Integrated Biobank of Luxembourg IBBL

Luxembourg, Luxembourg

Integrated Biobank of Luxembourg IBBL

Luxembourg, Luxembourg
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Kofanova O.A.,Integrated BioBank of Luxembourg IBBL | Davis K.,PPD Inc | Glazer B.,Quintiles | De Souza Y.,University of California at San Francisco | And 2 more authors.
Biopreservation and Biobanking | Year: 2014

The impact of shipping temperatures and preservation media used during transport of either peripheral blood mononuclear cells (PBMCs) or Jurkat cells was assessed, in view of implementing of a proficiency testing scheme on mononuclear cell viability. Samples were analyzed before and after shipment at different temperatures (ambient temperature, dry ice, and liquid nitrogen) and in different preservation media (serum with cryoprotectant, commercial cryopreservation solution, and room temperature transport medium). Sample quality was assessed by viability assays (Trypan Blue dye exclusion, flow cytometry, Cell Analysis System cell counting (CASY)), and by ELISpot functional assay. The liquid nitrogen storage and shipment were found to be the most stable conditions to preserve cell viability and functionality. However, we show that alternative high quality shipment conditions for viable cells are dry ice shipment and commercial cryopreservation solution. These were also cost-efficient shipment conditions, satisfying the requirements of a proficiency testing scheme for viable mononuclear cells. Room temperature transport medium dramatically and adversely affected the integrity of mononuclear cells. © Mary Ann Liebert, Inc. 2014.

Azuaje F.J.,CRP Sante | Heymann M.,Integrated BioBank of Luxembourg IBBL | Ternes A.-M.,CRP Sante | Wienecke-Baldacchino A.,University of Luxembourg | And 3 more authors.
Journal of Clinical Bioinformatics | Year: 2012

The 6 thBenelux Bioinformatics Conference (BBC11) held in Luxembourg on 12 and 13 December 2011 attracted around 200 participants, including internationally-renowned guest speakers and more than 100 peer-reviewed submissions from 3 continents. Researchers from the public and private sectors convened at BBC11 to discuss advances and challenges in a wide spectrum of application areas. A key theme of the conference was the contribution of bioinformatics to enable and accelerate translational and clinical research. The BBC11 stressed the need for stronger collaborating efforts across disciplines and institutions. The demonstration of the clinical relevance of systems approaches and of next-generation sequencing-based measurement technologies are among the existing opportunities for increasing impact in translational research. Translational bioinformatics will benefit from research models that strike a balance between the importance of protecting intellectual property and the need to openly access scientific and technological advances. The full conference proceedings are freely available at © 2012 Azuaje et al; licensee BioMed Central Ltd.

Kofanova O.A.,Integrated Biobank of Luxembourg IBBL | Betsou F.,Integrated Biobank of Luxembourg IBBL
Biopreservation and Biobanking | Year: 2013

Proteomic research requires high-quality, standardized samples. Quality control (QC) biomarkers, which are sensitive to the collection, processing or storage conditions, would be useful tools to identify compromised samples. This study evaluates the usefulness of renal lithostatine as a QC tool for urine sample processing in daily biobank work. Four factors (pre-analytical variations) were examined for their effect on renal lithostatine as measured by ELISA: time from sample collection to centrifugation, number of specimen freeze-thaw cycles, specimen preservation with protease inhibitors, and the inclusion or exclusion of urinary sediment. © 2013, Mary Ann Liebert, Inc.

Unger C.,Qiagen | Kofanova O.,Integrated Biobank of Luxembourg IBBL | Sokolowska K.,Integrated Biobank of Luxembourg IBBL | Lehmann D.,Qiagen | Betsou F.,Integrated Biobank of Luxembourg IBBL
Electrophoresis | Year: 2015

The analytical and clinical validity of analyses of RNA samples destined for clinical diagnosis and therapeutic management is directly impacted by RNA quality. RNA is affected by heat, enzymatic degradation, and Ultraviolet (UV) light. RNA from three eukaryotic cell lines was degraded by heat, RNase, or UV light. RNA integrity values obtained with the benchmark Agilent Bioanalyzer 2100 system were compared with those from the more recent QIAxcel Advanced system. The application of this novel method has allowed us to unravel differences between RNA biophysical and biochemical degradation modes. Agilent RNA integrity number (RIN) and QIAxcel RIS were comparable in heat-degraded and RNase III-degraded RNA. Agilent RIN and QIAxcel RIS were comparable at a RIN decision level of 7 in UV-degraded RNA but not overall. The QIAxcel RIS method was more precise than Agilent RIN for RIN<8, while the inverse was true for RIN≥8. Greater degradation of mRNA and rRNA in UV-damaged samples hampered the Agilent RIN calculation algorithm. Overall, RIS was more robust than RIN for assessing RNA integrity. The ΔΔCt-values for heat- and UV-degraded RNA samples showed slightly higher correlation with RIS than with RIN. RNA integrity can be used to categorize RNA samples for suitability for downstream gene expression analyses, independently of the RNA degradation mechanism. The new method QIAxcel is more robust and therefore allows more accurate categorization of compromised RNA samples. © 2015 WILEY-VCH Verlag GmbH & Co.

Kofanova O.A.,Integrated BioBank of Luxembourg IBBL | Fack F.,CRP Sante | Niclou S.P.,CRP Sante | Betsou F.,Integrated BioBank of Luxembourg IBBL
Biopreservation and Biobanking | Year: 2013

Preanalytical conditions applied during sample collection and processing can affect the detection or quantification of unstable phosphoprotein biomarkers. We evaluated the consequences of tissue stabilization and protein extraction methods on phosphoprotein analysis. The effects of stabilization techniques (heat stabilization, snap-freezing) and time on the levels of phosphoproteins, including phospho-Akt, p-ERK 1/2, p-IkBα, p-JNK, and p38 MAPK, were evaluated using a BioPlex phosphoprotein assay. Additionally, two different protein extraction protocols, using different extraction buffers (8 M urea buffer, or Bio-Rad buffer without urea) were tested. For snap-frozen samples, protein extraction yields were comparable with the two buffer systems. For heat-stabilized samples, total protein yields were significantly lower following extraction in non-urea buffer. However, the concentrations of specific phosphoproteins were significantly higher in heat-stabilized samples than in the corresponding snap-frozen samples, indicating that this tissue processing method better preserved phosphoproteins. Significant differences were found between the measured phosphoprotein levels in heat-stabilized and snap-frozen tissue, suggesting that alterations occur very rapidly after tissue excision. Our results suggest that heat stabilization can be used as a tissue processing method for subsequent phosphoprotein analyses, but also suggest that the BioPlex phosphoprotein assay could be used as a possible quality control method to assess tissue sample integrity. © Copyright 2013, Mary Ann Liebert, Inc. 2013.

Astrin J.J.,Zoological Research Museum Alexander Koenig ZFMK | Betsou F.,Integrated Biobank of Luxembourg IBBL
Biopreservation and Biobanking | Year: 2016

Biobanks have become indispensable tools for a wide array of life and environmental sciences, and biotechnology. To evaluate trends in biobanking, 20,000 bibliographic records were retrieved and analyzed between 1939 and 2014 from the Scopus database using a series of biobank-related search terms within titles and keywords. Since the 1990s, the field of biobanking has been, and still is, experiencing above-average growth in terms of publications, journals, and thematic orientations. Almost two-thirds of all indexed biobanking documents have been published in the last decade, with now >1,000 publications in 600 distinct journals per year. Around 50,000 individual authors can be identified who have so far contributed to the field of biobanking, with an average of 1.5 publications per author. Author affiliations follow an uneven distribution: 42% of the authors are based in Europe, 33% in North America, 13% in Asia, 5% in South America, 4% in Australasia, and 2% in Africa. Analyzing the most common title words revealed (as did the journals) a strong focus on blood banking, but other biospecimen types - especially seeds, cells, and tissues - have been gaining increasing weight recently. Among medical applications, transfusion dominates, followed by transplantation. While a noticeable increase in disease and especially health occurred at the beginning of the millennium, cohort and consent seem to have become high-relevance topics only in this decade. In terms of banked organisms, human dominates, followed by viruses and plants (especially represented through seed banking). A very rough estimate based on subject categories suggests that a third of all publications in biobanking focus on organisms other than humans. However, animal, fungal, and microbial biobanking are still underrepresented, especially when considering their shares in global biodiversity. © Copyright 2016, Mary Ann Liebert, Inc. 2016.

Ammerlaan W.,Integrated BioBank of Luxembourg IBBL | Trezzi J.-P.,Integrated BioBank of Luxembourg IBBL | Trezzi J.-P.,Luxembourg Center for Systems Biomedicine | Lescuyer P.,University of Geneva | And 3 more authors.
Biopreservation and Biobanking | Year: 2014

Background: Formal method validation for biospecimen processing in the context of accreditation in laboratories and biobanks is lacking. Serum and plasma processing protocols were validated for fitness-for-purpose in terms of key downstream endpoints, and this article demonstrates methodology for biospecimen processing method validation. Methods: Serum and plasma preparation from human blood was optimized for centrifugation conditions with respect to microparticle counts. Optimal protocols were validated for methodology and reproducibility in terms of acceptance criteria based on microparticle counts, DNA and hemoglobin concentration, and metabolomic and proteomic profiles. These parameters were also used to evaluate robustness for centrifugation temperature (4°C versus room temperature [RT]), deceleration (low, medium, high) and blood stability (after a 2-hour delay). Results: Optimal protocols were 10-min centrifugation for serum and 20-min for plasma at 2000 g, medium brake, RT. Methodology and reproducibility acceptance criteria were met for both protocols except for reproducibility of plasma metabolomics. Overall, neither protocol was robust for centrifugation at 4°C versus RT. RT gave higher microparticles and free DNA yields in serum, and fewer microparticles with less hemolysis in plasma. Overall, both protocols were robust for fast, medium, and low deceleration, with a medium brake considered optimal. Pre-centrifugation stability after a 2-hour delay was seen at both temperatures for hemoglobin concentration and proteomics, but not for microparticle counts. Conclusions: We validated serum and plasma collection methods suitable for downstream protein, metabolite, or free nucleic acid-based applications. Temperature and pre-centrifugation delay can influence analytic results, and laboratories and biobanks should systematically record these conditions in the scope of accreditation. © Copyright 2014, Mary Ann Liebert, Inc.

Kofanova O.A.,Integrated Biobank of Luxembourg IBBL | Mommaerts K.,Integrated Biobank of Luxembourg IBBL | Betsou F.,Integrated Biobank of Luxembourg IBBL
Biopreservation and Biobanking | Year: 2015

This biospecimen research case study illustrates the importance of a neglected pre-analytical factor, the polypropylene type of storage tubes. We measured amyloid β1-42 peptide and showed that a non-irradiated, homopolymer type of polypropylene has the lowest adsorption properties. © 2015, Mary Ann Liebert, Inc.

Kofanova O.A.,Integrated Biobank of Luxembourg IBBL | Mathieson W.,Imperial College London | Thomas G.A.,Imperial College London | Betsou F.,Integrated Biobank of Luxembourg IBBL
Biopreservation and Biobanking | Year: 2014

This case study illustrates the usefulness of the DNA fingerprinting method in biobank quality control (QC) procedures and emphasizes the need for detailed and accurate record keeping during processing of biological samples. It also underlines the value of independent third-party assessment to identify points at which errors are most likely to have occurred when unexpected results are obtained from biospecimens. © Copyright 2014, Mary Ann Liebert, Inc. 2014.

PubMed | Integrated BioBank of Luxembourg IBBL
Type: Journal Article | Journal: Biopreservation and biobanking | Year: 2016

This article is the fifth in a series of publications providing formal method validation for biospecimen processing. We report the optimization and validation of methodology to obtain nucleic acids of sufficient quantity and quality from blood.DNA was extracted using the Chemagic DNA Blood Kit on an MSM I. Extraction was optimized in terms of blood volume, elution buffer volume, and lysis conditions. The optimal protocol was validated for reproducibility, robustness (delay to buffy coat extraction, blood vs. buffy coat, and use of a magnetic rack), and performance (yield, purity, and concentration). RNA was extracted using a PAXgene Blood miRNA kit with a QiaCube. The protocol was validated for reproducibility, robustness (elution buffer, delay, and temperature before extraction), and performance (yield, purity, integrity, and miRNA content). Two platforms (QiaCube, Biorobot Universal) were further compared.For DNA extraction, a 4mL blood sample, manual lysis, and 300L elution buffer were found to be reproducible (CV <10% for DNA yield and A260nm/A280nm ratio) and robust (buffy coat vs. whole blood; immediate processing of buffy coat after lysis vs. storage for 1 week at 2-8C; and magnetic rack use). There was no difference between automated and manual lysis. RNA extracted with the PAXgene Blood miRNA kit on a QiaCube gave high yields and optimal reproducibility (low CV for RNA yield and integrity) with BR5 elution buffer (vs. water and TE). PAXgene tubes could be stored for up to 2 weeks at 2-8C. The Biorobot Universal System gave similar mean RNA yields with Qiacube and slightly lower but acceptable purity.We validated automated isolation of DNA with a Chemagic DNA Blood Kit on a magnetic bead-based MSM I, and of RNA with a PAXgene Blood miRNA kit on a silica membrane-based QiaCube or Biorobot (for low and high throughput, respectively).

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