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Grillo F, Ali M, Paudice M, Pigozzi S, Anselmi G, Scabini S, Sciallero S, Piol N, Mastracci L. Impact of formalin fixation on mismatch repair protein evaluation by immunohistochemistry. Virchows Arch 2023; 483:677-685. [PMID: 37773452 PMCID: PMC10673985 DOI: 10.1007/s00428-023-03661-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/29/2023] [Accepted: 09/15/2023] [Indexed: 10/01/2023]
Abstract
Mismatch repair/microsatellite instability (MMR/MSI) status in colorectal cancer (CRC) has become fundamental as a diagnostic, prognostic, and predictive factor. MMR immunohistochemistry (IHC) is considered a simple and reliable approach; however, its effectiveness depends on pre-analytic factors. Aim of this study was to investigate the impact of different fixation times/protocols on MMR protein IHC quality. Left over tissue from surgically resected CRC samples (cold ischemia time < 30 min) where fixed as follows: standard formalin fixation (24-48 h); hypo-fixation (<20 h); hyper-fixation (>90 h); cold (4°C) fixation (24-48 h); standard fixation for small sample size (0.5×0.5 cm). Samples for each group were collected from 30 resected CRC and the following parameters were evaluated on 600 immunohistochemical stains: intensity of expression; patchiness of staining; presence of central artefact. Forty-six immunoreactions were inadequate (score 0 intensity), the majority regarding MLH1 or PMS2 in the hypo-fixation group (47.8%), followed by the hyper-fixation group (28.1%); cold formalin fixation showed the least inadequate cases. Patchiness and central artefact were more frequent in hypo-fixation and standard fixation group compared to the others. MLH1 (closely followed by PMS2) performed worse with regard to immunostaining intensity (p=0.0002) in the standard and in the hypo-fixation group (p< 0.00001). Using a small sample size improved patchiness/central artefacts. This is the first study specifically created to evaluate the impact of fixation on MMR protein IHC, showing that both formalin hypo- and hyper-fixation can cause problems; 24-h formalin fixation as well as cold (4°C) formalin fixation are recommended for successful IHC MMR evaluation.
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Affiliation(s)
- Federica Grillo
- Pathology Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy.
- Pathology Unit, Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa and IRCCS Ospedale Policlinico San Martino, Genoa, Italy.
| | - Murad Ali
- Pathology Unit, Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa and IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Michele Paudice
- Pathology Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
- Pathology Unit, Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa and IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Simona Pigozzi
- Pathology Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
- Pathology Unit, Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa and IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Giorgia Anselmi
- Molecular Diagnostic Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Stefano Scabini
- Oncological Surgical Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Stefania Sciallero
- Medical Oncology Unit 1, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - Nataniele Piol
- Pathology Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Luca Mastracci
- Pathology Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
- Pathology Unit, Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa and IRCCS Ospedale Policlinico San Martino, Genoa, Italy
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Shaker N, Sardana R, Hamasaki S, Nohle DG, Ayers LW, Parwani AV. Accuracy of whole slide image based image analysis is adversely affected by preanalytical factors such as stained tissue slide and paraffin block age. J Pathol Inform 2022; 13:100121. [PMID: 36268058 PMCID: PMC9577058 DOI: 10.1016/j.jpi.2022.100121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/04/2022] [Accepted: 06/24/2022] [Indexed: 11/19/2022] Open
Abstract
Background Personalized medicine and accurate quantification of tumor and biomarker expression have become the cornerstone of cancer diagnostics. This requires Quality Control (QC) of research tissue samples to confirm adequate targeted tumor tissue sampling. Digitalization of stained tissue slides offer a precious way to archive, preserve, and retrieve necessary information when needed. This study is aimed to assess the most significant pre-analytic and analytic factors that might contribute to the efficacy of obtaining accurate whole slide images (WSIs) interpretation. Various studies are needed to identifysuch factors to allow for appropriate AI application and adequate tumor area/percentage quantification. Methods Hematoxylene and Eosine (H&E) satined WSIs collected from tissue specimens provided by the Cooperative Human Tissue Network (CHTN) Midwestern Division (CHTNMWD) were analyzed. Tissue specimens were processed, fixed, stained, and scanned contemporaneously (within 1 month). Two cohorts of malignant, colorectal cancer, 20X WSI (ScanscopeXT, Leica Biosystems, Illinois), were assembled. The study identified a "recent cohort" that included 76 WSIs created on 2018 or later. "Aged cohort" included 73 WSIs from specimens procured in the period of (2012-2014). Twenty recent WSIs of adenocarcinoma cases were used to construct WSIs analysis algorithms (VIS, Visiopharm A/S, Denmark) using machine learning to produce morphometric maps and calculate tissue and tumor areas. Results Algorithmic analysis of 69 WSIs from rescanned aged slides vs. that of contemporaneous WSIs concluded 18 (28%) similar finding in tumor areas (within 10%), 56 (82%) had identicaltissue areas, and 54 (79%) had similar tumor percentages. Conclusion WSIs of aged H&E slides and stained paraffin block re-cuts produce different tumor quantification compared to those of original scanned sslides most likely due to pre-analytical factors. The difference in tumor area detected between original and rescanned WSIs trended upward in the period between 2012 and 2014. Less tumor area was detected as the slides age. Recut and H&E-stained tissues from stored paraffin blocks may detect more tumor due to excess eosinophilia. These results highlights the value of documenting archives of H&E WSIs collected at the procurement time. Such images provide a superior archive over glass slides and Formalin-Fixed Paraffin-Embedded (FFPE) blocks and contribute betterg to WSIs analysis application.
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Affiliation(s)
- Nada Shaker
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
- Corresponding author.
| | - Ruhani Sardana
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Satoshi Hamasaki
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - David G. Nohle
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
- Cooperative Human Tissue Network (CHTN) Midwestern Division (MWD) State University (OSU), Columbus, OH, USA
| | - Leona W. Ayers
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
- Cooperative Human Tissue Network (CHTN) Midwestern Division (MWD) State University (OSU), Columbus, OH, USA
| | - Anil V. Parwani
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
- Cooperative Human Tissue Network (CHTN) Midwestern Division (MWD) State University (OSU), Columbus, OH, USA
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Yousif M, van Diest PJ, Laurinavicius A, Rimm D, van der Laak J, Madabhushi A, Schnitt S, Pantanowitz L. Artificial intelligence applied to breast pathology. Virchows Arch 2021; 480:191-209. [PMID: 34791536 DOI: 10.1007/s00428-021-03213-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 09/12/2021] [Accepted: 09/27/2021] [Indexed: 12/12/2022]
Abstract
The convergence of digital pathology and computer vision is increasingly enabling computers to perform tasks performed by humans. As a result, artificial intelligence (AI) is having an astoundingly positive effect on the field of pathology, including breast pathology. Research using machine learning and the development of algorithms that learn patterns from labeled digital data based on "deep learning" neural networks and feature-engineered approaches to analyze histology images have recently provided promising results. Thus far, image analysis and more complex AI-based tools have demonstrated excellent success performing tasks such as the quantification of breast biomarkers and Ki67, mitosis detection, lymph node metastasis recognition, tissue segmentation for diagnosing breast carcinoma, prognostication, computational assessment of tumor-infiltrating lymphocytes, and prediction of molecular expression as well as treatment response and benefit of therapy from routine H&E images. This review critically examines the literature regarding these applications of AI in the area of breast pathology.
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Affiliation(s)
- Mustafa Yousif
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
- Department of Pathology, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Paul J van Diest
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Arvydas Laurinavicius
- Department of Pathology, Pharmacology and Forensic Medicine, Faculty of Medicine, Vilnius University, and National Center of Pathology, Affiliate of Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
| | - David Rimm
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Jeroen van der Laak
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Anant Madabhushi
- Department of Biomedical Engineering, Case Western Reserve University, and Louis Stokes Cleveland Veterans Administration Medical Center, Cleveland, OH, USA
- Louis Stokes Cleveland Veterans Administration Medical Center, Cleveland, OH, USA
| | - Stuart Schnitt
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Breast Oncology Program, Dana-Farber/Brigham and Women's Cancer Center, Boston, MA, USA
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Zhang PF, Zheng XH, Li XZ, Sun L, Jia WH. Informatics Management of Tumor Specimens in the Era of Big Data: Challenges and Solutions. Biopreserv Biobank 2021; 19:531-542. [PMID: 34030478 DOI: 10.1089/bio.2020.0084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Biomedical data bear the potential to facilitate personalized diagnosis and precision treatment. In the era of Big Data, high-quality annotation of human specimens has become the primary mission of biobankers, especially for tumor biobanks with large amounts of "omics" and clinical data. However, the lack of agreed-upon standardization and the gap among heterogeneous databases make information application and communication a major challenge. International efforts are underway to develop national projects on informatics management. The aim of this review is to provide references in specimen annotation to regulate and take full advantage of biological and biomedical information. First, critical data categories that are vital for specimen applications, including sample attributes, clinical data, preanalytical variations, and analytical records, are systematically listed for subsequent data mining. Second, current standards and guidelines related to biospecimen information are reviewed, and proper standards for tumor biobanks are recommended. In particular, commonly-used approaches and functionalities of data management are summarized and discussed. This review highlights the importance of informatics management of tumor specimens, defines critical data types, recommends data standards, and presents the methodologies of data harmonization for biobankers to reach high quality annotation of biospecimens.
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Affiliation(s)
- Pei-Fen Zhang
- State Key Laboratory of Oncology in South China, Tumor Biobank, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, P. R. China
| | - Xiao-Hui Zheng
- State Key Laboratory of Oncology in South China, Tumor Biobank, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, P. R. China
| | - Xi-Zhao Li
- State Key Laboratory of Oncology in South China, Tumor Biobank, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, P. R. China
| | - Lin Sun
- Department of Information, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, P. R. China
| | - Wei-Hua Jia
- State Key Laboratory of Oncology in South China, Tumor Biobank, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, P. R. China
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Valihrach L, Androvic P, Kubista M. Circulating miRNA analysis for cancer diagnostics and therapy. Mol Aspects Med 2020; 72:100825. [DOI: 10.1016/j.mam.2019.10.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/01/2019] [Accepted: 10/07/2019] [Indexed: 12/12/2022]
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PREDICT: a checklist for preventing preanalytical diagnostic errors in clinical trials. ACTA ACUST UNITED AC 2019; 58:518-526. [DOI: 10.1515/cclm-2019-1089] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 10/22/2019] [Indexed: 12/13/2022]
Abstract
Abstract
Although the importance of guaranteeing a high level of preanalytical quality in routine diagnostic testing has already been largely acknowledged over the past decades, minor emphasis is currently being placed on the fact that accurate performance and standardization of many preanalytical activities are also necessary prerogatives of clinical trials. Reliable evidence exists that clear indications on how to manage the different preanalytical steps are currently lacking in many clinical trials protocols, nor have detailed authoritative documents been published or endorsed on this matter to the best of our knowledge. To fill this gap, the European Federation of Clinical Chemistry and Laboratory Medicine (EFLM) Working Group for Preanalytical Phase (WG-PRE) will provide here a specific checklist for preventing preanalytical diagnostic errors in clinical trials (PREDICT), especially focused on covering the most important preanalytical aspects of blood sample management in clinical studies, and thus encompassing test selection, patient preparation, sample collection, management and storage, sample transportation, as well as specimen retrieval before testing. The WG-PRE members sincerely hope that these recommendations will provide a useful contribution for increasing the success rate in clinical trials.
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Abu-Rabie P, Sheelan D, Laures A, Spaull J, Dowell S. Increasing the discrimination power of rapid evaporative ionisation mass spectrometry (REIMS) in analytical control tissue quality screening and cell line sample identification. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 35. [PMID: 31295371 DOI: 10.1002/rcm.8525] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 05/31/2019] [Accepted: 07/04/2019] [Indexed: 05/15/2023]
Abstract
RATIONALE Rapid Evaporative Ionisation Mass Spectrometry (REIMS) has been evaluated as a tool to improve analytical efficiency and add capability in areas within Pharmaceutical Research and Development (Pharma R&D). This article reports the comparison of single MS, and tandem MS/MS REIMS (REIMS and REIMS/MS) methodologies to investigate which mode produces maximum discrimination power for screening applications. METHODS Control tissue samples and cell line suspension samples were analysed using optimised REIMS and REIMS/MS to evaluate which technique produced optimal discrimination power for control tissue and cell line identification. The iKnife sampling tool and a prototype 'cell sampler' were utilised for tissue and cell analysis, respectively. The REIMS source was coupled to a hybrid Quadrupole-Time Of Flight (QTOF) mass spectrometer. Multivariate Analysis (MVA) was utilised to evaluate the resulting Mass Spectrometry (MS) data and discriminate between sample types. RESULTS Proof of concept investigations demonstrating that REIMS/MS offered increased MVA discrimination for sample identification, compared with REIMS, is presented for the first time. Control tissue data showed discrimination by timepoint classification over 0-144 h storage after removal from the host. Timepoint discrimination was optimised using REIMS/MS with a collision energy that effectively maximised ion fragmentation. Similar optimisation was observed when REIMS/MS was applied to the identification of cell lines. CONCLUSIONS The proof of concept results demonstrate that REIMS/MS can offer advantages over REIMS for control tissue quality screening, and cell line identification applications in Pharma R&D. Further work following this proof of concept investigation is being undertaken to implement the technology for these applications, utilising the optimised REIMS/MS methodology. REIMS/MS will also be used as an optimised tool for other applications.
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Affiliation(s)
- Paul Abu-Rabie
- Medicinal Science and Technology, GlaxoSmithKline R&D, Stevenage, SG1 2NY, UK
| | - Denver Sheelan
- Medicinal Science and Technology, GlaxoSmithKline R&D, Stevenage, SG1 2NY, UK
| | - Alice Laures
- Medicinal Science and Technology, GlaxoSmithKline R&D, Stevenage, SG1 2NY, UK
| | - John Spaull
- Medicinal Science and Technology, GlaxoSmithKline R&D, Stevenage, SG1 2NY, UK
| | - Simon Dowell
- Medicinal Science and Technology, GlaxoSmithKline R&D, Stevenage, SG1 2NY, UK
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Shamai G, Binenbaum Y, Slossberg R, Duek I, Gil Z, Kimmel R. Artificial Intelligence Algorithms to Assess Hormonal Status From Tissue Microarrays in Patients With Breast Cancer. JAMA Netw Open 2019; 2:e197700. [PMID: 31348505 PMCID: PMC6661721 DOI: 10.1001/jamanetworkopen.2019.7700] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
IMPORTANCE Immunohistochemistry (IHC) is the most widely used assay for identification of molecular biomarkers. However, IHC is time consuming and costly, depends on tissue-handling protocols, and relies on pathologists' subjective interpretation. Image analysis by machine learning is gaining ground for various applications in pathology but has not been proposed to replace chemical-based assays for molecular detection. OBJECTIVE To assess the prediction feasibility of molecular expression of biomarkers in cancer tissues, relying only on tissue architecture as seen in digitized hematoxylin-eosin (H&E)-stained specimens. DESIGN, SETTING, AND PARTICIPANTS This single-institution retrospective diagnostic study assessed the breast cancer tissue microarrays library of patients from Vancouver General Hospital, British Columbia, Canada. The study and analysis were conducted from July 1, 2015, through July 1, 2018. A machine learning method, termed morphological-based molecular profiling (MBMP), was developed. Logistic regression was used to explore correlations between histomorphology and biomarker expression, and a deep convolutional neural network was used to predict the biomarker expression in examined tissues. MAIN OUTCOMES AND MEASURES Positive predictive value (PPV), negative predictive value (NPV), and area under the receiver operating characteristics curve measures of MBMP for assessment of molecular biomarkers. RESULTS The database consisted of 20 600 digitized, publicly available H&E-stained sections of 5356 patients with breast cancer from 2 cohorts. The median age at diagnosis was 61 years for cohort 1 (412 patients) and 62 years for cohort 2 (4944 patients), and the median follow-up was 12.0 years and 12.4 years, respectively. Tissue histomorphology was significantly correlated with the molecular expression of all 19 biomarkers assayed, including estrogen receptor (ER), progesterone receptor (PR), and ERBB2 (formerly HER2). Expression of ER was predicted for 105 of 207 validation patients in cohort 1 (50.7%) and 1059 of 2046 validation patients in cohort 2 (51.8%), with PPVs of 97% and 98%, respectively, NPVs of 68% and 76%, respectively, and accuracy of 91% and 92%, respectively, which were noninferior to traditional IHC (PPV, 91%-98%; NPV, 51%-78%; and accuracy, 81%-90%). Diagnostic accuracy improved given more data. Morphological analysis of patients with ER-negative/PR-positive status by IHC revealed resemblance to patients with ER-positive status (Bhattacharyya distance, 0.03) and not those with ER-negative/PR-negative status (Bhattacharyya distance, 0.25). This suggests a false-negative IHC finding and warrants antihormonal therapy for these patients. CONCLUSIONS AND RELEVANCE For at least half of the patients in this study, MBMP appeared to predict biomarker expression with noninferiority to IHC. Results suggest that prediction accuracy is likely to improve as data used for training expand. Morphological-based molecular profiling could be used as a general approach for mass-scale molecular profiling based on digitized H&E-stained images, allowing quick, accurate, and inexpensive methods for simultaneous profiling of multiple biomarkers in cancer tissues.
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Affiliation(s)
- Gil Shamai
- Department of Electrical Engineering, Technion Israel Institute of Technology, Haifa, Israel
| | - Yoav Binenbaum
- Laboratory of Pediatric Oncology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Laboratory for Applied Cancer Research, Rambam Healthcare Campus, Rappaport Institute of Medicine and Research, Haifa, Israel
| | - Ron Slossberg
- Departmemt of Computer Science, Technion Israel Institute of Technology, Haifa, Israel
| | - Irit Duek
- Department of Otolaryngology-Head and Neck Surgery, Rambam Health Care Campus, Haifa, Israel
| | - Ziv Gil
- Laboratory for Applied Cancer Research, Rambam Healthcare Campus, Rappaport Institute of Medicine and Research, Haifa, Israel
- Department of Otolaryngology-Head and Neck Surgery, Rambam Health Care Campus, Haifa, Israel
| | - Ron Kimmel
- Departmemt of Computer Science, Technion Israel Institute of Technology, Haifa, Israel
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Omilian AR, Zirpoli GR, Cheng TYD, Yao S, Stein L, Davis W, Head KL, Nair P, Khoury T, Ambrosone CB, Bshara W. Storage Conditions and Immunoreactivity of Breast Cancer Subtyping Markers in Tissue Microarray Sections. Appl Immunohistochem Mol Morphol 2019; 28:267-273. [PMID: 31205070 DOI: 10.1097/pai.0000000000000756] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Loss of immunoreactivity in tissue sections has been shown to occur when slide sections are stored at room temperature for prolonged periods of time. We conducted a systematic investigation to determine the extent of staining loss in various storage conditions to determine an optimal storage method. We investigated 6 antibodies that are commonly used for breast cancer subtyping in research studies with immunohistochemistry (ER, PR, HER2, CK5/6, EGFR, and Ki67) in formalin-fixed paraffin-embedded breast tissue microarrays consisting of 148 patients. Tissue microarrays were sectioned at various time points: fresh, 1 week, 1 month, 6 months, and 12 months before staining. Slides sectioned at each time point were stored in 5 storage conditions: desiccator, paraffin dipped, 4°C, -20°C, and -80°C. Immunohistochemistry scores were assessed over time with McNemar Test and Bowker Test of Symmetry. Desiccator storage was the only storage condition that did not show any loss in immunoreactivity for any antibody or time point in our study. Paraffin coated slides were the most difficult storage method operationally and also showed the most loss in immunoreactivity. Storing sections in a desiccator was the most effective method for minimizing immunoreactivity loss. Cold storage at 4°C is an intermediate option that is not as protective as a desiccator, but offers the advantage of being accessible to virtually all research labs.
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Affiliation(s)
- Angela R Omilian
- Departments of Cancer Prevention and Control.,Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Gary R Zirpoli
- Slone Epidemiology Center, Boston University Medical Campus, Boston, MA
| | - Ting-Yuan David Cheng
- Departments of Cancer Prevention and Control.,Department of Epidemiology, University of Florida, Gainesville, FL
| | - Song Yao
- Departments of Cancer Prevention and Control
| | - Leighton Stein
- Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | | | - Karen L Head
- Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Priya Nair
- Departments of Cancer Prevention and Control
| | - Thaer Khoury
- Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | | | - Wiam Bshara
- Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, NY
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McCall SJ, Branton PA, Blanc VM, Dry SM, Gastier-Foster JM, Harrison JH, Jewell SD, Dash RC, Obeng RC, Rose J, Mateski DL, Liubinskas A, Robb JA, Ramirez NC, Shea K. The College of American Pathologists Biorepository Accreditation Program: Results from the First 5 Years. Biopreserv Biobank 2018; 16:16-22. [PMID: 29394087 PMCID: PMC5824654 DOI: 10.1089/bio.2017.0108] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The College of American Pathologists (CAP) developed the Biorepository Accreditation Program (BAP) in 2012. This program integrates best practices from the International Society for Biological and Environmental Biorepositories, the National Cancer Institute, the Organisation for Economic Cooperation and Development, the Center for Medicare and Medicaid Services, and the CAP Laboratory Accreditation Program. The goal of this elective program is to provide requirements for standardization in biorepository processes that will result in high-quality specimens that can be used to support research, drug discovery, and personalized medicine. CAP uses a peer inspection model to ensure the inspectors have proper expertise and to promote educational efforts through information sharing. Lead inspectors are comprised of pathologists, PhDs, and managers of biorepositories and they are often supported by CAP staff inspectors. Accreditation is a 3-year continuous cycle of quality with a peer inspection occurring at the start of year 1 and a self-inspection and CAP desk assessment at the start of year 2 and 3. At this time 53 biorepositories are fully CAP BAP accredited and 13 are in the process of obtaining accreditation. There are currently 273 established standards with requirement lists customized based on the scope of activities performed by a biorepository. A total of 90 inspections were completed between May 2012 and December 2016. Sixty-one were initial inspections and 29 were reinspections. A total of 527 deficiencies were identified in the areas of Equipment/Instrumentation (22%), Information Technology (18%), Specimen Handling and QC (15%), Quality Management (16%), Personnel (11%), Safety (10%), Facilities (6%), and Regulatory (2%). Assessment of common deficiencies identifies areas of focus for continuous improvement and educational opportunities. Overall success of the program is high based on the current enrollment of 66 biorepositories, anecdotal participant feedback and increasing national recognition of the BAP in federal documents.
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Affiliation(s)
- Shannon J. McCall
- Department of Pathology, Duke University Health System, Durham, North Carolina
| | - Philip A. Branton
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Victoria M. Blanc
- Central Biorepository, University of Michigan Medical School, Ann Arbor, Michigan
| | - Sarah M. Dry
- Department of Pathology and Laboratory Medicine, UCLA Medical Center, David Geffen School of Medicine, Los Angeles, California
| | - Julie M. Gastier-Foster
- Department of Pathology, Nationwide Childrens' Hospital and The Ohio State University, Columbus, Ohio
| | - James H. Harrison
- Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia
- Department of Pathology, University of Virginia, Charlottesville, Virginia
| | - Scott D. Jewell
- Program for Biospecimen Science, Van Andel Research Institute, Grand Rapids, Michigan
| | - Rajesh C. Dash
- Department of Pathology, Duke University Health System, Durham, North Carolina
| | | | - Joan Rose
- College of American Pathologists, Northfield, Illinois
| | | | | | - James A. Robb
- Consulting Pathologist and Former CAP Governor, Boca Raton, Florida
| | - Nilsa C. Ramirez
- Department of Pathology, Nationwide Childrens' Hospital and The Ohio State University, Columbus, Ohio
| | - Kathi Shea
- Brooks Life Science Systems, Indianapolis, Indiana
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Andry C, Duffy E, Moskaluk CA, McCall S, Roehrl MHA, Remick D. Biobanking-Budgets and the Role of Pathology Biobanks in Precision Medicine. Acad Pathol 2017; 4:2374289517702924. [PMID: 28725790 PMCID: PMC5497908 DOI: 10.1177/2374289517702924] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 02/28/2017] [Accepted: 03/04/2017] [Indexed: 12/29/2022] Open
Abstract
Biobanks have become an important component of the routine practice of pathology. At the 2016 meeting of the Association of Pathology Chairs, a series of presentations covered several important aspects of biobanking. An often overlooked aspect of biobanking is the fiscal considerations. A biobank budget must address the costs of consenting, procuring, processing, and preserving high-quality biospecimens. Multiple revenue streams will frequently be necessary to create a sustainable biobank; partnering with other key stakeholders has been shown to be successful at academic institutions which may serve as a model. Biobanking needs to be a deeply science-driven and innovating process so that specimens help transform patient-centered clinical and basic research (ie, fulfill the promise of precision medicine). Pathology’s role must be at the center of the biobanking process. This ensures that optimal research samples are collected while guaranteeing that clinical diagnostics are never impaired. Biobanks will continue to grow as important components in the mission of pathology, especially in the era of precision medicine.
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Affiliation(s)
- Chris Andry
- Boston Medical Center and Boston University School of Medicine, Boston, MA, USA
| | - Elizabeth Duffy
- Boston Medical Center and Boston University School of Medicine, Boston, MA, USA
| | | | - Shannon McCall
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | | | - Daniel Remick
- Boston Medical Center and Boston University School of Medicine, Boston, MA, USA
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12
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Robboy SJ, McLendon R. Structured Annual Faculty Review Program Accelerates Professional Development and Promotion: Long-Term Experience of the Duke University Medical Center's Pathology Department. Acad Pathol 2017; 4:2374289516689471. [PMID: 28725786 PMCID: PMC5497916 DOI: 10.1177/2374289516689471] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 12/10/2016] [Accepted: 12/17/2016] [Indexed: 11/15/2022] Open
Abstract
This retrospective observational study on faculty development analyzes the Duke University Pathology Department's 18-year experience with a structured mentoring program involving 51 junior faculty members. The majority had MD degrees only (55%). The percentage of young women faculty hires before 1998 was 25%, increasing to 72% after 2005. Diversity also broadened from 9% with varied heritages before 1998 to 37% since then. The mentoring process pivoted on an annual review process. The reviews generally helped candidates focus much earlier, identified impediments they individually felt, and provided new avenues to gain a national reputation for academic excellence. National committee membership effectively helped gain national exposure. Thirty-eight percent of the mentees served on College of American Pathologists (CAP) committees, exponential multiples of any other national society. Some used CAP resources to develop major programs, some becoming nationally and internationally recognized for their academic activities. Several faculty gained national recognition as thought leaders for publishing about work initiated to serve administrative needs in the Department. The review process identified the need for more protected time for research, issues with time constraints, and avoiding exploitation when collaborating with other departments. This review identified a rigorous faculty mentoring and review process that included annual career counseling, goal-oriented academic careers, monitored advancement to promotion, higher salaries, and national recognition. All contributed to high faculty satisfaction and low faculty turnover. We conclude that a rigorous annual faculty review program and its natural sequence, promotion, can greatly foster faculty satisfaction.
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Affiliation(s)
- Stanley J Robboy
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - Roger McLendon
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
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13
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Variability in, variability out: best practice recommendations to standardize pre-analytical variables in the detection of circulating and tissue microRNAs. ACTA ACUST UNITED AC 2017; 55:608-621. [DOI: 10.1515/cclm-2016-0471] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 09/05/2016] [Indexed: 01/02/2023]
Abstract
Abstract:microRNAs (miRNAs) hold promise as biomarkers for a variety of disease processes and for determining cell differentiation. These short RNA species are robust, survive harsh treatment and storage conditions and may be extracted from blood and tissue. Pre-analytical variables are critical confounders in the analysis of miRNAs: we elucidate these and identify best practices for minimizing sample variation in blood and tissue specimens. Pre-analytical variables addressed include patient-intrinsic variation, time and temperature from sample collection to storage or processing, processing methods, contamination by cells and blood components, RNA extraction method, normalization, and storage time/conditions. For circulating miRNAs, hemolysis and blood cell contamination significantly affect profiles; samples should be processed within 2 h of collection; ethylene diamine tetraacetic acid (EDTA) is preferred while heparin should be avoided; samples should be “double spun” or filtered; room temperature or 4 °C storage for up to 24 h is preferred; miRNAs are stable for at least 1 year at –20 °C or –80 °C. For tissue-based analysis, warm ischemic time should be <1 h; cold ischemic time (4 °C) <24 h; common fixative used for all specimens; formalin fix up to 72 h prior to processing; enrich for cells of interest; validate candidate biomarkers with in situ visualization. Most importantly, all specimen types should have standard and common workflows with careful documentation of relevant pre-analytical variables.
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14
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Bodenmiller B. Multiplexed Epitope-Based Tissue Imaging for Discovery and Healthcare Applications. Cell Syst 2016; 2:225-38. [PMID: 27135535 DOI: 10.1016/j.cels.2016.03.008] [Citation(s) in RCA: 159] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 03/10/2016] [Indexed: 12/15/2022]
Abstract
The study of organs and tissues on a molecular level is necessary as we seek an understanding of health and disease. Over the last few years, powerful highly multiplexed epitope-based imaging approaches that rely on the serial imaging of tissues with fluorescently labeled antibodies and the simultaneous analysis using metal-labeled antibodies have emerged. These techniques enable analysis of dozens of epitopes in thousands of cells in a single experiment providing a systems level view of normal and disease processes at the single-cell level with spatial resolution in tissues. In this Review, I discuss, first, the highly multiplexed epitope-based imaging approaches and the generated data. Second, I describe challenges that must be overcome to implement these imaging methods from bench to bedside, including issues with tissue processing and analyses of the large amounts of data generated. Third, I discuss how these methods can be integrated with readouts of genome, transcriptome, metabolome, and live cell information, and fourth, the novel applications possible in tissue biology, drug development, and biomarker discovery. I anticipate that highly multiplexed epitope-based imaging approaches will broadly complement existing imaging methods and will become a cornerstone of tissue biology and biomedical research and of precision medical applications.
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Affiliation(s)
- Bernd Bodenmiller
- Institute of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland.
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15
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Robboy SJ, Gupta S, Crawford JM, Cohen MB, Karcher DS, Leonard DGB, Magnani B, Novis DA, Prystowsky MB, Powell SZ, Gross DJ, Black-Schaffer WS. The Pathologist Workforce in the United States: II. An Interactive Modeling Tool for Analyzing Future Qualitative and Quantitative Staffing Demands for Services. Arch Pathol Lab Med 2016; 139:1413-30. [PMID: 26516939 DOI: 10.5858/arpa.2014-0559-oa] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT Pathologists are physicians who make diagnoses based on interpretation of tissue and cellular specimens (surgical/cytopathology, molecular/genomic pathology, autopsy), provide medical leadership and consultation for laboratory medicine, and are integral members of their institutions' interdisciplinary patient care teams. OBJECTIVE To develop a dynamic modeling tool to examine how individual factors and practice variables can forecast demand for pathologist services. DESIGN Build and test a computer-based software model populated with data from surveys and best estimates about current and new pathologist efforts. RESULTS Most pathologists' efforts focus on anatomic (52%), laboratory (14%), and other direct services (8%) for individual patients. Population-focused services (12%) (eg, laboratory medical direction) and other professional responsibilities (14%) (eg, teaching, research, and hospital committees) consume the rest of their time. Modeling scenarios were used to assess the need to increase or decrease efforts related globally to the Affordable Care Act, and specifically, to genomic medicine, laboratory consolidation, laboratory medical direction, and new areas where pathologists' expertise can add value. CONCLUSIONS Our modeling tool allows pathologists, educators, and policy experts to assess how various factors may affect demand for pathologists' services. These factors include an aging population, advances in biomedical technology, and changing roles in capitated, value-based, and team-based medical care systems. In the future, pathologists will likely have to assume new roles, develop new expertise, and become more efficient in practicing medicine to accommodate new value-based delivery models.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - W Stephen Black-Schaffer
- From the Department of Pathology, Duke University Medical Center, Durham, North Carolina (Dr Robboy); The Smart Cube, Noida, India (Mr Gupta); the Department of Pathology and Laboratory Medicine, North Shore-Long Island Jewish Health System, Manhasset, New York (Dr Crawford); the Department of Pathology, Huntsman Cancer Hospital, University of Utah, Salt Lake City (Dr Cohen); the Department of Pathology, George Washington University, Washington, DC (Dr Karcher); the Department of Pathology, University of Vermont College of Medicine, Burlington (Dr Leonard); the Department of Pathology, Tufts University School of Medicine, Boston, Massachusetts (Dr Magnani); Novis Consulting, Lee, New Hampshire (Dr Novis); the Department of Pathology, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, New York (Dr Prystowsky); the Department of Pathology and Genomic Medicine, The Methodist Hospital, Houston, Texas (Dr Powell); Policy Roundtable, College of American Pathologists, Washington, DC (Dr Gross); the Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston (Dr Black-Schaffer)
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16
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An investigation of the comparability of commercially sourced plasma and pharmaceutical study plasma, using total protein concentration. Bioanalysis 2016; 8:311-21. [PMID: 26808091 DOI: 10.4155/bio.15.248] [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: 11/17/2022] Open
Abstract
BACKGROUND Control blood plasma is regularly used in bioanalysis, biomarkers and proteomics, and is often obtained from commercial sources. It has always been assumed that this plasma will be comparable to plasma drawn during a drug development study. RESULTS When compared using total protein concentrations, plasma from only one species (dog) demonstrated statistical comparability, plasma from all other species tested (human, rabbit, mouse and rat) shows a statistically significant difference. CONCLUSION If endogenous components of blood plasma are being measured, or if an assay technique does not significantly limit matrix effects, any assay controls should be prepared using control plasma from the drug development site, or using commercial plasma that has been screened against drug development site plasma.
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17
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Ewaisha R, Gawryletz CD, Anderson KS. Crucial considerations for pipelines to validate circulating biomarkers for breast cancer. Expert Rev Proteomics 2016; 13:201-11. [PMID: 26653344 DOI: 10.1586/14789450.2016.1132170] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Despite decades of progress in breast imaging, breast cancer remains the second most common cause of cancer mortality in women. The rapidly proliferative breast cancers that are associated with high relapse rates and mortality frequently present in younger women, in unscreened individuals, or in the intervals between screening mammography. Biomarkers exist for monitoring metastatic disease, such as CEA, CA27.29 and CA15-3, but there are no circulating biomarkers clinically available for early detection, prognosis, or monitoring for clinical relapse. There has been significant progress in the discovery of potential circulating biomarkers, including proteins, autoantibodies, nucleic acids, exosomes, and circulating tumor cells, but the vast majority of these biomarkers have not progressed beyond initial research discovery, and none have yet been approved for clinical use in early stage disease. Here, the authors review the crucial considerations of developing pipelines for the rapid evaluation of circulating biomarkers for breast cancer.
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Affiliation(s)
- Radwa Ewaisha
- a Center for Personalized Diagnostics, Biodesign Institute , Arizona State University , Tempe , AZ , USA
| | - Chelsea D Gawryletz
- b Department of Medical Oncology , Mayo Clinic Arizona , Scottsdale , AZ , USA
| | - Karen S Anderson
- a Center for Personalized Diagnostics, Biodesign Institute , Arizona State University , Tempe , AZ , USA.,b Department of Medical Oncology , Mayo Clinic Arizona , Scottsdale , AZ , USA
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18
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Abstract
CONTEXT Genomic medicine requires the identification of biomarkers and therapeutic targets, which in turn, requires high-quality biospecimens. Achieving high-quality biospecimens requires implementing standard operating procedures to control the variations of preanalytic variables in biobanking. Currently, most biobanks do not control the variations of preanalytic variables when collecting, processing, and storing their biospecimens. However, those variations have been shown to affect the quality of biospecimens and gene expression profiling. OBJECTIVE To identify evidence-based preanalytic parameters that can be applied and those parameters that need further study. DATA SOURCES We searched the Biospecimen Research and PubMed databases using defined key words. We retrieved and reviewed 212 articles obtained through those searches. We included 58 articles (27%) according to our inclusion and exclusion criteria for this review. CONCLUSION -Preanalytic variables in biobanking can degrade the quality of biospecimens and alter gene expression profiling. Variables that require further study include the effect of surgical manipulation; the effect of warm ischemia; the allowable duration of delayed specimen processing; the optimal type, duration, and temperature of preservation and fixation; and the optimal storage duration of formalin-fixed, paraffin embedded specimens in a fit-for-purpose approach.
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Affiliation(s)
- Jane H Zhou
- From the Departments of Pathology (Drs Zhou and Sahin) and Head and Neck Surgery (Dr Myers), University of Texas MD Anderson Cancer Center, Houston. Dr Zhou is now with Human Genome Sequencing Center, Baylor College of Medicine, Houston
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19
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Robb JA, Bry L, Sluss PM, Wagar EA, Kennedy MF. A Call to Standardize Preanalytic Data Elements for Biospecimens, Part II. Arch Pathol Lab Med 2015; 139:1125-8. [PMID: 25594725 DOI: 10.5858/arpa.2014-0572-cp] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
CONTEXT Biospecimens must have appropriate clinical annotation (data) to ensure optimal quality for both patient care and research. Additional clinical preanalytic variables are the focus of this continuing study. OBJECTIVE To complete the identification of the essential preanalytic variables (data fields) that can, and in some instances should, be attached to every collected biospecimen by adding the additional specific variables for clinical chemistry and microbiology to our original 170 variables. DESIGN The College of American Pathologists Diagnostic Intelligence and Health Information Technology Committee sponsored a second Biorepository Working Group to complete the list of preanalytic variables for annotating biospecimens. Members of the second Biorepository Working Group are experts in clinical pathology and microbiology. Additional preanalytic area-specific variables were identified and ranked along with definitions and potential negative impacts if the variable is not attached to the biospecimen. The draft manuscript was reviewed by additional national and international stakeholders. RESULTS Four additional required preanalytic variables were identified specifically for clinical chemistry and microbiology biospecimens that can be used as a guide for site-specific implementation into patient care and research biorepository processes. CONCLUSIONS In our collective experience, selecting which of the many preanalytic variables to attach to any specific set of biospecimens used for patient care and/or research is often difficult. The additional ranked list should be of practical benefit when selecting preanalytic variables for a given biospecimen collection.
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Affiliation(s)
| | | | | | | | - Mary F Kennedy
- From the Department of Pathology, Brigham and Women's Hospital (Dr Bry), and the Department of Pathology, Massachusetts General Hospital (Dr Sluss), Boston; the Department of Pathology, MD Anderson Cancer Center, Houston, Texas (Dr Wagar); and the College of American Pathologists, Northfield, Illinois (Ms Kennedy). Dr Robb is a consulting pathologist in Boca Raton, Florida
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20
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Scalia CR, Gendusa R, Basciu M, Riva L, Tusa L, Musarò A, Veronese S, Formenti A, D'Angelo D, Ronzio AG, Cattoretti G, Bolognesi MM. Epitope recognition in the human-pig comparison model on fixed and embedded material. J Histochem Cytochem 2015. [PMID: 26209082 PMCID: PMC4823807 DOI: 10.1369/0022155415597738] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The conditions and the specificity by which an antibody binds to its target protein in routinely fixed and embedded tissues are unknown. Direct methods, such as staining in a knock-out animal or in vitro peptide scanning of the epitope, are costly and impractical. We aimed to elucidate antibody specificity and binding conditions using tissue staining and public genomic and immunological databases by comparing human and pig—the farmed mammal evolutionarily closest to humans besides apes. We used a database of 146 anti-human antibodies and found that antibodies tolerate partially conserved amino acid substitutions but not changes in target accessibility, as defined by epitope prediction algorithms. Some epitopes are sensitive to fixation and embedding in a species-specific fashion. We also find that half of the antibodies stain porcine tissue epitopes that have 60% to 100% similarity to human tissue at the amino acid sequence level. The reason why the remaining antibodies fail to stain the tissues remains elusive. Because of its similarity with the human, pig tissue offers a convenient tissue for quality control in immunohistochemistry, within and across laboratories, and an interesting model to investigate antibody specificity.
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Affiliation(s)
| | - Rossella Gendusa
- Azienda Ospedaliera San Gerardo, Monza, Italy (CRS, RG, LR, LT, AM, GC, MMB)
| | - Maria Basciu
- Dipartimento di Chirurgia e Medicina Traslazionale, Universitá degli Studi di Milano-Bicocca, Monza Italy (MB, GC)
| | - Lorella Riva
- Azienda Ospedaliera San Gerardo, Monza, Italy (CRS, RG, LR, LT, AM, GC, MMB)
| | - Lorenza Tusa
- Azienda Ospedaliera San Gerardo, Monza, Italy (CRS, RG, LR, LT, AM, GC, MMB)
| | - Antonella Musarò
- Azienda Ospedaliera San Gerardo, Monza, Italy (CRS, RG, LR, LT, AM, GC, MMB)
| | - Silvio Veronese
- Struttura Complessa di Anatomia Patologica, Dipartimento di Medicina di Laboratorio, Azienda Ospedaliera Ospedale Niguarda Ca' Granda, Milano Italy (SV)
| | - Angelo Formenti
- Servizio di Igiene degli Alimenti di Origine Animale, Dipartimento Veterinario, Azienda Sanitaria Locale di Monza e Brianza, Desio, Italy (AF, DD)
| | - Donatella D'Angelo
- Servizio di Igiene degli Alimenti di Origine Animale, Dipartimento Veterinario, Azienda Sanitaria Locale di Monza e Brianza, Desio, Italy (AF, DD)
| | - Angela Gabriella Ronzio
- Dipartimento di Prevenzione Veterinario, Distretto Veterinario 2 Legnano - Castano Primo, Azienda Sanitaria Locale Milano 1, Castano Primo, Italy (AGR)
| | - Giorgio Cattoretti
- Azienda Ospedaliera San Gerardo, Monza, Italy (CRS, RG, LR, LT, AM, GC, MMB),Dipartimento di Chirurgia e Medicina Traslazionale, Universitá degli Studi di Milano-Bicocca, Monza Italy (MB, GC)
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21
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Ellervik C, Vaught J. Preanalytical Variables Affecting the Integrity of Human Biospecimens in Biobanking. Clin Chem 2015; 61:914-34. [DOI: 10.1373/clinchem.2014.228783] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 04/13/2015] [Indexed: 12/20/2022]
Abstract
Abstract
BACKGROUND
Most errors in a clinical chemistry laboratory are due to preanalytical errors. Preanalytical variability of biospecimens can have significant effects on downstream analyses, and controlling such variables is therefore fundamental for the future use of biospecimens in personalized medicine for diagnostic or prognostic purposes.
CONTENT
The focus of this review is to examine the preanalytical variables that affect human biospecimen integrity in biobanking, with a special focus on blood, saliva, and urine. Cost efficiency is discussed in relation to these issues.
SUMMARY
The quality of a study will depend on the integrity of the biospecimens. Preanalytical preparations should be planned with consideration of the effect on downstream analyses. Currently such preanalytical variables are not routinely documented in the biospecimen research literature. Future studies using biobanked biospecimens should describe in detail the preanalytical handling of biospecimens and analyze and interpret the results with regard to the effects of these variables.
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Affiliation(s)
- Christina Ellervik
- Department of Research, Nykoebing Falster Hospital, Nykoebing Falster, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, MA
| | - Jim Vaught
- International Society for Biological and Environmental Repositories, Vancouver, Canada
- Editor-in-Chief, Biopreservation and Biobanking, Vancouver, Canada
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22
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Hassis ME, Niles RK, Braten MN, Albertolle ME, Ewa Witkowska H, Hubel CA, Fisher SJ, Williams KE. Evaluating the effects of preanalytical variables on the stability of the human plasma proteome. Anal Biochem 2015; 478:14-22. [PMID: 25769420 PMCID: PMC4492164 DOI: 10.1016/j.ab.2015.03.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 02/19/2015] [Accepted: 03/04/2015] [Indexed: 10/23/2022]
Abstract
High quality clinical biospecimens are vital for biomarker discovery, verification, and validation. Variations in blood processing and handling can affect protein abundances and assay reliability. Using an untargeted LC-MS approach, we systematically measured the impact of preanalytical variables on the plasma proteome. Time prior to processing was the only variable that affected the plasma protein levels. LC-MS quantification showed that preprocessing times <6h had minimal effects on the immunodepleted plasma proteome, but by 4 days significant changes were apparent. Elevated levels of many proteins were observed, suggesting that in addition to proteolytic degradation during the preanalytical phase, changes in protein structure are also important considerations for protocols using antibody depletion. As to processing variables, a comparison of single- vs double-spun plasma showed minimal differences. After processing, the impact ⩽3 freeze-thaw cycles was negligible regardless of whether freshly collected samples were processed in short succession or the cycles occurred during 14-17 years of frozen storage (-80 °C). Thus, clinical workflows that necessitate modest delays in blood processing times or employ different centrifugation steps can yield valuable samples for biomarker discovery and verification studies.
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Affiliation(s)
- Maria E Hassis
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA; Sandler-Moore Mass Spectrometry Core Facility, University of California San Francisco, San Francisco, CA 94143, USA; Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - Richard K Niles
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA; Sandler-Moore Mass Spectrometry Core Facility, University of California San Francisco, San Francisco, CA 94143, USA
| | - Miles N Braten
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA; Sandler-Moore Mass Spectrometry Core Facility, University of California San Francisco, San Francisco, CA 94143, USA; Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - Matthew E Albertolle
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA; Sandler-Moore Mass Spectrometry Core Facility, University of California San Francisco, San Francisco, CA 94143, USA; Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - H Ewa Witkowska
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA; Sandler-Moore Mass Spectrometry Core Facility, University of California San Francisco, San Francisco, CA 94143, USA; Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - Carl A Hubel
- Magee-Womens Research Institute and Department of Obstetrics, Gynecology & Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Susan J Fisher
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA; Sandler-Moore Mass Spectrometry Core Facility, University of California San Francisco, San Francisco, CA 94143, USA; Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA; Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA
| | - Katherine E Williams
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA; Sandler-Moore Mass Spectrometry Core Facility, University of California San Francisco, San Francisco, CA 94143, USA; Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA.
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23
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Gündisch S, Annaratone L, Beese C, Drecol E, Marchiò C, Quaglino E, Sapino A, Becker KF, Bussolati G. Critical roles of specimen type and temperature before and during fixation in the detection of phosphoproteins in breast cancer tissues. J Transl Med 2015; 95:561-71. [PMID: 25730369 PMCID: PMC4421866 DOI: 10.1038/labinvest.2015.37] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 12/09/2014] [Accepted: 12/31/2014] [Indexed: 12/21/2022] Open
Abstract
The most efficient approach for therapy selection to inhibit the deregulated kinases in cancer tissues is to measure their phosphorylation status prior to the treatment. The aim of our study was to evaluate the influence of pre-analytical parameters (cold ischemia time, temperature before and during tissue fixation, and sample type) on the levels of proteins and phosphoproteins in breast cancer tissues, focusing on the PI3 kinase/AKT pathway. The BALB-neuT mouse breast cancer model expressing HER2 and pAKT proteins and human biopsy and resection specimens were analyzed. By using quantitative reverse phase protein arrays (RPPA), 9 proteins and 16 phosphoproteins relevant to breast cancer biology were assessed. Cold temperatures before and during fixation resulted in a marked improvement in the preservation of the reactivity of biological markers (eg, ER, HER2) in general and, specifically, pHER2 and pAKT. Some phosphoproteins, eg, pHER2 and pAKT, were more sensitive to prolonged cold ischemia times than others (eg, pS6RP and pSTAT5). By comparing the phosphoprotein levels in core needle biopsies with those in resection specimens, we found a marked decrease in many phosphoproteins in the latter. Cold conditions can improve the preservation of proteins and phosphoproteins in breast cancer tissues. Biopsies ≤ 1 mm in size are the preferred sample type for assessing the activity of deregulated kinases for personalized cancer treatments because the phosphoprotein levels are better preserved compared with resection specimens. Each potential new (phospho)protein biomarker should be tested for its sensitivity to pre-analytical processing prior to the development of a diagnostic assay.
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Affiliation(s)
- Sibylle Gündisch
- Institute of Pathology, Technische Universität München, Trogerstrasse, Munich, Germany
| | - Laura Annaratone
- Department of Medical Sciences, University of Turin, Via Santena, Turin, Italy
| | - Christian Beese
- Institute of Pathology, Technische Universität München, Trogerstrasse, Munich, Germany
| | - Enken Drecol
- Institute of Pathology, Technische Universität München, Trogerstrasse, Munich, Germany
| | - Caterina Marchiò
- Department of Medical Sciences, University of Turin, Via Santena, Turin, Italy,Pathology Service, Azienda Ospedaliera Città della Salute e della Scienza di Torino, Via Santena, Turin, Italy
| | - Elena Quaglino
- Department of Molecular Biotechnologies and Health Sciences, University of Turin, Via Nizza, Turin, Italy
| | - Anna Sapino
- Department of Medical Sciences, University of Turin, Via Santena, Turin, Italy,Pathology Service, Azienda Ospedaliera Città della Salute e della Scienza di Torino, Via Santena, Turin, Italy
| | - Karl-Friedrich Becker
- Institute of Pathology, Technische Universität München, Trogerstrasse, Munich, Germany,Technische Universität München, Institute of Pathology, Trogerstrasse18, Munich, D-81675, Germany. E-mail:
| | - Gianni Bussolati
- Department of Medical Sciences, University of Turin, Via Santena, Turin, Italy,Department of Medical Sciences, University of Turin, Via Santena 7, Turin 10126, Italy. E-mail:
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24
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de Baca ME, Arnaout R, Brodsky V, Birdsong GG. Ordo ab Chao: framework for an integrated disease report. Arch Pathol Lab Med 2015; 139:165-70. [PMID: 25611099 DOI: 10.5858/arpa.2013-0561-cp] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT The volume of information that must be assimilated to appropriately manage patients with complex or chronic disease can make this task difficult because of the number of data points, their variable temporal availability, and the fact that they may reside in different systems or even institutions. OBJECTIVE .- To outline a framework for building an integrated disease report (IDR) that takes advantage of the capabilities of electronic reporting to create a single, succinct, interpretative report comprising all disease pertinent data. DESIGN Disease pertinent data of an IDR include pathology results, laboratory and radiology data, pathologic correlations, risk profiles, and therapeutic implications. We used cancer herein as a representative process for proposing what is, to our knowledge, the first example of standardized guidelines for such a report. The IDR was defined as a modular, dynamic, electronic summary of the most current state of a patient in regard to a particular illness such as lung cancer or diabetes, which includes all information relevant for patient management. RESULTS We propose the following 11 core data concepts that an IDR should include: patient identification; patient demographics; disease, diagnosis, and prognosis; tumor board dispositions and decisions; graphic timeline; preresection workup and therapy; resection workup; interpretative comment summarizing pertinent findings; biobanking data; postresection workup; and disease and patient status at follow-up. CONCLUSIONS A well-executed IDR should improve patient care and efficiency for health care team members. It would demonstrate the added value of pathology interpretation and likely contribute to a reduction in errors and improved patient safety by decreasing the risk that important data will be overlooked.
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Affiliation(s)
- Monica E de Baca
- From the Department of Hematopathology, Hematologics, Inc, Seattle, Washington (Dr de Baca); the Department of Pathology and Division of Clinical Informatics, Beth Israel Deaconess Medical Center, and the Department of Systems Biology, Harvard Medical School, Boston, Massachusetts (Dr Arnaout); the Department of Pathology and Laboratory Medicine, Weill Cornell Medical College-New York Presbyterian Hospital, New York (Dr Brodsky); and the Department of Pathology and Laboratory Medicine, Emory University School of Medicine/Grady Health System, Atlanta, Georgia (Dr Birdsong)
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Bass BP, Engel KB, Greytak SR, Moore HM. A review of preanalytical factors affecting molecular, protein, and morphological analysis of formalin-fixed, paraffin-embedded (FFPE) tissue: how well do you know your FFPE specimen? Arch Pathol Lab Med 2015; 138:1520-30. [PMID: 25357115 DOI: 10.5858/arpa.2013-0691-ra] [Citation(s) in RCA: 178] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT Formalin fixation and paraffin embedding is a timeless, cost-efficient, and widely adopted method of preserving human tissue biospecimens that has resulted in a substantial reservoir of formalin-fixed, paraffin-embedded blocks that represent both the pathology and preanalytical handling of the biospecimen. This reservoir of specimens is increasingly being used for DNA, RNA, and proteomic analyses. OBJECTIVE To evaluate the impact of preanalytical factors associated with the formalin fixation and paraffin embedding process on downstream morphological and molecular endpoints. DATA SOURCES We surveyed the existing literature using the National Cancer Institute's Biospecimen Research Database for published reports investigating the potential influence of preanalytical factors associated with the formalin fixation and paraffin embedding process on DNA, RNA, protein, and morphological endpoints. CONCLUSIONS Based on the literature evidence, the molecular, proteomic, and morphological endpoints can be altered in formalin-fixed, paraffin-embedded specimens by suboptimal processing conditions. While the direction and magnitude of effects associated with a given preanalytical factor were dependent on the analyte (DNA, RNA, protein, and morphology) and analytical platform, acceptable conditions are highlighted, and a summary of conditions that could preclude analysis is provided.
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Affiliation(s)
- B Paige Bass
- From the Kelly Government Solutions Program, Kelly Services, Rockville (Drs Bass and Greytak), and the Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda (Dr Moore), Maryland; and the Preferred Solutions Group, Arlington, Virginia (Dr Engel)
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Genomic assays for Epstein-Barr virus-positive gastric adenocarcinoma. Exp Mol Med 2015; 47:e134. [PMID: 25613731 PMCID: PMC4314585 DOI: 10.1038/emm.2014.93] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Accepted: 10/06/2014] [Indexed: 12/13/2022] Open
Abstract
A small set of gastric adenocarcinomas (9%) harbor Epstein–Barr virus (EBV) DNA within malignant cells, and the virus is not an innocent bystander but rather is intimately linked to pathogenesis and tumor maintenance. Evidence comes from unique genomic features of host DNA, mRNA, microRNA and CpG methylation profiles as revealed by recent comprehensive genomic analysis by The Cancer Genome Atlas Network. Their data show that gastric cancer is not one disease but rather comprises four major classes: EBV-positive, microsatellite instability (MSI), genomically stable and chromosome instability. The EBV-positive class has even more marked CpG methylation than does the MSI class, and viral cancers have a unique pattern of methylation linked to the downregulation of CDKN2A (p16) but not MLH1. EBV-positive cancers often have mutated PIK3CA and ARID1A and an amplified 9p24.1 locus linked to overexpression of JAK2, CD274 (PD-L1) and PDCD1LG2 (PD-L2). Multiple noncoding viral RNAs are highly expressed. Patients who fail standard therapy may qualify for enrollment in clinical trials targeting cancer-related human gene pathways or promoting destruction of infected cells through lytic induction of EBV genes. Genomic tests such as the GastroGenus Gastric Cancer Classifier are available to identify actionable variants in formalin-fixed cancer tissue of affected patients.
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Doroshow JH, Kummar S. Translational research in oncology--10 years of progress and future prospects. Nat Rev Clin Oncol 2014; 11:649-62. [PMID: 25286976 DOI: 10.1038/nrclinonc.2014.158] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
International efforts to sequence the genomes of various human cancers have been broadly deployed in drug discovery programmes. Diagnostic tests that predict the value of the molecularly targeted anticancer agents used in such programmes are conceived and validated in parallel with new small-molecule treatments and immunotherapies. This approach has been aided by better preclinical cancer models; an enhanced appreciation of the complex interactions that exist between tumour cells and their microenvironment; the elucidation of interactions between many of the genetic drivers of cancer, including oncogenes and tumour suppressors; and recent insights into the genetic heterogeneity of human tumours made possible by extraordinary improvements in DNA-sequencing techniques. These advances are being employed in the first generation of genomic clinical trials that will examine the feasibility of matching a broad range of systemic therapies to specific molecular tumour characteristics. More-extensive molecular characterization of tumours and their supporting matrices are anticipated to become standard aspects of oncological practice, permitting continuous molecular re-evaluations of human malignancies on a patient-by-patient and treatment-by-treatment basis. We review selected developments in translational cancer biology, diagnostics, and therapeutics that have occurred over the past decade and offer our thoughts on future prospects for the next few years.
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Affiliation(s)
- James H Doroshow
- 1] Division of Cancer Treatment and Diagnosis, Room 3A-44, Building 31, 31 Center Drive, National Cancer Institute, NIH, Bethesda, MD 20892, USA. [2] Developmental Therapeutics Branch of the Center for Cancer Research, Room 3A-44, Building 31, 31 Center Drive, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Shivaani Kummar
- Division of Cancer Treatment and Diagnosis, Room 3A-44, Building 31, 31 Center Drive, National Cancer Institute, NIH, Bethesda, MD 20892, USA
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Simpson RW, Berman MA, Foulis PR, Divaris DXG, Birdsong GG, Mirza J, Moldwin R, Spencer S, Srigley JR, Fitzgibbons PL. Cancer biomarkers: the role of structured data reporting. Arch Pathol Lab Med 2014; 139:587-93. [PMID: 25275812 DOI: 10.5858/arpa.2014-0082-ra] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT The College of American Pathologists has been producing cancer protocols since 1986 to aid pathologists in the diagnosis and reporting of cancer cases. Many pathologists use the included cancer case summaries as templates for dictation/data entry into the final pathology report. These summaries are now available in a computer-readable format with structured data elements for interoperability, packaged as "electronic cancer checklists." Most major vendors of anatomic pathology reporting software support this model. OBJECTIVES To outline the development and advantages of structured electronic cancer reporting using the electronic cancer checklist model, and to describe its extension to cancer biomarkers and other aspects of cancer reporting. DATA SOURCES Peer-reviewed literature and internal records of the College of American Pathologists. CONCLUSIONS Accurate and usable cancer biomarker data reporting will increasingly depend on initial capture of this information as structured data. This process will support the standardization of data elements and biomarker terminology, enabling the meaningful use of these datasets by pathologists, clinicians, tumor registries, and patients.
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Affiliation(s)
- Ross W Simpson
- From the Department of Pathology, Park Nicollet-Methodist Hospital, St Louis Park, Minnesota (Dr Simpson); the Department of Pathology, Jefferson Regional Medical Center, Jefferson Hills, Pennsylvania (Dr Berman); the University of South Florida Department of Pathology and Cell Biology, James A. Haley Veterans' Hospital, Tampa (Dr Foulis); the Department of Laboratory Medicine, Grand River Hospital, Kitchener, Ontario, Canada (Dr Divaris); the Department of Pathology, Grady Health System/Emory University School of Medicine, Atlanta, Georgia (Dr Birdsong); Capability & Specialty Advancement, College of American Pathologists, Northfield, Illinois (Drs Mirza, Moldwin, and Spencer); the Laboratory Medicine and Genetics Program, Trillium Health Partners, Mississauga, Ontario, Canada (Dr Srigley); and the Department of Pathology, St Jude Medical Center, Fullerton, California (Dr Fitzgibbons)
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Simon MA, de la Riva EE, Bergan R, Norbeck C, McKoy JM, Kulesza P, Dong X, Schink J, Fleisher L. Improving diversity in cancer research trials: the story of the Cancer Disparities Research Network. JOURNAL OF CANCER EDUCATION : THE OFFICIAL JOURNAL OF THE AMERICAN ASSOCIATION FOR CANCER EDUCATION 2014; 29:366-74. [PMID: 24519744 PMCID: PMC4029870 DOI: 10.1007/s13187-014-0617-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The participation of racial and ethnic minorities and underserved populations in clinical trials is a critical link between scientific innovation and improvements in health care delivery and health outcomes. However, these population groups continue to be underrepresented in research. We describe the development of the Cancer Disparities Research Network (CDRN) to improve minority and underserved populations' participation in biobanking research. Between February and October 2011, we conducted a regional assessment to identify challenges and opportunities for cancer trials and biobanking research across the CDRN. Representatives from ten CDRN biorepository facilities completed an online survey assessing their facilities' minority biospecimen collection, biobanking practices, and education/outreach initiatives. Representatives of eight facilities also participated in stakeholder interviews. The majority (70%) of facilities reported that specimens were available for research, although only one tenth of these specimens were from non-White patients. Most facilities collected a patient's age, gender, race, medical history, and ethnicity with samples; however, less than half also collected family health history, education level, household income, or primary language spoken. In addition, few institutions collected Asian or Hispanic subgroup information. Only a few reported biospecimen collection outreach programs specifically targeting minority and underserved populations. Biospecimen directors and administrators indicated that funding, biospecimen sharing procedures, and standardization barriers limited their facilities from collaborating in biospecimen collection programs, despite their great interest. These findings suggest that the CDRN can provide opportunities for collaboration, resource sharing, and fostering of research ideas to address cancer disparities in biospecimen research.
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Affiliation(s)
- Melissa A Simon
- Department of Obstetrics & Gynecology and Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, 633 N. St. Clair, Suite 1800, Chicago, IL, 60611, USA,
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Mora E, Robb JA, Stefanoff G, Mellado RH, Coppola D, Muñoz-Antonia T, Flores I. Proceedings of the 1st Puerto Rico Biobanking Workshop. Rev Recent Clin Trials 2014; 9:233-44. [PMID: 25626063 PMCID: PMC4635463 DOI: 10.2174/1574887110666150127105545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 12/02/2014] [Accepted: 12/08/2014] [Indexed: 05/02/2023]
Abstract
The 1st Puerto Rico Biobanking Workshop took place on August 20st, 2014 in the Auditorium of the Comprehensive Cancer Center of the University of Puerto Rico, Medical Sciences Campus in San Juan Puerto Rico. The program for this 1-day, live workshop included lectures by three biobanking experts, followed by presentations from existing biobanks in Puerto Rico and audience discussion. The need for increasing biobanking expertise in Puerto Rico stems from the fact that Hispanics in general are underrepresented in the biobanks in existence in the US, which limits the research conducted specifically to understand the molecular differences in cancer cells compared to other better studied populations. In turn, this lack of information impairs the development of better diagnostic and therapeutic approaches for our population. Dr. James Robb, M.D., F.C.A.P., consulting pathologist to the National Cancer Institute (NCI) and the Office of Biorepositories and Biospecimen Research (OBBR), opened the workshop with a discussion on the basic aspects of the science of biobanking (e.g., what is a biobank; its goals and objectives; protocols and procedures) in his talk addressing the importance of banking tissues for advancing biomedical research. Next, Dr. Gustavo Stefanoff, from the Cancer Institutes Network of Latin America (RINC by its name in Spanish), explained the mission, objectives, and structure of the Network of Latin-American and Caribbean Biobanks (REBLAC by its name in Spanish), which despite limited resources and many challenges, currently accrue high quality human tissue specimens and data to support cancer research in the region. Dr. Robert Hunter-Mellado, Professor of Internal Medicine, Universidad Central del Caribe, followed with an examination of the ethical and regulatory aspects of biobanking tissues for future research, including informed consent of subjects; protection of human subjects rights; and balancing risks and benefit ratios. In the afternoon, the directors of existing biobanks in Puerto Rico (the Puerto Rico Biobank, the Comprehensive Cancer Center biobank, and an HIV-focused biobank at Universidad Central del Caribe) presented their experiences and challenges with establishing biobanks for research in Puerto Rico. In sum, this workshop presented opportunities to share knowledge in the science of biobanking, for further training, and of networking among the participants (34 from 4 different institutions), which will strengthen the collaborative links between investigators studying cancer in Latin America, the Caribbean, and the US.
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Affiliation(s)
| | | | | | | | | | | | - Idhaliz Flores
- Department of Microbiology, Department of Ob-Gyn, Ponce Health Sciences University & School of Medicine, Ponce Research Institute, PO BOX 7004, Ponce, PR 00732.
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