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biobank and quality control

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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
#1
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
#2
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. We present FlashPCA2, a tool that can perform partial PCA on 1 million individuals faster than competing approaches, while requiring substantially less memory...
May 5, 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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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...
January 12, 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
#9
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
#10
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...
December 19, 2016: 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
#11
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
#12
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...
November 16, 2016: Prostate
https://www.readbyqxmd.com/read/27799821/vejle-diabetes-biobank-a-resource-for-studies-of-the-etiologies-of-diabetes-and-its-comorbidities
#13
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
#14
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
#15
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
https://www.readbyqxmd.com/read/27620695/multicentric-study-of-the-effect-of-pre-analytical-variables-in-the-quality-of-plasma-samples-stored-in-biobanks-using-different-complementary-proteomic-methods
#16
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
https://www.readbyqxmd.com/read/27599083/-institutional-biobank-as-a-pillar-of-medical-science
#17
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
https://www.readbyqxmd.com/read/27541936/quality-assurance-of-samples-and-processes-in-the-spanish-renal-research-network-redinren-biobank
#18
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...
December 2016: Biopreservation and Biobanking
https://www.readbyqxmd.com/read/27462375/genome-wide-dna-methylation-profiling-with-medip-seq-using-archived-dried-blood-spots
#19
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
https://www.readbyqxmd.com/read/27403896/applicability-of-under-vacuum-fresh-tissue-sealing-and-cooling-to-omics-analysis-of-tumor-tissues
#20
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...
December 2016: Biopreservation and Biobanking
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