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Chacon Alberty L, King M, Mesquita FCP, Hochman-Mendez C. Quality Assessment of Long-Term Cryopreserved Human Bone-Derived Marrow Mesenchymal Stromal Cell Samples: Experience from the Texas Heart Institute Biorepository and Biospecimen Profiling Core. Biopreserv Biobank 2024. [PMID: 39253842 DOI: 10.1089/bio.2023.0144] [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: 09/11/2024] Open
Abstract
In biomedical research, biorepositories are pivotal resources that safeguard and supply clinical samples for scientific investigators. Proper long-term cryopreservation conditions are essential to maintain biospecimen quality. In this study, we analyzed the efficacy of sample cryopreservation at the Texas Heart Institute Biorepository and Biospecimen Profiling Core (THI-BRC). Our assessments included a thorough review of internal processes, quality reports, and both internal and external audit outcomes. We examined the integrity of human bone marrow-derived multipotent mesenchymal stromal cells (BM-MSCs) that were cryopreserved for over 5 years. These samples originated from randomly selected clinical trial participants or commercially sourced cell lines. Parameters such as cell viability, DNA and RNA integrity, population doubling time, sterility, and BM-MSC-specific attributes such as surface antigen expression and differentiation potential were studied. BM-MSC samples cryopreserved for ∼6 months served as our control. Our results demonstrated that the 5-year cryopreserved samples maintained their integrity compared with the shorter-term stored control samples. Moreover, THI-BRC has met accreditation agency standards and has not received any repeated deficiencies over 7 years. Collectively, our findings affirm that THI-BRC's biospecimen storage protocols align with accepted standards as confirmed by the quality assessment of long-term stored clinical samples.
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Affiliation(s)
- Lourdes Chacon Alberty
- Biorepository and Biospecimen Profiling Core, The Texas Heart Institute, Houston, Texas, USA
- Regenerative Medicine Research, The Texas Heart Institute, Houston, Texas, USA
| | - Madelyn King
- Biorepository and Biospecimen Profiling Core, The Texas Heart Institute, Houston, Texas, USA
| | | | - Camila Hochman-Mendez
- Biorepository and Biospecimen Profiling Core, The Texas Heart Institute, Houston, Texas, USA
- Regenerative Medicine Research, The Texas Heart Institute, Houston, Texas, USA
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Radojevic DN, Todorovic MS, Vitosevic KM, Canovic V, Pavicevic M, Slovic ZS, Andric IM, Matic S, Todorovic DV. The changes in tissue histomorphology and quality of DNA in healthy human autopsied tissues stored at -20 °C and -150 °C. Leg Med (Tokyo) 2024; 67:102396. [PMID: 38237382 DOI: 10.1016/j.legalmed.2024.102396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 01/05/2024] [Indexed: 03/01/2024]
Abstract
The aim of this study was to compare the changes in tissue histomorphology and DNA quality in six different healthy tissues (brain, heart, lung, liver, spleen and kidney) exempted during autopsy of healthy individuals and storage at -20 °C and -150 °C three month. Tissue samples were obtained, divided by tissue and temperature group, and for each sample, tissue histomorphology and DNA (isolated from all tissues in duplicated - 72 samples of DNA) quality were analysed. Morphology of tissue samples was studied using H&E staining. DNA was isolated using the phenol-chloroform-isoamyl alcohol method. To assess the concentration and purity of the DNA samples, we used a spectrophotometer to measure absorbance at wavelengths of 280 nm and 260 nm. The fragments of human telomerase reverse transcriptase (hTERT) gene were amplified from the DNA using PCR reaction and then visualised using the 2 % agarose gel. Samples stored at -150 °C sustained the highest degree of histomorphological damage, while samples stored at -20 °C were less degraded, compared to control. The liver samples stored at -20 °C had a mean DNA concentration (1030.4 ± 51.5 ng/μl) higher than the samples of liver tissue stored at -150 °C (497.4 ± 167.1 ng/μl) (p < 0.001). Other tissues did not have statistically significantly different DNA concentration at both temperatures. Liver samples at -20 °C had degraded DNA, showed as the absence of hTERT gene in most of samples. Other tissue samples in both temperature groups had unfragmented DNA. Storing tissue samples at -20 °C is not inferior in terms of DNA yield and integrity, and possibly superior for tissue histomorphology, comparing with samples stored at -150⁰C.
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Affiliation(s)
- Dusan N Radojevic
- University of Kragujevac, Serbia, Faculty of Medical Sciences, Department of Genetics
| | - Milos S Todorovic
- University of Kragujevac, Serbia, Faculty of Medical Sciences, Department of Forensic medicine; University Clinical Center Kragujevac, Department of Forensic Medicine and Toxicology, Kragujevac, Serbia.
| | - Katarina M Vitosevic
- University of Kragujevac, Serbia, Faculty of Medical Sciences, Department of Forensic medicine; University Clinical Center Kragujevac, Department of Forensic Medicine and Toxicology, Kragujevac, Serbia
| | - Vanja Canovic
- University of Kragujevac, Serbia, Faculty of Medical Sciences, Department of Forensic medicine; University Clinical Center Kragujevac, Department of Forensic Medicine and Toxicology, Kragujevac, Serbia
| | - Milena Pavicevic
- University of Kragujevac, Serbia, Faculty of Science and Mathematics
| | - Zivana S Slovic
- University of Kragujevac, Serbia, Faculty of Medical Sciences, Department of Forensic medicine; University Clinical Center Kragujevac, Department of Forensic Medicine and Toxicology, Kragujevac, Serbia
| | - Ivana M Andric
- University of Kragujevac, Serbia, Faculty of Medical Sciences, Department of Forensic medicine
| | - Stevan Matic
- Institute of Pathology and Forensic Medicine, Military Medical Academy, Belgrade, Serbia
| | - Danijela V Todorovic
- University of Kragujevac, Serbia, Faculty of Medical Sciences, Department of Genetics
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McCall SJ, Lubensky IA, Moskaluk CA, Parwani A, Radin K, Ramirez NC, Von Menchhofen Z, Washington MK, LiVolsi VA. The Cooperative Human Tissue Network of the National Cancer Institute: Supporting Cancer Research for 35 Years. Mol Cancer Ther 2023; 22:1144-1153. [PMID: 37523711 PMCID: PMC10626893 DOI: 10.1158/1535-7163.mct-22-0714] [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: 11/04/2022] [Revised: 03/20/2023] [Accepted: 07/25/2023] [Indexed: 08/02/2023]
Abstract
The Cooperative Human Tissue Network was created by the NCI in 1987 to support a coordinated national effort to collect and distribute high quality, pathologist-validated human tissues for cancer research. Since then, the network has expanded to provide different types of tissue samples, blood and body fluid samples, immunohistologic and molecular sample preparations, tissue microarrays, and clinical datasets inclusive of biomarkers and molecular testing. From inception through the end of 2021, the network has distributed 1,375,041 biospecimens. It served 889 active investigators in 2021. The network has also taken steps to begin to optimize the representation of diverse communities among the distributed biospecimens. In this article, the authors review the 35-year history of this network, describe changes to the program over the last 15 years, and provide operational and scientific highlights from each of the divisions. Readers will learn how to engage with the network and about the continued evolution of the program for the future.
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Affiliation(s)
- Shannon J McCall
- Department of Pathology, Duke University School of Medicine and Duke Cancer Institute, Durham, North Carolina
| | | | | | - Anil Parwani
- Department of Pathology, The Ohio State University, Columbus, Ohio
| | | | | | | | - Mary K Washington
- Department of Pathology, Vanderbilt University, Nashville, Tennessee
| | - Virginia A LiVolsi
- Department of Pathology, University of Pennsylvania, Philadelphia, Pennsylvania
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Laberiano-Fernández C, Luján JM, de Carvalho Dornelas B, Benites MF, Quispe PG, Vásquez VA, Espinoza AG, Guerra EG, Álvarez GGA, Astigueta-Pérez J, de Dávila MTG, Zambrano SC, Rojas TV, Mariños A, González ES, Lazcano R, Lastra RR, Alvarado-Cabrero I, Miller HG, Bardales RH, Abad-Licham M. Highlights from the 7th Oncological Pathology Conference 'Pathological Anatomy in the context of the National Cancer Law: An overview of the Latin American experience', 15, 22 and 23 July 2022, Trujillo, Peru. Ecancermedicalscience 2022; 16:1462. [PMID: 36819804 PMCID: PMC9934878 DOI: 10.3332/ecancer.2022.1462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Indexed: 11/06/2022] Open
Abstract
The seventh session of the Oncological Pathology Conference (JoPaO) entitled 'Pathological Anatomy in the context of the National Cancer Law: An overview of the Latin American experience', was held virtually on July 15, 22 and 23. Peru was the headquarters for this event, where 17 national and international professors of high academic standing participated. They interacted in a multidisciplinary context through talks with national panellists and the general public. The recent promulgation of the 'National Cancer Law' fosters the development of discussion forums to analyse the national realities and uphold continuous learning about experiences in other Latin American countries with successful cancer programmes, in which pathology holds a principal role. The topics addressed during this JoPaO included the exchange of Latin American cancer management experiences, an emphasis on investments in and the development of strategic plans to improve care, the use of new technologies, laboratory quality control, and the need to advance scientific research.
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Affiliation(s)
| | - Joan Moreno Luján
- Peruvian Society of Medical Oncology, Lima 15037, Peru,https://orcid.org/0000-0003-2621-7198
| | - Bruno de Carvalho Dornelas
- Clinical Hospital of the Federal University of Uberlandia, Uberlândia, MG, 38405-320,,https://orcid.org/0000-0003-1404-8876
| | - Magali Franco Benites
- Ramiro Prialé Prialé National Hospital, Huancayo 12006, Peru,https://orcid.org/0000-0002-4872-1646
| | - Patricia Gutiérrez Quispe
- Carlos Alberto Seguín Escobedo National Hospital, EsSalud, Arequipa 04001, Peru,https://orcid.org/0000-0002-1491-1556
| | - Valeria Aguilar Vásquez
- Northern Regional Institute of Neoplastic Diseases, Trujillo 13008, Peru,https://orcid.org/0000-0001-6889-0175
| | - Andric Guerrero Espinoza
- Northern Regional Institute of Neoplastic Diseases, Trujillo 13008, Peru,https://orcid.org/0000-0002-2619-1920
| | - Elsa Guerra Guerra
- Alberto Sabogal Sologuren National Hospital, Callao 07011, Peru,https://orcid.org/0000-0002-6320-1278
| | | | - Juan Astigueta-Pérez
- Antenor Orrego Private University School of Medicine, Trujillo 13008, Peru,https://orcid.org/0000-0001-5984-3270
| | - Maria Teresa Garcia de Dávila
- Garrahan and British Paediatric Hospital of Buenos Aires, Buenos Aires C1245 CABA, Argentina,https://orcid.org/0000-0002-3561-5035
| | - Sandro Casavilca Zambrano
- National Institute of Neoplastic Diseases, Lima, Surquillo 15038, Peru,https://orcid.org/0000-0001-8406-739X
| | - Tatiana Vidaurre Rojas
- National Institute of Neoplastic Diseases, Lima, Surquillo 15038, Peru,https://orcid.org/0000-0003-1995-4560
| | - Alejandro Mariños
- MD Anderson Cancer Center, Houston, TX 77030, United States,https://orcid.org/0000-0001-8179-5789
| | - Emmanuel S González
- Dr. Enrique Baltodano Briceño Hospital (HEBB), CCSS, Liberia 50101, Costa Rica,https://orcid.org/0000-0001-6204-3231
| | - Rossana Lazcano
- MD Anderson Cancer Center, Houston, TX 77030, United States,https://orcid.org/0000-0001-9890-2325
| | - Ricardo R Lastra
- The University of Chicago Medical Center, Chicago, IL 60637, United States,https://orcid.org/0000-0003-0691-5685
| | - Isabel Alvarado-Cabrero
- Star Medica Central Hospital, Mexico,Mexican Oncology Hospital, Mexico City 14080, Mexico,https://orcid.org/0000-0003-4000-9280
| | - Henry Guerra Miller
- National Institute of Neoplastic Diseases, Lima, Surquillo 15038, Peru,https://orcid.org/0000-0002-4894-5631
| | - Ricardo H Bardales
- Outpatient Pathology Associates/Precision Pathology, Sacramento, CA 95826, United States,https://orcid.org/0000-0003-1238-8535
| | - Milagros Abad-Licham
- Northern Regional Institute of Neoplastic Diseases, Trujillo 13008, Peru,Antenor Orrego Private University School of Medicine, Trujillo 13008, Peru,Centre of Excellence in Pathological Oncology, Trujillo 13011, Perú,https://orcid.org/0000-0002-3530-6937
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Szechtman H, Dvorkin-Gheva A, Gomez-Marin A. A virtual library for behavioral performance in standard conditions-rodent spontaneous activity in an open field during repeated testing and after treatment with drugs or brain lesions. Gigascience 2022; 11:giac092. [PMID: 36261217 PMCID: PMC9581716 DOI: 10.1093/gigascience/giac092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/31/2022] [Accepted: 09/06/2022] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND Beyond their specific experiment, video records of behavior have future value-for example, as inputs for new experiments or for yet unknown types of analysis of behavior-similar to tissue or blood sample banks in life sciences where clinically derived or otherwise well-described experimental samples are stored to be available for some unknown potential future purpose. FINDINGS Research using an animal model of obsessive-compulsive disorder employed a standardized paradigm where the behavior of rats in a large open field was video recorded for 55 minutes on each test. From 43 experiments, there are 19,976 such trials that amount to over 2 years of continuous recording. In addition to videos, there are 2 video-derived raw data objects: XY locomotion coordinates and plots of animal trajectory. To motivate future use, the 3 raw data objects are annotated with a general schema-one that abstracts the data records from their particular experiment while providing, at the same time, a detailed list of independent variables bearing on behavioral performance. The raw data objects are deposited as 43 datasets but constitute, functionally, a library containing 1 large dataset. CONCLUSIONS Size and annotation schema give the library high reuse potential: in applications using machine learning techniques, statistical evaluation of subtle factors, simulation of new experiments, or as educational resource. Ultimately, the library can serve both as the seed and as the test bed to create a machine-searchable virtual library of linked open datasets for behavioral performance in defined conditions.
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Affiliation(s)
- Henry Szechtman
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Anna Dvorkin-Gheva
- Department of Pathology & Molecular Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Alex Gomez-Marin
- Department of Systems Neurobiology, Instituto de Neurociencias (CSIC-UMH), 03550 Sant Joan d'Alacant, Alicante, Spain
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Zhu Y, Jackson D, Hunter B, Beattie L, Turner L, Hambly BD, Jeremy RW, Malecki C, Robertson EN, Li A, Remedios C, Richmond D, Semsarian C, O'Sullivan JF, Bannon PG, Lal S. Models of cardiovascular surgery biobanking to facilitate translational research and precision medicine. ESC Heart Fail 2021; 9:21-30. [PMID: 34931483 PMCID: PMC8787984 DOI: 10.1002/ehf2.13768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 11/07/2021] [Accepted: 12/02/2021] [Indexed: 11/17/2022] Open
Abstract
Biobanking in health care has evolved over the last few decades from simple biological sample repositories to complex and dynamic units with multi‐organizational infrastructure networks and has become an essential tool for modern medical research. Cardiovascular tissue biobanking provides a unique opportunity to utilize cardiac and vascular samples for translational research into heart failure and other related pathologies. Current techniques for diagnosis, classification, and treatment monitoring of cardiac disease relies primarily on interpretation of clinical signs, imaging, and blood biomarkers. Further research at the disease source (i.e. myocardium and blood vessels) has been limited by a relative lack of access to quality human cardiac tissue and the inherent shortcomings of most animal models of heart disease. In this review, we describe a model for cardiovascular tissue biobanking and databasing, and its potential to facilitate basic and translational research. We share techniques to procure endocardial samples from patients with hypertrophic cardiomyopathy, heart failure with reduced ejection fraction, and heart failure with preserved ejection fraction, in addition to aortic disease samples. We discuss some of the issues with respect to data collection, privacy, biobank consent, and the governance of tissue biobanking. The development of tissue biobanks as described here has significant scope to improve and facilitate translational research in multi‐omic fields such as genomics, transcriptomics, proteomics, and metabolomics. This research heralds an era of precision medicine, in which patients with cardiovascular pathology can be provided with optimized and personalized medical care for the treatment of their individual phenotype.
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Affiliation(s)
- YingYan Zhu
- Department of Cardiothoracic Surgery Royal Prince Alfred Hospital Sydney New South Wales Australia
| | - Dan Jackson
- Department of Cardiothoracic Surgery Royal Prince Alfred Hospital Sydney New South Wales Australia
| | - Benjamin Hunter
- Cardiovascular Precision Laboratory The University of Sydney Sydney New South Wales 2006 Australia
- Charles Perkins Centre The University of Sydney Sydney New South Wales Australia
- Faculty of Medicine and Health The University of Sydney Sydney New South Wales Australia
| | - Lorna Beattie
- Department of Cardiothoracic Surgery Royal Prince Alfred Hospital Sydney New South Wales Australia
- The Baird Institute for Applied Heart and Lung Surgical Research Sydney New South Wales Australia
| | - Lisa Turner
- Department of Cardiothoracic Surgery Royal Prince Alfred Hospital Sydney New South Wales Australia
- The Baird Institute for Applied Heart and Lung Surgical Research Sydney New South Wales Australia
| | - Brett D. Hambly
- Charles Perkins Centre The University of Sydney Sydney New South Wales Australia
- Faculty of Medicine and Health The University of Sydney Sydney New South Wales Australia
| | - Richmond W. Jeremy
- Faculty of Medicine and Health The University of Sydney Sydney New South Wales Australia
- The Baird Institute for Applied Heart and Lung Surgical Research Sydney New South Wales Australia
- Department of Cardiology Royal Prince Alfred Hospital Sydney New South Wales Australia
| | - Cassandra Malecki
- Faculty of Medicine and Health The University of Sydney Sydney New South Wales Australia
| | - Elizabeth N. Robertson
- Faculty of Medicine and Health The University of Sydney Sydney New South Wales Australia
- Department of Cardiology Royal Prince Alfred Hospital Sydney New South Wales Australia
| | - Amy Li
- Faculty of Medicine and Health The University of Sydney Sydney New South Wales Australia
- Department of Pharmacy & Biomedical Sciences La Trobe University Melbourne Victoria Australia
| | - Cris Remedios
- Faculty of Medicine and Health The University of Sydney Sydney New South Wales Australia
| | - David Richmond
- Faculty of Medicine and Health The University of Sydney Sydney New South Wales Australia
- Department of Cardiology Royal Prince Alfred Hospital Sydney New South Wales Australia
| | - Christopher Semsarian
- Faculty of Medicine and Health The University of Sydney Sydney New South Wales Australia
- Department of Cardiology Royal Prince Alfred Hospital Sydney New South Wales Australia
- Agnes Ginges Centre for Molecular Cardiology Centenary Institute Sydney New South Wales Australia
| | - John F. O'Sullivan
- Cardiovascular Precision Laboratory The University of Sydney Sydney New South Wales 2006 Australia
- Charles Perkins Centre 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 Cardiology Royal Prince Alfred Hospital Sydney New South Wales Australia
- Heart Research Institute The University of Sydney Sydney New South Wales Australia
| | - Paul G. Bannon
- Department of Cardiothoracic Surgery Royal Prince Alfred Hospital Sydney New South Wales Australia
- Charles Perkins Centre The University of Sydney Sydney New South Wales Australia
- Faculty of Medicine and Health The University of Sydney Sydney New South Wales Australia
- The Baird Institute for Applied Heart and Lung Surgical Research Sydney New South Wales Australia
- RPA Institute of Academic Surgery (IAS) Royal Prince Alfred Hospital and the University of Sydney Sydney New South Wales Australia
| | - Sean Lal
- Cardiovascular Precision Laboratory The University of Sydney Sydney New South Wales 2006 Australia
- Charles Perkins Centre The University of Sydney Sydney New South Wales Australia
- Faculty of Medicine and Health The University of Sydney Sydney New South Wales Australia
- The Baird Institute for Applied Heart and Lung Surgical Research Sydney New South Wales Australia
- Department of Cardiology Royal Prince Alfred Hospital Sydney New South Wales Australia
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Li X, Han J, Zhang S, Chen K, Zhao L, He Y, Liu S. Artificial Intelligence for Screening Chinese Electronic Medical Record and Biobank Information. Biopreserv Biobank 2021; 19:386-393. [PMID: 34042506 DOI: 10.1089/bio.2020.0151] [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: 11/13/2022] Open
Abstract
Objective: To establish a structured and integrated platform of clinical data and biobank data, and a client to retrieve these data. Study Design: Initially, the hospital information system (HIS) and biobank information system (BIS) were integrated through the patients' ID numbers. Then, natural language processing (NLP) was used to process the integrated unstructured clinical information. A query interface was designed for this system, which enabled researchers to retrieve clinical or biobank data. Finally, several queries were listed and manually checked to test the retrieval performance of the system. Results: The construction of the biobank screening system (BSS) was completed, and the data were structured. The BSS took an average of 2 seconds to perform a search for target patients/samples. The retrieval results were consistent with the HIS and BIS. For complex queries, we manually checked the retrieved patients/samples, and the system's accuracy was 100%. Conclusion: This NLP-based system improved biological sample screening and using of clinical data. We will continue to improve this system, enhance resource sharing, and promote the development of translational medicine.
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Affiliation(s)
- Xiaoqing Li
- Department of Biobank, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiang Han
- Department of Biobank, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shaodian Zhang
- Synyi Research, Shanghai, China.,APEX Data and Knowledge Management Lab, Shanghai Jiao Tong University, Shanghai, China
| | | | - Liebin Zhao
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Child Health Advocacy Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yi He
- Department of Informatics, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shijian Liu
- Department of Biobank, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Child Health Advocacy Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Pak MG, Roh MS. Influence of Cold Ischemia Time and Storage Period on DNA Quality and Biomarker Research in Biobanked Colorectal Cancer Tissues. KOSIN MEDICAL JOURNAL 2020. [DOI: 10.7180/kmj.2020.35.1.26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Objectives Biobanking plays an important role in future research. Assessment and control of the preanalytical variables of biobanked tissues are fundamentals for the optimal use of biospecimens. Methods Forty-five colorectal cancer (CRC) tissues stored at −80°C in Bio-Resource Bank were evaluated to define the influence of cold ischemia time (CIT) and storage period (SP) on DNA quality in biobanked tissues. Three CITs (less than 30 minutes (CIT-1), 30–45 minutes (CIT-2), and 45–60 minutes (CIT-3)) and three SPs (less than 1 year (SP-1), 2–3 years (SP-2), and 4–5 years (SP-3)) were chosen. NanoDrop spectrophotometer was used to determine the 260/280 ratio for DNA purity. DNA integrity was analyzed by a UV transilluminator following electrophoresis on 2% agarose gel. To evaluate the practical usability of DNA for biomarker research, KRAS mutation status was assessed by PCR amplification. Results All DNA specimens had a 260/280 ratio ranging between 1.8 and 2.0 with the exception of one specimen (CIT-2/SP-2 group). For DNA integrity, DNA appeared as a compact, high-molecular-weight band with no or scanty low-molecular-weight smears. The concordance of KRAS mutation status between paired biobanked frozen tissues and formalin-fixed paraffin-embedded tissues was 100%. DNA remained stable in CRC tissues kept at room temperature for up to 1 hour and long-term storage up to 5 years. Conclusions Storage conditions of our biobank are suitable for long-term (at least five years) specimen preservation with high DNA quality. These results have practical implications that could affect banking guidelines.
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9
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Brogna R, Oldenhof H, Sieme H, Figueiredo C, Kerrinnes T, Wolkers WF. Increasing storage stability of freeze-dried plasma using trehalose. PLoS One 2020; 15:e0234502. [PMID: 32525915 PMCID: PMC7289390 DOI: 10.1371/journal.pone.0234502] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 05/26/2020] [Indexed: 12/13/2022] Open
Abstract
Preservation of blood plasma in the dried state would facilitate long-term storage and transport at ambient temperatures, without the need of to use liquid nitrogen tanks or freezers. The aim of this study was to investigate the feasibility of dry preservation of human plasma, using sugars as lyoprotectants, and evaluate macromolecular stability of plasma components during storage. Blood plasma from healthy donors was freeze dried using 0-10% glucose, sucrose, or trehalose, and stored at various temperatures. Differential scanning calorimetry was used to measure the glass transition temperatures of freeze-dried samples. Protein aggregation, the overall protein secondary structure, and oxidative damage were studied under different storage conditions. Differential scanning calorimetry measurements showed that plasma freeze-dried with glucose, sucrose and trehalose have glass transition temperatures of respectively 72±3.4°C, 46±11°C, 15±2.4°C. It was found that sugars diminish freeze-drying induced protein aggregation in a dose-dependent manner, and that a 10% (w/v) sugar concentration almost entirely prevents protein aggregation. Protein aggregation after rehydration coincided with relatively high contents of β-sheet structures in the dried state. Trehalose reduced the rate of protein aggregation during storage at elevated temperatures, and plasma that is freeze- dried plasma with trehalose showed a reduced accumulation of reactive oxygen species and protein oxidation products during storage. In conclusion, freeze-drying plasma with trehalose provides an attractive alternative to traditional cryogenic preservation.
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Affiliation(s)
- Raffaele Brogna
- Unit for Reproductive Medicine—Clinic for Horses, University of Veterinary Medicine Hannover, Hannover, Germany
- Biostabilization laboratory—Lower Saxony Centre for Biomedical Engineering, Implant Research and Development, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Harriëtte Oldenhof
- Unit for Reproductive Medicine—Clinic for Horses, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Harald Sieme
- Unit for Reproductive Medicine—Clinic for Horses, University of Veterinary Medicine Hannover, Hannover, Germany
| | | | | | - Willem F. Wolkers
- Unit for Reproductive Medicine—Clinic for Horses, University of Veterinary Medicine Hannover, Hannover, Germany
- Biostabilization laboratory—Lower Saxony Centre for Biomedical Engineering, Implant Research and Development, University of Veterinary Medicine Hannover, Hannover, Germany
- * E-mail:
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Dudez O, Dalstein V, Kanagaratnam L, Nasri S, Coquelet C, Fichel C, Bouland N, Lemaire E, Diebold MD, Marchal-Bressenot A, Boulagnon-Rombi C. Is the Mirror Image Method Really Useful in Tumor Tissue Bank Quality Control? Biopreserv Biobank 2019; 17:539-545. [PMID: 31233333 DOI: 10.1089/bio.2018.0123] [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: 11/12/2022] Open
Abstract
Oncology research projects are highly dependent on the quality of tumor samples stored in the biobank. Microscopic control is important to ensure the quality of the frozen sample (Does the sample correspond to tumor tissue? Does the sample contain a sufficient number of tumor cells for molecular analysis?). The aim of this study was to evaluate the value of the mirror image method in quality control of colonic adenocarcinoma samples stored in a tumor bank. Microscopic concordance for the differentiation grade, malignant and normal cell percentages, necrosis, mucinous component, and ulceration was assessed on 82 colon adenocarcinoma banked samples and their paired, formalin-fixed, paraffin-embedded mirror controls. Molecular concordance for KRAS status was evaluated in 76 of these 82 cases. Morphological correspondence between frozen and mirror samples was good for the mucinous component (intraclass correlation coefficient [ICC] = 0.81), moderate for differentiation (Cohen's kappa coefficient [k] = 0.67), fair for malignant cells (ICC = 0.44), and poor for ulceration (k = 0.08), normal tissue (ICC = 0.36), and necrosis (ICC = 0.13) percentages. Molecular correspondence for KRAS status was almost perfect (95% correspondence, k = 0.88) between frozen and mirror samples. In conclusion, the mirror sample method is not a good alternative for microscopic and molecular control of frozen colonic adenocarcinoma samples.
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Affiliation(s)
- Oriane Dudez
- Pathology Department, Academic Hospital, Reims, France
| | - Véronique Dalstein
- Pathology Department, Academic Hospital, Reims, France.,Champagne Ardenne Cancers' Molecular Genetic Platform, Reims, France.,Inserm UMR-S 903, Université de Reims Champagne Ardenne, Reims, France
| | | | - Saviz Nasri
- Champagne Ardenne Biobank, Academic Hospital, Reims, France
| | | | | | - Nicole Bouland
- Pathology Department, Medicine University, Reims, France
| | - Emeric Lemaire
- Pathology Department, Academic Hospital, Reims, France.,Inserm UMR-S 903, Université de Reims Champagne Ardenne, Reims, France
| | - Marie-Danièle Diebold
- Pathology Department, Academic Hospital, Reims, France.,Champagne Ardenne Biobank, Academic Hospital, Reims, France.,Pathology Department, Medicine University, Reims, France
| | - Aude Marchal-Bressenot
- Pathology Department, Academic Hospital, Reims, France.,Pathology Department, Medicine University, Reims, France
| | - Camille Boulagnon-Rombi
- Pathology Department, Academic Hospital, Reims, France.,Pathology Department, Medicine University, Reims, France.,UMR CNRS 7369, Reims University, Reims, France
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11
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Almarzooqi S, Campbell C. Genetic Research Using Archival Tissue: Ethical, Social, and Legal Considerations in the United Arab Emirates. Asian Bioeth Rev 2018; 10:219-230. [PMID: 33717288 DOI: 10.1007/s41649-018-0062-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 07/02/2018] [Indexed: 10/26/2022] Open
Abstract
Pathological archival tissue has been used as a source of research material for many years. The advancement in molecular techniques led to an escalated interest in genetic research on archival tissue. Research on archival tissue has been used without obtaining consents from patients, although the ethical justification for such a practice is unlikely to apply for genetic research that involves whole genome sequencing, for instance. Issues of confidentiality and patients' autonomy are being raised as institutions consider when approval for this type of research should be granted. In addition, patients' advocate is mandating some of these changes. In the context of the United Arab Emirates, this paper makes clear the current uncertainties arising from the use of archival tissue in genetic research, as it could be highly invasive of privacy interests and also fails to respect autonomous choice. It further explains what needs to change in order to support such research that is directed at promoting public good, but in a way that is not detrimental to the welfare of patients as research participants.
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Affiliation(s)
- Saeeda Almarzooqi
- Pathology Department, College of Medicine and Health Sciences, United Arab Emirates University, P.O. Box 17666, Al Ain, United Arab Emirates
| | - Carol Campbell
- College of Natural and Health Sciences, Zayed University, P.O. Box 144534, Abu Dhabi, United Arab Emirates
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12
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Moore N, Doty D, Zielstorff M, Kariv I, Moy LY, Gimbel A, Chevillet JR, Lowry N, Santos J, Mott V, Kratchman L, Lau T, Addona G, Chen H, Borenstein JT. A multiplexed microfluidic system for evaluation of dynamics of immune-tumor interactions. LAB ON A CHIP 2018; 18:1844-1858. [PMID: 29796561 DOI: 10.1039/c8lc00256h] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Recapitulation of the tumor microenvironment is critical for probing mechanisms involved in cancer, and for evaluating the tumor-killing potential of chemotherapeutic agents, targeted therapies and immunotherapies. Microfluidic devices have emerged as valuable tools for both mechanistic studies and for preclinical evaluation of therapeutic agents, due to their ability to precisely control drug concentrations and gradients of oxygen and other species in a scalable and potentially high throughput manner. Most existing in vitro microfluidic cancer models are comprised of cultured cancer cells embedded in a physiologically relevant matrix, collocated with vascular-like structures. However, the recent emergence of immune checkpoint inhibitors (ICI) as a powerful therapeutic modality against many cancers has created a need for preclinical in vitro models that accommodate interactions between tumors and immune cells, particularly for assessment of unprocessed tumor fragments harvested directly from patient biopsies. Here we report on a microfluidic model, termed EVIDENT (ex vivo immuno-oncology dynamic environment for tumor biopsies), that accommodates up to 12 separate tumor biopsy fragments interacting with flowing tumor-infiltrating lymphocytes (TILs) in a dynamic microenvironment. Flow control is achieved with a single pump in a simple and scalable configuration, and the entire system is constructed using low-sorption materials, addressing two principal concerns with existing microfluidic cancer models. The system sustains tumor fragments for multiple days, and permits real-time, high-resolution imaging of the interaction between autologous TILs and tumor fragments, enabling mapping of TIL-mediated tumor killing and testing of various ICI treatments versus tumor response. Custom image analytic algorithms based on machine learning reported here provide automated and quantitative assessment of experimental results. Initial studies indicate that the system is capable of quantifying temporal levels of TIL infiltration and tumor death, and that the EVIDENT model mimics the known in vivo tumor response to anti-PD-1 ICI treatment of flowing TILs relative to isotype control treatments for syngeneic mouse MC38 tumors.
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Affiliation(s)
- N Moore
- Materials and Microfabrication Directorate, Draper, Cambridge, MA 02139, USA.
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13
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Somers GR, Vargas SO, Coffin CM. Society for Pediatric Pathology Comment on Proposed Changes to Regulations on Research with Human Tissues (Docket ID#: HHS-OPHS-2015-0008). Pediatr Dev Pathol 2017; 19:428-430. [PMID: 26926166 DOI: 10.2350/16-03-1784-let.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Gino R Somers
- Division of Pathology Hospital for Sick Children & University of Toronto, Toronto, Canada
| | - Sara O Vargas
- Department of Pathology Boston Children's Hospital & Harvard Medical School, Boston, MA, USA
| | - Cheryl M Coffin
- Department of Pathology Vanderbilt Medical Center, Nashville, TN, USA
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14
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Multicenter fresh frozen tissue sampling in colorectal cancer: does the quality meet the standards for state of the art biomarker research? Cell Tissue Bank 2017; 18:425-431. [PMID: 28258397 PMCID: PMC5587614 DOI: 10.1007/s10561-017-9613-x] [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] [Received: 10/20/2016] [Accepted: 02/23/2017] [Indexed: 02/07/2023]
Abstract
The growing interest in the molecular subclassification of colorectal cancers is increasingly facilitated by large multicenter biobanking initiatives. The quality of tissue sampling is pivotal for successful translational research. This study shows the quality of fresh frozen tissue sampling within a multicenter cohort study for colorectal cancer (CRC) patients. Each of the seven participating hospitals randomly contributed ten tissue samples, which were collected following Standard Operating Procedures (SOP) using established techniques. To indicate if the amount of intact RNA is sufficient for molecular discovery research and prove SOP compliance, the RNA integrity number (RIN) was determined. Samples with a RIN < 6 were measured a second time and when consistently low a third time. The highest RIN was used for further analysis. 91% of the tissue samples had a RIN ≥ 6 (91%). The remaining six samples had a RIN between 5 and 6 (4.5%) or lower than 5 (4.5%). The median overall RIN was 7.3 (range 2.9-9.0). The median RIN of samples in the university hospital homing the biobank was 7.7 and the median RIN for the teaching hospitals was 7.3, ranging from 6.5 to 7.8. No differences were found in the outcome of different hospitals (p = 0.39). This study shows that the collection of high quality fresh frozen samples of colorectal cancers is feasible in a multicenter design with complete SOP adherence. Thus, using basic sampling techniques large patient cohorts can be organized for predictive and prognostic (bio)marker research for CRC.
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15
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Jacobson RS, Becich MJ, Bollag RJ, Chavan G, Corrigan J, Dhir R, Feldman MD, Gaudioso C, Legowski E, Maihle NJ, Mitchell K, Murphy M, Sakthivel M, Tseytlin E, Weaver J. A Federated Network for Translational Cancer Research Using Clinical Data and Biospecimens. Cancer Res 2015; 75:5194-201. [PMID: 26670560 PMCID: PMC4683415 DOI: 10.1158/0008-5472.can-15-1973] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Advances in cancer research and personalized medicine will require significant new bridging infrastructures, including more robust biorepositories that link human tissue to clinical phenotypes and outcomes. In order to meet that challenge, four cancer centers formed the Text Information Extraction System (TIES) Cancer Research Network, a federated network that facilitates data and biospecimen sharing among member institutions. Member sites can access pathology data that are de-identified and processed with the TIES natural language processing system, which creates a repository of rich phenotype data linked to clinical biospecimens. TIES incorporates multiple security and privacy best practices that, combined with legal agreements, network policies, and procedures, enable regulatory compliance. The TIES Cancer Research Network now provides integrated access to investigators at all member institutions, where multiple investigator-driven pilot projects are underway. Examples of federated search across the network illustrate the potential impact on translational research, particularly for studies involving rare cancers, rare phenotypes, and specific biologic behaviors. The network satisfies several key desiderata including local control of data and credentialing, inclusion of rich phenotype information, and applicability to diverse research objectives. The TIES Cancer Research Network presents a model for a national data and biospecimen network.
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Affiliation(s)
| | - Michael J Becich
- University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania
| | - Roni J Bollag
- Georgia Regents University Cancer Center, Augusta, Georgia
| | - Girish Chavan
- University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania
| | - Julia Corrigan
- University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania
| | - Rajiv Dhir
- University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania
| | - Michael D Feldman
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania
| | | | | | - Nita J Maihle
- Georgia Regents University Cancer Center, Augusta, Georgia
| | - Kevin Mitchell
- University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania
| | | | | | - Eugene Tseytlin
- University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania
| | - JoEllen Weaver
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania
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16
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Bregy A, Papadimitriou K, Faber DA, Shah AH, Gomez CR, Komotar RJ, Egea SC. Banking Brain Tumor Specimens Using a University Core Facility. Biopreserv Biobank 2015; 13:280-6. [PMID: 26280502 DOI: 10.1089/bio.2014.0106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Within the past three decades, the significance of banking human cancer tissue for the advancement of cancer research has grown exponentially. The purpose of this article is to detail our experience in collecting brain tumor specimens in collaboration with the University of Miami/Sylvester Tissue Bank Core Facility (UM-TBCF), to ensure the availability of high-quality samples of central nervous system tumor tissue for research. Successful tissue collection begins with obtaining informed consent from patients following institutional IRB and federal HIPAA guidelines, and it needs a well-trained professional staff and continued maintenance of high ethical standards and record keeping. Since starting in 2011, we have successfully banked 225 brain tumor specimens for research. Thus far, the most common tumor histology identified among those specimens has been glioblastoma (22.1%), followed by meningioma (18.1%). The majority of patients were White, non-Hispanics accounting for 45.1% of the patient population; Hispanic/Latinos accounted for 23%, and Black/African Americans accounted for 14%, which represent the particular population of the State of Florida according to the 2010 census data. The most common tumors found in each subgroup were as follows: Black/African American, glioblastoma and meningioma; Hispanic, metastasis and glioblastoma; White, glioblastoma and meningioma. The UM-TBCF is a valuable repository, offering high-quality tumor samples from a unique patient population.
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Affiliation(s)
- Amade Bregy
- 1 Department of Neurological Surgery, University of Miami Miller School of Medicine , Miami, Florida
| | - Kyriakos Papadimitriou
- 1 Department of Neurological Surgery, University of Miami Miller School of Medicine , Miami, Florida
| | - David A Faber
- 1 Department of Neurological Surgery, University of Miami Miller School of Medicine , Miami, Florida
| | - Ashish H Shah
- 1 Department of Neurological Surgery, University of Miami Miller School of Medicine , Miami, Florida
| | - Carmen R Gomez
- 2 Department of Pathology, University of Miami Miller School of Medicine , Miami, Florida
| | - Ricardo J Komotar
- 1 Department of Neurological Surgery, University of Miami Miller School of Medicine , Miami, Florida
| | - Sophie C Egea
- 1 Department of Neurological Surgery, University of Miami Miller School of Medicine , Miami, Florida
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17
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Li H, Guo Y, Sun B, Chen K. Histological Assessment of Tumor Tissue Samples via the Mirror Image Method. Biopreserv Biobank 2015; 13:25-30. [PMID: 25686044 DOI: 10.1089/bio.2014.0093] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Haixin Li
- Cancer Biobank, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Yan Guo
- Cancer Biobank, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Baocun Sun
- Department of Pathology, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Kexin Chen
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
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18
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Kheirollahi M, Dashti S, Khalaj Z, Nazemroaia F, Mahzouni P. Brain tumors: Special characters for research and banking. Adv Biomed Res 2015; 4:4. [PMID: 25625110 PMCID: PMC4300589 DOI: 10.4103/2277-9175.148261] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 02/25/2014] [Indexed: 12/21/2022] Open
Abstract
A brain tumor is an intracranial neoplasm within the brain or in the central spinal canal. Primary malignant brain tumors affect about 200,000 people worldwide every year. Brain cells have special characters. Due to the specific properties of brain tumors, including epidemiology, growth, and division, investigation of brain tumors and the interpretation of results is not simple. Research to identify the genetic alterations of human tumors improves our knowledge of tumor biology, genetic interactions, progression, and preclinical therapeutic assessment. Obtaining data for prevention, diagnosis, and therapy requires sufficient samples, and brain tumors have a wide range. As a result, establishing the bank of brain tumors is very important and essential.
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Affiliation(s)
- Majid Kheirollahi
- Department of Genetics and Molecular Biology and Pediatrics Inherited Diseases Research Center, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Sepideh Dashti
- Department of Genetics and Molecular Biology and Pediatrics Inherited Diseases Research Center, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Zahra Khalaj
- Department of Genetics and Molecular Biology and Pediatrics Inherited Diseases Research Center, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Fatemeh Nazemroaia
- Department of Genetics and Molecular Biology and Pediatrics Inherited Diseases Research Center, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Parvin Mahzouni
- Department of Pathology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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19
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Shalaby T, Fiaschetti G, Baumgartner M, Grotzer MA. MicroRNA signatures as biomarkers and therapeutic target for CNS embryonal tumors: the pros and the cons. Int J Mol Sci 2014; 15:21554-86. [PMID: 25421247 PMCID: PMC4264241 DOI: 10.3390/ijms151121554] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 11/07/2014] [Accepted: 11/08/2014] [Indexed: 12/19/2022] Open
Abstract
Embryonal tumors of the central nervous system represent a heterogeneous group of childhood cancers with an unknown pathogenesis; diagnosis, on the basis of histological appearance alone, is controversial and patients’ response to therapy is difficult to predict. They encompass medulloblastoma, atypical teratoid/rhabdoid tumors and a group of primitive neuroectodermal tumors. All are aggressive tumors with the tendency to disseminate throughout the central nervous system. The large amount of genomic and molecular data generated over the last 5–10 years encourages optimism that new molecular targets will soon improve outcomes. Recent neurobiological studies have uncovered the key role of microRNAs (miRNAs) in embryonal tumors biology and their potential use as biomarkers is increasingly being recognized and investigated. However the successful use of microRNAs as reliable biomarkers for the detection and management of pediatric brain tumors represents a substantial challenge. This review debates the importance of miRNAs in the biology of central nervous systemembryonal tumors focusing on medulloblastoma and atypical teratoid/rhabdoid tumors and highlights the advantages as well as the limitations of their prospective application as biomarkers and candidates for molecular therapeutic targets.
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Affiliation(s)
- Tarek Shalaby
- Department of Oncology, University Children's Hospital of Zurich, Steinwiesstrasse 75, Zurich 8032, Switzerland.
| | - Giulio Fiaschetti
- Department of Oncology, University Children's Hospital of Zurich, Steinwiesstrasse 75, Zurich 8032, Switzerland.
| | - Martin Baumgartner
- Department of Oncology, University Children's Hospital of Zurich, Steinwiesstrasse 75, Zurich 8032, Switzerland.
| | - Michael A Grotzer
- Department of Oncology, University Children's Hospital of Zurich, Steinwiesstrasse 75, Zurich 8032, Switzerland.
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20
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Establishment and maintenance of a standardized glioma tissue bank: Huashan experience. Cell Tissue Bank 2014; 16:271-81. [PMID: 24929994 DOI: 10.1007/s10561-014-9459-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 06/06/2014] [Indexed: 10/25/2022]
Abstract
Cerebral glioma is the most common brain tumor as well as one of the top ten malignant tumors in human beings. In spite of the great progress on chemotherapy and radiotherapy as well as the surgery strategies during the past decades, the mortality and morbidity are still high. One of the major challenges is to explore the pathogenesis and invasion of glioma at various "omics" levels (such as proteomics or genomics) and the clinical implications of biomarkers for diagnosis, prognosis or treatment of glioma patients. Establishment of a standardized tissue bank with high quality biospecimens annotated with clinical information is pivotal to the solution of these questions as well as the drug development process and translational research on glioma. Therefore, based on previous experience of tissue banks, standardized protocols for sample collection and storage were developed. We also developed two systems for glioma patient and sample management, a local database for medical records and a local image database for medical images. For future set-up of a regional biobank network in Shanghai, we also founded a centralized database for medical records. Hence we established a standardized glioma tissue bank with sufficient clinical data and medical images in Huashan Hospital. By September, 2013, tissues samples from 1,326 cases were collected. Histological diagnosis revealed that 73 % were astrocytic tumors, 17 % were oligodendroglial tumors, 2 % were oligoastrocytic tumors, 4 % were ependymal tumors and 4 % were other central nervous system neoplasms.
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21
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Chen HJ, Yang JJ, Fang LY, Huang MM, Yan HH, Zhang XC, Xu CR, Wu YL. Feasibility of computed tomography-guided core needle biopsy in producing state-of-the-art clinical management in Chinese lung cancer. Thorac Cancer 2014; 5:155-61. [PMID: 26766993 DOI: 10.1111/1759-7714.12076] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2013] [Accepted: 10/06/2013] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND A satisfactory biopsy determines the state-of-the-art management of lung cancer in this era of personalized medicine. This study aimed to investigate the suitability and efficacy of computed tomography (CT)-guided core needle biopsy in clinical management. METHODS A cohort of 353 patients with clinically suspected lung cancer was enrolled in the study. Patient factors and biopsy variables were recorded. Epidermal growth factor receptor (EGFR) gene mutations and echinoderm microtubule-associated protein-like 4 (EML4)-anaplastic lymphoma kinase (ALK) rearrangement were detected in tumor specimens. Adequacy of biopsic obtainment for clinical trial screening and tissue bank establishment were reviewed. RESULTS Overall diagnostic accuracy of malignancy achieved 98.5%. The median biopsy time of the cohort was 20 minutes. In patients with non-small cell lung cancer (NSCLC), 99.3% (287/289) were diagnosed as specific histologic subtypes, and two patients (0.7%) were determined as NSCLC not otherwise specified (NOS). EGFR mutations were analyzed in 81.7% (236/289) of patients with NSCLC, and 98.7% (233/236) showed conclusive results. EML4-ALK gene fusion was tested in 43.9% (127/289) of NSCLC patients, and 98.4% (125/127) showed conclusive results: 6.4% (8/125) of those had gene fusion. Ninety-six NSCLC patients participated in clinical trial screening and provided mandatory tumor slides for molecular profiling. Pathological evaluation was fulfilled in 90 patients (93.8%); 99.4% (320/322) of patients with malignancy provided extra tissue for the establishment of a tumor bank. CONCLUSIONS CT-guided core needle biopsy provided optimal clinical management in this era of translational medicine. The biopsic modality should be prioritized in selected lung cancer patients.
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Affiliation(s)
- Hua-Jun Chen
- Division of Pulmonary Oncology, Guangdong Lung Cancer Institute, Guangdong General Hospital & Guangdong Academy of Medical Sciences Guangzhou, China
| | - Jin-Ji Yang
- Division of Pulmonary Oncology, Guangdong Lung Cancer Institute, Guangdong General Hospital & Guangdong Academy of Medical Sciences Guangzhou, China
| | - Liang-Yi Fang
- Radiotherapy Department, Guangdong General Hospital & Guangdong Academy of Medical Sciences Guangzhou, China
| | - Min-Min Huang
- Radiotherapy Department, Guangdong General Hospital & Guangdong Academy of Medical Sciences Guangzhou, China
| | - Hong-Hong Yan
- Division of Pulmonary Oncology, Guangdong Lung Cancer Institute, Guangdong General Hospital & Guangdong Academy of Medical Sciences Guangzhou, China
| | - Xu-Chao Zhang
- Division of Pulmonary Oncology, Guangdong Lung Cancer Institute, Guangdong General Hospital & Guangdong Academy of Medical Sciences Guangzhou, China
| | - Chong-Rui Xu
- Division of Pulmonary Oncology, Guangdong Lung Cancer Institute, Guangdong General Hospital & Guangdong Academy of Medical Sciences Guangzhou, China
| | - Yi-Long Wu
- Division of Pulmonary Oncology, Guangdong Lung Cancer Institute, Guangdong General Hospital & Guangdong Academy of Medical Sciences Guangzhou, China
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22
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The procurement, storage, and quality assurance of frozen blood and tissue biospecimens in pathology, biorepository, and biobank settings. Clin Biochem 2014; 47:258-66. [PMID: 24424103 DOI: 10.1016/j.clinbiochem.2014.01.002] [Citation(s) in RCA: 167] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 01/04/2014] [Accepted: 01/04/2014] [Indexed: 01/19/2023]
Abstract
Well preserved frozen biospecimens are ideal for evaluating the genome, transcriptome, and proteome. While papers reviewing individual aspects of frozen biospecimens are available, we present a current overview of experimental data regarding procurement, storage, and quality assurance that can inform the handling of frozen biospecimens. Frozen biospecimen degradation can be influenced by factors independent of the collection methodology including tissue type, premortem agonal changes, and warm ischemia time during surgery. Rapid stabilization of tissues by snap freezing immediately can mitigate artifactually altered gene expression and, less appreciated, protein phosphorylation profiles. Collection protocols may be adjusted for specific tissue types as cellular ischemia tolerance varies widely. If data is not available for a particular tissue type, a practical goal is snap freezing within 20min. Tolerance for freeze-thaw events is also tissue type dependent. Tissue storage at -80°C can preserve DNA and protein for years but RNA can show degradation at 5years. For -80°C freezers, aliquots frozen in RNAlater or similar RNA stabilizing solutions are a consideration. It remains unresolved as to whether storage at -150°C provides significant advantages relative to that at -80°C. Histologic quality assurance of tissue biospecimens is typically performed at the time of surgery but should also be conducted on the aliquot to be distributed because of tissue heterogeneity. Biobanking protocols for blood and its components are highly dependent on intended use and multiple collection tube types may be needed. Additional quality assurance testing should be dictated by the anticipated downstream applications.
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Abstract
Powerful technologies critical to personalized medicine and targeted therapeutics require the analysis of carefully validated, procured, stored, and managed biospecimens. Reflecting advancements in biospecimen science, the National Cancer Institute and the International Society for Biological and Environmental Repositories are periodically publishing best practices that can guide the biobanker. The modern biobank will operate more like a clinical laboratory with formal accreditation, standard operating procedures, and quality assurance protocols. This chapter highlights practical issues of consent, procurement, storage, quality assurance, disbursement, funding, and space. Common topics of concern are discussed including the differences between clinical and research biospecimens, stabilization of biospecimens during procurement, optimal storage temperatures, and technical validation of biospecimen content and quality. With quickly expanding biospecimen needs and limited healthcare budgets, biobanks may need to be selective as to what is stored. Furthermore, a shift to room-temperature storage modalities where possible can reduce long-term space and fiscal requirements.
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Affiliation(s)
- William H Yong
- Translational Pathology Core Laboratory, Brain Tumor Translational Resource, Department of Pathology and Laboratory Medicine, Center for Health Sciences, David Geffen School of Medicine at UCLA, 10833 Le Conte Ave, 18-161 CHS, Los Angeles, CA, 90095, USA,
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24
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Grizzle WE, Bell WC, Sexton KC. Issues in collecting, processing and storing human tissues and associated information to support biomedical research. Cancer Biomark 2012; 9:531-49. [PMID: 22112494 DOI: 10.3233/cbm-2011-0183] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The availability of human tissues to support biomedical research is critical to advance translational research focused on identifying and characterizing approaches to individualized (personalized) medical care. Providing such tissues relies on three acceptable models - a tissue banking model, a prospective collection model and a combination of these two models. An unacceptable model is the "catch as catch can" model in which tissues are collected, processed and stored without goals or a plan or without standard operating procedures, i.e., portions of tissues are collected as available and processed and stored when time permits. In the tissue banking model, aliquots of tissues are collected according to SOPs. Usually specific sizes and types of tissues are collected and processed (e.g., 0.1 gm of breast cancer frozen in OCT). Using the banking model, tissues may be collected that may not be used and/or do not meet specific needs of investigators; however, at the time of an investigator request, tissues are readily available as is clinical information including clinical outcomes. In the model of prospective collection, tissues are collected based upon investigator requests including specific requirements of investigators. For example, the investigator may request that two 0.15 gm matching aliquots of breast cancer be minced while fresh, put in RPMI media with and without fetal calf serum, cooled to 4°C and shipped to the investigator on wet ice. Thus, the tissues collected prospectively meet investigator needs, all collected specimens are utilized and storage of specimens is minimized; however, investigators must wait until specimens are collected, and if needed, for clinical outcome. The operation of any tissue repository requires well trained and dedicated personnel. A quality assurance program is required which provides quality control information on the diagnosis of a specimen that is matched specifically to the specimen provided to an investigator instead of an overall diagnosis of the specimen via a surgical pathology report. This is necessary because a specific specimen may not match the diagnosis of the case due to many factors such as necrosis, unsuspected tumor invasion of apparently normal tissue, and areas of fibrosis which are mistaken grossly for tumor. Aliquots for quality control (QC) may or may not be collected at the time of collection and in some cases, QC may not occur until specimens are distributed to investigators. In establishing a tumor repository, multiple issues need to be considered. These include the available resources, long term support, space and equipment. The needs of the potential users need to be identified as to the types of tissues and services needed and the annotation expected. Other specific issues to be considered include collection of specimens potentially infected with blood borne pathogens (e.g., hepatitis B), charge back mechanisms, informatics needs and support, and investigator requirements (e.g., recognition of repository contributions in publications). In general, the repository should not perform the research of the investigators, but should provide the infrastructure necessary to support the research of the investigator. Thus, the goals of the repository must be established. Similarly, ethical and regulatory issues must be evaluated. In general, tissue repositories need ethical (e.g., IRB) and privacy (e.g., HIPAA) review. Also, safety issues need to be considered as well as how biohazards will be addressed by investigator-users. Considerations involving the transfer of specimens to other organization usually require a material transfer agreement (MTA). A MTA should address biohazards as well as indemnification. Thus, many issues must be considered and addressed in order to establish and operate successfully a biorepository.
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Affiliation(s)
- William E Grizzle
- Division of Anatomic Pathology, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA.
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Herpel E, Koleganova N, Schreiber B, Walter B, Kalle CV, Schirmacher P. Structural requirements of research tissue banks derived from standardized project surveillance. Virchows Arch 2012; 461:79-86. [DOI: 10.1007/s00428-012-1258-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 04/17/2012] [Accepted: 05/21/2012] [Indexed: 10/27/2022]
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Abstract
The future success of translational research is critically dependent on the procurement and availability of high-quality tissue specimens linked to accurate histopathologic and clinical information about the individual banked specimen. The international community has awakened to this critical need only recently. Three major roadblocks have hindered the success of previous biobank consortiums: (1) Ethical issues surrounding patient consent and ownership of intellectual property, (2) Failure to properly preserve the molecular content of the tissue, and failure to reliably document clinical data linked to the specimen, and (3) Management issues: inadequate funding, competition for use of the tissue, inadequate personnel and facilities, and absence of dedicated database software. This chapter reviews these critical roadblocks and discusses international efforts to provide strategies to implement high-quality biobanks.
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Affiliation(s)
- Eoin F Gaffney
- Department of Histopathology, Biobank Ireland Trust, St James's Hospital, Dublin, Ireland.
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Jackson C, Dixon-Woods M, Tobin M, Young B, Heney D, Pritchard-Jones K. Seeking consent to tissue banking: a survey of health professionals in childhood cancer. Eur J Cancer Care (Engl) 2011; 18:391-400. [PMID: 19594610 DOI: 10.1111/j.1365-2354.2008.01033.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
To identify the views of health professionals working in childhood cancer on seeking consent to tissue banking from potential donors. Self-completion questionnaires sent to 553 UK paediatric oncology health professionals. The response rate was 60%. Respondents (100%) were in favour of using tissue samples from children with cancer for research. A substantial minority (30%) had concerns about the impact of the law on their professional role in relation to tissue banking. Almost all (90%) reported that both the parent(s) and the child, if able, should be asked for consent, though the UK Human Tissue Act provides that a competent child's consent is sufficient. Most (94%) supported 'generic' rather than 'specific' consent. Barriers to obtaining consent included: (1) timing of the approach to families; (2) availability of suitable staff; (3) sensitivity of the issues; (4) difficulties of managing the process; and (5) problems of maintaining a paper trail. Many would welcome training on seeking consent. Personal knowledge and relationships with families are often seen as important in guiding the proper approach to consent rather than formalized rules. There is widespread support among health professionals for tissue banking in childhood cancer. In sensitive situations, disciplined exercise of professional discretion might better deliver on aspirations for regulation than rigid procedures.
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Affiliation(s)
- C Jackson
- Department of Health Sciences, University of Leicester, Leicester, UK
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Amin W, Singh H, Pople AK, Winters S, Dhir R, Parwani AV, Becich MJ. A decade of experience in the development and implementation of tissue banking informatics tools for intra and inter-institutional translational research. J Pathol Inform 2010; 1:S2153-3539(22)00104-3. [PMID: 20922029 PMCID: PMC2941965 DOI: 10.4103/2153-3539.68314] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2010] [Accepted: 06/18/2010] [Indexed: 11/15/2022] Open
Abstract
Context: Tissue banking informatics deals with standardized annotation, collection and storage of biospecimens that can further be shared by researchers. Over the last decade, the Department of Biomedical Informatics (DBMI) at the University of Pittsburgh has developed various tissue banking informatics tools to expedite translational medicine research. In this review, we describe the technical approach and capabilities of these models. Design: Clinical annotation of biospecimens requires data retrieval from various clinical information systems and the de-identification of the data by an honest broker. Based upon these requirements, DBMI, with its collaborators, has developed both Oracle-based organ-specific data marts and a more generic, model-driven architecture for biorepositories. The organ-specific models are developed utilizing Oracle 9.2.0.1 server tools and software applications and the model-driven architecture is implemented in a J2EE framework. Result: The organ-specific biorepositories implemented by DBMI include the Cooperative Prostate Cancer Tissue Resource (http://www.cpctr.info/), Pennsylvania Cancer Alliance Bioinformatics Consortium (http://pcabc.upmc.edu/main.cfm), EDRN Colorectal and Pancreatic Neoplasm Database (http://edrn.nci.nih.gov/) and Specialized Programs of Research Excellence (SPORE) Head and Neck Neoplasm Database (http://spores.nci.nih.gov/current/hn/index.htm). The model-based architecture is represented by the National Mesothelioma Virtual Bank (http://mesotissue.org/). These biorepositories provide thousands of well annotated biospecimens for the researchers that are searchable through query interfaces available via the Internet. Conclusion: These systems, developed and supported by our institute, serve to form a common platform for cancer research to accelerate progress in clinical and translational research. In addition, they provide a tangible infrastructure and resource for exposing research resources and biospecimen services in collaboration with the clinical anatomic pathology laboratory information system (APLIS) and the cancer registry information systems.
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Affiliation(s)
- Waqas Amin
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, USA
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Boudou-Rouquette P, Touibi N, Boëlle PY, Tiret E, Fléjou JF, Wendum D. Imprint cytology in tumor tissue bank quality control: an efficient method to evaluate tumor necrosis and to detect samples without tumor cells. Virchows Arch 2010; 456:443-7. [PMID: 20191289 DOI: 10.1007/s00428-010-0889-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2009] [Revised: 01/06/2010] [Accepted: 01/31/2010] [Indexed: 01/05/2023]
Abstract
Quality assessment of the tissue stored in a tumor biobank is crucial because it is estimated that approximately 10% of the frozen samples are unsuitable for a molecular analysis mainly because of sampling problems in the tissue. We studied the value of imprint cytology (IC) versus frozen section to quantify necrosis and tumor cells in the tissue. The amount of tumor cells and necrosis was assessed by one pathologist on the frozen sections and ICs independently on 100 consecutive tumor samples. It was expressed as a percentage on frozen sections and on a four-level semiquantitative scale for IC (0 to 3+). Overall agreement between the quantity of tumor cells on IC and on frozen section was fair (Kappa = 0.23). Sensitivity and specificity of IC to detect the absence of tumor cell on the frozen section were 57% (4/7) and 98% (91/93), respectively. Overall agreement between necrosis quantification on IC and on frozen section was substantial (Kappa = 0.66).Sensitivity and specificity of IC to detect significant necrosis (defined as more than 30% necrosis) were 100% (3/3) and 98% (95/97), respectively. We show that IC is efficient to semiquantify necrosis in a tumor sample and to detect significant necrosis. IC seems to be less efficient to quantify tumor cells.
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Affiliation(s)
- Pascaline Boudou-Rouquette
- Service d'Anatomie et Cytologie Pathologiques, AP-HP, Hôpital Saint-Antoine, 184 rue du faubourg St Antoine, 75571 Paris Cedex 12, France
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Yu YY, Zhu ZG. Significance of biological resource collection and tumor tissue bank creation. World J Gastrointest Oncol 2010; 2:5-8. [PMID: 21160810 PMCID: PMC2999151 DOI: 10.4251/wjgo.v2.i1.5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2009] [Revised: 07/04/2009] [Accepted: 07/11/2009] [Indexed: 02/05/2023] Open
Abstract
Progress in the molecular oncology of gastrointestinal carcinomas depends on high quality cancer tissues for research. Recent acceleration on new technological platforms as well as the “omics” revolution increases the demands on tissues and peripheral blood for research at the DNA, mRNA and protein levels. Tissue bank creation emerges as a priority. Tumor tissue banks are facilities that are organized to collect, store and distribute samples of tumor and normal tissue for further use in basic and translational cancer research. The samples are generally obtained immediately after excision, prior to fixation, to ensure optimal preservation of proteins and nucleic acids. It is possible for surgeons or pathologists to collect fresh tissue prospectively during their routine dissection procedures. Most tissue banks are “project-driven” tumor banks, which are specialized collections of tumor samples on which their research is based. Systematic collection of all available tumor tissue is much rarer. High quality tissue banks need the collaboration of clinicians and basic scientists, but also the informed consent of patients and ethical approval. Through the standard operation procedure, snap frozen fresh tissue collection, storage and quality control for cryopreserved tissues are the pivotal factors on tissue bank construction and maintaining. The purpose of the tissue bank creation is enhancing the quality and speed on both the basic and translational research on gastrointestinal cancer. The quality assurance and quality control are handled based on reviewing HE staining slides or touch imprint cytology by pathologists.
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Affiliation(s)
- Ying-Yan Yu
- Ying-Yan Yu, Zheng-Gang Zhu, Department of Surgery, Shanghai Institute of Digestive Surgery, School of Medicine, Shanghai Jiao Tong University, 200025 Shanghai, China
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Bell WC, Sexton KC, Grizzle WE. Organizational issues in providing high-quality human tissues and clinical information for the support of biomedical research. Methods Mol Biol 2010; 576:1-30. [PMID: 19882254 DOI: 10.1007/978-1-59745-545-9_1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
Superior-quality human tissues are required to support many types of biomedical research. To be useful optimally in supporting research, not only must these tissues be accurately diagnosed, but also the specific aliquots of tissue supplied to investigators must be accurately described as part of the quality control analysis of the tissue. Tissues should be collected, processed, and stored uniformly. Some tissues are provided to investigators from tissue banks for which tissues have been collected and processed according to standard operating procedures (SOPs) of the tissue bank. Other tissues provided to support research are collected and processed according to SOPs modified to meet investigator needs and requirements, i.e., prospective collection/processing. These different models of tissue collection require different goals, designs, and SOPs. The objectives of tissue repositories also vary based on the types of tissues provided (e.g., fresh tissue aliquots, fixed paraffin-embedded tissue, paraffin tissue sections, etc.) and how the tissues are to be used in research. For example, the potential use of tissues affects the need for extensive annotation of the specimen including both clinical information (e.g., clinical outcomes) and demographics. Specifically, if the tissues are to be used for extraction of proteins or basic studies of disease processes, less clinical information, if any, may be needed than if the tissues are to be used for the correlation of an aspect of the disease process with clinical outcome or response to a specific therapy. In this review, we describe, based on our experience, the major issues that should be addressed in designing and establishing a tissue repository.
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Affiliation(s)
- Walter C Bell
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
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De Paoli P. Institutional shared resources and translational cancer research. J Transl Med 2009; 7:54. [PMID: 19563639 PMCID: PMC2711056 DOI: 10.1186/1479-5876-7-54] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2009] [Accepted: 06/29/2009] [Indexed: 02/06/2023] Open
Abstract
The development and maintenance of adequate shared infrastructures is considered a major goal for academic centers promoting translational research programs. Among infrastructures favoring translational research, centralized facilities characterized by shared, multidisciplinary use of expensive laboratory instrumentation, or by complex computer hardware and software and/or by high professional skills are necessary to maintain or improve institutional scientific competitiveness. The success or failure of a shared resource program also depends on the choice of appropriate institutional policies and requires an effective institutional governance regarding decisions on staffing, existence and composition of advisory committees, policies and of defined mechanisms of reporting, budgeting and financial support of each resource. Shared Resources represent a widely diffused model to sustain cancer research; in fact, web sites from an impressive number of research Institutes and Universities in the U.S. contain pages dedicated to the SR that have been established in each Center, making a complete view of the situation impossible. However, a nation-wide overview of how Cancer Centers develop SR programs is available on the web site for NCI-designated Cancer Centers in the U.S., while in Europe, information is available for individual Cancer centers. This article will briefly summarize the institutional policies, the organizational needs, the characteristics, scientific aims, and future developments of SRs necessary to develop effective translational research programs in oncology. In fact, the physical build-up of SRs per se is not sufficient for the successful translation of biomedical research. Appropriate policies to improve the academic culture in collaboration, the availability of educational programs for translational investigators, the existence of administrative facilitations for translational research and an efficient organization supporting clinical trial recruitment and management represent essential tools, providing solutions to overcome existing barriers in the development of translational research in biomedical research centers.
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Affiliation(s)
- Paolo De Paoli
- Centro di Riferimento Oncologico, IRCCS, I-33081 Aviano PN Aviano, Italy.
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Somoza N, Torà M. [Biological safety in the storage and transport of biological specimens from patients with respiratory diseases used in research settings]. Arch Bronconeumol 2009; 45:187-95. [PMID: 19327879 DOI: 10.1016/j.arbres.2009.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2009] [Accepted: 02/05/2009] [Indexed: 02/04/2023]
Abstract
Major advances in genomics and proteomics have prompted the creation of biological specimen collections and biobanks for use in biomedical research. These specimen collections and the wealth of data they generate will allow longitudinal studies to be conducted and subproducts such as DNA or RNA to be obtained. They may even be used in future studies. To ensure specimen integrity, from the outset it is necessary to define procedures for sampling, transport and storage, the subproducts to be obtained, and the end purpose, as well as to address biosafety issues and arrange for suitable equipment monitoring. Strict control of these conditions will confer added value on the specimens, as quality and traceability would be assured. This article aims to provide a general overview of the recommendations concerning biological safety, transport, and storage of biological specimens for biomedical research into respiratory diseases in accordance with current legislation.
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Affiliation(s)
- Nuria Somoza
- Servicios Científico-Técnicos, IMIM-Hospital del Mar, Universitat Autònoma de Barcelona (UDIMAS-UAB), Barcelona, España
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Nirmalan NJ, Harnden P, Selby PJ, Banks RE. Development and validation of a novel protein extraction methodology for quantitation of protein expression in formalin-fixed paraffin-embedded tissues using western blotting. J Pathol 2009; 217:497-506. [PMID: 19156775 DOI: 10.1002/path.2504] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The development of efficient formaldehyde cross-link reversal strategies will make the vast diagnostic tissue archives of pathology departments amenable to prospective and retrospective translational research, particularly in biomarker-driven proteomic investigations. Heat-induced antigen retrieval strategies (HIARs) have achieved varying degrees of cross-link reversal, potentially enabling archival tissue usage for proteomic applications outside its current remit of immunohistochemistry (IHC). While most successes achieved so far have been based on retrieving tryptic peptide fragments using shot-gun proteomic approaches, attempts at extracting full-length, non-degraded, immunoreactive proteins from archival tissue have proved challenging. We have developed a novel heat-induced antigen retrieval strategy using SDS-containing Laemmli buffer for efficient intact protein recovery from formalin-fixed tissues for subsequent analysis by western blotting. Protocol optimization and comparison of extraction efficacies with frozen tissues and current leader methodology is presented. Quantitative validation of methodology was carried out in a cohort of matched tumour/normal, frozen/FFPE renal tissue samples from 10 patients, probed by western blotting for a selected panel of seven proteins known to be differentially expressed in renal cancer. Our data show that the protocol enables efficient extraction of non-degraded, full-length, immunoreactive protein, with tumour versus normal differential expression profiles for a majority of the panel of proteins tested being comparable to matched frozen tissue controls (rank correlation, r = 0.7292, p < 1.825e-09). However, the variability observed in extraction efficacies for some membrane proteins emphasizes the need for cautious interpretation of quantitative data from this subset of proteins. The method provides a viable, cost-effective quantitative option for the validation of potential biomarker panels through a range of clinical samples from existing diagnostic archives, provided that validation of the method is first carried out for the specific proteins under study.
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Affiliation(s)
- Niroshini J Nirmalan
- Clinical and Biomedical Proteomics Group, Cancer Research UK Clinical Centre, Leeds, UK
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Sandusky G, Dumaual C, Cheng L. Review Paper: Human Tissues for Discovery Biomarker Pharmaceutical Research: The Experience of the Indiana University Simon Cancer Center—Lilly Research Labs Tissue/Fluid BioBank. Vet Pathol 2009; 46:2-9. [DOI: 10.1354/vp.46-1-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- G. Sandusky
- Simon Cancer Center and Department of Pathology and Laboratory Medicine, Indiana University, Indianapolis, IN
| | - C. Dumaual
- Simon Cancer Center and Department of Pathology and Laboratory Medicine, Indiana University, Indianapolis, IN
| | - L. Cheng
- Simon Cancer Center and Department of Pathology and Laboratory Medicine, Indiana University, Indianapolis, IN
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CQ Sources/Bibliography. Camb Q Healthc Ethics 2008. [DOI: 10.1017/s0963180108080584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
These CQ Sources were compiled by Bette Anton.
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Bell WC, Young ES, Billings PE, Grizzle WE. The efficient operation of the surgical pathology gross room. Biotech Histochem 2008; 83:71-82. [PMID: 18568681 DOI: 10.1080/10520290802127610] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The gross room is the area where pathology specimens from operating rooms are transferred for pathology review and analysis, serving as the bridge between the treating physician and diagnostic surgical pathologist. Reaching the correct diagnosis for a specimen depends on the proper handling and processing of tissue transferred to this very busy area. We review here the basic function and management of the gross room including a brief discussion of common specimen types, biohazard exposure and safety, and collection of tissue for research.
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Affiliation(s)
- W C Bell
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35294-0007, USA
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Mangia A, Chiriatti A, Chiarappa P, Incalza MA, Antonaci G, Pilato B, Simone G, Tommasi S, Paradiso A. Touch imprint cytology in tumor tissue banks for the confirmation of neoplastic cellularity and for DNA extraction. Arch Pathol Lab Med 2008; 132:974-8. [PMID: 18517281 DOI: 10.5858/2008-132-974-ticitt] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2007] [Indexed: 11/06/2022]
Abstract
CONTEXT Learning the characteristics of frozen tissue samples stored in tumor banks for biological studies remains a problem. OBJECTIVE To assess the use of touch imprint cytology on fresh tissue samples as a rapid and reliable method of determining the presence and quantity of neoplastic cells before freezing. DESIGN Touch imprint cytology was performed on 259 specimens of operable breast cancer. Touch imprints were prepared from fresh tissue specimens before freezing samples for storage. Each tumor sample was imprinted on a glass slide and stained with hematoxylin-eosin. Tumor cellularity was quantified as negative, poor, moderate, or rich. RESULTS A significant correlation was found between samples with a tumor size greater than 2 cm and high tumor cellularity (P = .03; chi(2) test). Furthermore, 35% of ductal tumors showed higher tumor cellularity compared with lobular tumors (P < .001; chi(2) test). No association was found between lymph node status and tumor grade. When samples for which more than 2 imprints were available were examined, tumor cellularity among imprints of the same sample showed an overall agreement of 0.67 (P < .001; kappa statistic). It was also determined that the higher the cellularity, the higher the agreement. Our data also showed concordance of 0.87 (P < .001; kappa statistic) between touch imprint cytology imprints and histologic sections from contiguous tumor. Moreover, 11 randomly selected samples underwent DNA extraction, polymerase chain reaction, and sequencing to verify the feasibility of DNA analyses. We found that DNA from touch imprint cytology was amplifiable and suitable for direct sequencing. CONCLUSIONS Touch imprint cytology may represent an important step in the quality control of tumor cellularity of breast cancer specimens designed to be stored in tumor biobanks and a valid method for assessing the suitability of such tissue for further biomorphologic and biomolecular applications.
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Affiliation(s)
- Anita Mangia
- Clinical Experimental Oncology Laboratory, National Cancer Institute, Bari, Italy.
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Nirmalan NJ, Harnden P, Selby PJ, Banks RE. Mining the archival formalin-fixed paraffin-embedded tissue proteome: opportunities and challenges. MOLECULAR BIOSYSTEMS 2008; 4:712-20. [PMID: 18563244 DOI: 10.1039/b800098k] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The significant potential of tissue-based proteomic biomarker studies can be restricted by difficulties in accessing samples in optimal fresh-frozen form. While archival formalin-fixed tissue collections with attached clinical and outcome data represent a valuable alternate resource, the use of formalin as a fixative which induces protein cross-linking, has generally been assumed to render them unsuitable for proteomic studies. However, this view has been challenged recently with the publication of several papers accomplishing variable degrees of heat-induced reversal of cross-links. Although still in its infancy and requiring the quantitative optimisation of several critical parameters, formalin-fixed tissue proteomics holds promise as a powerful tool for biomarker-driven translational research. Here, we critically review the current status of research in the field, highlighting challenges which need to be addressed for robust quantitative application of protocols to ensure confident high impact inferences can be made.
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Affiliation(s)
- Niroshini J Nirmalan
- Clinical and Biomedical Proteomics Group, Cancer Research UK Clinical Centre, St James's University Hospital, Beckett Street, Leeds, UK
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Cavuşoğlu AC, Saydam S, Alakavuklar M, Canda T, Sevinç A, Kiliç Y, Harmancioğlu O, Koçdor MA, Kinay M, Alanyali H, Görken I, Balci P, Demirkan B, Sakizli M, Güner G. A pilot study for human tumor/DNA banking: returned more questions than answers. Med Oncol 2008; 25:471-3. [PMID: 18392956 DOI: 10.1007/s12032-008-9060-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2007] [Accepted: 06/22/2007] [Indexed: 12/01/2022]
Abstract
A pilot study was performed for setting up the Dokuz Eylül University Breast Tumor DNA Bank (DEUBTB) to facilitate the sharing of tumor DNA/RNA samples and related data from cases collected by collaborators specializing in the breast cancer diseases between 2004 and 2006. The pilot study aimed to provide answers for certain questions on: (1) ethical concerns (informing the volunteer for donating specimen, anonymizing the sample information, procedure on sample request), (2) obtaining and processing samples (technical issues, flowchart), (3) storing samples and their products (storing forms and conditions), (4) clinical database (which clinical data to store), (5) management organization (quality and quantity of personnel, flowchart for management relations), (6) financial issues (establishment and maintenance costs). When the bank had 64 samples, even though it is quite ready to supply samples for a research project, it revealed many questions on details that may be answered in more than one way, pointing that all biobanks need to be controlled by a higher degree of management party which develops and offers quality standards for these establishments.
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Affiliation(s)
- A Celebiler Cavuşoğlu
- Dokuz Eylül University Faculty of Medicine and Institute of Oncology, Izmir, Turkey.
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Neubauer H, Fehm T, Schütz C, Speer R, Solomayer E, Schrattenholz A, Cahill MA, Kurek R. Proteomic expression profiling of breast cancer. Recent Results Cancer Res 2007; 176:89-120. [PMID: 17607919 DOI: 10.1007/978-3-540-46091-6_9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Breast cancer is one of the most common cancers observed in women in industrialized Western countries. The development of novel diagnostic methods and the application of modern systemic therapies have significantly optimized early detection and therapy of breast cancer. However, many patients are currently overtreated. Traditionally, tumours have been categorized on the basis of histopathological criteria. However, staining pattern and intensity of cancer cells are not sufficient to reflect the molecular events driving tumour development and progression. Therefore, new genomic, transcriptomic and proteomic techniques are applied to clinical samples aiming to identify new targets for a therapy tailored for an individual patient. After an introduction to common genomic and transcriptomic profiling technologies and their relevance for clinical use, we will focus on analytical and preanalytical applications for the identification of new therapeutic targets by protein profiling, with a special emphasis on two-dimensional gel-technologies (2D-PAGE), particularly as they apply to the study of breast cancer.
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Sandusky GE, Teheny KH, Esterman M, Hanson J, Williams SD. Quality control of human tissues--experience from the Indiana University Cancer Center-Lilly Research Labs human tissue bank. Cell Tissue Bank 2007; 8:287-95. [PMID: 17387635 DOI: 10.1007/s10561-007-9037-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2006] [Accepted: 02/26/2007] [Indexed: 10/23/2022]
Abstract
The success of molecular research and its applications in both the clinical and basic research arenas is strongly dependent on the collection, handling, storage, and quality control of fresh human tissue samples. This tissue bank was set up to bank fresh surgically obtained human tissue using a Clinical Annotated Tissue Database (CATD) in order to capture the associated patient clinical data and demographics using a one way patient encryption scheme to protect patient identification. In this study, we determined that high quality of tissue samples is imperative for both genomic and proteomic molecular research. This paper also contains a brief compilation of the literature involved in the patient ethics, patient informed consent, patient de-identification, tissue collection, processing, and storage as well as basic molecular research generated from the tissue bank using good clinical practices. The current applicable rules, regulations, and guidelines for handling human tissues are briefly discussed. More than 6,610 cancer patients have been consented (97% of those that were contacted by the consenter) and 16,800 tissue specimens have been banked from these patients in 9 years. All samples collected in the bank were QC'd by a pathologist. Approximately 1,550 tissue samples have been requested for use in basic, clinical, and/or biomarker cancer research studies. Each tissue aliquot removed from the bank for a research study were evaluated by a second H&E, if the samples passed the QC, they were submitted for genomic and proteomic molecular analysis/study. Approximately 75% of samples evaluated were of high histologic quality and used for research studies. Since 2003, we changed the patient informed consent to allow the tissue bank to gather more patient clinical follow-up information. Ninety two percent of the patients (1,865 patients) signed the new informed consent form and agreed to be re-contacted for follow-up information on their disease state. In addition, eighty five percent of patients (1,584) agreed to be re-contacted to provide a biological fluid sample to be used for biomarker research.
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Affiliation(s)
- George E Sandusky
- Lilly Research Labs and Indiana University Cancer Center, Indianapolis, IN 46285, USA.
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Availability and quality of paraffin blocks identified in pathology archives: a multi-institutional study by the Shared Pathology Informatics Network (SPIN). BMC Cancer 2007; 7:37. [PMID: 17386082 PMCID: PMC1810540 DOI: 10.1186/1471-2407-7-37] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2006] [Accepted: 02/28/2007] [Indexed: 11/10/2022] Open
Abstract
Background Shared Pathology Informatics Network (SPIN) is a tissue resource initiative that utilizes clinical reports of the vast amount of paraffin-embedded tissues routinely stored by medical centers. SPIN has an informatics component (sending tissue-related queries to multiple institutions via the internet) and a service component (providing histopathologically annotated tissue specimens for medical research). This paper examines if tissue blocks, identified by localized computer searches at participating institutions, can be retrieved in adequate quantity and quality to support medical researchers. Methods Four centers evaluated pathology reports (1990–2005) for common and rare tumors to determine the percentage of cases where suitable tissue blocks with tumor were available. Each site generated a list of 100 common tumor cases (25 cases each of breast adenocarcinoma, colonic adenocarcinoma, lung squamous carcinoma, and prostate adenocarcinoma) and 100 rare tumor cases (25 cases each of adrenal cortical carcinoma, gastro-intestinal stromal tumor [GIST], adenoid cystic carcinoma, and mycosis fungoides) using a combination of Tumor Registry, laboratory information system (LIS) and/or SPIN-related tools. Pathologists identified the slides/blocks with tumor and noted first 3 slides with largest tumor and availability of the corresponding block. Results Common tumors cases (n = 400), the institutional retrieval rates (all blocks) were 83% (A), 95% (B), 80% (C), and 98% (D). Retrieval rate (tumor blocks) from all centers for common tumors was 73% with mean largest tumor size of 1.49 cm; retrieval (tumor blocks) was highest-lung (84%) and lowest-prostate (54%). Rare tumors cases (n = 400), each institution's retrieval rates (all blocks) were 78% (A), 73% (B), 67% (C), and 84% (D). Retrieval rate (tumor blocks) from all centers for rare tumors was 66% with mean largest tumor size of 1.56 cm; retrieval (tumor blocks) was highest for GIST (72%) and lowest for adenoid cystic carcinoma (58%). Conclusion Assessment shows availability and quality of archival tissue blocks that are retrievable and associated electronic data that can be of value for researchers. This study serves to compliment the data from which uniform use of the SPIN query tools by all four centers will be measured to assure and highlight the usefulness of archival material for obtaining tumor tissues for research.
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Ericsson C, Franzén B, Nistér M. Frozen tissue biobanks. Tissue handling, cryopreservation, extraction, and use for proteomic analysis. Acta Oncol 2007; 45:643-61. [PMID: 16938807 DOI: 10.1080/02841860600818047] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The potential and the limitations of protein analysis of tissue samples are surveyed. The complexity, concentration range and dynamics of the human proteome are reviewed, as is the effect of handling and cryopreservation. Protein extraction, solubilization, resolution and detection are discussed, in relation to the properties of the human proteome.
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Affiliation(s)
- Christer Ericsson
- Department of Oncology - Pathology, Karolinska Institutet, CCK R8:05, Karolinska University Hospital, Solna, 171 76 Stockholm, Sweden.
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Lopez-Guerrero JA, Riegman PHJ, Oosterhuis JW, Lam KH, Oomen MHA, Spatz A, Ratcliffe C, Knox K, Mager R, Kerr D, Pezzella F, van Damme B, van de Vijver M, van Boven H, Morente MM, Alonso S, Kerjaschki D, Pammer J, Carbone A, Gloghini A, Teodorovic I, Isabelle M, Passioukov A, Lejeune S, Therasse P, van Veen EB, Dinjens WNM, Llombart-Bosch A. TuBaFrost 4: access rules and incentives for a European tumour bank. Eur J Cancer 2006; 42:2924-9. [PMID: 17027256 DOI: 10.1016/j.ejca.2006.04.030] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2006] [Accepted: 04/04/2006] [Indexed: 01/21/2023]
Abstract
When designing infrastructure for a networked virtual tumour bank (samples remain at the collector institutes and sample data are collected in a searchable central database), it is apparent that this can only function properly after developing an adequate set of rules for use and access. These rules must include sufficient incentives for the tissue sample collectors to remain active within the network and maintain sufficient sample levels in the local bank. These requirements resulted in a key TuBaFrost rule, stating that the custodianship of the samples remains under the authority of the local collector. As a consequence, the samples and the decision to issue the samples to a requestor are not transferred to a large organisation but instead remain with the collector, thus allowing autonomous negotiation between collector and requestor, potential co-authorship in publications or compensation for collection and processing costs. Furthermore, it realises a streamlined cost effective network, ensuring tissue visibility and accessibility thereby improving the availability of large amounts of samples of highly specific or rare tumour types as well as providing contact opportunities for collaboration between scientists with cutting edge technology and tissue collectors. With this general purpose in mind, the rules and responsibilities for collectors, requestors and central office were generated.
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Affiliation(s)
- J A Lopez-Guerrero
- Unit of Molecular Biology, Fundación Instituto Valenciano de Oncología, C/Profesor Beltran Baguena, 8+11, Valencia, Spain.
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Morente MM, Mager R, Alonso S, Pezzella F, Spatz A, Knox K, Kerr D, Dinjens WNM, Oosterhuis JW, Lam KH, Oomen MHA, van Damme B, van de Vijver M, van Boven H, Kerjaschki D, Pammer J, Lopez-Guerrero JA, Llombart Bosch A, Carbone A, Gloghini A, Teodorovic I, Isabelle M, Passioukov A, Lejeune S, Therasse P, van Veen EB, Ratcliffe C, Riegman PHJ. TuBaFrost 2: Standardising tissue collection and quality control procedures for a European virtual frozen tissue bank network. Eur J Cancer 2006; 42:2684-91. [PMID: 17027255 DOI: 10.1016/j.ejca.2006.04.029] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2006] [Accepted: 04/04/2006] [Indexed: 11/18/2022]
Abstract
Tumour Bank Networking presents a great challenge for oncological research as in order to carry out large-scale, multi-centre studies with minimal intrinsic bias, each tumour bank in the network must have some fundamental similarities and be using the same standardised and validated procedures. The European Human Frozen Tumour Tissue Bank (TuBaFrost) has responded to this need by the promotion of an integrated platform of tumour banks in Europe. The operational framework for TuBaFrost has drawn upon the best practice of standard workflows and operating procedures employed by members of the TuBaFrost project and key initiatives worldwide.
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Affiliation(s)
- M M Morente
- Centro Nacional de Investigaciones Oncológicas, Melchor Fernández Almagro, 3, E-28029 Madrid, Spain.
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De Paoli P. Bio-banking in microbiology: from sample collection to epidemiology, diagnosis and research. FEMS Microbiol Rev 2005; 29:897-910. [PMID: 16219511 PMCID: PMC7110355 DOI: 10.1016/j.femsre.2005.01.005] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2004] [Revised: 01/17/2005] [Accepted: 01/31/2005] [Indexed: 12/03/2022] Open
Abstract
Millions of biological samples, including cells of human, animal or bacterial origin, viruses, serum/plasma or DNA/RNA, are stored every year throughout the world for diagnostics and research. The purpose of this review is to summarize the resources necessary to set up a bio-banking facility, the challenges and pitfalls of sample collection, and the most important techniques for separation and storage of samples. Biological samples can be stored for up to 30 years, but specific protocols are required to reduce the damage induced by preservation techniques. Software dedicated to biological banks facilitate sample registration and identification, the cataloguing of sample properties (type of sample/specimen, associated diseases and/or therapeutic protocols, environmental information, etc.), sample tracking, quality assurance and specimen availability. Bio-bank facilities must adopt good laboratory practices and a stringent quality control system and, when required, comply with ethical issues.
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Affiliation(s)
- Paolo De Paoli
- Division of Microbiology, Immunology and Virology, Centro di Riferimento Oncologico, IRCCS, via Pedemontana 12, 33170 Aviano, Italy.
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Fernandez CV, Magee F, Fraser RB. The crucial role of tumour specimen handling in childhood cancer outcomes. Paediatr Child Health 2005; 10:471-472. [PMID: 19668659 PMCID: PMC2722598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023] Open
Abstract
The significant advances achieved in the care of children with cancer have been the result of carefully conducted clinical trials in international cooperative group settings. Specialized biological testing of tumour specimens is now an essential component of risk and treatment assignment for many childhood cancers. Thus, the appropriate collection and handling of tumour specimens is crucial to maintaining and further advancing the excellent outcomes that we have achieved. We recommend that all children with a strongly suspected malignancy, or cases in which the situation is unclear, be discussed with a paediatric oncologist before obtaining a tumour specimen. When a tumour is discovered incidentally at surgery, we recommend that the tumour be placed in a saline-soaked gauze and a paediatric pathologist or oncologist contacted immediately. Further progress in understanding and treating childhood cancer is intimately linked to basic studies of biology, translational research and determining the role of biological markers in risk stratification. Early and careful collaboration between front-line physicians and tertiary care oncology specialists is essential to the continuing success of treatment of children with cancer.
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Affiliation(s)
| | - Fergall Magee
- Departments of Pediatrics and Pathology, BC’s Women’s and Children’s Hospital, Vancouver, British Columbia
| | - Robert B Fraser
- Pathology, IWK Health Centre, Dalhousie University, Halifax, Nova Scotia
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