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biobank and quality control

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https://www.readbyqxmd.com/read/28925747/protocol-and-quality-assurance-for-carotid-imaging-in-100-000-participants-of-uk-biobank-development-and-assessment
#1
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
#2
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)...
August 23, 2017: 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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
https://www.readbyqxmd.com/read/28145427/variability-in-assigning-pathogenicity-to-incidental-findings-insights-from-ldlr-sequence-linked-to-the-electronic-health-record-in-1013-individuals
#11
Maya S Safarova, Eric W Klee, Linnea M Baudhuin, Erin M Winkler, Michelle L Kluge, Suzette J Bielinski, Janet E Olson, Iftikhar J Kullo
Knowledge of variant pathogenicity is key to implementing genomic medicine. We describe variability between expert reviewers in assigning pathogenicity to sequence variants in LDLR, the causal gene in the majority of cases of familial hypercholesterolemia. LDLR was sequenced on the Illumina HiSeq platform (average read depth >200 × ) in 1013 Mayo Biobank participants recruited from 2012 to 2013. Variants with a minor allele frequency (MAF) <5% predicted to be functional or referenced in HGMD (Human Gene Mutation Database) or NCBI-ClinVar databases were reviewed...
April 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28114305/targeted-sequencing-of-lung-function-loci-in-chronic-obstructive-pulmonary-disease-cases-and-controls
#12
María Soler Artigas, Louise V Wain, Nick Shrine, Tricia M McKeever, Ian Sayers, Ian P Hall, Martin D Tobin
Chronic obstructive pulmonary disease (COPD) is the third leading cause of death worldwide; smoking is the main risk factor for COPD, but genetic factors are also relevant contributors. Genome-wide association studies (GWAS) of the lung function measures used in the diagnosis of COPD have identified a number of loci, however association signals are often broad and collectively these loci only explain a small proportion of the heritability. In order to examine the association with COPD risk of genetic variants down to low allele frequencies, to aid fine-mapping of association signals and to explain more of the missing heritability, we undertook a targeted sequencing study in 300 COPD cases and 300 smoking controls for 26 loci previously reported to be associated with lung function...
2017: PloS One
https://www.readbyqxmd.com/read/28080144/a-survey-of-the-current-situation-of-clinical-biobanks-in-china
#13
Haiyan Li, Mingyu Ni, Peng Wang, Xiaomin Wang
The development of biomedical research urgently needs the support of a large number of high-quality clinical biospecimens. Therefore, human biobanks at different levels have been established successively in China and other countries at a significantly increasing pace in recent years. To better understand the general current state of clinical biobanks in China, we surveyed 42 clinical biobanks based in hospitals and collected information involving their management systems, sharing mechanisms, quality control systems, and informational management systems using closed questionnaire methods...
June 2017: Biopreservation and Biobanking
https://www.readbyqxmd.com/read/28072712/seniorlab-a-prospective-observational-study-investigating-laboratory-parameters-and-their-reference-intervals-in-the-elderly
#14
Martin Risch, Urs Nydegger, Lorenz Risch
BACKGROUND: In clinical practice, laboratory results are often important for making diagnostic, therapeutic, and prognostic decisions. Interpreting individual results relies on accurate reference intervals and decision limits. Despite the considerable amount of resources in clinical medicine spent on elderly patients, accurate reference intervals for the elderly are rarely available. The SENIORLAB study set out to determine reference intervals in the elderly by investigating a large variety of laboratory parameters in clinical chemistry, hematology, and immunology...
January 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/27988499/the-effect-of-storage-temperature-fluctuations-on-the-stability-of-biochemical-analytes-in-blood-serum
#15
Helmuth Haslacher, Thomas Szekeres, Marlene Gerner, Elisabeth Ponweiser, Manuela Repl, Oswald F Wagner, Thomas Perkmann
BACKGROUND: Irreproducibility of scientific results constitutes an undesirably onerous economic burden and is in many cases caused by low-quality materials. Therefore, researchers are increasingly devoting their attention to the bioresources they use. In turn, those bioresources are required to validate their preanalytical processes in order to ensure best possible quality. The present study thus aimed to evaluate the impact of repeated temperature fluctuations, as they occur in most research biobanks due to repetitive opening and closing of freezer doors, on the stability of 26 biochemical analytes...
June 27, 2017: Clinical Chemistry and Laboratory Medicine: CCLM
https://www.readbyqxmd.com/read/27875525/precision-medicine-in-cancer-challenges-and-recommendations-from-an-eu-funded-cervical-cancer-biobanking-study
#16
Sanne Samuels, Balazs Balint, Heiko von der Leyen, Philippe Hupé, Leanne de Koning, Choumouss Kamoun, Windy Luscap-Rondof, Ulrike Wittkop, Ksenia Bagrintseva, Marina Popovic, Atttila Kereszt, Els Berns, Gemma G Kenter, Ekaterina S Jordanova, Maud Kamal, Susy Scholl
BACKGROUND: Cervical cancer (CC) remains a leading cause of gynaecological cancer-related mortality worldwide. CC pathogenesis is triggered when human papillomavirus (HPV) inserts into the genome, resulting in tumour suppressor gene inactivation and oncogene activation. Collecting tumour and blood samples is critical for identifying these genetic alterations. METHODS: BIO-RAIDs is the first prospective molecular profiling clinical study to include a substantial biobanking effort that used uniform high-quality standards and control of samples...
December 6, 2016: British Journal of Cancer
https://www.readbyqxmd.com/read/27862105/blind-biobanking-of-the-prostatectomy-specimen-critical-evaluation-of-the-existing-techniques-and-development-of-the-new-4-level-tissue-extraction-model-with-high-sampling-efficacy
#17
Yuri Tolkach, Okyaz Eminaga, Fabian Wötzel, Sebastian Huss, Olaf Bettendorf, Elke Eltze, Mahmoud Abbas, Florian Imkamp, Axel Semjonow
BACKGROUND: Fresh tissue is mandatory to perform high-quality translation studies. Several models for tissue extraction from prostatectomy specimens without guidance by frozen sections are already introduced. However, little is known about the sampling efficacy of these models, which should provide representative tissue in adequate volumes, account for multifocality and heterogeneity of tumor, not violate the routine final pathological examination, and perform quickly without frozen section-based histological control...
March 2017: Prostate
https://www.readbyqxmd.com/read/27799821/vejle-diabetes-biobank-a-resource-for-studies-of-the-etiologies-of-diabetes-and-its-comorbidities
#18
Eva Rabing Brix Petersen, Aneta Aleksandra Nielsen, Henry Christensen, Torben Hansen, Oluf Pedersen, Cramer Kjeldahl Christensen, Ivan Brandslund
AIMS: Carefully designed and established biobanks are considered one of the most essential resources to foster biomedical research as they provide cost-effective and rapid access to a vast variety of biological materials and related anthropometrics allowing for testing of various biomarkers as well as numerous original and pertinent bioclinical hypotheses related to human disease etiology and prognosis. The objective of the present study was to present the baseline data, design, and methods used for the establishment of the Vejle Diabetes Biobank...
2016: Clinical Epidemiology
https://www.readbyqxmd.com/read/27789671/applying-metabolomics-to-cardiometabolic-intervention-studies-and-trials-past-experiences-and-a-roadmap-for-the-future
#19
REVIEW
Naomi J Rankin, David Preiss, Paul Welsh, Naveed Sattar
Metabolomics and lipidomics are emerging methods for detailed phenotyping of small molecules in samples. It is hoped that such data will: (i) enhance baseline prediction of patient response to pharmacotherapies (beneficial or adverse); (ii) reveal changes in metabolites shortly after initiation of therapy that may predict patient response, including adverse effects, before routine biomarkers are altered; and( iii) give new insights into mechanisms of drug action, particularly where the results of a trial of a new agent were unexpected, and thus help future drug development...
October 2016: International Journal of Epidemiology
https://www.readbyqxmd.com/read/27672657/18s-ribosomal-rna-evaluation-as-preanalytical-quality-control-for-animal-dna
#20
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
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