA) research has demonstrated its potential as a non-invasive biomarker for cancer. However, the deployment of ctDNA assays in routine clinical practice remains challenging owing to variability in analytical approaches and the assessment of clinical significance. A well-developed, analytically valid ctDNA assay is a prerequisite for integrating ctDNA into cancer management, and an appropriate analytical technology is crucial for the development of a ctDNA assay. Other determinants including pre-analytical procedures, test validation, internal quality control (IQC), and continual proficiency testing (PT) are also important for the accuracy of ctDNA assays. In the present review, we will focus on the most widely used ctDNA detection technologies and the key quality management measures used to assure the accuracy of ctDNA assays. The aim of this review is to provide useful information for technology selection during ctDNA assay development and assure a reliable test result in clinical practice.
Collapse
|
22
|
Zill OA, Banks KC, Fairclough SR, Mortimer SA, Vowles JV, Mokhtari R, Gandara DR, Mack PC, Odegaard JI, Nagy RJ, Baca AM, Eltoukhy H, Chudova DI, Lanman RB, Talasaz A. The Landscape of Actionable Genomic Alterations in Cell-Free Circulating Tumor DNA from 21,807 Advanced Cancer Patients. Clin Cancer Res 2018; 24:3528-3538. [DOI: 10.1158/1078-0432.ccr-17-3837] [Citation(s) in RCA: 211] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 03/19/2018] [Accepted: 05/11/2018] [Indexed: 11/16/2022]
|
23
|
Carneiro BA, Pamarthy S, Shah AN, Sagar V, Unno K, Han H, Yang XJ, Costa RB, Nagy RJ, Lanman RB, Kuzel TM, Ross JS, Gay L, Elvin JA, Ali SM, Cristofanilli M, Chae YK, Giles FJ, Abdulkadir SA. Anaplastic Lymphoma Kinase Mutation ( ALK F1174C) in Small Cell Carcinoma of the Prostate and Molecular Response to Alectinib. Clin Cancer Res 2018; 24:2732-2739. [PMID: 29559559 DOI: 10.1158/1078-0432.ccr-18-0332] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 02/27/2018] [Accepted: 03/15/2018] [Indexed: 12/13/2022]
Abstract
Purpose: Small cell carcinoma of the prostate (SCCP) is an aggressive disease that can arise de novo or by transdifferentiation from prostate adenocarcinoma. Alterations in anaplastic lymphoma kinase (ALK) gene are involved in neuroblastoma, lung cancer, and other malignancies, but its role in SCCP has not been documented. We describe a patient with refractory de novo SCCP with ALK F1174C-activating mutation who obtained clinical benefit from treatment with ALK inhibitor.Experimental Design: Next-generation sequencing (NGS) was used to analyze primary and circulating tumor DNA (ctDNA). Prostate cancer databases were queried for alterations in ALK gene, mRNA, and its impact in clinical outcomes. In vitro prostate cell line/organoid models were generated by lentiviral-mediated expression of ALK and ALK F1174C and assessed for response to ALK inhibitors crizotinib and alectinib.Results: NGS analysis of the primary tumor and ctDNA of a 39-year-old patient with refractory SSCP identified ALK F1174C mutation. Treatment with second-generation ALK inhibitor alectinib resulted in radiographic stable disease for over 6 months, symptomatic improvement, and significant molecular response as reflected by declining ctDNA allele fraction. Analysis of prostate cancer datasets showed that ALK amplification was associated with poor outcome. In prostate cancer cells and organoids, ALK F1174C expression enhanced growth and induced expression of the neuroendocrine marker neuron-specific enolase. Alectinib was more effective than crizotinib in inhibiting ALK F1174C-expressing cell growth.Conclusions: These findings implicate ALK-activating mutations in SCCP pathogenesis and suggest the therapeutic potential of targeting ALK molecular alterations in some patients with SCCP. Clin Cancer Res; 24(12); 2732-9. ©2018 AACR.
Collapse
Affiliation(s)
- Benedito A Carneiro
- Division of Hematology/Oncology, Lifespan Cancer Institute, the Warren Alpert Medical School, Brown University, Providence, Rhode Island.
| | - Sahithi Pamarthy
- The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Ami N Shah
- Developmental Therapeutics Program, Division of Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Vinay Sagar
- The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Kenji Unno
- The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - HuiYing Han
- The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Ximing J Yang
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Rubens B Costa
- Developmental Therapeutics Program, Division of Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | | | | | - Timothy M Kuzel
- Rush University Medical Center, Division of Hematology/Oncology, Chicago, Illinois
| | - Jeffrey S Ross
- Foundation Medicine Inc., Cambridge, Massachusetts.,Upstate Medical University, Syracuse, New York
| | - Laurie Gay
- Foundation Medicine Inc., Cambridge, Massachusetts
| | | | - Siraj M Ali
- Foundation Medicine Inc., Cambridge, Massachusetts
| | - Massimo Cristofanilli
- The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Young K Chae
- The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Developmental Therapeutics Program, Division of Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | | | - Sarki A Abdulkadir
- The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| |
Collapse
|
24
|
Strickler JH, Loree JM, Ahronian LG, Parikh AR, Niedzwiecki D, Pereira AAL, McKinney M, Korn WM, Atreya CE, Banks KC, Nagy RJ, Meric-Bernstam F, Lanman RB, Talasaz A, Tsigelny IF, Corcoran RB, Kopetz S. Genomic Landscape of Cell-Free DNA in Patients with Colorectal Cancer. Cancer Discov 2018; 8:164-173. [PMID: 29196463 PMCID: PMC5809260 DOI: 10.1158/2159-8290.cd-17-1009] [Citation(s) in RCA: 202] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 11/14/2017] [Accepted: 11/29/2017] [Indexed: 01/10/2023]
Abstract
"Liquid biopsy" approaches analyzing cell-free DNA (cfDNA) from the blood of patients with cancer are increasingly utilized in clinical practice. However, it is not yet known whether cfDNA sequencing from large cohorts of patients with cancer can detect genomic alterations at frequencies similar to those observed by direct tumor sequencing, and whether this approach can generate novel insights. Here, we report next-generation sequencing data from cfDNA of 1,397 patients with colorectal cancer. Overall, frequencies of genomic alterations detected in cfDNA were comparable to those observed in three independent tissue-based colorectal cancer sequencing compendia. Our analysis also identified a novel cluster of extracellular domain (ECD) mutations in EGFR, mediating resistance by blocking binding of anti-EGFR antibodies. Patients with EGFR ECD mutations displayed striking tumor heterogeneity, with 91% harboring multiple distinct resistance alterations (range, 1-13; median, 4). These results suggest that cfDNA profiling can effectively define the genomic landscape of cancer and yield important biological insights.Significance: This study provides one of the first examples of how large-scale genomic profiling of cfDNA from patients with colorectal cancer can detect genomic alterations at frequencies comparable to those observed by direct tumor sequencing. Sequencing of cfDNA also generated insights into tumor heterogeneity and therapeutic resistance and identified novel EGFR ectodomain mutations. Cancer Discov; 8(2); 164-73. ©2017 AACR.This article is highlighted in the In This Issue feature, p. 127.
Collapse
Affiliation(s)
| | - Jonathan M Loree
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Leanne G Ahronian
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Aparna R Parikh
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | | | | | | | - W Michael Korn
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Caris Life Sciences, Phoenix, Arizona
| | - Chloe E Atreya
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | | | | | | | | | | | - Igor F Tsigelny
- University of California, San Diego, San Diego, California
- CureMatch Inc., San Diego, California
| | - Ryan B Corcoran
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts.
| | - Scott Kopetz
- The University of Texas MD Anderson Cancer Center, Houston, Texas.
| |
Collapse
|
25
|
Hench IB, Hench J, Tolnay M. Liquid Biopsy in Clinical Management of Breast, Lung, and Colorectal Cancer. Front Med (Lausanne) 2018; 5:9. [PMID: 29441349 PMCID: PMC5797586 DOI: 10.3389/fmed.2018.00009] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/15/2018] [Indexed: 12/12/2022] Open
Abstract
Examination of tumor molecular characteristics by liquid biopsy is likely to greatly influence personalized cancer patient management. Analysis of circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), and tumor-derived exosomes, all collectively referred to as “liquid biopsies,” are not only a modality to monitor treatment efficacy, disease progression, and emerging therapy resistance mechanisms, but they also assess tumor heterogeneity and evolution in real time. We review the literature concerning the examination of ctDNA and CTC in a diagnostic setting, evaluating their prognostic, predictive, and monitoring capabilities. We discuss the advantages and limitations of various leading ctDNA/CTC analysis technologies. Finally, guided by the results of clinical trials, we discuss the readiness of cell-free DNA and CTC as routine biomarkers in the context of various common types of neoplastic disease. At this moment, one cannot conclude whether or not liquid biopsy will become a mainstay in oncology practice.
Collapse
Affiliation(s)
- Ivana Bratić Hench
- Institute for Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Jürgen Hench
- Institute for Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Markus Tolnay
- Institute for Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| |
Collapse
|
26
|
Zaporozhchenko IA, Ponomaryova AA, Rykova EY, Laktionov PP. The potential of circulating cell-free RNA as a cancer biomarker: challenges and opportunities. Expert Rev Mol Diagn 2018; 18:133-145. [DOI: 10.1080/14737159.2018.1425143] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Ivan A. Zaporozhchenko
- Laboratory of Molecular Medicine, Institute of Chemical Biology and Fundamental Medicine of SB RAS, Novosibirsk, Russia
- Laboratory of Biomedical Technologies, Centre of New Surgical Technologies, E.N. Meshalkin Siberian Federal Biomedical Research Center, Novosibirsk, Russia
| | - Anastasia A. Ponomaryova
- Laboratory of Immunology, Tomsk Cancer Research Institute of SB RAMS, Tomsk, Russia
- Department of Applied Physics, National Research Tomsk Polytechnic University, Tomsk, Russia
| | - Elena Yu Rykova
- Laboratory of Molecular Medicine, Institute of Chemical Biology and Fundamental Medicine of SB RAS, Novosibirsk, Russia
- Laboratory of Biomedical Technologies, Centre of New Surgical Technologies, E.N. Meshalkin Siberian Federal Biomedical Research Center, Novosibirsk, Russia
| | - Pavel P. Laktionov
- Laboratory of Molecular Medicine, Institute of Chemical Biology and Fundamental Medicine of SB RAS, Novosibirsk, Russia
- Laboratory of Biomedical Technologies, Centre of New Surgical Technologies, E.N. Meshalkin Siberian Federal Biomedical Research Center, Novosibirsk, Russia
| |
Collapse
|
27
|
Lopez A, Harada K, Mizrak Kaya D, Dong X, Song S, Ajani JA. Liquid biopsies in gastrointestinal malignancies: when is the big day? Expert Rev Anticancer Ther 2017; 18:19-38. [DOI: 10.1080/14737140.2018.1403320] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Anthony Lopez
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Gastroenterology and Hepatology and Inserm U954, Nancy University Hospital, Lorraine University, Vandoeuvre-lès-Nancy, France
| | - Kazuto Harada
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dilsa Mizrak Kaya
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiaochuan Dong
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shumei Song
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jaffer A. Ajani
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| |
Collapse
|
28
|
Posadas EM, Limvorasak S, Figlin RA. Targeted therapies for renal cell carcinoma. Nat Rev Nephrol 2017; 13:496-511. [DOI: 10.1038/nrneph.2017.82] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
|
29
|
Lee J, Blumenthal GM, Hohl RJ, Huang SM. Cancer Therapy: Shooting for the Moon. Clin Pharmacol Ther 2017; 101:552-558. [PMID: 28418166 PMCID: PMC5525193 DOI: 10.1002/cpt.655] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 02/06/2017] [Indexed: 11/15/2022]
Affiliation(s)
- Jsh Lee
- Office of the Director, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - G M Blumenthal
- Office of Hematology & Oncology Products, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
| | - R J Hohl
- Penn State Cancer Institute, Pennsylvania State University, Hershey, Pennsylvania, USA
| | - S-M Huang
- Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
| |
Collapse
|