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Kratz JD, Zhang W, Patel M, Uboha NV. Challenges in biomarker-based clinical trials for patients with gastrointestinal malignancies. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2022. [DOI: 10.1080/23808993.2022.2106852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Affiliation(s)
- Jeremy D. Kratz
- Carbone Cancer Center, University of Wisconsin, Madison, WI, USA
- Division of Hematology, Medical Oncology and Palliative care, Department of Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
- US Department of Veterans Affairs, William S. Middleton Memorial Veterans Hospital, Madison, Wisconsin, USA
| | - Wei Zhang
- Carbone Cancer Center, University of Wisconsin, Madison, WI, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Monica Patel
- Carbone Cancer Center, University of Wisconsin, Madison, WI, USA
- Division of Hematology, Medical Oncology and Palliative care, Department of Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
| | - Nataliya V. Uboha
- Carbone Cancer Center, University of Wisconsin, Madison, WI, USA
- Division of Hematology, Medical Oncology and Palliative care, Department of Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
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Hoshitsuki K, Rathod S, Ramsey MJ, Zhu L, Moreland LW, Fernandez CA. Adalimumab Immunogenicity Is Negatively Correlated with Anti-Hinge Antibody Levels in Patients with Rheumatoid Arthritis. J Pharmacol Exp Ther 2020; 375:488-497. [PMID: 33008870 DOI: 10.1124/jpet.120.000179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 09/16/2020] [Indexed: 12/16/2022] Open
Abstract
Patients with rheumatoid arthritis (RA) are frequently treated with anti-tumor necrosis factor-α immunoglobulin therapy but develop neutralizing antibodies against these drugs, necessitating therapeutic monitoring of drug concentrations and anti-drug antibodies. Patients with RA have multiple factors related to their autoimmune disposition that interfere with conventionally used methods to detect anti-drug antibodies. Currently deployed analytical methods have significant limitations that hinder clinical interpretation and/or routine use, and no method can detect immunogenicity and drug levels simultaneously to provide clinically meaningful recommendations. Given these limitations, the objective of this study was to identify sources of and associations with assay interference in patients with RA. We designed a modular immunogenicity and drug concentration detection technology to identify the factors that interfere with the detection of adalimumab and anti-adalimumab antibodies in a cohort of 206 patients with RA. Patients were included from the University of Pittsburgh Rheumatoid Arthritis Comparative Effectiveness Research registry. In this cohort, we analyzed clinical and plasma factors associated with anti-adalimumab and anti-hinge antibodies. A novel flow cytometry-based assay was developed and validated that simultaneously measures adalimumab and anti-adalimumab antibody concentrations, overcoming many of the interference factors that are limitations of conventional assays, including anti-fragment crystallizable (Fc) and anti-hinge antibodies. C-reactive protein (P = 0.035), Disease Activity Score-28 (DAS28) score (P = 0.002), and disease activity category (P = 0.009) were significantly associated with anti-adalimumab antibodies but not with anti-hinge antibodies (P > 0.05). Anti-hinge antibodies were inversely associated with drug-neutralizing antibodies (P = 0.002). In patients with RA, anti-hinge antibodies may have a potential protective effect against the development of anti-adalimumab antibodies. SIGNIFICANCE STATEMENT: Using a novel cytometric assay that simultaneously measures drug and anti-drug antibodies, we overcame many interferences that hinder the clinical interpretation of adalimumab immunogenicity testing. Our investigation in patients with RA demonstrated that immunogenicity impaired the pharmacological action of adalimumab via analysis of RA disease severity markers. We also demonstrate that patients with anti-hinge antibodies had lower anti-adalimumab antibody levels and decreased drug neutralization. Our results suggest that anti-hinge antibodies can predict adalimumab immunogenicity before the start of therapy.
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Affiliation(s)
- Keito Hoshitsuki
- Center for Pharmacogenetics and Department of Pharmaceutical Sciences (K.H., S.R., M.J.R., C.A.F.) and Rheumatology and Clinical Immunology (L.Z., L.W.M.), University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Sanjay Rathod
- Center for Pharmacogenetics and Department of Pharmaceutical Sciences (K.H., S.R., M.J.R., C.A.F.) and Rheumatology and Clinical Immunology (L.Z., L.W.M.), University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Manda J Ramsey
- Center for Pharmacogenetics and Department of Pharmaceutical Sciences (K.H., S.R., M.J.R., C.A.F.) and Rheumatology and Clinical Immunology (L.Z., L.W.M.), University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Lei Zhu
- Center for Pharmacogenetics and Department of Pharmaceutical Sciences (K.H., S.R., M.J.R., C.A.F.) and Rheumatology and Clinical Immunology (L.Z., L.W.M.), University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Larry W Moreland
- Center for Pharmacogenetics and Department of Pharmaceutical Sciences (K.H., S.R., M.J.R., C.A.F.) and Rheumatology and Clinical Immunology (L.Z., L.W.M.), University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Christian A Fernandez
- Center for Pharmacogenetics and Department of Pharmaceutical Sciences (K.H., S.R., M.J.R., C.A.F.) and Rheumatology and Clinical Immunology (L.Z., L.W.M.), University of Pittsburgh, Pittsburgh, Pennsylvania
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Grossman D, Okwundu N, Bartlett EK, Marchetti MA, Othus M, Coit DG, Hartman RI, Leachman SA, Berry EG, Korde L, Lee SJ, Bar-Eli M, Berwick M, Bowles T, Buchbinder EI, Burton EM, Chu EY, Curiel-Lewandrowski C, Curtis JA, Daud A, Deacon DC, Ferris LK, Gershenwald JE, Grossmann KF, Hu-Lieskovan S, Hyngstrom J, Jeter JM, Judson-Torres RL, Kendra KL, Kim CC, Kirkwood JM, Lawson DH, Leming PD, Long GV, Marghoob AA, Mehnert JM, Ming ME, Nelson KC, Polsky D, Scolyer RA, Smith EA, Sondak VK, Stark MS, Stein JA, Thompson JA, Thompson JF, Venna SS, Wei ML, Swetter SM. Prognostic Gene Expression Profiling in Cutaneous Melanoma: Identifying the Knowledge Gaps and Assessing the Clinical Benefit. JAMA Dermatol 2020; 156:1004-1011. [PMID: 32725204 PMCID: PMC8275355 DOI: 10.1001/jamadermatol.2020.1729] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Importance Use of prognostic gene expression profile (GEP) testing in cutaneous melanoma (CM) is rising despite a lack of endorsement as standard of care. Objective To develop guidelines within the national Melanoma Prevention Working Group (MPWG) on integration of GEP testing into the management of patients with CM, including (1) review of published data using GEP tests, (2) definition of acceptable performance criteria, (3) current recommendations for use of GEP testing in clinical practice, and (4) considerations for future studies. Evidence Review The MPWG members and other international melanoma specialists participated in 2 online surveys and then convened a summit meeting. Published data and meeting abstracts from 2015 to 2019 were reviewed. Findings The MPWG members are optimistic about the future use of prognostic GEP testing to improve risk stratification and enhance clinical decision-making but acknowledge that current utility is limited by test performance in patients with stage I disease. Published studies of GEP testing have not evaluated results in the context of all relevant clinicopathologic factors or as predictors of regional nodal metastasis to replace sentinel lymph node biopsy (SLNB). The performance of GEP tests has generally been reported for small groups of patients representing particular tumor stages or in aggregate form, such that stage-specific performance cannot be ascertained, and without survival outcomes compared with data from the American Joint Committee on Cancer 8th edition melanoma staging system international database. There are significant challenges to performing clinical trials incorporating GEP testing with SLNB and adjuvant therapy. The MPWG members favor conducting retrospective studies that evaluate multiple GEP testing platforms on fully annotated archived samples before embarking on costly prospective studies and recommend avoiding routine use of GEP testing to direct patient management until prospective studies support their clinical utility. Conclusions and Relevance More evidence is needed to support using GEP testing to inform recommendations regarding SLNB, intensity of follow-up or imaging surveillance, and postoperative adjuvant therapy. The MPWG recommends further research to assess the validity and clinical applicability of existing and emerging GEP tests. Decisions on performing GEP testing and patient management based on these results should only be made in the context of discussion of testing limitations with the patient or within a multidisciplinary group.
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Affiliation(s)
- Douglas Grossman
- Huntsman Cancer Institute, Salt Lake City, Utah
- Department of Dermatology, University of Utah, Salt Lake City
- Department of Oncological Sciences, University of Utah, Salt Lake City
| | | | - Edmund K Bartlett
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael A Marchetti
- Dermatology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Megan Othus
- Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Daniel G Coit
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Rebecca I Hartman
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Department of Dermatology, Harvard Medical School, Boston, Massachusetts
| | - Sancy A Leachman
- Department of Dermatology and Knight Cancer Institute, Oregon Health & Science University, Portland
| | - Elizabeth G Berry
- Department of Dermatology and Knight Cancer Institute, Oregon Health & Science University, Portland
| | - Larissa Korde
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland
| | - Sandra J Lee
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Department of Data Sciences, Harvard Medical School, Boston, Massachusetts
| | - Menashe Bar-Eli
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston
| | - Marianne Berwick
- Departments of Dermatology and Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque
| | - Tawnya Bowles
- Department of Surgery, Division of Surgical Oncology, University of Utah, Salt Lake City
| | - Elizabeth I Buchbinder
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Department of Internal Medicine, Harvard Medical School, Boston, Massachusetts
| | - Elizabeth M Burton
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston
| | - Emily Y Chu
- Department of Dermatology, Perelman School of Medicine University of Pennsylvania, Philadelphia
| | | | - Julia A Curtis
- Department of Dermatology, University of Utah, Salt Lake City
| | - Adil Daud
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco
- Department of Hematology/Oncology, University of California, San Francisco
| | - Dekker C Deacon
- Department of Dermatology, University of Utah, Salt Lake City
| | - Laura K Ferris
- Department of Dermatology and University of Pittsburgh Clinical and Translational Science Institute, Pittsburgh, Pennsylvania
| | - Jeffrey E Gershenwald
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston
| | - Kenneth F Grossmann
- Huntsman Cancer Institute, Salt Lake City, Utah
- Department of Medicine, Division of Oncology, University of Utah, Salt Lake City
| | - Siwen Hu-Lieskovan
- Huntsman Cancer Institute, Salt Lake City, Utah
- Department of Medicine, Division of Oncology, University of Utah, Salt Lake City
| | - John Hyngstrom
- Huntsman Cancer Institute, Salt Lake City, Utah
- Department of Surgery, Division of Surgical Oncology, University of Utah, Salt Lake City
| | - Joanne M Jeter
- Department of Internal Medicine and The Ohio State University Comprehensive Cancer Center, Columbus
| | - Robert L Judson-Torres
- Huntsman Cancer Institute, Salt Lake City, Utah
- Department of Dermatology, University of Utah, Salt Lake City
| | - Kari L Kendra
- Department of Internal Medicine and The Ohio State University Comprehensive Cancer Center, Columbus
| | - Caroline C Kim
- Department of Dermatology, Tufts Medical Center, Boston, Massachusetts
- Partners Healthcare, Newton Wellesley Dermatology Associates, Wellesley, Massachusetts
| | - John M Kirkwood
- Department of Internal Medicine and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - David H Lawson
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Winship Cancer Institute of Emory University, Atlanta, Georgia
| | | | - Georgina V Long
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Department of Medical Oncology, Royal North Shore Hospital, Sydney, New South Wales, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
| | - Ashfaq A Marghoob
- Dermatology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Janice M Mehnert
- Department of Medical Oncology, Robert Wood Johnson University Hospital, New Brunswick, New Jersey
- Rutgers Cancer Institute of New Jersey, New Brunswick
| | - Michael E Ming
- Department of Dermatology, Perelman School of Medicine University of Pennsylvania, Philadelphia
| | - Kelly C Nelson
- Department of Dermatology, The University of Texas MD Anderson Cancer Center, Houston
| | - David Polsky
- Department of Dermatology, Ronald O. Perelman Department of Dermatology, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York University School of Medicine, New York, New York
| | - Richard A Scolyer
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, New South Wales, Australia
| | - Eric A Smith
- Department of Pathology, University of Utah, Salt Lake City
| | - Vernon K Sondak
- Department of Cutaneous Oncology, Moffitt Cancer Center & Research Institute, Tampa, Florida
- Department of Oncologic Sciences, University of South Florida Morsani College of Medicine, Tampa
| | - Mitchell S Stark
- The University of Queensland Diamantina Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Australia
| | - Jennifer A Stein
- Department of Dermatology, Ronald O. Perelman Department of Dermatology, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York University School of Medicine, New York, New York
| | - John A Thompson
- Fred Hutchinson Cancer Research Center, Seattle, Washington
- Department of Oncology, University of Washington, Seattle
- Seattle Cancer Care Alliance, Seattle, Washington
| | - John F Thompson
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Suraj S Venna
- Inova Schar Cancer Institute, Department of Medicine, Virginia Commonwealth University, Fairfax
| | - Maria L Wei
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco
- Department of Dermatology, University of California, San Francisco
- Dermatology Service, Veterans Affairs Medical Center, San Francisco, California
| | - Susan M Swetter
- Stanford University Medical Center and Cancer Institute, Stanford, California
- Dermatology Service, Veterans Affairs Palo Alto Health Care System, Palo Alto, California
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Beesley LJ, Hawkins PG, Amlani LM, Bellile EL, Casper KA, Chinn SB, Eisbruch A, Mierzwa ML, Spector ME, Wolf GT, Shuman AG, Taylor JMG. Individualized survival prediction for patients with oropharyngeal cancer in the human papillomavirus era. Cancer 2019; 125:68-78. [PMID: 30291798 PMCID: PMC6309492 DOI: 10.1002/cncr.31739] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 08/07/2018] [Accepted: 08/08/2018] [Indexed: 12/19/2022]
Abstract
BACKGROUND Accurate, individualized prognostication in patients with oropharyngeal squamous cell carcinoma (OPSCC) is vital for patient counseling and treatment decision making. With the emergence of human papillomavirus (HPV) as an important biomarker in OPSCC, calculators incorporating this variable have been developed. However, it is critical to characterize their accuracy prior to implementation. METHODS Four OPSCC calculators were identified that integrate HPV into their estimation of 5-year overall survival. Treatment outcomes for 856 patients with OPSCC who were evaluated at a single institution from 2003 through 2016 were analyzed. Predicted survival probabilities were generated for each patient using each calculator. Calculator performance was assessed and compared using Kaplan-Meier plots, receiver operating characteristic curves, concordance statistics, and calibration plots. RESULTS Correlation between pairs of calculators varied, with coefficients ranging from 0.63 to 0.90. Only 3 of 6 pairs of calculators yielded predictions within 10% of each other for at least 50% of patients. Kaplan-Meier curves of calculator-defined risk groups demonstrated reasonable stratification. Areas under the receiver operating characteristic curve ranged from 0.74 to 0.80, and concordance statistics ranged from 0.71 to 0.78. Each calculator demonstrated superior discriminatory ability compared with clinical staging according to the seventh and eighth editions of the American Joint Committee on Cancer staging manual. Among models, the Denmark calculator was found to be best calibrated to observed outcomes. CONCLUSIONS Existing calculators exhibited reasonable estimation of survival in patients with OPSCC, but there was considerable variability in predictions for individual patients, which limits the clinical usefulness of these calculators. Given the increasing role of personalized treatment in patients with OPSCC, further work is needed to improve accuracy and precision, possibly through the identification and incorporation of additional biomarkers.
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Affiliation(s)
- Lauren J Beesley
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Peter G Hawkins
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Lahin M Amlani
- Department of Otolaryngology-Head and Neck Surgery, University of Michigan Medical School, Ann Arbor, Michigan
| | - Emily L Bellile
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Keith A Casper
- Department of Otolaryngology-Head and Neck Surgery, University of Michigan Medical School, Ann Arbor, Michigan
| | - Steven B Chinn
- Department of Otolaryngology-Head and Neck Surgery, University of Michigan Medical School, Ann Arbor, Michigan
| | - Avraham Eisbruch
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Michelle L Mierzwa
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Matthew E Spector
- Department of Otolaryngology-Head and Neck Surgery, University of Michigan Medical School, Ann Arbor, Michigan
| | - Gregory T Wolf
- Department of Otolaryngology-Head and Neck Surgery, University of Michigan Medical School, Ann Arbor, Michigan
| | - Andrew G Shuman
- Department of Otolaryngology-Head and Neck Surgery, University of Michigan Medical School, Ann Arbor, Michigan
| | - Jeremy M G Taylor
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan
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Koo KM, Wang J, Richards RS, Farrell A, Yaxley JW, Samaratunga H, Teloken PE, Roberts MJ, Coughlin GD, Lavin MF, Mainwaring PN, Wang Y, Gardiner RA, Trau M. Design and Clinical Verification of Surface-Enhanced Raman Spectroscopy Diagnostic Technology for Individual Cancer Risk Prediction. ACS NANO 2018; 12:8362-8371. [PMID: 30028592 DOI: 10.1021/acsnano.8b03698] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The use of emerging nanotechnologies, such as plasmonic nanoparticles in diagnostic applications, potentially offers opportunities to revolutionize disease management and patient healthcare. Despite worldwide research efforts in this area, there is still a dearth of nanodiagnostics which have been successfully translated for real-world patient usage due to the predominant sole focus on assay analytical performance and lack of detailed investigations into clinical performance in human samples. In a bid to address this pressing need, we herein describe a comprehensive clinical verification of a prospective label-free surface-enhanced Raman scattering (SERS) nanodiagnostic assay for prostate cancer (PCa) risk stratification. This contribution depicts a roadmap of (1) designing a SERS assay for robust and accurate detection of clinically validated PCa RNA targets; (2) employing a relevant and proven PCa clinical biomarker model to test our nanodiagnostic assay; and (3) investigating the clinical performance on independent training ( n = 80) and validation ( n = 40) cohorts of PCa human patient samples. By relating the detection outcomes to gold-standard patient biopsy findings, we established a PCa risk scoring system which exhibited a clinical sensitivity and specificity of 0.87 and 0.90, respectively [area-under-curve of 0.84 (95% confidence interval: 0.81-0.87) for differentiating high- and low-risk PCa] in the validation cohort. We envision that our SERS nanodiagnostic design and clinical verification approach may aid in the individualized prediction of PCa presence and risk stratification and may overall serve as an archetypical strategy to encourage comprehensive clinical evaluation of nanodiagnostic innovations.
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Affiliation(s)
- Kevin M Koo
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology , University of Queensland , Brisbane , QLD 4072 , Australia
| | - Jing Wang
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology , University of Queensland , Brisbane , QLD 4072 , Australia
| | - Renée S Richards
- The University of Queensland, Centre for Clinical Research , Brisbane , QLD 4029 , Australia
- QIMR Berghofer Medical Research Institute , Brisbane , QLD 4006 , Australia
| | - Aine Farrell
- The University of Queensland, Centre for Clinical Research , Brisbane , QLD 4029 , Australia
| | - John W Yaxley
- The University of Queensland, Centre for Clinical Research , Brisbane , QLD 4029 , Australia
- Department of Urology , Royal Brisbane and Women's Hospital , Brisbane , QLD 4029 , Australia
| | - Hema Samaratunga
- The University of Queensland, Centre for Clinical Research , Brisbane , QLD 4029 , Australia
- Aquesta Specialized Uropathology, Brisbane , QLD 4066 , Australia
- Princess Alexandra Hospital , Brisbane , QLD 4102 , Australia
| | - Patrick E Teloken
- Department of Urology , Royal Brisbane and Women's Hospital , Brisbane , QLD 4029 , Australia
- Princess Alexandra Hospital , Brisbane , QLD 4102 , Australia
| | - Matthew J Roberts
- The University of Queensland, Centre for Clinical Research , Brisbane , QLD 4029 , Australia
- Department of Urology , Royal Brisbane and Women's Hospital , Brisbane , QLD 4029 , Australia
| | - Geoffrey D Coughlin
- Department of Urology , Royal Brisbane and Women's Hospital , Brisbane , QLD 4029 , Australia
| | - Martin F Lavin
- The University of Queensland, Centre for Clinical Research , Brisbane , QLD 4029 , Australia
| | - Paul N Mainwaring
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology , University of Queensland , Brisbane , QLD 4072 , Australia
| | - Yuling Wang
- Department of Molecular Sciences, Faculty of Science and Engineering , Macquarie University , Sydney , NSW 2109 , Australia
| | - Robert A Gardiner
- The University of Queensland, Centre for Clinical Research , Brisbane , QLD 4029 , Australia
- Department of Urology , Royal Brisbane and Women's Hospital , Brisbane , QLD 4029 , Australia
- Edith Cowan University , Perth , WA 6027 , Australia
- Griffith University , Brisbane , QLD 4111 , Australia
| | - Matt Trau
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology , University of Queensland , Brisbane , QLD 4072 , Australia
- School of Chemistry and Molecular Biosciences , University of Queensland , Brisbane , QLD 4072 , Australia
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de Graaf G, Postmus D, Westerink J, Buskens E. The early economic evaluation of novel biomarkers to accelerate their translation into clinical applications. COST EFFECTIVENESS AND RESOURCE ALLOCATION 2018; 16:23. [PMID: 29946228 PMCID: PMC6006586 DOI: 10.1186/s12962-018-0105-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 06/02/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Translating prognostic and diagnostic biomarker candidates into clinical applications takes time, is very costly, and many candidates fail. It is therefore crucial to be able to select those biomarker candidates that have the highest chance of successfully being adopted in the clinic. This requires an early estimate of the potential clinical impact and commercial value. In this paper, we aim to demonstratively evaluate a set of novel biomarkers in terms of clinical impact and commercial value, using occurrence of cardiovascular disease (CVD) in type-2 diabetes (DM2) patients as a case study. METHODS We defined a clinical application for the novel biomarkers, and subsequently used data from a large cohort study in The Netherlands in a modeling exercise to assess the potential clinical impact and headroom for the biomarkers. RESULTS The most likely application of the biomarkers would be to identify DM2 patients with a low CVD risk and subsequently withhold statin treatment. As a result, one additional CVD event in every 75 patients may be expected. The expected downstream savings resulted in a headroom for a point-of-care device ranging from €119.09 at a willingness to accept of €0 for one additional CVD event, to €0 at a willingness to accept of €15,614 or more. CONCLUSION It is feasible to evaluate novel biomarkers on outcomes directly relevant to technological development and clinical adoption. Importantly, this may be attained at the same point in time and using the same data as used for the evaluation of association with disease and predictive power.
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Affiliation(s)
- Gimon de Graaf
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, PO Box 30.001, 9700 RB Groningen, The Netherlands
| | - Douwe Postmus
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, PO Box 30.001, 9700 RB Groningen, The Netherlands
| | - Jan Westerink
- Department of Vascular Medicine, University Medical Center Utrecht, PO Box 85.500, 3508 GA Utrecht, The Netherlands
| | - Erik Buskens
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, PO Box 30.001, 9700 RB Groningen, The Netherlands
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Selby PJ, Banks RE, Gregory W, Hewison J, Rosenberg W, Altman DG, Deeks JJ, McCabe C, Parkes J, Sturgeon C, Thompson D, Twiddy M, Bestall J, Bedlington J, Hale T, Dinnes J, Jones M, Lewington A, Messenger MP, Napp V, Sitch A, Tanwar S, Vasudev NS, Baxter P, Bell S, Cairns DA, Calder N, Corrigan N, Del Galdo F, Heudtlass P, Hornigold N, Hulme C, Hutchinson M, Lippiatt C, Livingstone T, Longo R, Potton M, Roberts S, Sim S, Trainor S, Welberry Smith M, Neuberger J, Thorburn D, Richardson P, Christie J, Sheerin N, McKane W, Gibbs P, Edwards A, Soomro N, Adeyoju A, Stewart GD, Hrouda D. Methods for the evaluation of biomarkers in patients with kidney and liver diseases: multicentre research programme including ELUCIDATE RCT. PROGRAMME GRANTS FOR APPLIED RESEARCH 2018. [DOI: 10.3310/pgfar06030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BackgroundProtein biomarkers with associations with the activity and outcomes of diseases are being identified by modern proteomic technologies. They may be simple, accessible, cheap and safe tests that can inform diagnosis, prognosis, treatment selection, monitoring of disease activity and therapy and may substitute for complex, invasive and expensive tests. However, their potential is not yet being realised.Design and methodsThe study consisted of three workstreams to create a framework for research: workstream 1, methodology – to define current practice and explore methodology innovations for biomarkers for monitoring disease; workstream 2, clinical translation – to create a framework of research practice, high-quality samples and related clinical data to evaluate the validity and clinical utility of protein biomarkers; and workstream 3, the ELF to Uncover Cirrhosis as an Indication for Diagnosis and Action for Treatable Event (ELUCIDATE) randomised controlled trial (RCT) – an exemplar RCT of an established test, the ADVIA Centaur® Enhanced Liver Fibrosis (ELF) test (Siemens Healthcare Diagnostics Ltd, Camberley, UK) [consisting of a panel of three markers – (1) serum hyaluronic acid, (2) amino-terminal propeptide of type III procollagen and (3) tissue inhibitor of metalloproteinase 1], for liver cirrhosis to determine its impact on diagnostic timing and the management of cirrhosis and the process of care and improving outcomes.ResultsThe methodology workstream evaluated the quality of recommendations for using prostate-specific antigen to monitor patients, systematically reviewed RCTs of monitoring strategies and reviewed the monitoring biomarker literature and how monitoring can have an impact on outcomes. Simulation studies were conducted to evaluate monitoring and improve the merits of health care. The monitoring biomarker literature is modest and robust conclusions are infrequent. We recommend improvements in research practice. Patients strongly endorsed the need for robust and conclusive research in this area. The clinical translation workstream focused on analytical and clinical validity. Cohorts were established for renal cell carcinoma (RCC) and renal transplantation (RT), with samples and patient data from multiple centres, as a rapid-access resource to evaluate the validity of biomarkers. Candidate biomarkers for RCC and RT were identified from the literature and their quality was evaluated and selected biomarkers were prioritised. The duration of follow-up was a limitation but biomarkers were identified that may be taken forward for clinical utility. In the third workstream, the ELUCIDATE trial registered 1303 patients and randomised 878 patients out of a target of 1000. The trial started late and recruited slowly initially but ultimately recruited with good statistical power to answer the key questions. ELF monitoring altered the patient process of care and may show benefits from the early introduction of interventions with further follow-up. The ELUCIDATE trial was an ‘exemplar’ trial that has demonstrated the challenges of evaluating biomarker strategies in ‘end-to-end’ RCTs and will inform future study designs.ConclusionsThe limitations in the programme were principally that, during the collection and curation of the cohorts of patients with RCC and RT, the pace of discovery of new biomarkers in commercial and non-commercial research was slower than anticipated and so conclusive evaluations using the cohorts are few; however, access to the cohorts will be sustained for future new biomarkers. The ELUCIDATE trial was slow to start and recruit to, with a late surge of recruitment, and so final conclusions about the impact of the ELF test on long-term outcomes await further follow-up. The findings from the three workstreams were used to synthesise a strategy and framework for future biomarker evaluations incorporating innovations in study design, health economics and health informatics.Trial registrationCurrent Controlled Trials ISRCTN74815110, UKCRN ID 9954 and UKCRN ID 11930.FundingThis project was funded by the NIHR Programme Grants for Applied Research programme and will be published in full inProgramme Grants for Applied Research; Vol. 6, No. 3. See the NIHR Journals Library website for further project information.
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Affiliation(s)
- Peter J Selby
- Clinical and Biomedical Proteomics Group, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
- Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Rosamonde E Banks
- Clinical and Biomedical Proteomics Group, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Walter Gregory
- Leeds Institute of Clinical Trials Research, University of Leeds, Leeds, UK
| | - Jenny Hewison
- Leeds Institute of Health Sciences, University of Leeds, Leeds, UK
| | - William Rosenberg
- Institute for Liver and Digestive Health, Division of Medicine, University College London, London, UK
| | - Douglas G Altman
- Centre for Statistics in Medicine, University of Oxford, Oxford, UK
| | - Jonathan J Deeks
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Christopher McCabe
- Department of Emergency Medicine, University of Alberta Hospital, Edmonton, AB, Canada
| | - Julie Parkes
- Primary Care and Population Sciences Academic Unit, University of Southampton, Southampton, UK
| | | | | | - Maureen Twiddy
- Leeds Institute of Health Sciences, University of Leeds, Leeds, UK
| | - Janine Bestall
- Leeds Institute of Health Sciences, University of Leeds, Leeds, UK
| | | | - Tilly Hale
- LIVErNORTH Liver Patient Support, Newcastle upon Tyne, UK
| | - Jacqueline Dinnes
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Marc Jones
- Leeds Institute of Clinical Trials Research, University of Leeds, Leeds, UK
| | | | | | - Vicky Napp
- Leeds Institute of Clinical Trials Research, University of Leeds, Leeds, UK
| | - Alice Sitch
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Sudeep Tanwar
- Institute for Liver and Digestive Health, Division of Medicine, University College London, London, UK
| | - Naveen S Vasudev
- Clinical and Biomedical Proteomics Group, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
- Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Paul Baxter
- Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, UK
| | - Sue Bell
- Leeds Institute of Clinical Trials Research, University of Leeds, Leeds, UK
| | - David A Cairns
- Clinical and Biomedical Proteomics Group, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | | | - Neil Corrigan
- Leeds Institute of Clinical Trials Research, University of Leeds, Leeds, UK
| | - Francesco Del Galdo
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
| | - Peter Heudtlass
- Leeds Institute of Clinical Trials Research, University of Leeds, Leeds, UK
| | - Nick Hornigold
- Clinical and Biomedical Proteomics Group, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Claire Hulme
- Leeds Institute of Health Sciences, University of Leeds, Leeds, UK
| | - Michelle Hutchinson
- Clinical and Biomedical Proteomics Group, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Carys Lippiatt
- Department of Specialist Laboratory Medicine, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | | | - Roberta Longo
- Leeds Institute of Health Sciences, University of Leeds, Leeds, UK
| | - Matthew Potton
- Leeds Institute of Clinical Trials Research, University of Leeds, Leeds, UK
| | - Stephanie Roberts
- Clinical and Biomedical Proteomics Group, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Sheryl Sim
- Clinical and Biomedical Proteomics Group, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Sebastian Trainor
- Clinical and Biomedical Proteomics Group, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Matthew Welberry Smith
- Clinical and Biomedical Proteomics Group, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
- Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - James Neuberger
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | | | - Paul Richardson
- Royal Liverpool and Broadgreen University Hospitals NHS Trust, Liverpool, UK
| | - John Christie
- Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Neil Sheerin
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - William McKane
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Paul Gibbs
- Portsmouth Hospitals NHS Trust, Portsmouth, UK
| | | | - Naeem Soomro
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | | | - Grant D Stewart
- NHS Lothian, Edinburgh, UK
- Academic Urology Group, University of Cambridge, Cambridge, UK
| | - David Hrouda
- Charing Cross Hospital, Imperial College Healthcare NHS Trust, London, UK
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8
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Lucas JL, Tacheny EA, Ferris A, Galusha M, Srivastava AK, Ganguly A, Williams PM, Sachs MC, Thurin M, Tricoli JV, Ricker W, Gildersleeve JC. Development and validation of a Luminex assay for detection of a predictive biomarker for PROSTVAC-VF therapy. PLoS One 2017; 12:e0182739. [PMID: 28771597 PMCID: PMC5542629 DOI: 10.1371/journal.pone.0182739] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 07/24/2017] [Indexed: 11/19/2022] Open
Abstract
Cancer therapies can provide substantially improved survival in some patients while other seemingly similar patients receive little or no benefit. Strategies to identify patients likely to respond well to a given therapy could significantly improve health care outcomes by maximizing clinical benefits while reducing toxicities and adverse effects. Using a glycan microarray assay, we recently reported that pretreatment serum levels of IgM specific to blood group A trisaccharide (BG-Atri) correlate positively with overall survival of cancer patients on PROSTVAC-VF therapy. The results suggested anti-BG-Atri IgM measured prior to treatment could serve as a biomarker for identifying patients likely to benefit from PROSTVAC-VF. For continued development and clinical application of serum IgM specific to BG-Atri as a predictive biomarker, a clinical assay was needed. In this study, we developed and validated a Luminex-based clinical assay for measuring serum IgM specific to BG-Atri. IgM levels were measured with the Luminex assay and compared to levels measured using the microarray for 126 healthy individuals and 77 prostate cancer patients. This assay provided reproducible and consistent results with low %CVs, and tolerance ranges were established for the assay. IgM levels measured using the Luminex assay were found to be highly correlated to the microarray results with R values of 0.93–0.95. This assay is a Laboratory Developed Test (LDT) and is suitable for evaluating thousands of serum samples in CLIA certified laboratories that have validated the assay. In addition, the study demonstrates that discoveries made using neoglycoprotein-based microarrays can be readily migrated to a clinical assay.
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Affiliation(s)
- Julie L. Lucas
- MRIGlobal, Gaithersburg, Maryland, United States of America
| | | | - Allison Ferris
- MRIGlobal, Gaithersburg, Maryland, United States of America
| | | | - Apurva K. Srivastava
- Pharmacodynamics Biomarker Program, Applied/Developmental Research Directorate Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, United States of America
| | - Aniruddha Ganguly
- Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - P. Mickey Williams
- Molecular Characterization and Clinical Assay Development Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Michael C. Sachs
- Biostatistics Branch, Biometric Research Program, NCI, NIH, Bethesda, Maryland, United States of America
| | - Magdalena Thurin
- Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - James V. Tricoli
- Diagnostic Biomarkers and Technology Branch, Cancer Diagnosis Program Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, Maryland, United States of America
| | - Winnie Ricker
- Information Management Services, Inc., Rockville, Maryland, United States of America
| | - Jeffrey C. Gildersleeve
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, United States of America
- * E-mail:
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Amadi C, Gatenby P. Barrett’s oesophagus: Current controversies. World J Gastroenterol 2017; 23:5051-5067. [PMID: 28811703 PMCID: PMC5537175 DOI: 10.3748/wjg.v23.i28.5051] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 04/03/2017] [Accepted: 07/04/2017] [Indexed: 02/06/2023] Open
Abstract
Oesophageal adenocarcinoma is rapidly increasing in Western countries. This tumour frequently presents late in its course with metastatic disease and has a very poor prognosis. Barrett’s oesophagus is an acquired condition whereby the native squamous mucosa of the lower oesophagus is replaced by columnar epithelium following prolonged gastro-oesophageal reflux and is the recognised precursor lesion for oesophageal adenocarcinoma. There are multiple national and society guidelines regarding screening, surveillance and management of Barrett’s oesophagus, however all are limited regarding a clear evidence base for a well-demonstrated benefit and cost-effectiveness of surveillance, and robust risk stratification for patients to best use resources. Currently the accepted risk factors upon which surveillance intervals and interventions are based are Barrett’s segment length and histological interpretation of the systematic biopsies. Further patient risk factors including other demographic features, smoking, gender, obesity, ethnicity, patient age, biomarkers and endoscopic adjuncts remain under consideration and are discussed in full. Recent evidence has been published to support earlier endoscopic intervention by means of ablation of the metaplastic Barrett’s segment when the earliest signs of dysplasia are detected. Further work should concentrate on establishing better risk stratification and primary and secondary preventative strategies to reduce the risk of adenocarcinoma of the oesophagus.
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10
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Considerations of developing an NGS assay for clinical applications in precision oncology: The NCI-MATCH NGS assay experience. Curr Probl Cancer 2017. [DOI: 10.1016/j.currproblcancer.2017.05.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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11
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Hernández P, Gorrochategui J, Primo D, Robles A, Rojas JL, Espinosa AB, Gómez C, Martínez-López J, Bennett TA, Ballesteros J. Drug Discovery Testing Compounds in Patient Samples by Automated Flow Cytometry. SLAS Technol 2017; 22:325-337. [PMID: 28340541 PMCID: PMC5464399 DOI: 10.1177/2472630317700346] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Functional ex vivo assays that predict a patient’s clinical response to anticancer drugs for guiding cancer treatment have long been a goal, but few have yet proved to be reliable. To address this, we have developed an automated flow cytometry platform for drug screening that evaluates multiple endpoints with a robust data analysis system that can capture the complex mechanisms of action across different compounds. This system, called PharmaFlow, is used to test peripheral blood or bone marrow samples from patients diagnosed with hematological malignancies. Functional assays that use the whole sample, retaining all the microenvironmental components contained in the sample, offer an approach to ex vivo testing that may give results that are clinically relevant. This new approach can help to predict the patients’ response to existing treatments or to drugs under development, for hematological malignancies or other tumors. In addition, relevant biomarkers can be identified that determine the patient’s sensitivity, resistance, or toxicity to a given treatment. We propose that this approach, which better recapitulates the human microenvironment, constitutes a more predictive assay for personalized medicine and preclinical drug discovery.
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Affiliation(s)
| | | | | | | | | | | | | | - Joaquín Martínez-López
- 1 Vivia Biotech, Tres Cantos, Madrid, Spain.,2 Hematology Service, Hospital 12 de Octubre, Madrid, Spain
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12
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Jensen K, Krusenstjerna-Hafstrøm R, Lohse J, Petersen KH, Derand H. A novel quantitative immunohistochemistry method for precise protein measurements directly in formalin-fixed, paraffin-embedded specimens: analytical performance measuring HER2. Mod Pathol 2017; 30:180-193. [PMID: 27767098 DOI: 10.1038/modpathol.2016.176] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 08/18/2016] [Accepted: 08/23/2016] [Indexed: 12/16/2022]
Abstract
In clinical routine pathology today, detection of protein in intact formalin-fixed, paraffin-embedded tissue is limited to immunohistochemistry, which is semi-quantitative. This study presents a new and reliable quantitative immunohistochemistry method, qIHC, based on a novel amplification system that enables quantification of protein directly in formalin-fixed, paraffin-embedded tissue by counting of dots. The qIHC technology can be combined with standard immunohistochemistry, and assessed using standard bright-field microscopy or image analysis. The objective was to study analytical performance of the qIHC method. qIHC was tested under requirements for an analytical quantitative test, and compared with ELISA and flow cytometry for quantitative protein measurements. Human epidermal growth factor receptor 2 (HER2) protein expression was measured in five different cell lines with HER2 expression from undetectable with immunohistochemistry to strong positive staining (IHC 3+). Repeatability, reproducibility, robustness, linearity, dynamic range, sensitivity, and quantification limits were evaluated. Reproducibility and robustness were assessed in a setup to resemble daily work in a laboratory using a commercial immunohistochemistry platform. In addition, qIHC was correlated to standard HER2 immunohistochemistry in 44 breast cancer specimens. For all evaluated parameters, qIHC performance was either comparable or better than the reference methods. Furthermore, qIHC has a lower limit of detection than both immunohistochemistry and the ELISA reference method, and demonstrated ability to measure HER2 accurately and precise within a large dynamic range. In conclusion, the results show that qIHC provides a sensitive, quantitative, accurate, and robust assay for measurement of protein expression in formalin-fixed, paraffin-embedded cell lines, and tissue.
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Affiliation(s)
- Kristian Jensen
- Dako Denmark A/S, an Agilent Technologies Company, Produktionsvej 42, Glostrup, Denmark
| | | | - Jesper Lohse
- Dako Denmark A/S, an Agilent Technologies Company, Produktionsvej 42, Glostrup, Denmark
| | - Kenneth H Petersen
- Dako Denmark A/S, an Agilent Technologies Company, Produktionsvej 42, Glostrup, Denmark
| | - Helene Derand
- Dako Denmark A/S, an Agilent Technologies Company, Produktionsvej 42, Glostrup, Denmark
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13
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Puchades-Carrasco L, Pineda-Lucena A. Metabolomics in pharmaceutical research and development. Curr Opin Biotechnol 2015; 35:73-7. [DOI: 10.1016/j.copbio.2015.04.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 04/06/2015] [Accepted: 04/07/2015] [Indexed: 12/26/2022]
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14
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Duffy MJ, Sturgeon CM, Sölétormos G, Barak V, Molina R, Hayes DF, Diamandis EP, Bossuyt PMM. Validation of new cancer biomarkers: a position statement from the European group on tumor markers. Clin Chem 2015; 61:809-20. [PMID: 25882892 DOI: 10.1373/clinchem.2015.239863] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 04/02/2015] [Indexed: 11/06/2022]
Abstract
BACKGROUND Biomarkers are playing increasingly important roles in the detection and management of patients with cancer. Despite an enormous number of publications on cancer biomarkers, few of these biomarkers are in widespread clinical use. CONTENT In this review, we discuss the key steps in advancing a newly discovered cancer candidate biomarker from pilot studies to clinical application. Four main steps are necessary for a biomarker to reach the clinic: analytical validation of the biomarker assay, clinical validation of the biomarker test, demonstration of clinical value from performance of the biomarker test, and regulatory approval. In addition to these 4 steps, all biomarker studies should be reported in a detailed and transparent manner, using previously published checklists and guidelines. Finally, all biomarker studies relating to demonstration of clinical value should be registered before initiation of the study. SUMMARY Application of the methodology outlined above should result in a more efficient and effective approach to the development of cancer biomarkers as well as the reporting of cancer biomarker studies. With rigorous application, all stakeholders, and especially patients, would be expected to benefit.
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Affiliation(s)
- Michael J Duffy
- Clinical Research Centre, St Vincent's University Hospital and UCD School of Medicine and Medical Science, Conway Institute of Bimolecular and Biomedical Research, University College Dublin, Dublin, Ireland;
| | - Catharine M Sturgeon
- Department of Clinical Biochemistry, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - György Sölétormos
- Department of Clinical Biochemistry, University of Copenhagen North Zealand Hospital, Hillerød, Denmark
| | - Vivian Barak
- Oncology Department, Hadassah University Hospital, Jerusalem, Israel
| | - Rafael Molina
- Hospital Clinic, University of Barcelona, Barcelona, Spain
| | - Daniel F Hayes
- University of Michigan Comprehensive Cancer Center, Ann Arbor, MI
| | - Eleftherios P Diamandis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Patrick M M Bossuyt
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
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Abstract
Although there is ample literature reporting on the identification of molecular biomarkers for head and neck squamous cell carcinoma, none is currently recommended for routine clinical use. A major reason for this lack of progress is the difficulty in designing studies in head and neck cancer to clearly establish the clinical utility of biomarkers. Consequently, biomarker studies frequently stall at the initial discovery phase. In this article, we focus on biomarkers for use in clinical management, including selection of therapy. Using several contemporary examples, we identify some of the common deficiencies in study design that hinder success in biomarker development for this disease area, and we suggest some potential solutions. The purpose of this article is to provide guidance that can assist investigators to more efficiently move promising biomarkers in head and neck cancer from discovery to clinical practice
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Parkinson DR, McCormack RT, Keating SM, Gutman SI, Hamilton SR, Mansfield EA, Piper MA, Deverka P, Frueh FW, Jessup JM, McShane LM, Tunis SR, Sigman CC, Kelloff GJ. Evidence of clinical utility: an unmet need in molecular diagnostics for patients with cancer. Clin Cancer Res 2014; 20:1428-44. [PMID: 24634466 DOI: 10.1158/1078-0432.ccr-13-2961] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This article defines and describes best practices for the academic and business community to generate evidence of clinical utility for cancer molecular diagnostic assays. Beyond analytical and clinical validation, successful demonstration of clinical utility involves developing sufficient evidence to demonstrate that a diagnostic test results in an improvement in patient outcomes. This discussion is complementary to theoretical frameworks described in previously published guidance and literature reports by the U.S. Food and Drug Administration, Centers for Disease Control and Prevention, Institute of Medicine, and Center for Medical Technology Policy, among others. These reports are comprehensive and specifically clarify appropriate clinical use, adoption, and payer reimbursement for assay manufacturers, as well as Clinical Laboratory Improvement Amendments-certified laboratories, including those that develop assays (laboratory developed tests). Practical criteria and steps for establishing clinical utility are crucial to subsequent decisions for reimbursement without which high-performing molecular diagnostics will have limited availability to patients with cancer and fail to translate scientific advances into high-quality and cost-effective cancer care. See all articles in this CCR Focus section, "The Precision Medicine Conundrum: Approaches to Companion Diagnostic Co-development."
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Affiliation(s)
- David R Parkinson
- Authors' Affiliations: New Enterprise Associates, Inc., Menlo Park; CCS Associates, Mountain View; Myraqa, Redwood Shores, California; Johnson & Johnson/Veridex, LLC, Raritan, New Jersey; University of Texas, MD Anderson Cancer Center, Houston, Texas; Center for Diagnostics and Radiologic Health, Office of In Vitro Diagnostics, Personalized Medicine Program, Silver Spring; Center for Medical Technology Policy, Baltimore; Opus Three LLC; National Cancer Institute, Division of Cancer Treatment and Diagnosis, Rockville, Maryland; and Kaiser Permanente Research Affiliates Evidence-Based Practice Center, Kaiser Permanente Center for Health Research, Portland, Oregon
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A risk-management approach for effective integration of biomarkers in clinical trials: perspectives of an NCI, NCRI, and EORTC working group. Lancet Oncol 2014; 15:e184-93. [DOI: 10.1016/s1470-2045(13)70607-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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18
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Wilt TJ, Scardino PT, Carlsson SV, Basch E. Prostate-specific antigen screening in prostate cancer: perspectives on the evidence. J Natl Cancer Inst 2014; 106:dju010. [PMID: 24594482 DOI: 10.1093/jnci/dju010] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Timothy J Wilt
- Affiliations of authors: Minneapolis VA Center for Chronic Disease Outcomes Research and the University of Minnesota School of Medicine, Minneapolis, MN (TJW); Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, NY (PTS, SVC); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (EB)
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True LD. Methodological requirements for valid tissue-based biomarker studies that can be used in clinical practice. Virchows Arch 2014; 464:257-63. [PMID: 24487786 PMCID: PMC4009398 DOI: 10.1007/s00428-013-1531-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 12/13/2013] [Indexed: 12/25/2022]
Abstract
Paralleling the growth of ever more cost efficient methods to sequence the whole genome in minute fragments of tissue has been the identification of increasingly numerous molecular abnormalities in cancers--mutations, amplifications, insertions and deletions of genes, and patterns of differential gene expression, i.e., overexpression of growth factors and underexpression of tumor suppressor genes. These abnormalities can be translated into assays to be used in clinical decision making. In general terms, the result of such an assay is subject to a large number of variables regarding the characteristics of the available sample, particularities of the used assay, and the interpretation of the results. This review discusses the effects of these variables on assays of tissue-based biomarkers, classified by macromolecule--DNA, RNA (including micro RNA, messenger RNA, long noncoding RNA, protein, and phosphoprotein). Since the majority of clinically applicable biomarkers are immunohistochemically detectable proteins this review focuses on protein biomarkers. However, the principles outlined are mostly applicable to any other analyte. A variety of preanalytical variables impacts on the results obtained, including analyte stability (which is different for different analytes, i.e., DNA, RNA, or protein), period of warm and of cold ischemia, fixation time, tissue processing, sample storage time, and storage conditions. In addition, assay variables play an important role, including reagent specificity (notably but not uniquely an issue concerning antibodies used in immunohistochemistry), technical components of the assay, quantitation, and assay interpretation. Finally, appropriateness of an assay for clinical application is an important issue. Reference is made to publicly available guidelines to improve on biomarker development in general and requirements for clinical use in particular. Strategic goals are formulated in order to improve on the quality of biomarker reporting, including issues of analyte quality, experimental detail, assay efficiency and precision, and assay appropriateness.
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Affiliation(s)
- Lawrence D True
- Department of Pathology, University of Washington Medical Center, 1959 NE Pacific St., Box 356100, Seattle, WA, USA,
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Abstract
The use of biomarkers to identify patients who can benefit from treatment with a specific anticancer agent has the potential to both improve patient care and accelerate drug development. The development of targeted agents and their accompanying biomarkers frequently occurs contemporaneously, and confidence in a putative biomarker's performance might, therefore, be insufficient to restrict the definitive testing of a new agent to the subgroup of biomarker-positive patients. This Review considers which clinical trial designs and analysis strategies are appropriate for use in phase III, biomarker-driven, randomized clinical trials, on the basis of pre-existing evidence that the biomarker can successfully identify patients who will respond to the treatment in question. The types of interim monitoring that are appropriate for these trials are also discussed. In addition, enrichment strategies based on the use of prognostic biomarkers to separate a population into subgroups with better and worse outcomes, regardless of treatment, are described. Finally, the possibility of formally using a biomarker during phase II drug development, to select what type of biomarker-driven strategy should be used in the phase III trial, is discussed.
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Timmer MR, Sun G, Gorospe EC, Leggett CL, Lutzke L, Krishnadath KK, Wang KK. Predictive biomarkers for Barrett's esophagus: so near and yet so far. Dis Esophagus 2013; 26:574-81. [PMID: 23316980 PMCID: PMC4466900 DOI: 10.1111/dote.12015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Barrett's esophagus (BE) is the strongest risk factor for the development of esophageal adenocarcinoma. However, the risk of cancer progression is difficult to ascertain in individuals, as a significant number of patients with BE do not necessarily progress to esophageal adenocarcinoma. There are several issues with the current strategy of using dysplasia as a marker of disease progression. It is subject to sampling error during biopsy acquisition and interobserver variability among gastrointestinal pathologists. Ideal biomarkers with high sensitivity and specificity are needed to accurately detect high-risk BE patients for early intervention and appropriate cost-effective surveillance. To date, there are no available molecular tests in routine clinical practice despite known genetic and epigenetic aberrations in the Barrett's epithelium. In this review, we present potential biomarkers for the prediction of malignant progression in BE. These include markers of genomic instability, tumor suppressor loci abnormalities, epigenetic changes, proliferation markers, cell cycle predictors, and immunohistochemical markers. Further work in translating biomarkers for routine clinical use may eventually lead to accurate risk stratification.
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Affiliation(s)
- M. R. Timmer
- Barrett’s Esophagus Unit, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA,Department of Gastroenterology and Hepatology, Academic Medical Center, Amsterdam, The Netherlands
| | - G. Sun
- Barrett’s Esophagus Unit, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA,Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, Beijing, China
| | - E. C. Gorospe
- Barrett’s Esophagus Unit, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - C. L. Leggett
- Barrett’s Esophagus Unit, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - L. Lutzke
- Barrett’s Esophagus Unit, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - K. K. Krishnadath
- Department of Gastroenterology and Hepatology, Academic Medical Center, Amsterdam, The Netherlands
| | - K. K. Wang
- Barrett’s Esophagus Unit, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
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22
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Staedtler F, Hartmann N, Letzkus M, Bongiovanni S, Scherer A, Marc P, Johnson KJ, Schumacher MM. Robust and tissue-independent gender-specific transcript biomarkers. Biomarkers 2013; 18:436-45. [PMID: 23829492 DOI: 10.3109/1354750x.2013.811538] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
CONTEXT Correct gender assignment in humans at the molecular level is crucial in many scientific disciplines and applied areas. MATERIALS AND METHODS Candidate gender markers were identified through supervised statistical analysis of genome wide microarray expression data from human blood samples (N = 123, 58 female, 65 male) as a training set. The potential of the markers to predict undisclosed tissue donor gender was tested on microarray data from 13 healthy and 11 cancerous human tissue collections (internal) and external datasets from samples of varying tissue origin. The abundance of some genes in the marker panel was quantified by RT-PCR as alternative analytical technology. RESULTS We identified and qualified predictive, gender-specific transcript markers based on a set of five genes (RPS4Y1, EIF1AY, DDX3Y, KDM5D and XIST). CONCLUSION Gene expression marker panels can be used as a robust tissue- and platform-independent predictive approach for gender determination.
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Affiliation(s)
- Frank Staedtler
- Novartis Institutes for BioMedical Research (NIBR), Biomarker Development, Basel, Switzerland.
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23
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Actionable gene expression-based patient stratification for molecular targeted therapy in hepatocellular carcinoma. PLoS One 2013; 8:e64260. [PMID: 23785399 PMCID: PMC3681850 DOI: 10.1371/journal.pone.0064260] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 04/09/2013] [Indexed: 12/15/2022] Open
Abstract
Background The effectiveness of molecular targeted agents is modest in hepatocellular carcinoma (HCC). Efficacy of molecular targeted therapies has been better in cancer patients with high expression of actionable molecules defined as cognate target molecules. However, patient stratification based on the actionable molecules dictating the effectiveness of targeted drugs has remained understudied in HCC. Experimental Design & Results Paired tumor and non-tumoral tissues derived from a total of 130 HCC patients were studied. Real-time RT-PCR was used to analyze the mRNA expression of actionable molecules in the tissues. mRNA levels of EGFR, VEGFR2, PDGFRβ, FGFR1, and mTOR were up-regulated in tumors compared to non-tumors in 35.4, 42.3, 61.5, 24.6, and 50.0% of patients, respectively. Up-regulation of EGFR was observed at early stage and tended to gradually decrease toward late stages (BCLC stage A: 41.9%; B: 30.8%; C: 17.6%). Frequency of VEGFR2 expression in tumors at stage C was lower than that in the other stages (BCLC stage A: 45.9%; B: 41.0%; C: 29.4%). PDGFRβ and mTOR were observed to be up-regulated in more than 50% of tumors in all the stages whereas FGFR1 was up-regulated in only about 20% of HCC irrespective of stages. A cluster analysis of actionable gene expression revealed that HCC can be categorized into different subtypes that predict the effectiveness of molecular targeted agents and combination therapies in clinical trials. Analysis of in vitro sensitivity to sorafenib demonstrated that HCC cells with up-regulation of PDGFRβ and c-Raf mRNA are more susceptible to sorafenib treatment in a dose and time-dependent manner than cells with low expression of the genes. Conclusions mRNA expression analysis of actionable molecules could provide the rationale for new companion diagnostics-based therapeutic strategies in the treatment of HCC.
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24
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Duffy MJ, Crown J. Companion biomarkers: paving the pathway to personalized treatment for cancer. Clin Chem 2013; 59:1447-56. [PMID: 23656699 DOI: 10.1373/clinchem.2012.200477] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Companion biomarkers are biomarkers that are used in combination with specific therapies and that prospectively help predict likely response or severe toxicity. In this article we review the role of companion biomarkers in guiding treatment in patients with cancer. CONTENT In addition to the established companion biomarkers such as estrogen receptors and HER2 (human epidermal growth factor receptor 2) in breast cancer, several new companion biomarkers have become available in recent years. These include v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (KRAS) mutations for the selection of patients with advanced colorectal cancer who are unlikely to benefit from anti-epidermal growth factor receptor antibodies (cetuximab or panitumumab), epidermal growth factor receptor (EGFR) mutations for selecting patients with advanced non-small cell lung cancer (NSCLC) for treatment with tyrosine kinase inhibitors (gefitinib or erlotinib), v-raf murine sarcoma viral oncogene homolog B1 (BRAF) mutations for selecting patients with advanced melanoma for treatment with anti-BRAF agents (vemurafenib and dabrafenib), and anaplastic lymphoma receptor tyrosine kinase (ALK) translocations for identifying patients with NSCLC likely to benefit from crizotinib. SUMMARY The availability of companion biomarkers should improve drug efficacy, decrease toxicity, and lead to a more individualized approach to cancer treatment.
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Affiliation(s)
- Michael J Duffy
- UCD School of Medicine and Medical Science, Conway Institute, University College Dublin, Ireland
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25
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Thomas A, Rajan A, Lopez-Chavez A, Wang Y, Giaccone G. From targets to targeted therapies and molecular profiling in non-small cell lung carcinoma. Ann Oncol 2013; 24:577-85. [PMID: 23131389 PMCID: PMC3574546 DOI: 10.1093/annonc/mds478] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Revised: 08/13/2012] [Accepted: 08/14/2012] [Indexed: 12/22/2022] Open
Abstract
Although tumor molecular-profile-directed therapy appears promising in early clinical studies, there are many practical challenges to its successful clinical application in non-small-cell lung cancer (NSCLC). These challenges may be broadly classified as those relating to tumor (heterogeneity), tissue (acquisition and processing), testing (assays for molecular profiling) and trials (clinical evaluation of molecular markers and drugs). Strategies to overcome these challenges include (i) understanding the biological basis of tumor heterogeneity and of carcinogenesis in the large subset of patients with no currently evident driver events; (ii) technological advances in minimally invasive acquisition of tumor and next-generation sequencing (NGS) which would enable single-platform analysis of molecular alterations in limited tissue at a reasonable turnaround time (TAT); (iii) deliberation in early stages of drug development as well as clinical trial design to identify, validate and assess the clinical utility of biomarkers in conjunction with drugs and (iv) collaboration to improve understanding of and accrual to trials enrolling patients with rare molecular alterations.
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Affiliation(s)
- A. Thomas
- Medical Oncology Branch, National Cancer Institute, Bethesda
| | - A. Rajan
- Medical Oncology Branch, National Cancer Institute, Bethesda
| | - A. Lopez-Chavez
- Division of Hematology/Medical Oncology, Oregon Health and Science University, Portland, USA
| | - Y. Wang
- Medical Oncology Branch, National Cancer Institute, Bethesda
| | - G. Giaccone
- Medical Oncology Branch, National Cancer Institute, Bethesda
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26
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Poste G. Biospecimens, biomarkers, and burgeoning data: the imperative for more rigorous research standards. Trends Mol Med 2012; 18:717-22. [PMID: 23122852 DOI: 10.1016/j.molmed.2012.09.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Revised: 08/04/2012] [Accepted: 09/11/2012] [Indexed: 12/26/2022]
Abstract
Knowledge of the altered molecular landscapes in disease offers great promise for developing biomarker-based tests to improve diagnosis and optimize treatment. Progress in biomarker research has been frustratingly slow due to the poor clinical trial design and the lack of standards for specimen collection, biomarker analysis, and data reporting. The ability of high throughput genomics, proteomics, and other 'omics' platforms to profile a large number of analytes in a single assay, together with the pending prospect of rapid expansion of whole exome and whole genome sequencing for clinical use, is increasing the technical and logistical complexity of biomarker validation. Harnessing these new technologies and improved productivity in biomarker validation will depend on adopting systems-based approaches and require major changes in the organization and funding strategies for biomarker research. A systems approach will require new multi-institution collaborations, the integration of diverse technical and clinical activities, greater engagement of industry, and education of regulators, clinicians, and payers about how to use biomarkers for improved patient management and clinical outcomes.
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Affiliation(s)
- George Poste
- Complex Adaptive Systems Initiative, Arizona State University, 1475 N. Scottsdale Rd, Suite 361, Scottsdale, AZ 85257, USA.
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27
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Poste G, Carbone DP, Parkinson DR, Verweij J, Hewitt S, Jessup JM. Leveling the playing field: bringing development of biomarkers and molecular diagnostics up to the standards for drug development. Clin Cancer Res 2012; 18:1515-23. [PMID: 22422403 PMCID: PMC3307147 DOI: 10.1158/1078-0432.ccr-11-2206] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Molecular diagnostics are becoming increasingly important in clinical research to stratify or identify molecularly profiled patient cohorts for targeted therapies, to modify the dose of a therapeutic, and to assess early response to therapy or monitor patients. Molecular diagnostics can also be used to identify the pharmacogenetic risk of adverse drug reactions. The articles in this CCR Focus section on molecular diagnosis describe the development and use of markers to guide medical decisions regarding cancer patients. They define sources of preanalytic variability that need to be minimized, as well as the regulatory and financial challenges involved in developing diagnostics and integrating them into clinical practice. They also outline a National Cancer Institute program to assist diagnostic development. Molecular diagnostic clinical tests require rigor in their development and clinical validation, with sensitivity, specificity, and validity comparable to those required for the development of therapeutics. These diagnostics must be offered at a realistic cost that reflects both their clinical value and the costs associated with their development. When genome-sequencing technologies move into the clinic, they must be integrated with and traceable to current technology because they may identify more efficient and accurate approaches to drug development. In addition, regulators may define progressive drug approval for companion diagnostics that requires further evidence regarding efficacy and safety before full approval can be achieved. One way to accomplish this is to emphasize phase IV postmarketing, hypothesis-driven clinical trials with biological characterization that would permit an accurate definition of the association of low-prevalence gene alterations with toxicity or response in large cohorts.
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Affiliation(s)
- George Poste
- Chief Scientist, Complex Adaptive Systems Initiative, Arizona State University, 1475 North Scottsdale Road, Suite 361 Scottsdale, Arizona 85257
| | - David P. Carbone
- Professor of Medicine and Cancer Biology, Director, Thoracic/Head and Neck Program and Thoracic Oncology Center, Vanderbilt-Ingram Cancer Center, 691 Preston Building, Nashville, TN 37232-6838
| | - David R. Parkinson
- Chief Executive Officer, Nodality, Inc., 201 Gateway Boulevard, South San Francisco, CA 94080
| | - Jaap Verweij
- Chairman, Dept. of Medical Oncology and Daniel den Hoed Cancer Center, Erasmus University Medical Center, PO Box 2040, 3000 CA ROTTERDAM, Netherlands
| | - Stephen Hewitt
- Director, Tissue Array Research Program (TARP), Laboratory of Pathology, Advanced Technology Center, National Cancer Institute, Gaithersburg, MD
| | - J. Milburn Jessup
- Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD
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28
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Schilsky RL, Doroshow JH, LeBlanc M, Conley BA. Development and use of integral assays in clinical trials. Clin Cancer Res 2012; 18:1540-6. [PMID: 22422406 PMCID: PMC3307146 DOI: 10.1158/1078-0432.ccr-11-2202] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Clinical trials that include integral biomarkers to determine eligibility, assign treatment, or assess outcome must employ robust assays to measure the molecular analyte of interest. The decision to develop a biomarker assay into a test suitable for use in humans should be driven by clinical need, that is, there should be a clear clinical purpose for undertaking the test development. Supporting in vitro or in vivo research on the ability of the marker to distinguish subgroups of patients with a given characteristic is necessary. The magnitude of the difference in treatment effect expected with use of the marker should be sufficient to support differential treatment prescription for marker-positive and -negative patients. Analytical and clinical validation of the marker assay should be completed before the clinical trial is initiated to ensure that the assay is stable enough for clinical use throughout the trial. Clinical use of the assay requires that it be performed in a Clinical Laboratory Improvement Amendments-accredited laboratory, and the need to apply for an Investigational Device Exemption from the U.S. Food and Drug Administration should be considered. In this article we elaborate on the steps required to get a biomarker assay ready for use as an integral component of a clinical trial and give an example of the use of an integral assay in a phase III trial.
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Affiliation(s)
- Richard L. Schilsky
- Chief, Section of Hematology-Oncology and Deputy Director, Comprehensive Cancer Center, Biological Sciences Division, 5841 S. Maryland Ave, MC 2115, University of Chicago, Chicago, IL 60637, USA. Phone: (773) 834-3914
| | - James H. Doroshow
- Director, Division of Cancer Treatment and Diagnosis, and Deputy Director, National Cancer Institute; Department of Health and Human Services, Building 31, 3A44, Bethesda, MD 20892; Phone 301-496-4291;
| | - Michael LeBlanc
- Fred Hutchinson Cancer Research Center 1100 Fairview Ave N, M3-C102, Seattle, WA 98109; Phone 206-667-6089;
| | - Barbara A. Conley
- Division of Cancer Treatment and Diagnosis, National Cancer Institute; Department of Health and Human Services, 6035A Executive Plaza North, Rockville, MD 20892; Phone: 301-496-8639;
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29
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Meshinchi S, Hunger SP, Aplenc R, Adamson PC, Jessup JM. Lessons learned from the investigational device exemption review of Children's Oncology Group trial AAML1031. Clin Cancer Res 2012; 18:1547-54. [PMID: 22422407 PMCID: PMC3310885 DOI: 10.1158/1078-0432.ccr-11-2205] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The U.S. Food and Drug Administration is now exerting its regulatory authority over the use of molecular diagnostics and related assays for medical decision making in clinical trials, by performing pre-Investigational Device Exemption reviews in all phases of clinical trials. In this review, we assess the analytical performance of the assay for the diagnostic, and consider how that performance affects the diagnostic and the patient and their risks and benefits from treatment. We also discuss the process involved in the first review of a new Children's Oncology Group phase III trial in acute myelogenous leukemia. The lessons learned and recommendations for how to prepare for and incorporate this new level of regulatory review into the protocol development process are presented.
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Affiliation(s)
- Soheil Meshinchi
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Stephen P. Hunger
- Center for Cancer and Blood Disorders, Children's Hospital Colorado and the Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado; phone 720-777-8855;
| | - Richard Aplenc
- The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania
| | - Peter C. Adamson
- The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; The Children's Oncology Group, Arcadia, CA
| | - J. Milburn Jessup
- Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD
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30
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Andre F, Nowak F, Arnedos M, Lacroix L, Viens P, Calvo F. Biomarker Discovery, Development, and Implementation in France: A Report from the French National Cancer Institute and Cooperative Groups. Clin Cancer Res 2012; 18:1555-60. [DOI: 10.1158/1078-0432.ccr-11-2201] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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