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biobank and quality control

Cory Ann Leonard, Marina L Meli, Marilisa Novacco, Nicole Borel
The 18S ribosomal RNA (rRNA) gene is present in all eukaryotic cells. In this study, we evaluated the use of this gene to verify the presence of PCR-amplifiable host (animal) DNA as an indicator of sufficient sample quality for quantitative real-time PCR (qPCR) analysis. We compared (i) samples from various animal species, tissues, and sample types, including swabs; (ii) multiple DNA extraction methods; and (iii) both fresh and formalin-fixed paraffin-embedded (FFPE) samples. Results showed that 18S ribosomal RNA gene amplification was possible from all tissue samples evaluated, including avian, reptile, and FFPE samples and most swab samples...
2016: BioMed Research International
Jesús Mateos, Isabel Carneiro, Fernando Corrales, Felix Elortza, Alberto Paradela, Manuel Sánchez Del Pino, Ibon Iloro, Miguel Marcilla, Maria Isabel Mora, Luz Valero, Sergio Ciordia, Verónica Fernández, Maria Antonia Fortuño, Isabel García-Sánchez, Rosario Martínez, Maria Angeles Muñoz, Clara Rodriguez, Nieves Doménech
: Analytical proteomics has experienced exponential progress in the last decade and can be expected to lead research studies on diagnostic and therapeutic biomarkers in the near future. Because the development of this type of analysis requires the use of a large number of human samples with a minimum of quality requirements, our objective was to identify appropriate indicators for quality control of plasma samples stored in biobanks for research in proteomics. To accomplish this, plasma samples from 100 healthy donors were obtained and processed according to the pre-analytical variables of: a) time delay for the first centrifugation of the original blood sample (4 or 24h) and b) number of freeze/thaw cycles (1, 2 or 3) of the processed plasma samples...
September 9, 2016: Journal of Proteomics
María Lourdes Garza-Rodríguez, Antonio Alí Pérez-Maya, Daniela Estefanía Monsivais-Ovalle, Juan Francisco Velázquez-Vadillo, Hugo Alberto Barrera-Saldaña
A biobank facility is one of the most valuable means that academic medical organizations have to offer researchers for improving the competitiveness of their medical research. We describe the implementation of our institutional biobank. Our efforts focused on the design and equipment of work areas, staff training, quality control, bioethical and regulatory issues, generating research collaborations and developing funding strategies. We implemented an institutional biobank at the School of Medicine of the Autonomous University of Nuevo León, Mexico...
August 2016: Salud Pública de México
Laura Calleros-Basilio, María Alicia Cortés, Andrea García-Jerez, Alicia Luengo-Rodríguez, Ana Orozco-Agudo, José Manuel Valdivielso, Diego Rodríguez-Puyol, Manuel Rodríguez-Puyol
BACKGROUND: Biobanks are useful platforms to build bridges between basic, translational, and clinical research and clinical care. They are repositories of high-quality human biological samples ideal for evaluating their histological characteristics and also their genome, transcriptome, and proteome. The Spanish Renal Research Network Biobank contains more than 76,500 well-preserved frozen samples of a wide variety of kidney diseases, collected from 5450 patients seen by over 70 nephrology services throughout the Spanish territory...
August 19, 2016: Biopreservation and Biobanking
Nicklas H Staunstrup, Anna Starnawska, Mette Nyegaard, Lene Christiansen, Anders L Nielsen, Anders Børglum, Ole Mors
BACKGROUND: In utero and early-life experienced environmental exposures are suggested to play an important role in many multifactorial diseases potentially mediated through lasting effects on the epigenome. As the epigenome in addition remains modifiable throughout life, identifying specific disease-relevant biomarkers may prove challenging. This has led to an increased interest in epigenome-wide association studies using dried blood spots (DBS) routinely collected in perinatal screening programs...
2016: Clinical Epigenetics
Silvia Veneroni, Matteo Dugo, Maria Grazia Daidone, Egidio Iorio, Barbara Valeri, Patrizia Pinciroli, Maida De Bortoli, Edoardo Marchesi, Patrizia Miodini, Elena Taverna, Alessandro Ricci, Silvana Canevari, Giuseppe Pelosi, Italia Bongarzone
CONTEXT: Biobanks of frozen human normal and malignant tissues represent a valuable source for "omics" analysis in translational cancer research and molecular pathology. However, the success of molecular and cellular analysis strongly relies on the collection, handling, storage procedures, and quality control of fresh human tissue samples. OBJECTIVE: We tested whether under vacuum storage (UVS) effectively preserves tissues during the time between surgery and storage for "omics" analyses...
July 12, 2016: Biopreservation and Biobanking
Jean-Pierre Trezzi, Alexandre Bulla, Camille Bellora, Michael Rose, Pierre Lescuyer, Michael Kiehntopf, Karsten Hiller, Fay Betsou
INTRODUCTION: Metabolome analysis is complicated by the continuous dynamic changes of metabolites in vivo and ex vivo. One of the main challenges in metabolomics is the robustness and reproducibility of results, partially driven by pre-analytical variations. OBJECTIVES: The objective of this study was to analyse the impact of pre-centrifugation time and temperature, and to determine a quality control marker in plasma samples. METHODS: Plasma metabolites were measured by gas chromatography-mass spectrometry (GC-MS) and analysed with the MetaboliteDetector software...
2016: Metabolomics: Official Journal of the Metabolomic Society
Anna Carobene, Marta Strollo, Niels Jonker, Gerhard Barla, William A Bartlett, Sverre Sandberg, Marit Sverresdotter Sylte, Thomas Røraas, Una Ørvim Sølvik, Pilar Fernandez-Calle, Jorge Díaz-Garzón, Francesca Tosato, Mario Plebani, Abdurrahman Coşkun, Mustafa Serteser, Ibrahim Unsal, Ferruccio Ceriotti
BACKGROUND: Biological variation (BV) data have many fundamental applications in laboratory medicine. At the 1st Strategic Conference of the European Federation of Clinical Chemistry and Laboratory Medicine (EFLM) the reliability and limitations of current BV data were discussed. The EFLM Working Group on Biological Variation is working to increase the quality of BV data by developing a European project to establish a biobank of samples from healthy subjects to be used to produce high quality BV data...
October 1, 2016: Clinical Chemistry and Laboratory Medicine: CCLM
Thibaut Galissier, Christophe Schneider, Saviz Nasri, Lukshe Kanagaratnam, Caroline Fichel, Christelle Coquelet, Marie-Danièle Diebold, Reza Kianmanesh, Georges Bellon, Stéphane Dedieu, Aude Marchal Bressenot, Camille Boulagnon-Rombi
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...
2016: PloS One
Annika Karch, Claus Vogelmeier, Tobias Welte, Robert Bals, Hans-Ulrich Kauczor, Jürgen Biederer, Joachim Heinrich, Holger Schulz, Sven Gläser, Rolf Holle, Henrik Watz, Stephanie Korn, Nina Adaskina, Frank Biertz, Charlotte Vogel, Jørgen Vestbo, Emiel F M Wouters, Klaus Friedrich Rabe, Sandra Söhler, Armin Koch, Rudolf A Jörres
BACKGROUND: The German COPD cohort study COSYCONET ("COPD and SYstemic consequences-COmorbidities NETwork") investigates the interaction of lung disease, comorbidities and systemic inflammation. Recruitment took place from 2010 to 2013 in 31 study centers. In addition to the baseline visit, follow-up visits are scheduled at 6, 18, 36 and 54 months after baseline. The study also comprises a biobank, image bank, and includes health economic data. Here we describe the study design of COSYCONET and present baseline data of our COPD cohort...
May 2016: Respiratory Medicine
Wei Gan, Robin G Walters, Michael V Holmes, Fiona Bragg, Iona Y Millwood, Karina Banasik, Yiping Chen, Huaidong Du, Andri Iona, Anubha Mahajan, Ling Yang, Zheng Bian, Yu Guo, Robert J Clarke, Liming Li, Mark I McCarthy, Zhengming Chen
AIMS/HYPOTHESIS: Genome-wide association studies (GWAS) have discovered many risk variants for type 2 diabetes. However, estimates of the contributions of risk variants to type 2 diabetes predisposition are often based on highly selected case-control samples, and reliable estimates of population-level effect sizes are missing, especially in non-European populations. METHODS: The individual and cumulative effects of 59 established type 2 diabetes risk loci were measured in a population-based China Kadoorie Biobank (CKB) study of 93,000 Chinese adults, including >7,100 diabetes cases...
July 2016: Diabetologia
Fay Betsou, Alexandre Bulla, Sang Yun Cho, Judith Clements, Rodrigo Chuaqui, Domenico Coppola, Yvonne De Souza, Annemieke De Wilde, William Grizzle, Fiorella Guadagni, Elaine Gunter, Stacey Heil, Verity Hodgkinson, Joseph Kessler, Michael Kiehntopf, Hee Sung Kim, Iren Koppandi, Katheryn Shea, Rajeev Singh, Marc Sobel, Stella Somiari, Demetri Spyropoulos, Mars Stone, Gunnel Tybring, Klara Valyi-Nagy, Gert Van den Eynden, Lalita Wadhwa
This technical report presents quality control (QC) assays that can be performed in order to qualify clinical biospecimens that have been biobanked for use in research. Some QC assays are specific to a disease area. Some QC assays are specific to a particular downstream analytical platform. When such a qualification is not possible, QC assays are presented that can be performed to stratify clinical biospecimens according to their biomolecular quality.
April 5, 2016: Biopreservation and Biobanking
Nuno Rosa, Jéssica Marques, Eduardo Esteves, Mónica Fernandes, Vera M Mendes, Ângela Afonso, Sérgio Dias, Joaquim Polido Pereira, Bruno Manadas, Maria José Correia, Marlene Barros
Biobank saliva sample quality depends on specific criteria applied to collection, processing, and storage. In spite of the growing interest in saliva as a diagnostic fluid, few biobanks currently store large collections of such samples. The development of a standard operating procedure (SOP) for saliva collection and quality control is fundamental for the establishment of a new saliva biobank, which stores samples to be made available to the saliva research community. Different collection methods were tested regarding total volume of protein obtained, protein content, and protein profiles, and the results were used to choose the best method for protein studies...
August 2016: Biopreservation and Biobanking
Hilde K Ofte, Erling Tronvik, Karl B Alstadhaug
BACKGROUND: Cluster headache (CH) is regarded as a chronobiological disorder. The hypothalamic biological clock may thus be involved in the pathophysiology, but few studies have actually investigated this in CH patients. A variable number tandem repeat (VNTR) polymorphism of the PER3 clock gene has been associated to preferred daily rhythm (chronotype) in several studies. We aimed to study the distribution of PER3 VNTR polymorphisms and chronotypes in a CH population. METHODS: We used blood samples from a biobank of CH patients for genetic tests, and invited all tested patients to complete the Horne-Ostberg Morningness-eveningness Questionnaire (MEQ), the Pittsburgh sleep quality Index (PSQI) and the Shift Work Index...
2015: Journal of Headache and Pain
Michaela Th Mayrhofer, Petr Holub, Andrea Wutte, Jan-Eric Litton
BBMRI-ERIC, the Biobanking and BioMolecular Resources Research Infrastructure-European Research Infrastructure Consortium, is a new form of umbrella organization for biobanking in Europe. For rare and common diseases alike, it aims at providing fair access to quality-controlled human biological samples and associated biomedical and biomolecular data. Such access enables basic mechanisms underlying diseases to be studied, which is indispensable for the development of new biomarkers and drugs. In the context of the European Research Area (ERA), biobanks, which were identified as a particular European strength, contribute to Europe's cohesion policy through capacity-building in the BBMRI-ERIC member countries...
March 2016: Bundesgesundheitsblatt, Gesundheitsforschung, Gesundheitsschutz
Romy Kirsten, Michael Hummel
Active research sites in biomedicine need professionally structured, sustainable biobanks that represent established resources and technology platforms across different locations and disciplines. Currently, the funding of research biobanks is not uniformly regulated, mainly because of the different focuses, services and concepts. On the other hand, the samples and associated data of biobanks gain significant value over time, and therefore their long-term storage should be envisaged right from the start.The sustainability of biobank structures can be viewed from various perspectives, but financial sustainability certainly represents the most demanding challenge...
March 2016: Bundesgesundheitsblatt, Gesundheitsforschung, Gesundheitsschutz
Esther Herpel, Sabrina Schmitt, Michael Kiehntopf
During the last years, many biobanks that collect and provide biomaterials as well as associated phenotypical data have been established on national and international levels. However, due to the heterogeneity in structure and process landscape between biobanks, quality issues arise, which might affect equivalence of sample quality and thus usability of biomaterials for scientific research projects as well as interoperability of biobanks.Here, we will give an overview on the influence of biobanking procedures on sample quality and on potential quality control measures for research biobanks, mainly focusing on tissue and liquid biomaterials...
March 2016: Bundesgesundheitsblatt, Gesundheitsforschung, Gesundheitsschutz
Roland Jahns
Particularly in the past decade which has been marked by efforts to foster individualized/personalized medicine the need for well-characterized high-quality collections of human biological material has significantly increased. When establishing and operating a human biobank the interests and the "freedom" of biomedical research must always be weighed against the interests and rights of patients and/or donors; in this process ethical aspects should be considered systematically. In addition, the importance of quality control and quality assurance has largely increased in human biobanking, both from a scientific and even more from an ethical point of view, because donated biological materials are potentially stored for decades and (on request) might serve for currently not foreseeable biomedical research purposes...
March 2016: Bundesgesundheitsblatt, Gesundheitsforschung, Gesundheitsschutz
Amanda Rush, Jennifer A Byrne
OBJECTIVES: Inadequate research biospecimen quality may adversely impact research translation to clinical practice. Despite the development and endorsement of external quality assurance (QA) programs and biospecimen quality reporting tools, there has been little examination of relevant biobank practices. DESIGN AND METHODS: An online survey was designed to describe the use and communication of QA and quality control (QC) measures within an Australian cancer biobank cohort (n=21), classified according to access policy...
April 2016: Clinical Biochemistry
Timothy J Geddes, Billie E Ketelsen, Samreen Ahmed, Barbara L Pruetz, Laura E Fortier
Given the high demands on a multidisciplinary approach to sample collection, and despite the rigorous quality assurance and quality control measures designed to minimize sample misidentification in our state of the art biorepository, the potential for error is still a concern. Measures to deal with potential uncertainties are a necessary part of every successful biobanking operation. The Beaumont BioBank and associated Core Molecular Laboratory have developed procedures to address these rare incidents. Here we present a case study of occurrences in the Beaumont BioBank in which the identity of samples was uncertain and a resolution workflow was implemented to quickly remove the ambiguity...
February 2016: Biopreservation and Biobanking
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