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Kaufhold-Wedel C, Hummel M, Brobeil A, Schirmacher P, Schmitt S. [Quality assurance in tissue biobanking-an overview]. PATHOLOGIE (HEIDELBERG, GERMANY) 2022; 43:365-371. [PMID: 35925305 DOI: 10.1007/s00292-022-01078-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/30/2022] [Indexed: 06/15/2023]
Abstract
Tissue biobanks are important resource and technology platforms for biomedical research, which deals with molecular pathogenesis and the prevention, diagnosis and treatment of diseases.Due to this central role in the standardised collection, storage and distribution of human tissue and its derivatives, a practised quality management is one of the most important measures to achieve and maintain a comprehensive quality assurance of all biobanking processes. At the same time, this promotes acceptance and credibility. External quality assurance of biobanks can be achieved through accreditation. Within the German biobanking community, increasing harmonisation of biobanking processes has also been achieved through the provision of various quality assurance measures by the German Biobank Node (GBN).In the following, challenges and opportunities in the implementation of a comprehensive quality assurance in biobanking will be discussed and solutions for tissue biobanking will be presented using the example of the tissue bank of the National Centre for Tumour Diseases (NCT).
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Affiliation(s)
- Carolin Kaufhold-Wedel
- BioMaterialBank Heidelberg, Pathologisches Institut, Universitätsklinikum Heidelberg, Heidelberg, Deutschland
- Gewebebank des Nationalen Centrum für Tumorerkrankungen (NCT) Heidelberg, Heidelberg, Deutschland
| | - Michael Hummel
- German Biobank Node, Charité - Universitätsmedizin Berlin, Berlin, Deutschland
| | - Alexander Brobeil
- Gewebebank des Nationalen Centrum für Tumorerkrankungen (NCT) Heidelberg, Heidelberg, Deutschland
- Pathologisches Institut, Universitätsklinikum Heidelberg, Heidelberg, Deutschland
| | - Peter Schirmacher
- Pathologisches Institut, Universitätsklinikum Heidelberg, Heidelberg, Deutschland
| | - Sabrina Schmitt
- BioMaterialBank Heidelberg, Pathologisches Institut, Universitätsklinikum Heidelberg, Heidelberg, Deutschland.
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Willers C, Lynch T, Chand V, Islam M, Lassere M, March L. A Versatile, Secure, and Sustainable All-in-One Biobank-Registry Data Solution: The A3BC REDCap Model. Biopreserv Biobank 2021; 20:244-259. [PMID: 34807733 DOI: 10.1089/bio.2021.0098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Introduction: A key element in the big data revolution is large-scale biobanking and the associated development of high-quality data collections and supporting informatics solutions. As such, in establishing the Australian Arthritis and Autoimmune Biobank Collaborative (A3BC), we sought to establish a low-cost, nation-scale data management system capable of managing a multisite biobank registry with complex longitudinal sample and data requirements. Materials and Methods: We assessed several international commercial and nonprofit software platforms using standardized system requirement criteria and follow-up interviews. Vendor compliance scoring was prioritized to meet our project-critical requirements. Consumer/end-user codesign was integral to refining our system requirements for optimized adoption. Customization of the selected software solution was performed to optimize field auto-population between participant timepoints and forms, using modules that are transferable and that do not impact core code. Institutional and independent testing was used to ensure data security. Results: We selected the widely used research web application Research Electronic Data Capture (REDCap), which is "free" (under nonprofit license agreement terms), highly configurable, and customizable to a variety of biobank and registry needs and can be developed/maintained by biobank users with modest IT skill, time, and cost. We created a secure, comprehensive participant-centric biobank-registry database that includes: (1) best practice data security measures (incl. multisite access login using institutional user credentials), (2) permission-to-contact and dynamic itemized electronic consent, (3) a complete chain of custody from consent to longitudinal biospecimen data collection to publication, (4) complex longitudinal patient-reported surveys, (5) integration of record-level extracted/linked participant data, (6) significant form auto-population for streamlined data capture, and (7) native dashboards for operational visualizations. Conclusion: We recommend the versatile, reusable, and sustainable informatics model we have developed in REDCap for prospective chronic disease biobanks or registry biobanks (of local to national complexity) supporting holistic research into disease prediction, precision medicine, and prevention strategies.
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Affiliation(s)
- Craig Willers
- Institute of Bone and Joint Research, The Australian Arthritis and Autoimmune Biobank Collaborative, Kolling Institute, University of Sydney, Sydney, Australia
| | - Tom Lynch
- Institute of Bone and Joint Research, The Australian Arthritis and Autoimmune Biobank Collaborative, Kolling Institute, University of Sydney, Sydney, Australia
| | - Vibhasha Chand
- Public Health and Preventive Medicine, Monash University, Clayton, Australia
| | - Mohammad Islam
- Information and Communications Technology, University of Sydney, Sydney, Australia
| | - Marissa Lassere
- School of Population Health, University of New South Wales, Sydney, Australia
| | - Lyn March
- Institute of Bone and Joint Research, The Australian Arthritis and Autoimmune Biobank Collaborative, Kolling Institute, University of Sydney, Sydney, Australia
- Department of Rheumatology, Royal North Shore Hospital, St Leonards, Australia
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Yekula A, Muralidharan K, Kang KM, Wang L, Balaj L, Carter BS. From laboratory to clinic: Translation of extracellular vesicle based cancer biomarkers. Methods 2020; 177:58-66. [PMID: 32061674 DOI: 10.1016/j.ymeth.2020.02.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/21/2020] [Accepted: 02/03/2020] [Indexed: 02/08/2023] Open
Abstract
The past decade has witnessed a rapid growth in the field of extracellular vesicle (EV) based biomarkers for the diagnosis and monitoring of cancer. Several studies have reported novel EV based biomarkers, but the technical and clinical validation phase has been hampered by general challenges common to biomedical research field as well as specific challenges inherent to the nanoparticle field. This has led to more common failures than success stories in the biomarker discovery pipeline. As a result, more attention must be focused on the process of biomarker discovery, verification, and validation to allow for translation and application of novel EV based research to patient care. Herein, we briefly discuss the hurdles and potential solutions in EV biomarker discovery and verification and validation, and clinical translation.
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Affiliation(s)
- Anudeep Yekula
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School and Harvard Medical School, Boston, MA, United States.
| | - Koushik Muralidharan
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School and Harvard Medical School, Boston, MA, United States.
| | - Keiko M Kang
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School and Harvard Medical School, Boston, MA, United States; School of Medicine, University of California, San Diego, La Jolla, CA, United States.
| | - Lan Wang
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School and Harvard Medical School, Boston, MA, United States.
| | - Leonora Balaj
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School and Harvard Medical School, Boston, MA, United States.
| | - Bob S Carter
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School and Harvard Medical School, Boston, MA, United States.
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Findeisen P, Hemanna S, Maharjan RS, Mindt S, Costina V, Hofheinz R, Neumaier M. Mass spectrometry based analytical quality assessment of serum and plasma specimens with patterns of endo- and exogenous peptides. Clin Chem Lab Med 2019; 57:668-678. [DOI: 10.1515/cclm-2018-0811] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 11/05/2018] [Indexed: 12/23/2022]
Abstract
Abstract
Background
Inappropriate preanalytical sample handling is a major threat for any biomarker discovery approach. Blood specimens have a genuine proteolytic activity that leads to a time dependent decay of peptidic quality control markers (QCMs). The aim of this study was to identify QCMs for direct assessment of sample quality (DASQ) of serum and plasma specimens.
Methods
Serum and plasma specimens of healthy volunteers and tumor patients were spiked with two synthetic reporter peptides (exogenous QCMs) and aged under controlled conditions for up to 24 h. The proteolytic fragments of endogenous and exogenous QCMs were monitored for each time point by mass spectrometry (MS). The decay pattern of peptides was used for supervised classification of samples according to their respective preanalytical quality.
Results
The classification accuracy for fresh specimens (1 h) was 96% and 99% for serum and plasma specimens, respectively, when endo- and exogenous QCMs were used for the calculations. However, classification of older specimens was more difficult and overall classification accuracy decreased to 79%.
Conclusions
MALDI-TOF MS is a simple and robust method that can be used for DASQ of serum and plasma specimens in a high throughput manner. We propose DASQ as a fast and simple step that can be included in multicentric large-scale projects to ensure the homogeneity of sample quality.
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Enteric dysbiosis and fecal calprotectin expression in premature infants. Pediatr Res 2019; 85:361-368. [PMID: 30631136 PMCID: PMC6377820 DOI: 10.1038/s41390-018-0254-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 10/19/2018] [Accepted: 11/14/2018] [Indexed: 12/26/2022]
Abstract
BACKGROUND Premature infants often develop enteric dysbiosis with a preponderance of Gammaproteobacteria, which has been related to adverse clinical outcomes. We investigated the relationship between increasing fecal Gammaproteobacteria and mucosal inflammation, measured by fecal calprotectin (FC). METHODS Stool samples were collected from very-low-birth weight (VLBW) infants at ≤2, 3, and 4 weeks' postnatal age. Fecal microbiome was surveyed using polymerase chain reaction amplification of the V4 region of 16S ribosomal RNA, and FC was measured by enzyme immunoassay. RESULTS We enrolled 45 VLBW infants (gestation 27.9 ± 2.2 weeks, birth weight 1126 ± 208 g) and obtained stool samples at 9.9 ± 3, 20.7 ± 4.1, and 29.4 ± 4.9 days. FC was positively correlated with the genus Klebsiella (r = 0.207, p = 0.034) and its dominant amplicon sequence variant (r = 0.290, p = 0.003), but not with the relative abundance of total Gammaproteobacteria. Klebsiella colonized the gut in two distinct patterns: some infants started with low Klebsiella abundance and gained these bacteria over time, whereas others began with very high Klebsiella abundance. CONCLUSION In premature infants, FC correlated with relative abundance of a specific pathobiont, Klebsiella, and not with that of the class Gammaproteobacteria. These findings indicate a need to define dysbiosis at genera or higher levels of resolution.
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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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Ho TTB, Groer MW, Kane B, Yee AL, Torres BA, Gilbert JA, Maheshwari A. Dichotomous development of the gut microbiome in preterm infants. MICROBIOME 2018; 6:157. [PMID: 30208950 PMCID: PMC6136210 DOI: 10.1186/s40168-018-0547-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 09/03/2018] [Indexed: 05/31/2023]
Abstract
BACKGROUND Preterm infants are at risk of developing intestinal dysbiosis with an increased proportion of Gammaproteobacteria. In this study, we sought the clinical determinants of the relative abundance of feces-associated Gammaproteobacteria in very low birth weight (VLBW) infants. Fecal microbiome was characterized at ≤ 2 weeks and during the 3rd and 4th weeks after birth, by 16S rRNA amplicon sequencing. Maternal and infant clinical characteristics were extracted from electronic medical records. Data were analyzed by linear mixed modeling and linear regression. RESULTS Clinical data and fecal microbiome profiles of 45 VLBW infants (gestational age 27.9 ± 2.2 weeks; birth weight 1126 ± 208 g) were studied. Three stool samples were analyzed for each infant at mean postnatal ages of 9.9 ± 3, 20.7 ± 4.1, and 29.4 ± 4.9 days. The average relative abundance of Gammaproteobacteria was 42.5% (0-90%) at ≤ 2 weeks, 69.7% (29.9-86.9%) in the 3rd, and 75.5% (54.5-86%) in the 4th week (p < 0.001). Hierarchical and K-means clustering identified two distinct subgroups: cluster 1 started with comparatively low abundance that increased with time, whereas cluster 2 began with a greater abundance at ≤ 2 weeks (p < 0.001) that decreased over time. Both groups resembled each other by the 3rd week. Single variants of Klebsiella and Staphylococcus described variance in community structure between clusters and were shared between all infants, suggesting a common, hospital-derived source. Fecal Gammaproteobacteria was positively associated with vaginal delivery and antenatal steroids. CONCLUSIONS We detected a dichotomy in gut microbiome assembly in preterm infants: some preterm infants started with low relative gammaproteobacterial abundance in stool that increased as a function of postnatal age, whereas others began with and maintained high abundance. Vaginal birth and antenatal steroids were identified as predictors of Gammaproteobacteria abundance in the early (≤ 2 weeks) and later (3rd and 4th weeks) stool samples, respectively. These findings are important in understanding the development of the gut microbiome in premature infants.
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Affiliation(s)
- Thao T. B. Ho
- Department of Pediatrics, Morsani College of Medicine, University of South Florida, Tampa, FL USA
| | - Maureen W. Groer
- Department of Pediatrics, Morsani College of Medicine, University of South Florida, Tampa, FL USA
- College of Nursing, University of South Florida, Tampa, FL USA
| | - Bradley Kane
- College of Nursing, University of South Florida, Tampa, FL USA
| | - Alyson L. Yee
- Interdisciplinary Scientist Training Program, University of Chicago, Chicago, IL USA
- Microbiome Center, University of Chicago, Chicago, IL USA
- Department of Surgery, University of Chicago, Chicago, IL USA
| | - Benjamin A. Torres
- Department of Pediatrics, Morsani College of Medicine, University of South Florida, Tampa, FL USA
| | - Jack A. Gilbert
- Microbiome Center, University of Chicago, Chicago, IL USA
- Department of Surgery, University of Chicago, Chicago, IL USA
- Argonne National Laboratory, Chicago, IL USA
| | - Akhil Maheshwari
- Department of Pediatrics, Morsani College of Medicine, University of South Florida, Tampa, FL USA
- Department of Pediatrics, Johns Hopkins University, 1800 Orleans St, JHCC 8530, Baltimore, MD 21287 USA
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Neumeister VM, Juhl H. Tumor Pre-Analytics in Molecular Pathology: Impact on Protein Expression and Analysis. CURRENT PATHOBIOLOGY REPORTS 2018; 6:265-274. [PMID: 30595971 PMCID: PMC6290693 DOI: 10.1007/s40139-018-0179-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Purpose of Review Precision medicine promises patient tailored, individualized diagnosis and treatment of diseases and relies on clinical specimen integrity and accuracy of companion diagnostic testing. Therefore, pre-analytics, which are defined as the collection, processing, and storage of clinical specimens, are critically important to enable optimal diagnostics, molecular profiling, and clinical decision-making around harvested specimens. This review article discusses the impact of tumor pre-analytics on molecular pathology focusing on biospecimen protein expression and analysis. Recent Findings Due to busy clinical schedules and workflows that have been established for many years and to lack of standardization and limited assessment tools to quantify variability in pre-analytical processing, the effects of pre-analytics on biospecimen integrity are often overlooked. Several studies have recently emphasized an emerging crisis in science and reproducibility of results. Summary Biomarker instability due to pre-analytical variables affects comprehensive analysis and molecular phenotyping of patients’ tissue. This problematic emphasizes the critical need for standardized protocols and technologies to be applied in the clinical and research setting.
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Affiliation(s)
| | - Hartmut Juhl
- Indivumed, GmbH, Falkenried 88, D-20251 Hamburg, Germany
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Szarvas T, Nyirády P, Ogawa O, Furuya H, Rosser CJ, Kobayashi T. Urinary Protein Markers for the Detection and Prognostication of Urothelial Carcinoma. Methods Mol Biol 2018; 1655:251-273. [PMID: 28889391 DOI: 10.1007/978-1-4939-7234-0_19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Bladder cancer diagnosis and surveillance is mainly based on cystoscopy and urine cytology. However, both methods have significant limitations; urine cytology has a low sensitivity for low-grade tumors, while cystoscopy is uncomfortable for the patients. Therefore, in the last decade urine analysis was the subject of intensive research resulting in the identification of many potential biomarkers for the detection, surveillance, or prognostic stratification of bladder cancer. Current trends move toward the development of multiparametric models to improve the diagnostic accuracy compared with single molecular markers. Recent technical advances for high-throughput and more sensitive measurements have led to the development of multiplex assays showing potential for more efficient tools toward future clinical application. In this review, we focus on the findings of urinary protein research in the context of detection and prognostication of bladder cancer. Furthermore, we provide an up-to-date overview on the recommendations for the quality evaluation of published studies as well as for the conduction of future urinary biomarker studies.
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Affiliation(s)
- Tibor Szarvas
- Department of Urology, Semmelweis University, Üllői út 78/b 1082, Budapest, Hungary.
| | - Péter Nyirády
- Department of Urology, Semmelweis University, Üllői út 78/b 1082, Budapest, Hungary
| | - Osamu Ogawa
- Department of Urology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hideki Furuya
- Clinical and Translational Research Program, University of Hawaii Cancer Center, 701 Ilalo St, Rm 327, Honolulu, HI, 96813, USA
| | - Charles J Rosser
- Clinical and Translational Research Program, University of Hawaii Cancer Center, 701 Ilalo St, Rm 327, Honolulu, HI, 96813, USA
| | - Takashi Kobayashi
- Department of Urology, Kyoto University Graduate School of Medicine, Kyoto, Japan
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Galissier T, Schneider C, Nasri S, Kanagaratnam L, Fichel C, Coquelet C, Diebold MD, Kianmanesh R, Bellon G, Dedieu S, Marchal Bressenot A, Boulagnon-Rombi C. Biobanking of Fresh-Frozen Human Adenocarcinomatous and Normal Colon Tissues: Which Parameters Influence RNA Quality? PLoS One 2016; 11:e0154326. [PMID: 27124490 PMCID: PMC4849710 DOI: 10.1371/journal.pone.0154326] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 04/12/2016] [Indexed: 12/01/2022] Open
Abstract
Medical research projects become increasingly dependent on biobanked tissue of high quality because the reliability of gene expression is affected by the quality of extracted RNA. Hence, the present study aimed to determine if clinical, surgical, histological, and molecular parameters influence RNA quality of normal and tumoral frozen colonic tissues. RNA Quality Index (RQI) was evaluated on 241 adenocarcinomas and 115 matched normal frozen colon tissues collected between October 2006 and December 2012. RQI results were compared to patients’ age and sex, tumor site, kind of surgery, anastomosis failure, adenocarcinoma type and grade, tumor cell percentage, necrosis extent, HIF-1α and cleaved caspase-3 immunohistochemistry, and BRAF, KRAS and microsatellites status. The RQI was significantly higher in colon cancer tissue than in matched normal tissue. RQI from left-sided colonic cancers was significantly higher than RQI from right-sided cancers. The RNA quality was not affected by ischemia and storage duration. According to histological control, 7.9% of the samples were unsatisfactory because of inadequate sampling. Biobanked tumoral tissues with RQI ≥5 had lower malignant cells to stromal cells ratio than samples with RQI <5 (p <0.05). Cellularity, necrosis extent and mucinous component did not influence RQI results. Cleaved caspase-3 and HIF-1α immunolabelling were not correlated to RQI. BRAF, KRAS and microsatellites molecular status did not influence RNA quality. Multivariate analysis revealed that the tumor location, the surgical approach (laparoscopy versus open colectomy) and the occurrence of anastomotic leakage were the only parameters influencing significantly RQI results of tumor samples. We failed to identify parameter influencing RQI of normal colon samples. These data suggest that RNA quality of colonic adenocarcinoma biospecimens is determined by clinical and surgical parameters. More attention should be paid during the biobanking procedure of right-sided colon cancer or laparoscopic colectomy specimen. Histological quality control remains essential to control sampling accuracy.
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Affiliation(s)
- Thibaut Galissier
- Laboratoire d’Anatomie Pathologique, Centre Hospitalier Universitaire, Reims, France
| | - Christophe Schneider
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire, MEDyC, Reims, France
- Laboratoire SiRMa, Université de Reims Champagne-Ardenne, UFR Sciences Exactes et Naturelles, Reims, France
| | - Saviz Nasri
- Tumorothèque de Champagne Ardenne, Reims, France
| | - Lukshe Kanagaratnam
- Unité d’Aide Méthodologique, Centre Hospitalier Universitaire, Reims, France
| | - Caroline Fichel
- Laboratoire d’Anatomie Pathologique, Université de Reims Champagne-Ardenne, UFR Médecine, Reims, France
| | | | - Marie-Danièle Diebold
- Laboratoire d’Anatomie Pathologique, Centre Hospitalier Universitaire, Reims, France
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire, MEDyC, Reims, France
- Tumorothèque de Champagne Ardenne, Reims, France
- Laboratoire d’Anatomie Pathologique, Université de Reims Champagne-Ardenne, UFR Médecine, Reims, France
| | - Reza Kianmanesh
- Service de Chirurgie Digestive, Centre Hospitalier Universitaire, Reims, France
| | - Georges Bellon
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire, MEDyC, Reims, France
- Laboratoire de Biochimie, Centre Hospitalier Universitaire, Reims, France
| | - Stéphane Dedieu
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire, MEDyC, Reims, France
- Laboratoire SiRMa, Université de Reims Champagne-Ardenne, UFR Sciences Exactes et Naturelles, Reims, France
| | - Aude Marchal Bressenot
- Laboratoire d’Anatomie Pathologique, Centre Hospitalier Universitaire, Reims, France
- Laboratoire d’Anatomie Pathologique, Université de Reims Champagne-Ardenne, UFR Médecine, Reims, France
| | - Camille Boulagnon-Rombi
- Laboratoire d’Anatomie Pathologique, Centre Hospitalier Universitaire, Reims, France
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire, MEDyC, Reims, France
- Laboratoire d’Anatomie Pathologique, Université de Reims Champagne-Ardenne, UFR Médecine, Reims, France
- * E-mail:
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Abstract
Biobanking involves the collection, processing, storage, and distribution of biological specimens and the policies and procedures necessary to accomplish those aims successfully. Although biobanking may also involve collections for environmental studies or museum archives, most efforts to standardize biobanking practices have been directed toward human biomedical research. Initially focused primarily on collecting samples for diagnostic purposes in pathology settings, biobanks have evolved into complex organizations engaged in advancing personalized (or precision) medicine and translational research. This evolution has involved the development of biobanking best practices and the transformation of a field driven by empirical approaches into the emerging area of biospecimen science. It has become increasingly important to develop evidence-based practices for collecting biospecimens and data that can be shared with confidence with international collaborators. Aside from these technical approaches, other factors play crucial roles, such as ethical and regulatory issues, business planning and sustainability, and approaches to data collection and sharing.
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Affiliation(s)
- Jim Vaught
- International Society for Biological and Environmental Repositories, Vancouver, British Columbia V5Z 1B3, Canada.,Biopreservation & Biobanking, Kensington, Maryland 20895;
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12
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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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Quinlan PR, Groves M, Jordan LB, Stobart H, Purdie CA, Thompson AM. The Informatics Challenges Facing Biobanks: A Perspective from a United Kingdom Biobanking Network. Biopreserv Biobank 2015; 13:363-70. [PMID: 26418270 PMCID: PMC4675179 DOI: 10.1089/bio.2014.0099] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The challenges facing biobanks are changing from simple collections of materials to quality-assured fit-for-purpose clinically annotated samples. As a result, informatics awareness and capabilities of a biobank are now intrinsically related to quality. A biobank may be considered a data repository, in the form of raw data (the unprocessed samples), data surrounding the samples (processing and storage conditions), supplementary data (such as clinical annotations), and an increasing ethical requirement for biobanks to have a mechanism for researchers to return their data. The informatics capabilities of a biobank are no longer simply knowing sample locations; instead the capabilities will become a distinguishing factor in the ability of a biobank to provide appropriate samples. There is an increasing requirement for biobanking systems (whether in-house or commercially sourced) to ensure the informatics systems stay apace with the changes being experienced by the biobanking community. In turn, there is a requirement for the biobanks to have a clear informatics policy and directive that is embedded into the wider decision making process. As an example, the Breast Cancer Campaign Tissue Bank in the UK was a collaboration between four individual and diverse biobanks in the UK, and an informatics platform has been developed to address the challenges of running a distributed network. From developing such a system there are key observations about what can or cannot be achieved by informatics in isolation. This article will highlight some of the lessons learned during this development process.
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Affiliation(s)
- Philip R Quinlan
- 1 Dundee Cancer Centre, Ninewells Hospital and Medical School , Dundee, United Kingdom .,2 School of Veterinary Medicine and Science, University of Nottingham , Leicestershire, United Kingdom .,3 Computer Science, University of Nottingham , Leicestershire, United Kingdom .,4 Advanced Data Analysis Centre, University of Nottingham , Leicestershire, United Kingdom
| | - Martin Groves
- 1 Dundee Cancer Centre, Ninewells Hospital and Medical School , Dundee, United Kingdom
| | - Lee B Jordan
- 5 NHS Tayside, Ninewells Hospital and Medical School , Dundee, United Kingdom
| | - Hilary Stobart
- 6 Independent Cancer Patients Voice , London, United Kingdom
| | - Colin A Purdie
- 5 NHS Tayside, Ninewells Hospital and Medical School , Dundee, United Kingdom
| | - Alastair M Thompson
- 1 Dundee Cancer Centre, Ninewells Hospital and Medical School , Dundee, United Kingdom .,7 Department of Surgical Oncology, MD Anderson Cancer Centre , Houston, Texas
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14
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Paraizo Leite RE, Tenenholz Grinberg L. Closing the gap between brain banks and proteomics to advance the study of neurodegenerative diseases. Proteomics Clin Appl 2015; 9:832-7. [PMID: 26059592 DOI: 10.1002/prca.201400192] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Revised: 05/01/2015] [Accepted: 05/27/2015] [Indexed: 11/05/2022]
Abstract
Neurodegenerative diseases (NDs), such as Alzheimer's disease and Parkinson's disease, are among the most debilitating neurological disorders, and as life expectancy rises quickly around the world, the scientific and clinical challenges of dealing with them will also increase dramatically, putting increased pressure on the biomedical community to come up with innovative solutions for the understanding, diagnosis, and treatment of these conditions. Despite several decades of intensive research, there is still little that can be done to prevent, cure, or even slow down the progression of NDs in most patients. There is an urgent need to develop new lines of basic and applied research that can be quickly translated into clinical application. One way to do this is to apply the tools of proteomics to well-characterized samples of human brain tissue, but a closer partnership must still be forged between proteomic scientists, brain banks, and clinicians to explore the maximum potential of this approach. Here, we analyze the challenges and potential benefits of using human brain tissue for proteomics research toward NDs.
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Affiliation(s)
- Renata Elaine Paraizo Leite
- Physiopathology in Aging Lab/Brazilian Aging Brain Study Group-LIM22, University of Sao Paulo Medical School, Sao Paulo, Brazil.,Discipline of Geriatrics, University of Sao Paulo Medical School, Sao Paulo, Brazil
| | - Lea Tenenholz Grinberg
- Physiopathology in Aging Lab/Brazilian Aging Brain Study Group-LIM22, University of Sao Paulo Medical School, Sao Paulo, Brazil.,Department of Neurology, Memory and Aging Center, University of California, San Francisco, CA, USA
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15
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Mendy M, Caboux E, Sylla BS, Dillner J, Chinquee J, Wild C. Infrastructure and facilities for human biobanking in low- and middle-income countries: a situation analysis. Pathobiology 2015; 81:252-260. [PMID: 25792214 DOI: 10.1159/000362093] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE To collect information on biobanking facilities in low- and middle-income countries (LMICs) as a first step towards establishing an LMIC biobank and cohort building network (BCNet) to support research, with a focus on cancer control. METHOD Sixty centres were identified from sources including cancer centres, universities, hospitals, and public health facilities and invited to participate in a survey between December 2012 and March 2013. RESULTS Of the 27 centres (45%) that responded, most have existed for <10 years. They store between 1,000 and 1,000,000 research samples as well as samples remaining after clinical diagnosis. Sample storage is mostly in freezers, although 45% (9/20) of the centres do not have regular access to electricity. Biobank managers, sample management systems, and mechanisms for follow-up using linkages are uncommon. Many (80%; 21/26) of the centres have regulations to govern research, but regulations for the use of biobank resources (samples and data) are not well developed. CONCLUSIONS Biobanking facilities are being developed in LMICs. Shortcomings in international visibility, sample sharing regulations, standardization, quality assurance, and sample management systems could be alleviated by international networking. Stakeholders need to work together to increase access to high-quality biological resources for scientific research.
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Affiliation(s)
- Maimuna Mendy
- International Agency for Research on Cancer, Lyon, France
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16
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Integration, Networking, and Global Biobanking in the Age of New Biology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 864:1-9. [DOI: 10.1007/978-3-319-20579-3_1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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17
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Quinlan PR, Mistry G, Bullbeck H, Carter A. A data standard for sourcing fit-for-purpose biological samples in an integrated virtual network of biobanks. Biopreserv Biobank 2014; 12:184-91. [PMID: 24785371 DOI: 10.1089/bio.2013.0089] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Human tissue biobanks are at the epicenter of clinical research, responsible for providing both clinical samples and annotated data. There is a need for large numbers of samples to provide statistical power to research studies, especially since treatment and diagnosis are becoming ever more personalized. A single biobank cannot provide sufficient numbers of samples to capture the full spectrum of any disease. Currently there is no infrastructure in the United Kingdom (UK) to integrate biobanks. Therefore the National Cancer Research Institute (NCRI) Confederation of Cancer Biobanks (CCB) Working Group 3 looked to establish a data standard to enable biobanks to communicate about the samples they hold and so facilitate the formation of an integrated national network of biobanks. The Working Group examined the existing data standards available to biobanks, such as the MIABIS standard, and compared these to the aims of the working group. The CCB-developed data standard has brought many improvements: (1) Where existing data standards have been developed, these have been incorporated, ensuring compatibility with other initiatives; (2) the standard was written with the expectation that it will be extended for specific disease areas, such as the Breast Cancer Campaign Tissue Bank (BCCTB) and the Strategic Tissue Repository Alliances Through Unified Methods (STRATUM) project; and (3) biobanks will be able to communicate about specific samples, as well as aggregated statistics. The development of this data standard will allow all biobanks to integrate and share information about the samples they hold, facilitating the possibility of a national portal for researchers to find suitable samples for research. In addition, the data standard will allow other clinical services, such as disease registries, to communicate with biobanks in a standardized format allowing for greater cross-discipline data sharing.
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Affiliation(s)
- Philip R Quinlan
- 1 University of Dundee , Division of Cancer Research, Ninewells Hospital and Medical School, Dundee, United Kingdom
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