1
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van der Wijngaart H, Jagga S, Dekker H, de Goeij R, Piersma SR, Pham TV, Knol JC, Zonderhuis BM, Holland HJ, Jiménez CR, Verheul HMW, Vanapalli S, Labots M. Advancing wide implementation of precision oncology: A liquid nitrogen-free snap freezer preserves molecular profiles of biological samples. Cancer Med 2023; 12:10979-10989. [PMID: 36916528 DOI: 10.1002/cam4.5781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/18/2023] [Accepted: 02/24/2023] [Indexed: 03/16/2023] Open
Abstract
PURPOSE In precision oncology, tumor molecular profiles guide selection of therapy. Standardized snap freezing of tissue biospecimens is necessary to ensure reproducible, high-quality samples that preserve tumor biology for adequate molecular profiling. Quenching in liquid nitrogen (LN2 ) is the golden standard method, but LN2 has several limitations. We developed a LN2 -independent snap freezer with adjustable cold sink temperature. To benchmark this device against the golden standard, we compared molecular profiles of biospecimens. METHODS Cancer cell lines and core needle normal tissue biopsies from five patients' liver resection specimens were used to compare mass spectrometry (MS)-based global phosphoproteomic and RNA sequencing profiles and RNA integrity obtained by both freezing methods. RESULTS Unsupervised cluster analysis of phosphoproteomic and transcriptomic profiles of snap freezer versus LN2 -frozen K562 samples and liver biopsies showed no separation based on freezing method (with Pearson's r 0.96 (range 0.92-0.98) and >0.99 for K562 profiles, respectively), while samples with +2 h bench-time formed a separate cluster. RNA integrity was also similar for both snap freezing methods. Molecular profiles of liver biopsies were clearly identified per individual patient regardless of the applied freezing method. Two to 25 s freezing time variations did not induce profiling differences in HCT116 samples. CONCLUSION The novel snap freezer preserves high-quality biospecimen and allows identification of individual patients' molecular profiles, while overcoming important limitations of the use of LN2 . This snap freezer may provide a useful tool in clinical cancer research and practice, enabling a wider implementation of (multi-)omics analyses for precision oncology.
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Affiliation(s)
- Hanneke van der Wijngaart
- Department of Medical Oncology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Sahil Jagga
- Applied Thermal Sciences, Faculty of Science and Technology, University of Twente, Enschede, The Netherlands
| | - Henk Dekker
- Department of Medical Oncology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Richard de Goeij
- Department of Medical Oncology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Sander R Piersma
- Department of Medical Oncology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Thang V Pham
- Department of Medical Oncology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Jaco C Knol
- Department of Medical Oncology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Babs M Zonderhuis
- Department of Surgery, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Harry J Holland
- Applied Thermal Sciences, Faculty of Science and Technology, University of Twente, Enschede, The Netherlands
| | - Connie R Jiménez
- Department of Medical Oncology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Henk M W Verheul
- Department of Medical Oncology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Srinivas Vanapalli
- Applied Thermal Sciences, Faculty of Science and Technology, University of Twente, Enschede, The Netherlands
| | - Mariette Labots
- Department of Medical Oncology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
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2
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Servais MD, Galtier F, Nouvel A, Rebuffat S, Laget J, Géan A, Provost N, Lorcy F, Rigau V, Couderc G, Géraud P, Nocca D, Builles N, De Préville N, Lajoix AD. Addressing the quality challenge of a human biospecimen biobank through the creation of a quality management system. PLoS One 2022; 17:e0278780. [PMID: 36584180 PMCID: PMC9803146 DOI: 10.1371/journal.pone.0278780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 11/22/2022] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND The objective of the COMET (COllection of MEtabolic Tissues) biobank project is to create a high-quality collection of insulin-sensitive tissues (liver, muscle, adipose tissues, and epiploic artery) and blood sample derivatives (plasma, serum, DNA and RNA), collected from 270 grade 2-3 obese patients undergoing bariatric surgery. Relevant data on patient such as clinical/biological characteristics and sample handling are also collected. For this, our aim was to establish a Quality Management System (QMS) to meet the reliability and quality requirements necessary for its scientific exploitation. MATERIALS AND METHODS The COMET QMS includes: (1) Quality Assurance to standardize all stages of the biobanking process, (2) Quality Controls on samples from the first patients included in order to validate the sample management process and ensure reproducible quality; and 3) "in process" Quality Controls to ensure the reliability of the storage procedures and the stability of the samples over time. RESULTS For serum and plasma, several corrective actions, such as temperature handling and centrifugation conditions, were made to the protocol and led to improvement of the volume and quality of samples. Regarding DNA, all samples evaluated achieved a satisfactory level of purity and integrity and most of them yielded the required DNA quantity. All frozen tissue samples had RNAs of good purity. RNA quality was confirmed by RIN, achieving values in most cases over 7 and efficient amplification of housekeeping genes by RT-qPCR, with no significant differences among samples from the same tissue type. In the "in process" Quality Controls, DNA, RNA, and histological integrity of tissues showed no differences among samples after different preservation times. CONCLUSION Quality Control results have made it possible to validate the entire biobank process and confirm the utility of implementing QMS to guarantee the quality of a biospecimen collection.
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Affiliation(s)
| | - Florence Galtier
- INSERM, Clinical Investigation Center 1411, St Eloi Hospital, University Hospital of Montpellier, Montpellier, France
- Department of Endocrinology, Lapeyronie Hospital, University Hospital of Montpellier, Montpellier, France
- Biocommunication in Cardio-Metabolism (BC2M), University of Montpellier, Montpellier, France
| | - Agathe Nouvel
- Biocommunication in Cardio-Metabolism (BC2M), University of Montpellier, Montpellier, France
| | - Sandra Rebuffat
- Biocommunication in Cardio-Metabolism (BC2M), University of Montpellier, Montpellier, France
| | - Jonas Laget
- Biocommunication in Cardio-Metabolism (BC2M), University of Montpellier, Montpellier, France
| | | | | | - Frédéric Lorcy
- Biological Resources Center, Anatomy and Cytology Laboratory, University Hospital of Montpellier, Montpellier, France
| | - Valérie Rigau
- Biological Resources Center, Anatomy and Cytology Laboratory, University Hospital of Montpellier, Montpellier, France
| | - Guilhem Couderc
- Biological Resources Center, Tissue Bank, University Hospital of Montpellier, Montpellier, France
| | - Philippe Géraud
- INSERM, Clinical Investigation Center 1411, St Eloi Hospital, University Hospital of Montpellier, Montpellier, France
| | - David Nocca
- Department of Digestive Surgery, University Hospital of Montpellier, Montpellier, France
| | - Nicolas Builles
- Biological Resources Center, Tissue Bank, University Hospital of Montpellier, Montpellier, France
| | | | - Anne-Dominique Lajoix
- Biocommunication in Cardio-Metabolism (BC2M), University of Montpellier, Montpellier, France
- * E-mail:
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3
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Role of Biobanks for Cancer Research and Precision Medicine in Hepatocellular Carcinoma. J Gastrointest Cancer 2021; 52:1232-1247. [PMID: 34807351 DOI: 10.1007/s12029-021-00759-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/05/2021] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Hepatocellular carcinoma (HCC) is a highly complex and deadly cancer. There is an urgent need for new and effective treatment modalities. Since the primary goal in the management of cancer is to cure and improve survival, personalized therapy can increase survival, reduce mortality rates, and improve quality of life. Biobanks hold potential in leading to breakthroughs in biomedical research and precision medicine (PM). They serve as a biorepository, collecting, processing, storing, and supplying specimens and relevant data for basic, translational, and clinical research. OBJECTIVE We aimed to highlight the fundamental role of biobanks, harboring high quality, sustainable collections of patient samples in adequate size and variability, for developing diagnostic, prognostic, and predictive biomarkers to develop and PM approaches in the management of HCC. METHOD We obtained information from previously published articles and BBMRI directory. RESULTS AND CONCLUSION Biobanking of high-quality biospecimens along with patient clinical information provides a fundamental scientific infrastructure for basic, translational, and clinical research. Biobanks that control and eliminate pre-analytical variability of biospecimens, provide a platform to identify reliable biomarkers for the application of PM. We believe, establishing HCC biobanks will empower to underpin molecular mechanisms of HCC and generate strategies for PM. Thus, first, we will review current therapy approaches in HCC care. Then, we will summarize challenges in HCC management. Lastly, we will focus on the best practices for establishing HCC biobanking to support research, translational medicine in the light of new experimental research conducted with the aim of delivering PM for HCC patients.
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4
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Eggeling F, Hoffmann F. Microdissection—An Essential Prerequisite for Spatial Cancer Omics. Proteomics 2020; 20:e2000077. [DOI: 10.1002/pmic.202000077] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/12/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Ferdinand Eggeling
- Department of OtorhinolaryngologyMALDI Imaging and Core Unit Proteome AnalysisDFG Core Unit Jena Biophotonic and Imaging Laboratory (JBIL)Jena University Hospital Am Klinikum 1 Jena 07747 Germany
| | - Franziska Hoffmann
- Department of OtorhinolaryngologyMALDI Imaging and Core Unit Proteome AnalysisDFG Core Unit Jena Biophotonic and Imaging Laboratory (JBIL)Jena University Hospital Am Klinikum 1 Jena 07747 Germany
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5
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Enriching Personalized Endometrial Cancer Research with the Harmonization of Biobanking Standards. Cancers (Basel) 2019; 11:cancers11111734. [PMID: 31694311 PMCID: PMC6896027 DOI: 10.3390/cancers11111734] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/31/2019] [Accepted: 11/02/2019] [Indexed: 12/14/2022] Open
Abstract
Endometrial cancer is the commonest gynecological cancer, with an incidence predicted to escalate by a further 50–100% before 2025, due to the rapid rise in risk factors such as obesity and increased life expectancy. Endometrial cancer associated mortality is also rising, depicting the need for translatable research to improve our understanding of the disease. Rapid translation of scientific discoveries will facilitate the development of new diagnostic, prognostic and therapeutic strategies. Biobanks play a vital role in providing biospecimens with accompanying clinical data for personalized translational research. Wide variation in collection, and pre-analytic variations in processing and storage of bio-specimens result in divergent and irreproducible data from multiple studies that are unsuitable for collation to formulate robust conclusions. Harmonization of biobanking standards is thus vital, in facilitating international multi-center collaborative studies with valuable outcomes to improve personalized treatments. This review will detail the pitfalls in the biobanking of biosamples from women with cancer in general, and describe the recent international harmonization project that developed standardized research tools to overcome these challenges and to enhance endometrial cancer research, which will facilitate future development of personalized novel diagnostic strategies and treatments.
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6
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Dapic I, Baljeu-Neuman L, Uwugiaren N, Kers J, Goodlett DR, Corthals GL. Proteome analysis of tissues by mass spectrometry. MASS SPECTROMETRY REVIEWS 2019; 38:403-441. [PMID: 31390493 DOI: 10.1002/mas.21598] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 06/17/2019] [Indexed: 06/10/2023]
Abstract
Tissues and biofluids are important sources of information used for the detection of diseases and decisions on patient therapies. There are several accepted methods for preservation of tissues, among which the most popular are fresh-frozen and formalin-fixed paraffin embedded methods. Depending on the preservation method and the amount of sample available, various specific protocols are available for tissue processing for subsequent proteomic analysis. Protocols are tailored to answer various biological questions, and as such vary in lysis and digestion conditions, as well as duration. The existence of diverse tissue-sample protocols has led to confusion in how to choose the best protocol for a given tissue and made it difficult to compare results across sample types. Here, we summarize procedures used for tissue processing for subsequent bottom-up proteomic analysis. Furthermore, we compare protocols for their variations in the composition of lysis buffers, digestion procedures, and purification steps. For example, reports have shown that lysis buffer composition plays an important role in the profile of extracted proteins: the most common are tris(hydroxymethyl)aminomethane, radioimmunoprecipitation assay, and ammonium bicarbonate buffers. Although, trypsin is the most commonly used enzyme for proteolysis, in some protocols it is supplemented with Lys-C and/or chymotrypsin, which will often lead to an increase in proteome coverage. Data show that the selection of the lysis procedure might need to be tissue-specific to produce distinct protocols for individual tissue types. Finally, selection of the procedures is also influenced by the amount of sample available, which range from biopsies or the size of a few dozen of mm2 obtained with laser capture microdissection to much larger amounts that weight several milligrams.
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Affiliation(s)
- Irena Dapic
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | | | - Naomi Uwugiaren
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Jesper Kers
- Department of Pathology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam Cardiovascular Sciences (ACS), Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA
| | - David R Goodlett
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
- University of Maryland, 20N. Pine Street, Baltimore, MD 21201
| | - Garry L Corthals
- van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
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7
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Clavreul A, Soulard G, Lemée JM, Rigot M, Fabbro-Peray P, Bauchet L, Figarella-Branger D, Menei P. The French glioblastoma biobank (FGB): a national clinicobiological database. J Transl Med 2019; 17:133. [PMID: 31014363 PMCID: PMC6480741 DOI: 10.1186/s12967-019-1859-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 03/27/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Glioblastomas (GB) are the most common and lethal primary brain tumors. Significant progress has been made toward identifying potential risk factors for GB and diagnostic and prognostic biomarkers. However, the current standard of care for newly diagnosed GB, the Stupp protocol, has remained unchanged for over a decade. Large-scale translational programs based on a large clinicobiological database are required to improve our understanding of GB biology, potentially facilitating the development of personalized and specifically targeted therapies. With this goal in mind, a well-annotated clinicobiological database housing data and samples from GB patients has been set up in France: the French GB biobank (FGB). METHODS The biobank contains data and samples from adult GB patients from 24 centers in France providing written informed consent. Clinical and biomaterial data are stored in anonymized certified electronic case report forms. Biological samples (including frozen and formalin-fixed paraffin-embedded tumor tissues, blood samples, and hair) are conserved in certified biological resource centers or tumor tissue banks at each participating center. RESULTS Clinical data and biological materials have been collected for 1087 GB patients. A complete set of samples (tumor, blood and hair) is available for 66%, and at least one frozen tumor sample is available for 88% of the GB patients. CONCLUSIONS This large biobank is unique in Europe and can support the large-scale translational projects required to improve GB care. Additional biological materials, such as peritumoral brain zone and fecal samples, will be collected in the future, to respond to research needs.
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Affiliation(s)
- Anne Clavreul
- Département de Neurochirurgie, CHU, 4 rue Larrey, 49 933, Angers Cedex 9, France.,CRCINA, INSERM, Université de Nantes, Université d'Angers, Angers, France
| | - Gwénaëlle Soulard
- Département de Neurochirurgie, CHU, 4 rue Larrey, 49 933, Angers Cedex 9, France.,CRCINA, INSERM, Université de Nantes, Université d'Angers, Angers, France
| | - Jean-Michel Lemée
- Département de Neurochirurgie, CHU, 4 rue Larrey, 49 933, Angers Cedex 9, France.,CRCINA, INSERM, Université de Nantes, Université d'Angers, Angers, France
| | - Marion Rigot
- Département Promotion, Direction de la Recherche, CHU Nantes, Nantes, France
| | - Pascale Fabbro-Peray
- Département de Biostatistique, Epidémiologie, Santé Publique, CHU Nîmes, Nîmes, France.,Unité de recherche EA2415, Université de Montpellier, Montpellier, France
| | - Luc Bauchet
- Département de Neurochirurgie, Hôpital Gui de Chauliac, CHU Montpellier, Université de Montpellier, Montpellier, France.,Institut des Neurosciences de Montpellier INSERM U1051, Montpellier, France
| | - Dominique Figarella-Branger
- APHM, Hôpital de la Timone, Service d'Anatomie Pathologique et de Neuropathologie, Marseille, France.,Aix-Marseille Univ, CNRS, INP, Inst Neurophysiopathol, Marseille, France
| | - Philippe Menei
- Département de Neurochirurgie, CHU, 4 rue Larrey, 49 933, Angers Cedex 9, France. .,CRCINA, INSERM, Université de Nantes, Université d'Angers, Angers, France.
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8
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Sana G, Madigan JP, Gartner JJ, Fourrez M, Lin J, Qutob N, Narayan J, Shukla S, Ambudkar SV, Xia D, Rosenberg SA, Gottesman MM, Samuels Y, Gillet JP. Exome Sequencing of ABCB5 Identifies Recurrent Melanoma Mutations that Result in Increased Proliferative and Invasive Capacities. J Invest Dermatol 2019; 139:1985-1992.e10. [PMID: 30905807 PMCID: PMC6708748 DOI: 10.1016/j.jid.2019.01.036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 12/19/2018] [Accepted: 01/02/2019] [Indexed: 02/09/2023]
Abstract
ABCB5 is an ABC transporter that was shown to confer low-level multidrug resistance in cancer. In this study, we show that ABCB5 was mutated in 13.75% of the 640 melanoma samples analyzed. Besides nonsense mutations, two mutation hotspots were found in the ABCB5 protein, in the drug-binding pocket and the nucleotide-binding domains. Four mutations, which are representative of the mutation pattern, were selected. ATPase assays showed that these mutations resulted in a decrease in basal ATP hydrolysis by ABCB5. To select informative melanoma cell lines, mutational profiles of the clinical samples were further analyzed. This study showed mutations in the tumor suppressor CDKN2A gene and the NRAS oncogene in 62.5% and 75%, respectively of the samples that had mutations in the ABCB5 gene. No mutation was found in the tumor suppressor PTEN gene, whereas the activating V600E mutation in the BRAF oncogene was found in 25% of the samples with a mutated ABCB5 gene. Studies in four melanoma cell lines with various genetic backgrounds showed an increase in the proliferation and migration capacity of mutant ABCB5-expressing cells, suggesting that ABCB5 plays a role in the development of melanoma as a tumor suppressor gene.
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Affiliation(s)
- Géraldine Sana
- Laboratory of Molecular Cancer Biology, Molecular Physiology Research Unit (URPHYM), Namur Research Institute for Life Sciences, Faculty of Medicine, Department of Biomedical Sciences, University of Namur, Namur, Belgium
| | - James P Madigan
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Jared J Gartner
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Marie Fourrez
- Laboratory of Molecular Cancer Biology, Molecular Physiology Research Unit (URPHYM), Namur Research Institute for Life Sciences, Faculty of Medicine, Department of Biomedical Sciences, University of Namur, Namur, Belgium
| | - Jimmy Lin
- Washington University School of Medicine, Genome Technology Access Center, Genomics and Pathology Services, St. Louis, Missouri, USA
| | - Nouar Qutob
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Jitendra Narayan
- Laboratory of Evolutionary Genetics and Ecology (LEGE), Faculty of Sciences, Department of Biology, University of Namur, Namur, Belgium
| | - Suneet Shukla
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Suresh V Ambudkar
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Di Xia
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Steven A Rosenberg
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Michael M Gottesman
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA.
| | - Yardena Samuels
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Jean-Pierre Gillet
- Laboratory of Molecular Cancer Biology, Molecular Physiology Research Unit (URPHYM), Namur Research Institute for Life Sciences, Faculty of Medicine, Department of Biomedical Sciences, University of Namur, Namur, Belgium.
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9
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van Limbeek MAJ, Jagga S, Holland H, Ledeboer K, Ter Brake M, Vanapalli S. Cooling of a vial in a snapfreezing device without using sacrificial cryogens. Sci Rep 2019; 9:3510. [PMID: 30837583 PMCID: PMC6400931 DOI: 10.1038/s41598-019-40115-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 02/08/2019] [Indexed: 11/21/2022] Open
Abstract
A fresh and frozen high-quality patient bio-sample is required in molecular medicine for the identification of disease-associated mechanism at molecular levels. A common cooling procedure is immersing the tissue enclosed in a vial in a coolant such as liquid nitrogen. This procedure is not user friendly and is laborious as reducing the lag time from excision time to freezing depends on the logistic organizational structure within a hospital. Moreover snapfreezing must be done as soon as possible after tissue excision to preserve the tissue quality for molecular tests. Herein, we report an electrically powered snap freezing device as an alternative to quenching the vial in liquid nitrogen and therefore can be used directly at the location where the tissue is acquired. This device also facilitates the study of the effect of freezing conditions on the various molecular processes in the samples. Cooling experiments of a vial in the snap freezing device show that the cooling rates similar to or faster than quenching in liquid nitrogen are feasible. We performed experiments with several set point conditions and compared the results with a mathematical model.
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Affiliation(s)
- Michiel A J van Limbeek
- Energy, Materials and Systems Group, University of Twente, 7500 AE, Enschede, The Netherlands.,Physics of Fluids Group, MESA+ Institute, University of Twente, 7500 AE, Enschede, The Netherlands
| | - Sahil Jagga
- Energy, Materials and Systems Group, University of Twente, 7500 AE, Enschede, The Netherlands
| | - Harry Holland
- Energy, Materials and Systems Group, University of Twente, 7500 AE, Enschede, The Netherlands
| | - Koen Ledeboer
- Energy, Materials and Systems Group, University of Twente, 7500 AE, Enschede, The Netherlands
| | - Marcel Ter Brake
- Energy, Materials and Systems Group, University of Twente, 7500 AE, Enschede, The Netherlands
| | - Srinivas Vanapalli
- Energy, Materials and Systems Group, University of Twente, 7500 AE, Enschede, The Netherlands.
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10
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Zhang X, Han QY, Zhao ZS, Zhang JG, Zhou WJ, Lin A. Biobanking of Fresh-Frozen Gastric Cancer Tissues: Impact of Long-Term Storage and Clinicopathological Variables on RNA Quality. Biopreserv Biobank 2019; 17:58-63. [PMID: 30457887 DOI: 10.1089/bio.2018.0038] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Xia Zhang
- Biological Resource Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, People's Republic of China
| | - Qiu-Yue Han
- Biological Resource Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, People's Republic of China
| | - Zhang-Sheng Zhao
- Biological Resource Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, People's Republic of China
| | - Jian-Gang Zhang
- Biological Resource Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, People's Republic of China
| | - Wen-Jun Zhou
- Biological Resource Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, People's Republic of China
| | - Aifen Lin
- Biological Resource Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, People's Republic of China
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11
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Gao H, Liu Y, Ding J, Yang J, Zhang B, Hu Y, Ge M, Ye Q. A Nucleic Acid Quality Control Strategy for Frozen Tissues from a Biobank of High-Risk Pregnancy. Biopreserv Biobank 2018; 17:18-26. [PMID: 30256683 DOI: 10.1089/bio.2018.0041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The preservation of placental and fetal tissues will contribute to studying the pathogenesis of high-risk pregnancy diseases. However, few studies have focused on the effects of different preservation methods and cold ischemia time (CIT) on the quality of nucleic acids. An available quality control (QC) strategy will be beneficial to evaluate these effects for high-risk pregnancy biobanks. METHODS We established an evaluation strategy of nucleic acid QC by analyzing total RNA and genomic DNA (gDNA). Through this strategy, the effects of CIT, cryoprotectants (CPAs), and freeze/thaw cycles on the yield and integrity of placental RNA were analyzed. In addition, the effects of CIT on the yield and integrity of fetal DNA were determined. RESULTS For placental samples, there was no significant difference in RNA integrity (CIT <2 hours). After several freeze/thaw cycles, the RNA quality number values of placental samples in the CPA-free group and in the RNasin (TRIzol) group were decreased. For fetal samples, the DNA integrity of different organs (CIT <24 hours) was completely satisfactory, but it declined with the extension of CIT. Furthermore, different organs had different tolerances to cold ischemia, and the rank was as follows: skin, heart, liver, and placenta. In addition, the content of medium-length (600 bp) and long (1310 bp) fragments of gDNA were mainly reduced with the extension of CIT. CONCLUSION The RNA integrity of placental tissue was affected by CIT significantly. It is recommended that placenta should be cryopreserved within 2 hours (4°C) from isolation. To ensure DNA quality of fetal tissues, the samples are suggested to be frozen within 24 hours (4°C) from isolation. On the contrary, if samples have a long CIT, skin is superior to other organs in the aspect of biobanking donor's genetic information.
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Affiliation(s)
- Hong Gao
- 1 Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China.,2 Biobank of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China
| | - Yanhong Liu
- 1 Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China.,2 Biobank of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China
| | - Jie Ding
- 1 Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China.,2 Biobank of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China
| | - Jun Yang
- 1 Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China
| | - Biao Zhang
- 1 Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China
| | - Yue Hu
- 1 Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China.,2 Biobank of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China
| | - Meiling Ge
- 1 Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China.,2 Biobank of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China
| | - Qing Ye
- 1 Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China.,2 Biobank of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China
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12
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Zheng XH, Zhang SD, Zhang PF, Li XZ, Hu YZ, Tian T, Zhu L, Wang RZ, Jia WH. Tumor Cell Content and RNA Integrity of Surgical Tissues from Different Types of Tumors and Its Correlation with Ex Vivo and In Vivo Ischemia. Ann Surg Oncol 2018; 25:3764-3770. [PMID: 30225832 DOI: 10.1245/s10434-018-6697-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Indexed: 12/18/2022]
Abstract
BACKGROUND Tissues from tumor patients are important resources for promoting cancer research, and therefore many biobanks have been established to collect tumor tissues; however, the quality of tumor tissues after surgical resection has not been well documented. METHODS A total of 896 cases of tissues from 12 types of tumors were chosen for this study. First, histopathological examination was conducted to evaluate the tumor cell content; second, microchip electrophoresis was used to determine the RNA integrity number (RIN) in 466 cases of tissues with a tumor cell content ≥ 75%; and, finally, a correlation test was used to analyze the effect of ischemia on RNA integrity in 384 cases of tissues with a recorded ischemia time. RESULTS Tumor tissues from 12 different organs had different tumor cell contents and RNA integrity. The liver had the highest percentage (69.7%) of tissue samples with a tumor cell content ≥ 75%, and the highest percentage (96%) of samples with an RIN ≥ 7. RNA integrity was not correlated with limited ex vivo ischemia time (5-60 min) in any of the 12 types of tumors. In contrast, a significant correlation with in vivo ischemia time was observed in several types of tumors. CONCLUSIONS Not every sample of excised tumor tissue has a sufficient amount of tumor cells and enough RNA integrity. In vivo ischemia has a more significant influence on RNA integrity, and tumor tissues have different tolerances to pre-analytical variables. Those conducting translational research should pay attention to pre-analytical variables when collecting and utilizing tumor tissues.
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Affiliation(s)
- Xiao-Hui Zheng
- Tumor Biobank, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, People's Republic of China.,Affiliated Tumor Hospital of Xinjiang Medical University, Ürümqi, Xinjiang, People's Republic of China
| | - Shao-Dan Zhang
- Tumor Biobank, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, People's Republic of China
| | - Pei-Fen Zhang
- Tumor Biobank, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, People's Republic of China
| | - Xi-Zhao Li
- Tumor Biobank, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, People's Republic of China
| | - Ye-Zhu Hu
- Tumor Biobank, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, People's Republic of China
| | - Tian Tian
- Tumor Biobank, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, People's Republic of China
| | - Lin Zhu
- Affiliated Tumor Hospital of Xinjiang Medical University, Ürümqi, Xinjiang, People's Republic of China
| | - Ruo-Zheng Wang
- Affiliated Tumor Hospital of Xinjiang Medical University, Ürümqi, Xinjiang, People's Republic of China.
| | - Wei-Hua Jia
- Tumor Biobank, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, People's Republic of China. .,Affiliated Tumor Hospital of Xinjiang Medical University, Ürümqi, Xinjiang, People's Republic of China.
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13
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Susman S, Berindan-Neagoe I, Petrushev B, Pirlog R, Florian IS, Mihu CM, Berce C, Craciun L, Grewal R, Tomuleasa C. The role of the pathology department in the preanalytical phase of molecular analyses. Cancer Manag Res 2018; 10:745-753. [PMID: 29695931 PMCID: PMC5903845 DOI: 10.2147/cmar.s150851] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
After introducing the new molecules for the treatment of patients with tumoral pathology, the therapeutical decision will be taken depending on the molecular profile performed upon the harvested tissues. This major modification makes the molecular and morphological analysis an essential part in the clinical management of patients and the pathologist plays an important role in this process. The quality and reproducibility of the results are imperative today and they depend on both the reliability of the molecular techniques and the quality of the tissue we use in the process. Also, the genomics and proteomics techniques, used increasingly often, require high-quality tissues, and pathology laboratories play a very significant role in the management of all phases of this process. In this paper the parameters which must be followed in order to obtain optimal results within the techniques which analyze nucleic acids and proteins were reviewed.
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Affiliation(s)
- Sergiu Susman
- Department of Pathology, Imogen Research Center.,Department of Morphological Sciences
| | | | - Bobe Petrushev
- Research Center for Functional Genomics and Translational Medicine
| | | | - Ioan-Stefan Florian
- Department of Neurosurgery, Iuliu Hatieganu University of Medicine and Pharmacy
| | | | - Cristian Berce
- Research Center for Functional Genomics and Translational Medicine
| | | | - Ravnit Grewal
- Department of Hematology, Ion Chiricuta Oncology Institute
| | - Ciprian Tomuleasa
- Research Center for Functional Genomics and Translational Medicine.,Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Department of Haematopathology, Tygerberg Academic Hospital, Tygerberg, South Africa
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14
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Arni S, de Wijn R, Garcia–Villegas R, Bitanihirwe BK, Caviezel C, Weder W, Hillinger S. A strategy to analyse activity-based profiling of tyrosine kinase substrates in OCT-embedded lung cancer tissue. Anal Biochem 2018; 547:77-83. [DOI: 10.1016/j.ab.2018.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 01/31/2018] [Accepted: 02/01/2018] [Indexed: 01/11/2023]
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15
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Riegman PHJ, Bosch AL, Riegman PHJ, Dinjens WNM, 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, Lopez-Guerrero JA, Bosch AL, Carbone A, Gloghini A, Teodorovic I, Isabelle M, Jaminé D, Passioukov A, Lejeune S, Therasse P, van Veen EB, Lam KH, Oosterhuis JW. OECI TuBaFrost Tumor Biobanking. TUMORI JOURNAL 2018; 94:160-3. [DOI: 10.1177/030089160809400205] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
OECI TuBaFrost harbors a complete infrastructure for the exchange of frozen tumor samples between European countries. OECI TuBaFrost consists of: • A code of conduct on how to exchange human residual samples in Europe • A central database application accessible over the Internet ( www.tubafrost.org ) where data can be uploaded and searched from samples that can be selected and ordered • Access rules with incentives for collectors • Standardization needed to enable the analysis of high quality samples derived from different centers • Virtual Microscopy to support sample selection with difficult pathology The entire infrastructure was, after completion, which was entirely financed by the European Commission, implemented in the OECI. But so far it has not been used to its capacity. A recent survey held amongst the OECI members shed light on the causes. The main conclusion is that all responders see OECI TuBaFrost as a good platform for exchange of samples, however, the biggest bottleneck found was that potential users are too unfamiliar with the communication between their own biobank tracking system and the TuBaFrost central database application. Therefore, new future plans are drawn. In addition, new infrastructure plans have been developed and the first preparatory steps have been set. For biobanks the BBMRI project has started aiming for Pan-European Biobanking and Biomolecular Resources Research Infrastructure.
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Affiliation(s)
- Peter HJ Riegman
- Department of Pathology, Josephine Nefkens Institute, Erasmus Medical Center Rotterdam, The Netherlands
| | | | | | | | - MHA Oomen
- Erasmus MC, Rotterdam, The Netherlands
| | - A Spatz
- Institut Gustave Roussy, Villejuif, France
| | - C Ratcliffe
- National Translational Cancer Research Network, University of Oxford, Radcliffe Infirmary, Oxford, United Kingdom
| | - K Knox
- National Translational Cancer Research Network, University of Oxford, Radcliffe Infirmary, Oxford, United Kingdom
| | - R Mager
- National Translational Cancer Research Network, University of Oxford, Radcliffe Infirmary, Oxford, United Kingdom
- Nuffield Department of Clinical Laboratory Sciences, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - D Kerr
- National Translational Cancer Research Network, University of Oxford, Radcliffe Infirmary, Oxford, United Kingdom
| | - F. Pezzella
- Nuffield Department of Clinical Laboratory Sciences, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | | | | | - H van Boven
- Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - MM Morente
- Centro Nacional de Investigaciones Oncologicas, Madrid, Spain
| | - S Alonso
- Centro Nacional de Investigaciones Oncologicas, Madrid, Spain
| | - D Kerjaschki
- Allgemeines Krankenhaus, University of Vienna, Austria
| | - J Pammer
- Allgemeines Krankenhaus, University of Vienna, Austria
| | | | | | - A Carbone
- Centro di Riferimento Oncologico, Aviano (PN), Italy
| | - A Gloghini
- Centro di Riferimento Oncologico, Aviano (PN), Italy
| | | | | | - D Jaminé
- EORTC Data Center, Brussels, Belgium
| | | | - S Lejeune
- EORTC Data Center, Brussels, Belgium
| | | | | | - KH Lam
- Erasmus MC, Rotterdam, The Netherlands
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16
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Eminaga O, Semjonow A, Oezguer E, Herden J, Akbarov I, Tok A, Engelmann U, Wille S. An Electronic Specimen Collection Protocol Schema (eSCPS). Methods Inf Med 2018; 53:29-38. [PMID: 24317441 DOI: 10.3414/me13-01-0035] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 11/04/2013] [Indexed: 11/09/2022]
Abstract
SummaryBackground: The integrity of collection protocols in biobanking is essential for a high-quality sample preparation process. However, there is not currently a well-defined universal method for integrating collection protocols in the biobanking information system (BIMS). Therefore, an electronic schema of the collection protocol that is based on Extensible Markup Language (XML) is required to maintain the integrity and enable the exchange of collection protocols.Materials and Methods: The development and implementation of an electronic specimen collection protocol schema (eSCPS) was performed at two institutions (Muenster and Cologne) in three stages. First, we analyzed the infrastructure that was already established at both the biorepository and the hospital information systems of these institutions and determined the requirements for the sufficient preparation of specimens and documentation. Second, we designed an eSCPS according to these requirements. Fi -nally, a prospective study was conducted to implement and evaluate the novel schema in the current BIMS.Results: We designed an eSCPS that provides all of the relevant information about collection protocols. Ten electronic collection protocols were generated using the supplementary Protocol Editor tool, and these protocols were successfully implemented in the existing BIMS. Moreover, an electronic list of collection protocols for the current studies being performed at each institution was included, new collection protocols were added, and the existing protocols were redesigned to be modifiable. The documentation time was significantly reduced after implementing the eSCPS (5 ± 2 min vs. 7 ± 3 min; p = 0.0002).Conclusion: The eSCPS improves the integrity and facilitates the exchange of specimen collection protocols in the existing open-source BIMS.
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Affiliation(s)
- O Eminaga
- Okyaz Eminaga, M.D., Department of Urology/Prostate Center, University Hospital Cologne, Kerpener Street 62, 50937 Cologne, Germany, E-mail:
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17
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Ostrom QT, Devine K, Fulop J, Wolinsky Y, Liao P, Stetson L, Couce M, Sloan AE, Barnholtz-Sloan JS. Brain tumor biobanking in the precision medicine era: building a high-quality resource for translational research in neuro-oncology. Neurooncol Pract 2017; 4:220-228. [PMID: 29692920 PMCID: PMC5909804 DOI: 10.1093/nop/npw029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The growth of precision medicine has made access to biobanks with high-quality, well-annotated neuro-oncology biospecimens critical. Developing and maintaining neuro-oncology biobanks is best accomplished through multidisciplinary collaboration between clinicians and researchers. Balancing the needs and leveraging the skills of all stakeholders in this multidisciplinary effort is of utmost importance. Collaboration with a multidisciplinary team of clinicians, health care team members, and institutions, as well as patients and their families, is essential for access to participants in order to obtain informed consent, collect samples under strict standard operating procedures, and accurate and relevant clinical annotation. Once a neuro-oncology biobank is established, development and implementation of policies related to governance and distribution of biospecimens (both within and outside the institution) is of critical importance for sustainability. Proper implementation of a governance process helps to ensure that the biospecimens and data can be utilized in research with the largest potential benefit. New NIH and peer-reviewed journal policies related to public sharing of 'omic' data generated from stored biospecimens create new ethical challenges that must be addressed in developing informed consents, protocols, and standard operating procedures. In addition, diversification of sources of funding for the biobanks is needed for long-term sustainability.
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Affiliation(s)
- Quinn T Ostrom
- Case Comprehensive Cancer Center, Wearn 152, Case Western Reserve University School of Medicine, 11100 Euclid Avenue, Cleveland, Ohio 44106 (Q.T.O., K.D., J.F., P.L., L.S., A.E.S., J.S.B.S.); Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, 2103 Cornell Rd, WRB 2-532, Cleveland, Ohio 44106-7295 (Y.W.); Department of Pathology, University Hospitals Case Medical Center, Cleveland, Ohio 44106 (M.C.); Brain Tumor and Neuro-oncology Center, Department of Neurosurgery, University Hospitals Case Medical Center, Case Western Reserve School of Medicine, 11100 Euclid Ave, Cleveland, Ohio 44106 (A.E.S., J.S.B.S.)
| | - Karen Devine
- Case Comprehensive Cancer Center, Wearn 152, Case Western Reserve University School of Medicine, 11100 Euclid Avenue, Cleveland, Ohio 44106 (Q.T.O., K.D., J.F., P.L., L.S., A.E.S., J.S.B.S.); Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, 2103 Cornell Rd, WRB 2-532, Cleveland, Ohio 44106-7295 (Y.W.); Department of Pathology, University Hospitals Case Medical Center, Cleveland, Ohio 44106 (M.C.); Brain Tumor and Neuro-oncology Center, Department of Neurosurgery, University Hospitals Case Medical Center, Case Western Reserve School of Medicine, 11100 Euclid Ave, Cleveland, Ohio 44106 (A.E.S., J.S.B.S.)
| | - Jordonna Fulop
- Case Comprehensive Cancer Center, Wearn 152, Case Western Reserve University School of Medicine, 11100 Euclid Avenue, Cleveland, Ohio 44106 (Q.T.O., K.D., J.F., P.L., L.S., A.E.S., J.S.B.S.); Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, 2103 Cornell Rd, WRB 2-532, Cleveland, Ohio 44106-7295 (Y.W.); Department of Pathology, University Hospitals Case Medical Center, Cleveland, Ohio 44106 (M.C.); Brain Tumor and Neuro-oncology Center, Department of Neurosurgery, University Hospitals Case Medical Center, Case Western Reserve School of Medicine, 11100 Euclid Ave, Cleveland, Ohio 44106 (A.E.S., J.S.B.S.)
| | - Yingli Wolinsky
- Case Comprehensive Cancer Center, Wearn 152, Case Western Reserve University School of Medicine, 11100 Euclid Avenue, Cleveland, Ohio 44106 (Q.T.O., K.D., J.F., P.L., L.S., A.E.S., J.S.B.S.); Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, 2103 Cornell Rd, WRB 2-532, Cleveland, Ohio 44106-7295 (Y.W.); Department of Pathology, University Hospitals Case Medical Center, Cleveland, Ohio 44106 (M.C.); Brain Tumor and Neuro-oncology Center, Department of Neurosurgery, University Hospitals Case Medical Center, Case Western Reserve School of Medicine, 11100 Euclid Ave, Cleveland, Ohio 44106 (A.E.S., J.S.B.S.)
| | - Peter Liao
- Case Comprehensive Cancer Center, Wearn 152, Case Western Reserve University School of Medicine, 11100 Euclid Avenue, Cleveland, Ohio 44106 (Q.T.O., K.D., J.F., P.L., L.S., A.E.S., J.S.B.S.); Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, 2103 Cornell Rd, WRB 2-532, Cleveland, Ohio 44106-7295 (Y.W.); Department of Pathology, University Hospitals Case Medical Center, Cleveland, Ohio 44106 (M.C.); Brain Tumor and Neuro-oncology Center, Department of Neurosurgery, University Hospitals Case Medical Center, Case Western Reserve School of Medicine, 11100 Euclid Ave, Cleveland, Ohio 44106 (A.E.S., J.S.B.S.)
| | - Lindsay Stetson
- Case Comprehensive Cancer Center, Wearn 152, Case Western Reserve University School of Medicine, 11100 Euclid Avenue, Cleveland, Ohio 44106 (Q.T.O., K.D., J.F., P.L., L.S., A.E.S., J.S.B.S.); Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, 2103 Cornell Rd, WRB 2-532, Cleveland, Ohio 44106-7295 (Y.W.); Department of Pathology, University Hospitals Case Medical Center, Cleveland, Ohio 44106 (M.C.); Brain Tumor and Neuro-oncology Center, Department of Neurosurgery, University Hospitals Case Medical Center, Case Western Reserve School of Medicine, 11100 Euclid Ave, Cleveland, Ohio 44106 (A.E.S., J.S.B.S.)
| | - Marta Couce
- Case Comprehensive Cancer Center, Wearn 152, Case Western Reserve University School of Medicine, 11100 Euclid Avenue, Cleveland, Ohio 44106 (Q.T.O., K.D., J.F., P.L., L.S., A.E.S., J.S.B.S.); Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, 2103 Cornell Rd, WRB 2-532, Cleveland, Ohio 44106-7295 (Y.W.); Department of Pathology, University Hospitals Case Medical Center, Cleveland, Ohio 44106 (M.C.); Brain Tumor and Neuro-oncology Center, Department of Neurosurgery, University Hospitals Case Medical Center, Case Western Reserve School of Medicine, 11100 Euclid Ave, Cleveland, Ohio 44106 (A.E.S., J.S.B.S.)
| | - Andrew E Sloan
- Case Comprehensive Cancer Center, Wearn 152, Case Western Reserve University School of Medicine, 11100 Euclid Avenue, Cleveland, Ohio 44106 (Q.T.O., K.D., J.F., P.L., L.S., A.E.S., J.S.B.S.); Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, 2103 Cornell Rd, WRB 2-532, Cleveland, Ohio 44106-7295 (Y.W.); Department of Pathology, University Hospitals Case Medical Center, Cleveland, Ohio 44106 (M.C.); Brain Tumor and Neuro-oncology Center, Department of Neurosurgery, University Hospitals Case Medical Center, Case Western Reserve School of Medicine, 11100 Euclid Ave, Cleveland, Ohio 44106 (A.E.S., J.S.B.S.)
| | - Jill S Barnholtz-Sloan
- Case Comprehensive Cancer Center, Wearn 152, Case Western Reserve University School of Medicine, 11100 Euclid Avenue, Cleveland, Ohio 44106 (Q.T.O., K.D., J.F., P.L., L.S., A.E.S., J.S.B.S.); Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, 2103 Cornell Rd, WRB 2-532, Cleveland, Ohio 44106-7295 (Y.W.); Department of Pathology, University Hospitals Case Medical Center, Cleveland, Ohio 44106 (M.C.); Brain Tumor and Neuro-oncology Center, Department of Neurosurgery, University Hospitals Case Medical Center, Case Western Reserve School of Medicine, 11100 Euclid Ave, Cleveland, Ohio 44106 (A.E.S., J.S.B.S.)
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18
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Li JH, Chen J, Mu XJ, Shao QL, Zhou YQ, Yan LJ. Effect of tissue frozen on quantitative optical properties using optical coherence tomography. APPLIED OPTICS 2017; 56:8335-8339. [PMID: 29091612 DOI: 10.1364/ao.56.008335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 09/19/2017] [Indexed: 06/07/2023]
Abstract
The purpose is to demonstrate the optical charactering concerning nasopharyngeal tissue of pig by fresh sections and frozen correlating sections with optical coherence tomography (OCT). After being imaged on a fresh specimen, samples are then stored in low temperature refrigerators (-80°C) for one year for the second OCT measurement. The OCT structure of the epithelium, lamina propria, and the basement membrane are still resolvable; the median scattering coefficients and anisotropy factors fitting from OCT images based on the multiple scattering effects for epithelium are 27.6 mm-1 [interquartile range (IQR) 23.6 to 29.3 mm-1] versus 22.5 mm-1 (IQR 20.5 to 24.4 mm-1), 0.86 (IQR 0.81 to 0.9) versus 0.88 (IQR 0.87 to 0.9) for fresh and frozen tissue, respectively; and 10.2 mm-1 (IQR 8.1 to 13.6 mm-1) versus 9.6 mm-1 (IQR 8.1 to 13.8 mm-1), 0.96 (IQR 0.93 to 0.98) versus 0.92 (IQR 0.9 to 0.98) for lamina propria, respectively. The results show that the frozen storage method can be used for OCT research.
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19
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Arni S, Le THN, de Wijn R, Garcia-Villegas R, Dankers M, Weder W, Hillinger S. Ex vivo multiplex profiling of protein tyrosine kinase activities in early stages of human lung adenocarcinoma. Oncotarget 2017; 8:68599-68613. [PMID: 28978141 PMCID: PMC5620281 DOI: 10.18632/oncotarget.19803] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Accepted: 07/17/2017] [Indexed: 11/25/2022] Open
Abstract
Despite constant improvement in existing therapeutic efforts, the overall survival rate of lung cancer patients remains low. Enzyme activities may identify new therapeutically targetable biomarkers and overcome the marked lack of correlation between cellular abundance of translated proteins and corresponding mRNA expression levels. We analysed tyrosine kinase activities to classify lung adenocarcinoma (LuAdCa) resection specimens based on their underlying changes in cellular processes and pathways that are agents of or result from malignant transformation. We characterised 71 same-patient pairs of early-stage LuAdCa and non-neoplastic LuAdCa resection specimen lysates in the presence or absence of a tyrosine kinase inhibitor. We performed ex vivo multiplex tyrosine phosphorylation assays using 144 selected microarrayed kinase substrates. The obtained 76 selected phosphotyrosine signature peptides were subsequently analysed in terms of follow-up treatments and outcomes recorded in the patient files. For tumour, node, metastasis (TNM) stage 1 LuAdCa patients, we noticed a larger tyrosine kinase inhibitor-induced decrease in tyrosine phosphorylation for long-term as opposed to short-term disease survivors, for which 26 of 76 selected peptides were significantly (p < 0.01, FDR < 3%) more inhibited in the long-term survivors. Using statistical class prediction analysis, we obtained a 'prognostic-signature' for long- versus short-term disease survivors and correctly predicted the survival status of 73% of our patients. Our translational approach may assist clinical disease management after surgical resection and may help to direct patients for an optimal treatment strategy.
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Affiliation(s)
- Stephan Arni
- Department of Thoracic Surgery, University Hospital Zürich, Zürich, Switzerland
| | - Thi Hong Nhung Le
- Department of Thoracic Surgery, University Hospital Zürich, Zürich, Switzerland
| | - Rik de Wijn
- PamGene International B.V., 's-Hertogenbosch, The Netherlands
| | - Refugio Garcia-Villegas
- Department of Physiology, Biophysics and Neuroscience, Centro de Investigación y de Estudios Avanzados del IPN, Mexico City, Mexico
| | - Martjin Dankers
- PamGene International B.V., 's-Hertogenbosch, The Netherlands
| | - Walter Weder
- Department of Thoracic Surgery, University Hospital Zürich, Zürich, Switzerland
| | - Sven Hillinger
- Department of Thoracic Surgery, University Hospital Zürich, Zürich, Switzerland
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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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Ahmad-Nejad P, Duda A, Sucker A, Werner M, Bronsert P, Stickeler E, Reifenberger G, Malzkorn B, Oberländer M, Habermann JK, Bruch HP, Linnebacher M, Schadendorf D, Neumaier M. Assessing quality and functionality of DNA isolated from FFPE tissues through external quality assessment in tissue banks. Clin Chem Lab Med 2016; 53:1927-34. [PMID: 26053008 DOI: 10.1515/cclm-2014-1202] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 04/30/2015] [Indexed: 11/15/2022]
Abstract
BACKGROUND Biobanks are becoming increasingly important for assessment of disease risk as well as identification and validation of new diagnostic biomarkers and druggable targets. The validity of data obtained from biobanks is critically limited by the biomaterial quality of the biological samples. External quality assessment (EQA) programs suitable to comprehensively measure the biomaterial quality in archived materials are currently lacking. We report on quantitative assay designs for the analysis of both structural and functional integrity of DNAs that were applied in a first pilot EQA within the priority program on tumor tissue biobanking funded by the German Cancer Aid. METHODS Participating biobanks isolated DNAs from a standardized set of 10 samples comprising sections of four different formalin-fixed paraffin-embedded tissues using their standard operating procedures. Isolated DNAs and analytical results were returned and analyzed centrally for nucleic acids yield, purity, fragmentation and amplificability at a quantitative level using dedicated assay designs. RESULTS The amount of extracted DNA varied in isolates ranging between 1.5 μg and 25.8 μg. Quantification of DNA fragmentation and amplificability allowed to highlight considerable discrepancies in DNA quality. Amplicons yielded from the isolates of these identical EQA samples ranged from 105 to 411 bp suggesting differences between residual inhibitors of downstream enzymatic reactions. CONCLUSIONS The quality of extraction of bioanalytes from biomaterial archives is heterogeneous even for stable biomolecules like DNA isolated with highly standardized methods. EQAs are appropriate tools to uncover strengths and weaknesses in biobanks in a systematic fashion. Biomaterial integrity is insufficiently reflected by standard methods, but needs to be assessed to improve biobank interoperability. Finally, our results also point towards the problem of measuring the quality of more delicate biomolecules like proteins or metabolites.
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Lucena-Aguilar G, Sánchez-López AM, Barberán-Aceituno C, Carrillo-Ávila JA, López-Guerrero JA, Aguilar-Quesada R. DNA Source Selection for Downstream Applications Based on DNA Quality Indicators Analysis. Biopreserv Biobank 2016; 14:264-70. [PMID: 27158753 PMCID: PMC4991598 DOI: 10.1089/bio.2015.0064] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
High-quality human DNA samples and associated information of individuals are necessary for biomedical research. Biobanks act as a support infrastructure for the scientific community by providing a large number of high-quality biological samples for specific downstream applications. For this purpose, biobank methods for sample preparation must ensure the usefulness and long-term functionality of the products obtained. Quality indicators are the tool to measure these parameters, the purity and integrity determination being those specifically used for DNA. This study analyzes the quality indicators in DNA samples derived from 118 frozen human tissues in optimal cutting temperature (OCT) reactive, 68 formalin-fixed paraffin-embedded (FFPE) tissues, 119 frozen blood samples, and 26 saliva samples. The results obtained for DNA quality are discussed in association with the usefulness for downstream applications and availability of the DNA source in the target study. In brief, if any material is valid, blood is the most approachable option of prospective collection of samples providing high-quality DNA. However, if diseased tissue is a requisite or samples are available, the recommended source of DNA would be frozen tissue. These conclusions will determine the best source of DNA, according to the planned downstream application. Furthermore our results support the conclusion that a complete procedure of DNA quantification and qualification is necessary to guarantee the appropriate management of the samples, avoiding low confidence results, high costs, and a waste of samples.
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Affiliation(s)
- Gema Lucena-Aguilar
- 1 Andalusian Public Health System Biobank, Armilla, Spain .,2 Instituto de Investigación Biosanitaria de Granada , Armilla, Spain
| | - Ana María Sánchez-López
- 1 Andalusian Public Health System Biobank, Armilla, Spain .,2 Instituto de Investigación Biosanitaria de Granada , Armilla, Spain
| | | | - José Antonio Carrillo-Ávila
- 1 Andalusian Public Health System Biobank, Armilla, Spain .,2 Instituto de Investigación Biosanitaria de Granada , Armilla, Spain
| | - José Antonio López-Guerrero
- 3 Laboratory of Molecular Biology, Fundación Instituto Valenciano de Oncología , Valencia, Spain .,4 Biobank, Fundación Instituto Valenciano de Oncología , Valencia, Spain
| | - Rocío Aguilar-Quesada
- 1 Andalusian Public Health System Biobank, Armilla, Spain .,2 Instituto de Investigación Biosanitaria de Granada , Armilla, Spain
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23
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A critical analysis of cancer biobank practices in relation to biospecimen quality. Biophys Rev 2015; 7:369-378. [PMID: 28510101 DOI: 10.1007/s12551-015-0178-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 09/17/2015] [Indexed: 12/26/2022] Open
Abstract
There are concerns that a substantial proportion of published research data is not reproducible, which may partially explain the frequent failure to translate pre-clinical results to clinical care. High-quality cancer biospecimens are needed for robust, reproducible research findings, with most researchers obtaining these specimens from cancer biobanks or tumour banks. This review provides an overview of the types of quality control (QC) activities conducted within cancer biobanks that pertain to biospecimen quality and of biospecimen quality reporting tools, including SPREC and BRISQ. We examine how QC assay results and other biospecimen data are communicated from biobanks to researchers, and whether these activities lead to improved biospecimen quality reporting within the literature and/or to improved research outcomes. We also discuss operational factors that limit QC activities within biobanks and evidence gaps requiring further research. In summary, whereas the provision of quality biospecimens is a common aim of cancer biobanks, QC activities remain underreported and are rarely discussed in the literature, compared with other aspects of biobank operations. Further research is required to determine how biobanks can most efficiently optimise biospecimen quality, and how communication between biobanks and researchers can be improved.
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24
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Wang Y, Zheng H, Chen J, Zhong X, Wang Y, Wang Z, Wang Y. The Impact of Different Preservation Conditions and Freezing-Thawing Cycles on Quality of RNA, DNA, and Proteins in Cancer Tissue. Biopreserv Biobank 2015; 13:335-47. [PMID: 26484573 DOI: 10.1089/bio.2015.0029] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- Yaogeng Wang
- Laboratory of Molecular Diagnosis of Cancer, West China Hospital, Sichuan University, Chengdu, China
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Hong Zheng
- Laboratory of Molecular Diagnosis of Cancer, West China Hospital, Sichuan University, Chengdu, China
| | - Jie Chen
- Laboratory of Molecular Diagnosis of Cancer, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaorong Zhong
- Laboratory of Molecular Diagnosis of Cancer, West China Hospital, Sichuan University, Chengdu, China
| | - Yu Wang
- Laboratory of Molecular Diagnosis of Cancer, West China Hospital, Sichuan University, Chengdu, China
| | - Zhu Wang
- Laboratory of Molecular Diagnosis of Cancer, West China Hospital, Sichuan University, Chengdu, China
| | - Yanping Wang
- Laboratory of Molecular Diagnosis of Cancer, West China Hospital, Sichuan University, Chengdu, China
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
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25
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Corso G, Garosi L, Marrelli D, Roviello F. Assessment of a tumor bank: a thirty years experience of the University of Siena (Italy). Cell Tissue Bank 2014; 16:283-6. [PMID: 24984986 DOI: 10.1007/s10561-014-9460-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 06/24/2014] [Indexed: 02/05/2023]
Abstract
Tumor biobank plays a pivotal role in cancer biomedical research. The collection of a high variety of biological samples, including DNA, RNA, tissues, cells, blood, plasma and other body fluids, represents a necessary step to plan new strategies in the improvement of oncological patient care. Since 1985, a consolidated experience in biobanking management has been developed at the University of Siena (Italy). During these years, some information about clinico-pathology, surgery and a high number of human bispecimens have been collected. Herein, we described our experience in sampling management to improve the cancer research and the patient care.
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Affiliation(s)
- G Corso
- Unit of Surgical Oncology, Department of Surgical Medical Science and Neurosciences, University of Siena, 53100, Siena, Italy,
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26
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Ma R, Fredriksson I, Karthik GM, Winn G, Darai-Ramqvist E, Bergh J, Hartman J. Superficial scrapings from breast tumors is a source for biobanking and research purposes. J Transl Med 2014; 94:796-805. [PMID: 24776644 DOI: 10.1038/labinvest.2014.65] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Accepted: 04/01/2014] [Indexed: 01/13/2023] Open
Abstract
Breast cancer is a unique tumor disease in terms of the stringent requirement of predictive biomarker assessments. As recommended by current international guidelines, the established markers consist of estrogen receptor (ER), progesterone receptor, human epidermal growth factor and Ki67, and are primarily analyzed by immunohistochemistry. However, new diagnostic methods based on microarray or next-generation sequencing on DNA and mRNA level are gaining ground. These analyses require fresh-frozen tumor tissue that is generally not available from tumors <10 mm in diameter, comprising almost 25% of all resected breast cancer at our department. We here present a simple and standardized method to generate material from small tumors without risking the histopathological examination. Furthermore, we show that the quality of this material is sufficient for subsequent analysis on mRNA, DNA, and epigenetic level. We were also able to use this method for isolation and expansion of cancer stem cells from the majority of tumors. Consequently, researches can be provided with clinically relevant material for translational studies. In conclusion, this method opens up a new possibility for usage of valuable fresh tumor material for research purposes, biobanking, and next-generation sequencing.
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Affiliation(s)
- Ran Ma
- Departments of Oncology and Pathology, Cancer Center Karolinska, Karolinska Institutet, Stockholm, Sweden
| | - Irma Fredriksson
- 1] Departments of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden [2] Departments of Breast and Endocrine Surgery, Karolinska Institutet, Stockholm, Sweden
| | | | - Gregory Winn
- Departments of Clinical Pathology and Cytology, Karolinska University Hospital, Stockholm, Sweden
| | - Eva Darai-Ramqvist
- Departments of Clinical Pathology and Cytology, Karolinska University Hospital, Stockholm, Sweden
| | - Jonas Bergh
- 1] Departments of Oncology and Pathology, Cancer Center Karolinska, Karolinska Institutet, Stockholm, Sweden [2] Radiumhemmet - Karolinska Oncology, Karolinska University Hospital, Stockholm, Sweden
| | - Johan Hartman
- 1] Departments of Oncology and Pathology, Cancer Center Karolinska, Karolinska Institutet, Stockholm, Sweden [2] Departments of Clinical Pathology and Cytology, Karolinska University Hospital, Stockholm, Sweden
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27
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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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Kap M, Oomen M, Arshad S, de Jong B, Riegman P. Fit for purpose frozen tissue collections by RNA integrity number-based quality control assurance at the Erasmus MC tissue bank. Biopreserv Biobank 2014; 12:81-90. [PMID: 24749874 DOI: 10.1089/bio.2013.0051] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
About 5000 frozen tissue samples are collected each year by the Erasmus Medical Center tissue bank. Two percent of these samples are randomly selected annually for RNA isolation and RNA Integrity Number (RIN) measurement. A similar quality assessment was conducted during centralization of a 20-year-old tissue collection from the cancer institute, a 15-year-old liver sample archive (-80°C), and a 13-year-old clinical pathology frozen biopsy archive (Liquid Nitrogen). Samples were divided into either high-quality (RIN ≥6.5) or low-quality overall categories, or into four "fit-for-purpose" quality groups: RIN <5: not reliable for demanding downstream analysis; 5 ≤RIN <6: suitable for RT-qPCR; 6 ≤RIN <8: suitable for gene array analysis; and RIN ≥8: suitable for all downstream techniques. In general, low RIN values were correlated with fatty, fibrous, pancreatic, or necrotic tissue. When the percentage of samples with RIN ≥6.5 is higher than 90%, the tissue bank performance is adequate. The annual 2011 quality control assessment showed that 90.3% (n=93) of all samples had acceptable RIN values; 97.4% (n=39) of the cancer institute collection had RIN values above 6.5; and 88.6% (n=123) of samples from the liver sample archive collection had RIN values higher than 6.5. As the clinical pathology biopsy collection contained only 58.8% (n=24) acceptable samples, the procurement protocols used for these samples needed immediate evaluation. When the distribution of RIN values of the different collections were compared, no significant differences were found, despite differences in average storage time and temperature. According to the principle of "fit-for-purpose" distribution, the vast majority of samples are considered good enough for most downstream techniques. In conclusion, an annual tissue bank quality control procedure provides useful information on tissue sample quality and sheds light on where and if improvements need to be made.
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Affiliation(s)
- Marcel Kap
- Department of Pathology, Erasmus Medical Center , Rotterdam, The Netherlands
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29
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Torata N, Ohuchida K, Akagawa S, Cui L, Kozono S, Mizumoto K, Aishima S, Oda Y, Tanaka M. Tissue tablet method: an efficient tissue banking procedure applicable to both molecular analysis and frozen tissue microarray. Hum Pathol 2014; 45:143-52. [DOI: 10.1016/j.humpath.2013.08.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 08/15/2013] [Accepted: 08/21/2013] [Indexed: 11/28/2022]
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Somatic mutations in MAP3K5 attenuate its proapoptotic function in melanoma through increased binding to thioredoxin. J Invest Dermatol 2013; 134:452-460. [PMID: 24008424 PMCID: PMC3947167 DOI: 10.1038/jid.2013.365] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 06/24/2013] [Accepted: 07/12/2013] [Indexed: 12/13/2022]
Abstract
Patients with advanced metastatic melanoma have poor prognosis and the genetics underlying its pathogenesis are poorly understood. High throughput sequencing has allowed comprehensive discovery of somatic mutations in cancer samples. Here, upon analysis of our whole-genome and whole-exome sequencing data of 29 melanoma samples we identified several genes that harbor recurrent non-synonymous mutations. These included MAP3K5, which in a prevalence screen of 288 melanomas was found to harbor a R256C substitution in 5 cases. All MAP3K5 mutated samples were wild-type for BRAF, suggesting a mutual exclusivity for these mutations. Functional analysis of the MAP3K5 R256C mutation revealed attenuation of MKK4 activation through increased binding of the inhibitory protein thioredoxin (TXN/TRX-1/Trx); resulting in increased proliferation and anchorage-independent growth of melanoma cells. This mutation represents a potential target for the design of new therapies to treat melanoma.
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31
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Mathot L, Wallin M, Sjöblom T. Automated serial extraction of DNA and RNA from biobanked tissue specimens. BMC Biotechnol 2013; 13:66. [PMID: 23957867 PMCID: PMC3751724 DOI: 10.1186/1472-6750-13-66] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 08/15/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND With increasing biobanking of biological samples, methods for large scale extraction of nucleic acids are in demand. The lack of such techniques designed for extraction from tissues results in a bottleneck in downstream genetic analyses, particularly in the field of cancer research. We have developed an automated procedure for tissue homogenization and extraction of DNA and RNA into separate fractions from the same frozen tissue specimen. A purpose developed magnetic bead based technology to serially extract both DNA and RNA from tissues was automated on a Tecan Freedom Evo robotic workstation. RESULTS 864 fresh-frozen human normal and tumor tissue samples from breast and colon were serially extracted in batches of 96 samples. Yields and quality of DNA and RNA were determined. The DNA was evaluated in several downstream analyses, and the stability of RNA was determined after 9 months of storage. The extracted DNA performed consistently well in processes including PCR-based STR analysis, HaloPlex selection and deep sequencing on an Illumina platform, and gene copy number analysis using microarrays. The RNA has performed well in RT-PCR analyses and maintains integrity upon storage. CONCLUSIONS The technology described here enables the processing of many tissue samples simultaneously with a high quality product and a time and cost reduction for the user. This reduces the sample preparation bottleneck in cancer research. The open automation format also enables integration with upstream and downstream devices for automated sample quantitation or storage.
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Affiliation(s)
- Lucy Mathot
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, SE-751 85, Uppsala, Sweden
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Caenazzo L, Tozzo P, Pegoraro R. Biobanking research on oncological residual material: a framework between the rights of the individual and the interest of society. BMC Med Ethics 2013; 14:17. [PMID: 23547565 PMCID: PMC3616854 DOI: 10.1186/1472-6939-14-17] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 03/20/2013] [Indexed: 12/29/2022] Open
Abstract
Background The tissue biobanking of specific biological residual materials, which constitutes a useful resource for medical/scientific research, has raised some ethical issues, such as the need to define which kind of consent is applicable for biological residual materials biobanks. Discussion Biobank research cannot be conducted without considering arguments for obtaining the donors’ consent: in this paper we discuss to what extent consent in biobank research on oncological residual materials has to be required, and what type of consent would be appropriate in this context, considering the ethical principles of donation, solidarity, protection of the donors’ rights and the requirements of scientific progress. Regarding the relationship between informed consent and tissue collection, storage and research, we have focused on two possible choices related to the treatment of data and samples in the biobank: irreversible and reversible anonymization of the samples, distinguishing between biobank research on residual materials for which obtaining consent is necessary and justified, and biobank research for which it is not. The procedures involve different approaches and possible solutions that we will seek to define. The consent for clinical research reported in the Helsinki Declaration regards research involving human beings and for this reason it is subordinate to specific and detailed information on the research projects. Summary An important ethical aspect in regard to the role of Biobanks is encouraging sample donation. For donors, seeing human samples being kept rather than discarded, and seeing them become useful for research highlights the importance of the human body and improves the attitude towards donation. This process might also facilitate the giving of informed consent more willingly, and with greater trust.
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Affiliation(s)
- Luciana Caenazzo
- Department of Molecular Medicine, University of Padova, Via Falloppio 50, 35121 Padua, Italy.
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von Teichman A, Storz M, Dettwiler S, Moch H, Schraml P. Whole genome and transcriptome amplification: practicable tools for sustainable tissue biobanking? Virchows Arch 2012; 461:571-80. [PMID: 23007645 DOI: 10.1007/s00428-012-1315-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Revised: 08/24/2012] [Accepted: 09/03/2012] [Indexed: 12/18/2022]
Abstract
The use of whole genome amplification (WGA) and whole transcriptome amplification (WTA) techniques enables the enrichment of DNA and RNA from very small amounts of tissue. Here, we tested the suitability of WGA and WTA for tumor tissue biobanking. DNA and RNA from 13 standardized and seven non-standardized frozen and 12 formalin-fixed, paraffin-embedded (FFPE) clear cell renal cell carcinoma specimens (>9 years old) served to test the robustness of the WGA and WTA products by reidentifying von Hippel-Lindau (VHL) gene mutations known to exist in these samples. The enrichment of DNA and RNA from frozen tissue was up to 1,291-fold and 423-fold, respectively. The sizes and yields (10- to 73-fold) of the amplified DNA obtained from the 12 FFPE samples were generally lower. The quality of the RNA from the FFPE samples was too low to reliably perform WTA. Our results demonstrate that frozen tumor tissue is very suitable for WGA and WTA. All 20 VHL mutations were verified with WGA. Notably, we were able to show that 18 of the 20 (90 %) VHL mutations are also transcribed. In FFPE tumor tissue, 8 of 12 cases (67 %) showed the expected mutations after the first WGA. Accurate WTA with FFPE material is sophisticated and strongly depends on the modification and degradation status of the fixed tissue. We conclude that for sustainable tissue biobanking, the use of WGA and WTA is a unique opportunity to provide researchers with sufficient amounts of nucleic acids, preferably from limited frozen tissue material.
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Affiliation(s)
- Adriana von Teichman
- Institute of Surgical Pathology, University Hospital Zurich, Schmelzbergstrasse 12, 8091 Zurich, Switzerland
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Bao WG, Zhang X, Zhang JG, Zhou WJ, Bi TN, Wang JC, Yan WH, Lin A. Biobanking of fresh-frozen human colon tissues: impact of tissue ex-vivo ischemia times and storage periods on RNA quality. Ann Surg Oncol 2012; 20:1737-44. [PMID: 22711177 DOI: 10.1245/s10434-012-2440-1] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Indexed: 11/18/2022]
Abstract
BACKGROUND Biobanking plays an important role in translational cancer research. The impact of tissue ex-vivo ischemia time and storage period on RNA integrity is not well documented. METHODS Fresh-frozen colon tissues were collected in Taizhou Hospital of Zhejiang Province in China since 2004. Fifty-one colon cancer tissues with tumor cell content higher than 70 % and matched normal tissues during four storage periods (less than 15 months, 16-20 months, 21-25 months, and 26-40 months) were chosen to detect RNA quality. Fresh colon cancer tissues from 5 patients were cut into pieces and kept at room temperature or on ice for 0.5, 1, 2, and 4 h before snap freezing. RNA integrity was determined by microcapillary electrophoresis by the RNA integrity number (RIN) algorithm. RESULTS Sixty-seven percent of normal colon tissues and 94 % of colon cancer specimens yielded RNA with a RIN of ≥7. Matched colon cancer and normal tissues showed significant difference in RNA quality. RNA remained stable in colon cancer tissues kept at room temperature and on ice for up to 4 h, and long-term storage of banked colon specimens did not negatively influence RNA quality (RNA with RIN of ≥7 banked less than 15 months, 83 %; 16-20 months, 78 %; 21-25 months, 77 %; 26-40 months, 90 %). CONCLUSIONS Frozen colon tissues yield high-quality RNA in approximately 80 % of specimens. Ex-vivo ischemia times and storage periods did not adversely affect RNA quality. This study showed that standard operation protocols and the maintenance of high-quality tissue repositories were the keys to translational medicine research.
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Affiliation(s)
- Wei-Guang Bao
- Human Tissue Bank, Taizhou Hospital of Zhejiang Province, Wenzhou Medical College, Zhejiang, China
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35
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Issues of banking breast cancer cells to generate mammospheres. Cell Tissue Bank 2012; 14:153-8. [DOI: 10.1007/s10561-012-9320-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 05/23/2012] [Indexed: 01/06/2023]
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Exome sequencing identifies GRIN2A as frequently mutated in melanoma. Nat Genet 2011; 43:442-6. [PMID: 21499247 PMCID: PMC3161250 DOI: 10.1038/ng.810] [Citation(s) in RCA: 369] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Accepted: 03/24/2011] [Indexed: 02/03/2023]
Abstract
The incidence of melanoma is increasing more than any other cancer, and knowledge of its genetic alterations is limited. To systematically analyze such alterations, we performed whole-exome sequencing of 14 matched normal and metastatic tumor DNAs. Using stringent criteria, we identified 68 genes that appeared to be somatically mutated at elevated frequency, many of which are not known to be genetically altered in tumors. Most importantly, we discovered that TRRAP harbored a recurrent mutation that clustered in one position (p. Ser722Phe) in 6 out of 167 affected individuals (∼4%), as well as a previously unidentified gene, GRIN2A, which was mutated in 33% of melanoma samples. The nature, pattern and functional evaluation of the TRRAP recurrent mutation suggest that TRRAP functions as an oncogene. Our study provides, to our knowledge, the most comprehensive map of genetic alterations in melanoma to date and suggests that the glutamate signaling pathway is involved in this disease.
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Lu XF, Ma X, Zhou JQ, Chen FQ, Yang QP, Wei MY, Liu YM, Yang Y, Zhou WP. Establishment and management of a liver tissue bank in China. Shijie Huaren Xiaohua Zazhi 2011; 19:1187-1190. [DOI: 10.11569/wcjd.v19.i11.1187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
AIM: To develop a standardized and well-rounded liver tissue bank available for hepatology research using well-characterized and optimally preserved liver tumor tissue samples.
METHODS: Standardized operational procedures were developed, and samples such as fresh-frozen surgical tissue samples, pre- and postoperative whole blood, urine and paraffin section samples were collected. Using the National Liver Tissue Bank (NLTB) data management platform, the database can be accessed and renewed automatically or manually with the Hospital Information System (HIS).
RESULTS: From Mar 2009 to Dec 2010, over 4000 individuals had been enrolled as liver tumor donors to the NLTB, including 2 500 cases of newly diagnosed hepatocellular carcinoma (HCC), and 1 500 cases of diagnosed begin or malignant liver tumors. Database access and sample preservation can be managed easily and correctly with the data management platform.
CONCLUSION: We established a standard liver tissue bank using high-quality well-characterized samples, which will become the cornerstone for hepatology research, especially the diagnosis and treatment of HCC and other liver diseases.
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Baranyai Z, Mersich T, Dede K, Besznyák I, Zaránd A, Teknos D, Nagy P, Salamon F, Nagy P, Nagy Z, Kótai Z, Szász M, Lukács L, Szállási Z, Jósa V, Jakab F. [From project-based sample collection to biobank]. Orv Hetil 2011; 152:606-9. [PMID: 21436025 DOI: 10.1556/oh.2011.29068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The research group takes samples for molecular genetical examinations from tumors removed during operations within ischemic time interval. Samples are stored in liquid nitrogen. Clinical data of these patients are recorded in an informatics system developed by the group. Patients are followed in an out-patient clinic set up for this purpose not financed by the National Health Insurance Fund. Tissue samples and follow up data are used to cooperate with molecular genetical laboratories.
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Affiliation(s)
- Zsolt Baranyai
- Fővárosi Önkormányzat Uzsoki Utcai Kórháza Sebészet-Érsebészeti Osztály Budapest Uzsoki u. 29. 1145 Tumorgenetika Biobank Klaszter Budapest.
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39
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Biobanking of fresh frozen tissue from clinical surgical specimens: transport logistics, sample selection, and histologic characterization. Methods Mol Biol 2011; 675:299-306. [PMID: 20949397 DOI: 10.1007/978-1-59745-423-0_16] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
Abstract
Access to high-quality fresh frozen tissue is critical for translational cancer research and molecular -diagnostics. Here we describe a workflow for the collection of frozen solid tissue samples derived from fresh human patient specimens after surgery. The routines have been in operation at Uppsala University Hospital since 2001. We have integrated cryosection and histopathologic examination of each biobank sample into the biobank manual. In this way, even small, macroscopically ill-defined lesions can be -procured without a diagnostic hazard due to the removal of uncharacterized tissue from a clinical -specimen. Also, knowledge of the histomorphology of the frozen tissue sample - tumor cell content, stromal components, and presence of necrosis - is pivotal before entering a biobank case into costly molecular profiling studies.
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Abstract
Since RNA is believed to be the most vulnerable molecular component of unfixed tissue, preserved RNA integrity can be used as a general quality indicator in fresh frozen tissue biobanks. As the size of samples and biopsies often is small, in the range of millimeters or milligrams, it is important to implement quality control procedures adapted to minute the amounts of tissue. To this end, we here describe RNA extraction from one or a few frozen tissue sections and subsequent analysis of structural RNA integrity by microcapillary gel electrophoresis.
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Affiliation(s)
- Johan Botling
- Rudbeck Laboratory, Department of Genetics and Pathology, University Hospital, Uppsala, Sweden
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41
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Yang Y, Liu YM, Wei MY, Wu YF, Gao JH, Liu L, Zhou WP, Wang HY, Wu MC. The liver tissue bank and clinical database in China. ACTA ACUST UNITED AC 2010; 4:443-7. [PMID: 21088930 DOI: 10.1007/s11684-010-0190-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2010] [Accepted: 09/27/2010] [Indexed: 10/18/2022]
Abstract
To develop a standardized and well-rounded material available for hepatology research, the National Liver Tissue Bank (NLTB) Project began in 2008 in China to make well-characterized and optimally preserved liver tumor tissue and clinical database. From Dec 2008 to Jun 2010, over 3000 individuals have been enrolled as liver tumor donors to the NLTB, including 2317 cases of newly diagnosed hepatocellular carcinoma (HCC) and about 1000 cases of diagnosed benign or malignant liver tumors. The clinical database and sample store can be managed easily and correctly with the data management platform used. We believe that the high-quality samples with detailed information database will become the cornerstone of hepatology research especially in studies exploring the diagnosis and new treatments for HCC and other liver diseases.
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Affiliation(s)
- Yuan Yang
- Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, 200438, China
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42
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Goebell PJ, Morente MM. New concepts of biobanks--strategic chance for uro-oncology. Urol Oncol 2010; 28:449-57. [PMID: 20610282 DOI: 10.1016/j.urolonc.2010.03.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2009] [Revised: 03/17/2010] [Accepted: 03/18/2010] [Indexed: 02/04/2023]
Abstract
Cancer, as well as other common diseases, is a complex condition that not only causes a major threat to human health, but also represents a huge burden to society in terms of healthcare cost and loss of economic productivity. Treatment improvements remain elusive, since the causes of cancer are due to a huge number of small and possibly additive effects arising from genetic susceptibility, lifestyle, and environmental conditions. Thus, progress in translational cancer research investigating these changes and their complex interaction is highly dependent on large series of cases (affected and unaffected individuals) including high quality samples and their associated data. Therefore, large and well-organized biobanks have been established, are underway, or are planned in many countries and institutions. The integration of these resources with powerful molecular and "omics" approaches, integrated bioinformatic tools hold the promise to further advance our knowledge of disease development, thus leading to better prevention and treatment strategies. However, these valuable and irreplaceable collections typically suffer from underutilization, due to fragmentation of the collections and their accessibility, lack of common management strategies, including consensus on standard operating procedures, unique policies of utilization, and distribution as well as missing input on a broad basis reflecting research needs on an interdisciplinary, multi-institutional fashion beyond project-driven interest. The uro-oncologic community has not yet contributed to these efforts to its full potential, and broad knowledge on the contemporary developments in the field of biobanking and input into these efforts are still missing. This review presents an overview on biobanking and may serve as an update to be integrated into future discussions on managing biobanks involving uro-oncology. It is based on the discussions at the last meeting of the International Bladder Cancer Network in Barcelona (Spain) in fall 2008 and has been also largely influenced by the works and discussions of the Marble Arch International Working Group on Biobanking for Biomedical Research.
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Affiliation(s)
- Peter J Goebell
- Department of Urology, University Clinic of Erlangen, Erlangen, Germany.
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43
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Andersson K, Bray F, Arbyn M, Storm H, Zanetti R, Hallmans G, Coebergh JW, Dillner J. The interface of population-based cancer registries and biobanks in etiological and clinical research--current and future perspectives. Acta Oncol 2010; 49:1227-34. [PMID: 20583946 DOI: 10.3109/0284186x.2010.496792] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
BACKGROUND The availability of quality assured, population-based cancer registries and biobanks with high quality samples makes it possible to conduct research on large samples sets with long follow-up within a reasonable time frame. Defined quality for both cancer registries and biobanks is essential for enabling high quality biobank-based research. Recent networking projects have brought these infrastructures together to promote the combined use of cancer registries and biobanks in cancer research. MATERIALS AND METHODS In this report we review the current status and future perspectives of cancer registries and biobanks and how the interface between them should be developed to optimally further cancer research. RESULTS AND DISCUSSION Major conclusions for future improvements are that the research exploiting cancer registries and biobanks, and the research that is building and optimising the infrastructure, should evolve together for maximally relevant progress. Population-based and sustainable biobanks that continuously and consecutively store all samples ("Biological registries") under strict quality control are needed. There is also a need for increased education, information and visibility of the interdisciplinary sciences required for optimal exploitation of these resources.
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Riegman PH, de Jong BW, Llombart-Bosch A. The Organization of European Cancer Institute Pathobiology Working Group and its Support of European Biobanking Infrastructures for Translational Cancer Research. Cancer Epidemiol Biomarkers Prev 2010; 19:923-6. [DOI: 10.1158/1055-9965.epi-10-0062] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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45
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Jackson DH, Banks RE. Banking of clinical samples for proteomic biomarker studies: A consideration of logistical issues with a focus on pre-analytical variation. Proteomics Clin Appl 2010; 4:250-70. [DOI: 10.1002/prca.200900220] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2009] [Revised: 12/20/2009] [Accepted: 12/20/2009] [Indexed: 01/07/2023]
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Ocak S, Sos ML, Thomas RK, Massion PP. High-throughput molecular analysis in lung cancer: insights into biology and potential clinical applications. Eur Respir J 2009; 34:489-506. [PMID: 19648524 DOI: 10.1183/09031936.00042409] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
During the last decade, high-throughput technologies including genomic, epigenomic, transcriptomic and proteomic have been applied to further our understanding of the molecular pathogenesis of this heterogeneous disease, and to develop strategies that aim to improve the management of patients with lung cancer. Ultimately, these approaches should lead to sensitive, specific and noninvasive methods for early diagnosis, and facilitate the prediction of response to therapy and outcome, as well as the identification of potential novel therapeutic targets. Genomic studies were the first to move this field forward by providing novel insights into the molecular biology of lung cancer and by generating candidate biomarkers of disease progression. Lung carcinogenesis is driven by genetic and epigenetic alterations that cause aberrant gene function; however, the challenge remains to pinpoint the key regulatory control mechanisms and to distinguish driver from passenger alterations that may have a small but additive effect on cancer development. Epigenetic regulation by DNA methylation and histone modifications modulate chromatin structure and, in turn, either activate or silence gene expression. Proteomic approaches critically complement these molecular studies, as the phenotype of a cancer cell is determined by proteins and cannot be predicted by genomics or transcriptomics alone. The present article focuses on the technological platforms available and some proposed clinical applications. We illustrate herein how the "-omics" have revolutionised our approach to lung cancer biology and hold promise for personalised management of lung cancer.
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Affiliation(s)
- S Ocak
- Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt-Ingram Cancer Center, Nashville, TN 37232-6838, USA
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47
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Voidonikolas G, Gingras MC, Hodges S, McGuire AL, Chen C, Gibbs RA, Brunicardi FC, Fisher WE. Developing a tissue resource to characterize the genome of pancreatic cancer. World J Surg 2009; 33:723-31. [PMID: 19137368 DOI: 10.1007/s00268-008-9877-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
With recent advances in DNA sequencing technology, medicine is entering an era in which a personalized genomic approach to diagnosis and treatment of disease is feasible. However, discovering the role of altered DNA sequences in various disease states will be a challenging task. The genomic approach offers great promise for diseases, such as pancreatic cancer, in which the effect of current diagnostic and treatment modalities is disappointing. To facilitate the characterization of the genome of pancreatic cancer, high-quality and well-annotated tissue repositories are needed. This article summarizes the basic principles that guide the creation of such a repository, including sample processing and preservation techniques, sample size and composition, and collection of clinical data elements.
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Affiliation(s)
- Georgios Voidonikolas
- Michael E. DeBakey Department of Surgery, Baylor College of Medicine, 1709 Dryden, Suite 1500, Houston, TX 77030, USA
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48
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Bathe OF. Molecular determinants of outcomes: linking tissue banks to outcomes databases. J Surg Oncol 2009; 99:513-6. [PMID: 19466742 DOI: 10.1002/jso.21152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In the past, most outcomes research has focused on defining the clinicopathological determinants of outcomes. More recently, it has become apparent that the molecular features of tumor (as well as the genetic makeup of the patient) significantly influence outcomes, including responsiveness to therapy and prognosis. In view of this, there is a need for more research on the molecular determinants of outcomes. Research biorepositories are important vehicles for this type of research and they could potentially accelerate this work. For biomarker research to affect patient care, it is critical to effectively link patient outcomes data with descriptions of the molecular features of tumors. Effective linkage of outcomes data with tissue banks will dramatically accelerate biomarker research.
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Affiliation(s)
- Oliver F Bathe
- Departments of Surgery and Oncology, University of Calgary, AB, Canada.
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49
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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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50
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A banking strategy toward customized therapy in breast cancer. Cell Tissue Bank 2009; 10:301-8. [DOI: 10.1007/s10561-009-9124-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2008] [Accepted: 01/15/2009] [Indexed: 11/25/2022]
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