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biobank and quality control

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https://www.readbyqxmd.com/read/29801446/the-protocol-of-a-population-based-prospective-cohort-study-in-southwest-of-iran-to-analyze-common-non-communicable-diseases-shahrekord-cohort-study
#1
Arsalan Khaledifar, Morteza Hashemzadeh, Kamal Solati, Hosseion Poustchi, Valentina Bollati, Ali Ahmadi, Soleiman Kheiri, Keihan Ghatreh Samani, Mehdi Banitalebi, Morteza Sedehi, Reza Malekzadeh
BACKGROUND: Prospective cohort studies are considered ideal choices to study multiple outcomes and risk factors for Non-communicable diseases (NCDs). Our aim is to set-up the protocol and analyze risk factors, incidence rates, prevalence, trends, and the models of environmental and genetic determinants of NCDs and their outcomes as well as interaction among such determinants. METHODS: Shahrekord cohort study (SCS) that is a population-based prospective, study on a cohort consisting of people aged 35-70 years started in November 2015 in Iran...
May 25, 2018: BMC Public Health
https://www.readbyqxmd.com/read/29764892/intense-exercise-for-survival-among-men-with-metastatic-castrate-resistant-prostate-cancer-interval-gap4-a-multicentre-randomised-controlled-phase-iii-study-protocol
#2
Robert U Newton, Stacey A Kenfield, Nicolas H Hart, June M Chan, Kerry S Courneya, James Catto, Stephen P Finn, Rosemary Greenwood, Daniel C Hughes, Lorelei Mucci, Stephen R Plymate, Stephan F E Praet, Emer M Guinan, Erin L Van Blarigan, Orla Casey, Mark Buzza, Sam Gledhill, Li Zhang, Daniel A Galvão, Charles J Ryan, Fred Saad
INTRODUCTION: Preliminary evidence supports the beneficial role of physical activity on prostate cancer outcomes. This phase III randomised controlled trial (RCT) is designed to determine if supervised high-intensity aerobic and resistance exercise increases overall survival (OS) in patients with metastatic castrate-resistant prostate cancer (mCRPC). METHODS AND ANALYSIS: Participants (n=866) must have histologically documented metastatic prostate cancer with evidence of progressive disease on androgen deprivation therapy (defined as mCRPC)...
May 14, 2018: BMJ Open
https://www.readbyqxmd.com/read/29733683/biobanking-in-a-challenging-african-environment-unique-experience-from-the-siren-project
#3
Rufus O Akinyemi, Kazeem Akinwande, Samuel Diala, Osi Adeleye, Abiodun Ajose, Kehinde Issa, Dorcas Owusu, Isaac Boamah, Isah Suleiman Yahaya, Abdulraheem Olayemi Jimoh, Lucius Imoh, Gregory Fakunle, Albert Akpalu, Fred Sarfo, Kolawole Wahab, Emmanuel Sanya, Lukman Owolabi, Reginald Obiako, Godwin Osaigbovo, Morenikeji Komolafe, Michael Fawale, Philip Adebayo, Paul Olowoyo, Yahaya Obiabo, Taofiki Sunmonu, Ijezie Chukwuonye, Olayemi Balogun, Basirat Adeoye, Florence Oladele, Peter Olowoniyi, Frederick Adeyemi, Arthur Lezzi, Ajibola Tunde Falayi, Michael Fasanya, Kolawole Ogunwale, Olabisi Adeola, Omolara Olomu, Olumayowa Aridegbe, Ruth Laryea, Ezinne Uvere, Moyinoluwalogo Faniyan, Ezinne Melikam, Raelle Tagge, Onoja Akpa, Joshua Akinyemi, Oyedunni Arulogun, Hemant K Tiwari, Bruce Ovbiagele, Mayowa Owolabi
Africa was previously insufficiently represented in the emerging discipline of biobanking despite commendable early efforts. However, with the Human, Heredity, and Health in Africa (H3Africa) initiative, biorepository science has been bolstered, regional biobanks are springing up, and awareness about biobanks is growing on the continent. The Stroke Investigative Research and Educational Network (SIREN) project is a transnational, multicenter, hospital and community-based study involving over 3000 cases and 3000 controls recruited from 16 sites in Ghana and Nigeria...
May 7, 2018: Biopreservation and Biobanking
https://www.readbyqxmd.com/read/29626450/female-specific-association-between-variants-on-chromosome-9-and-self-reported-diagnosis-of-irritable-bowel-syndrome
#4
Ferdinando Bonfiglio, Tenghao Zheng, Koldo Garcia-Etxebarria, Fatemeh Hadizadeh, Luis Bujanda, Francesca Bresso, Lars Agreus, Anna Andreasson, Aldona Dlugosz, Greger Lindberg, Peter T Schmidt, Pontus Karling, Bodil Ohlsson, Magnus Simren, Susanna Walter, Gerardo Nardone, Rosario Cuomo, Paolo Usai-Satta, Francesca Galeazzi, Matteo Neri, Piero Portincasa, Massimo Bellini, Giovanni Barbara, Anna Latiano, Matthias Hübenthal, Vincent Thijs, Mihai G Netea, Daisy Jonkers, Lin Chang, Emeran A Mayer, Mira M Wouters, Guy Boeckxstaens, Michael Camilleri, Andre Franke, Alexandra Zhernakova, Mauro D'Amato
BACKGROUND & AIMS: Genetic factors are believed to affect risk for irritable bowel syndrome (IBS), but there have been no sufficiently powered and adequately sized studies. To identify DNA variants associated with IBS risk, we performed a genome-wide association study (GWAS) of the large UK Biobank population-based cohort, which includes genotype and health data from 500,000 participants. METHODS: We studied 7,287,191 high-quality single nucleotide polymorphisms in individuals who self-reported a doctor's diagnosis of IBS (cases; n = 9576) compared to the remainder of the cohort (controls; n = 336,499) (mean age of study subjects, 40-69 years)...
April 5, 2018: Gastroenterology
https://www.readbyqxmd.com/read/29615218/placental-promoter-methylation-of-dna-repair-genes-and-prenatal-exposure-to-particulate-air-pollution-an-environage-cohort-study
#5
Kristof Y Neven, Nelly D Saenen, Letitzia Tarantini, Bram G Janssen, Wouter Lefebvre, Charlotte Vanpoucke, Valentina Bollati, Tim S Nawrot
BACKGROUND: Exposure to particulate air pollution has been linked with risk of carcinogenesis. Damage to repair pathways might have long-term adverse health effects. We aimed to investigate the association of prenatal exposure to air pollution with placental mutation rate and the DNA methylation of key placental DNA repair genes. METHODS: This cohort study used data from the ongoing ENVironmental Influence ON early AGEing (ENVIRONAGE) birth cohort, which enrols pairs of mothers and neonates (singleton births only) at the East-Limburg Hospital (Genk, Belgium)...
April 2018: Lancet. Planetary Health
https://www.readbyqxmd.com/read/29567661/quality-control-of-serum-and-plasma-by-quantification-of-4e-14z-sphingadienine-c18-1-phosphate-uncovers-common-preanalytical-errors-during-handling-of-whole-blood
#6
Xinyu Liu, Miriam Hoene, Peiyuan Yin, Louise Fritsche, Peter Plomgaard, Jakob S Hansen, Christos T Nakas, Andreas M Niess, Jens Hudemann, Michael Haap, Maimuna Mendy, Cora Weigert, Xiaolin Wang, Andreas Fritsche, Andreas Peter, Hans-Ulrich Häring, Guowang Xu, Rainer Lehmann
BACKGROUND: Nonadherence to standard operating procedures (SOPs) during handling and processing of whole blood is one of the most frequent causes affecting the quality of serum and plasma. Yet, the quality of blood samples is of the utmost importance for reliable, conclusive research findings, valid diagnostics, and appropriate therapeutic decisions. METHODS: UHPLC-MS-driven nontargeted metabolomics was applied to identify biomarkers that reflected time to processing of blood samples, and a targeted UHPLC-MS analysis was used to quantify and validate these biomarkers...
May 2018: Clinical Chemistry
https://www.readbyqxmd.com/read/29148831/is-your-biobank-up-to-standards-a-review-of-the-national-canadian-tissue-repository-network-required-operational-practice-standards-and-the-controlled-documents-of-a-certified-biobank
#7
Victoria Hartman, Tania Castillo-Pelayo, Sindy Babinszky, Simon Dee, Jodi Leblanc, Lise Matzke, Sheila O'Donoghue, Jane Carpenter, Candace Carter, Amanda Rush, Jennifer Byrne, Rebecca Barnes, Anne-Marie Mes-Messons, Peter Watson
Ongoing quality management is an essential part of biobank operations and the creation of high quality biospecimen resources. Adhering to the standards of a national biobanking network is a way to reduce variability between individual biobank processes, resulting in cross biobank compatibility and more consistent support for health researchers. The Canadian Tissue Repository Network (CTRNet) implemented a set of required operational practices (ROPs) in 2011 and these serve as the standards and basis for the CTRNet biobank certification program...
February 2018: Biopreservation and Biobanking
https://www.readbyqxmd.com/read/29148824/biobanking-of-fresh-frozen-cancer-tissue-rna-is-stable-independent-of-tissue-type-with-less-than-1-hour-of-cold-ischemia
#8
Sang Yong Song, Jonghyun Jun, Miyeon Park, Seo Kyu Park, Wonju Choi, Kyunghee Park, Kee-Taek Jang, Myoyong Lee
BACKGROUND: The effects of preanalytical variables in tissue processing and storage periods on RNA quality of tissues have been well documented in each type of cancer. However, few studies have been performed on a comparative assessment of the impacts across different cancer tissues, even though it is well known that RNase activity is highly variable in various tissue types and RNase-rich tissues have been found to yield low-quality RNA. METHODS: We investigated the impacts of cold ischemia times and long-term storage on RNA integrity in various types of cancer tissue, which had been fresh-frozen and collected at the Samsung Medical Center Biobank...
February 2018: Biopreservation and Biobanking
https://www.readbyqxmd.com/read/29079522/image-processing-and-quality-control-for-the-first-10-000-brain-imaging-datasets-from-uk-biobank
#9
Fidel Alfaro-Almagro, Mark Jenkinson, Neal K Bangerter, Jesper L R Andersson, Ludovica Griffanti, Gwenaëlle Douaud, Stamatios N Sotiropoulos, Saad Jbabdi, Moises Hernandez-Fernandez, Emmanuel Vallee, Diego Vidaurre, Matthew Webster, Paul McCarthy, Christopher Rorden, Alessandro Daducci, Daniel C Alexander, Hui Zhang, Iulius Dragonu, Paul M Matthews, Karla L Miller, Stephen M Smith
UK Biobank is a large-scale prospective epidemiological study with all data accessible to researchers worldwide. It is currently in the process of bringing back 100,000 of the original participants for brain, heart and body MRI, carotid ultrasound and low-dose bone/fat x-ray. The brain imaging component covers 6 modalities (T1, T2 FLAIR, susceptibility weighted MRI, Resting fMRI, Task fMRI and Diffusion MRI). Raw and processed data from the first 10,000 imaged subjects has recently been released for general research access...
February 1, 2018: NeuroImage
https://www.readbyqxmd.com/read/29076399/cerebrospinal-fluid-and-blood-biomarkers-for-neurodegenerative-dementias-an-update-of-the-consensus-of-the-task-force-on-biological-markers-in-psychiatry-of-the-world-federation-of-societies-of-biological-psychiatry
#10
Piotr Lewczuk, Peter Riederer, Sid E O'Bryant, Marcel M Verbeek, Bruno Dubois, Pieter Jelle Visser, Kurt A Jellinger, Sebastiaan Engelborghs, Alfredo Ramirez, Lucilla Parnetti, Clifford R Jack, Charlotte E Teunissen, Harald Hampel, Alberto Lleó, Frank Jessen, Lidia Glodzik, Mony J de Leon, Anne M Fagan, José Luis Molinuevo, Willemijn J Jansen, Bengt Winblad, Leslie M Shaw, Ulf Andreasson, Markus Otto, Brit Mollenhauer, Jens Wiltfang, Martin R Turner, Inga Zerr, Ron Handels, Alexander G Thompson, Gunilla Johansson, Natalia Ermann, John Q Trojanowski, Ilker Karaca, Holger Wagner, Patrick Oeckl, Linda van Waalwijk van Doorn, Maria Bjerke, Dimitrios Kapogiannis, H Bea Kuiperij, Lucia Farotti, Yi Li, Brian A Gordon, Stéphane Epelbaum, Stephanie J B Vos, Catharina J M Klijn, William E Van Nostrand, Carolina Minguillon, Matthias Schmitz, Carla Gallo, Andrea Lopez Mato, Florence Thibaut, Simone Lista, Daniel Alcolea, Henrik Zetterberg, Kaj Blennow, Johannes Kornhuber
In the 12 years since the publication of the first Consensus Paper of the WFSBP on biomarkers of neurodegenerative dementias, enormous advancement has taken place in the field, and the Task Force takes now the opportunity to extend and update the original paper. New concepts of Alzheimer's disease (AD) and the conceptual interactions between AD and dementia due to AD were developed, resulting in two sets for diagnostic/research criteria. Procedures for pre-analytical sample handling, biobanking, analyses and post-analytical interpretation of the results were intensively studied and optimised...
June 2018: World Journal of Biological Psychiatry
https://www.readbyqxmd.com/read/28925747/protocol-and-quality-assurance-for-carotid-imaging-in-100-000-participants-of-uk-biobank-development-and-assessment
#11
Sean Coffey, Adam J Lewandowski, Steve Garratt, Rudy Meijer, Steven Lynum, Ram Bedi, James Paterson, Mohammad Yaqub, J Alison Noble, Stefan Neubauer, Steffen E Petersen, Naomi Allen, Cathie Sudlow, Rory Collins, Paul M Matthews, Paul Leeson
Background Ultrasound imaging is able to quantify carotid arterial wall structure for the assessment of cerebral and cardiovascular disease risks. We describe a protocol and quality assurance process to enable carotid imaging at large scale that has been developed for the UK Biobank Imaging Enhancement Study of 100,000 individuals. Design An imaging protocol was developed to allow measurement of carotid intima-media thickness from the far wall of both common carotid arteries. Six quality assurance criteria were defined and a web-based interface (Intelligent Ultrasound) was developed to facilitate rapid assessment of images against each criterion...
January 1, 2017: European Journal of Preventive Cardiology
https://www.readbyqxmd.com/read/28836039/fully-automated-left-ventricular-mass-and-volume-mri-analysis-in-the-uk-biobank-population-cohort-evaluation-of-initial-results
#12
Avan Suinesiaputra, Mihir M Sanghvi, Nay Aung, Jose Miguel Paiva, Filip Zemrak, Kenneth Fung, Elena Lukaschuk, Aaron M Lee, Valentina Carapella, Young Jin Kim, Jane Francis, Stefan K Piechnik, Stefan Neubauer, Andreas Greiser, Marie-Pierre Jolly, Carmel Hayes, Alistair A Young, Steffen E Petersen
UK Biobank, a large cohort study, plans to acquire 100,000 cardiac MRI studies by 2020. Although fully-automated left ventricular (LV) analysis was performed in the original acquisition, this was not designed for unsupervised incorporation into epidemiological studies. We sought to evaluate automated LV mass and volume (Siemens syngo InlineVF versions D13A and E11C), against manual analysis in a substantial sub-cohort of UK Biobank participants. Eight readers from two centers, trained to give consistent results, manually analyzed 4874 UK Biobank cases for LV end-diastolic volume (EDV), end-systolic volume (ESV), stroke volume (SV), ejection fraction (EF) and LV mass (LVM)...
February 2018: International Journal of Cardiovascular Imaging
https://www.readbyqxmd.com/read/28683736/security-controls-in-an-integrated-biobank-to-protect-privacy-in-data-sharing-rationale-and-study-design
#13
Takako Takai-Igarashi, Kengo Kinoshita, Masao Nagasaki, Soichi Ogishima, Naoki Nakamura, Sachiko Nagase, Satoshi Nagaie, Tomo Saito, Fuji Nagami, Naoko Minegishi, Yoichi Suzuki, Kichiya Suzuki, Hiroaki Hashizume, Shinichi Kuriyama, Atsushi Hozawa, Nobuo Yaegashi, Shigeo Kure, Gen Tamiya, Yoshio Kawaguchi, Hiroshi Tanaka, Masayuki Yamamoto
BACKGROUND: With the goal of realizing genome-based personalized healthcare, we have developed a biobank that integrates personal health, genome, and omics data along with biospecimens donated by volunteers of 150,000. Such a large-scale of data integration involves obvious risks of privacy violation. The research use of personal genome and health information is a topic of global discussion with regard to the protection of privacy while promoting scientific advancement. The present paper reports on our plans, current attempts, and accomplishments in addressing security problems involved in data sharing to ensure donor privacy while promoting scientific advancement...
July 6, 2017: BMC Medical Informatics and Decision Making
https://www.readbyqxmd.com/read/28633629/prevalence-of-and-risk-factors-for-severe-cognitive-and-sleep-symptoms-in-me-cfs-and-ms
#14
Vageesh Jain, Amit Arunkumar, Caroline Kingdon, Eliana Lacerda, Luis Nacul
BACKGROUND: There are considerable phenotypic and neuroimmune overlaps between myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) and multiple sclerosis (MS). While the precise aetiologies of both MS and ME/CFS are unclear, evidence suggests that deterioration in cognitive function is widely prevalent in patients with either condition. Little is known about differing risk factors or exposures, which may lead to severe cognitive or sleep symptoms. This study aims to gauge the extent of cognitive and sleep symptoms in ME/CFS and MS patients participating in the UK ME/CFS Biobank and identify the characteristics of those experiencing severe symptoms...
June 20, 2017: BMC Neurology
https://www.readbyqxmd.com/read/28604319/establishing-an-academic-biobank-in-a-resource-challenged-environment
#15
Cassandra Claire Soo, Freedom Mukomana, Scott Hazelhurst, Michele Ramsay
Past practices of informal sample collections and spreadsheets for data and sample management fall short of best-practice models for biobanking, and are neither cost effective nor efficient to adequately serve the needs of large research studies. The biobank of the Sydney Brenner Institute for Molecular Bioscience serves as a bioresource for institutional, national and international research collaborations. It provides high-quality human biospecimens from African populations, secure data and sample curation and storage, as well as monitored sample handling and management processes, to promote both non-communicable and infectious-disease research...
May 24, 2017: South African Medical Journal, Suid-Afrikaanse Tydskrif Vir Geneeskunde
https://www.readbyqxmd.com/read/28480134/common-and-rare-genetic-markers-of-lipid-variation-in-subjects-with-type-2-diabetes-from-the-accord-clinical-trial
#16
Skylar W Marvel, Daniel M Rotroff, Michael J Wagner, John B Buse, Tammy M Havener, Howard L McLeod, Alison A Motsinger-Reif
BACKGROUND: Individuals with type 2 diabetes are at an increased risk of cardiovascular disease. Alterations in circulating lipid levels, total cholesterol (TC), low-density lipoprotein (LDL), high-density lipoprotein (HDL), and triglycerides (TG) are heritable risk factors for cardiovascular disease. Here we conduct a genome-wide association study (GWAS) of common and rare variants to investigate associations with baseline lipid levels in 7,844 individuals with type 2 diabetes from the ACCORD clinical trial...
2017: PeerJ
https://www.readbyqxmd.com/read/28475694/flashpca2-principal-component-analysis-of-biobank-scale-genotype-datasets
#17
Gad Abraham, Yixuan Qiu, Michael Inouye
Motivation: Principal component analysis (PCA) is a crucial step in quality control of genomic data and a common approach for understanding population genetic structure. With the advent of large genotyping studies involving hundreds of thousands of individuals, standard approaches are no longer feasible. However, when the full decomposition is not required, substantial computational savings can be made. Results: We present FlashPCA2, a tool that can perform partial PCA on 1 million individuals faster than competing approaches, while requiring substantially less memory...
September 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28372841/improved-accuracy-of-an-tandem-liquid-chromatography-mass-spectrometry-method-measuring-24r-25-dihydroxyvitamin-d3-and-25-hydroxyvitamin-d-metabolites-in-serum-using-unspiked-controls-and-its-application-to-determining-cross-reactivity-of-a-chemiluminescent
#18
Kirsten G Dowling, George Hull, Jouko Sundvall, Christel Lamberg-Allardt, Kevin D Cashman
Measurement of serum 25-hydroxyvitamin D [25(OH)D] is considered the best indicator of vitamin D status. Two minor vitamin D metabolites are common interferences encountered in 25(OH)D assays. The first is 3-epi-25-hydroxyvitamin D3 [3-epi-25(OH)D3], which if not chromatographically resolved from 25-hydroxyvitamin D3 [25(OH)D3], can overestimate 25(OH)D concentrations. The second is 24R,25-dihydroxyvitamin D3 [24R,25(OH)2D3], which can cross-react with the antibodies in 25(OH)D immunoassays. Our aim was to develop an LC-MS/MS method capable of detecting both 3-epi-25(OH)D3 and 24R,25(OH)2D3 in serum without the use of a derivatization agent...
May 12, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28335817/gene-expression-differences-between-paxgene-and-tempus-blood-rna-tubes-are-highly-reproducible-between-independent-samples-and-biobanks
#19
Anne Heidi Skogholt, Einar Ryeng, Sten Even Erlandsen, Frank Skorpen, Svanhild A Schønberg, Pål Sætrom
BACKGROUND: Gene expression profiling from blood is sensitive to technology choices. For example, the main blood RNA collection systems-the PAXgene and Tempus tubes-differently influence RNA expression signatures. The aim of this study was to establish a common RNA isolation protocol for these two systems and investigate if it could reduce the differences in gene expression between them. RESULTS: We collected identical blood samples on the PAXgene and Tempus systems and retrieved blood samples from two independent biobanks-NOWAC and HUNT3-which are based on PAXgene and Tempus, respectively...
March 23, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/28255773/cell-lines-authentication-and-mycoplasma-detection-as-minimun-quality-control-of-cell-lines-in-biobanking
#20
C Corral-Vázquez, R Aguilar-Quesada, P Catalina, G Lucena-Aguilar, G Ligero, B Miranda, J A Carrillo-Ávila
Establishment of continuous cell lines from human normal and tumor tissues is an extended and useful methodology for molecular characterization of cancer pathophysiology and drug development in research laboratories. The exchange of these cell lines between different labs is a common practice that can compromise assays reliability due to contamination with microorganism such as mycoplasma or cells from different flasks that compromise experiment reproducibility and reliability. Great proportions of cell lines are contaminated with mycoplasma and/or are replaced by cells derived for a different origin during processing or distribution process...
June 2017: Cell and Tissue Banking
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