Abstract
Animal Specimen Repositories
Istituto Zooprofilattico Sperimentale di Brescia, Brescia, Italy
Background: Mesenchymal stem cells (MSCs) are frequently used in veterinary medicine to repair orthopaedic injuries, particularly in race horses. MSCs can be isolated from different tissues, but the most commonly used for clinical applications are derived from adipose tissue or bone marrow. A branch of our cell culture bank was dedicated to the storage of MSCs, in order to treat tendon injuries in horses.
Methods: MSCs have been isolated from fat tissue and bone marrow, propagated in vitro not more than four passages and tested for multi-potentiality. Before freezing, every batch was subjected to safety controls. Only the batches free from contaminations (viruses, eubacteria and mycoplasma) were banked. MSCs were used not only for autologous but also for allogeneic implantation. For implantation, cells were suspended in autologous Platelet Rich Plasma (PRP) and inoculated into the damaged tendon. After MSCs treatment, horses were subjected to a rehabilitative period and to ecographic controls. A sample of every batch was conserved in the bank to be preserved either for a subsequent treatment or in case of complaint.
Results: Currently the MSC bank consists of 100 batches of cells. Each ampoule contains an average of 7 × 106 MSCs. Ecographic examinations showed good tendon regeneration and some of the treated animals have started competitions.
Conclusions: The MSC bank at IZSLER is organized in accordance with quality parameters. The prepared cells have shown to be useful for clinical application regarding tendon repair.
Ezemvelo KZN Wildlife, Cascades, Kwazulu Natal, South Africa
Populations that are founded from a small surviving parent population that has gone through a numerical bottleneck can, if not properly managed, end up suffering from a decline in genetic diversity. This in turn could lead to inbreeding depression and a loss of fitness which if severe enough could lead to population extinction. The main objective of managing such a population is to have a meta-population exchange strategy that minimizes loss of heterozygosity and inbreeding. The establishment of a number of Genetic or Gene Specimen Banks in southern Africa has, as one of its outputs, facilitated the setting-up of genetic management standards and informing management as to the ongoing genetic status of selected endangered wildlife populations e.g. Black rhinoceros, Diceros bicornis minor. Specimens derived from currently abundant species would in turn also be valuable should a catastrophic decline in numbers befall the species, such as occurred with the Indian white-backed vulture Gyps bengalensis. The purpose of Gene Banks also includes archival banking; forensics investigations; contributing to the International Barcode of Life (iBOL) Initiative; biodiversity discovery; game ranch management; identifying hybrid species. Field officers are tasked with the logistics of collecting the appropriate specimens and data and transporting them to the Gene Bank. The Gene Bank is tasked with sample processing, management and control, as a national asset of the country and to the benefit of society.
Agricultural Research Council, Irene, Gauteng, South Africa
Introduction: Access to DNA derived from livestock and wildlife play a vital role in molecular genetics and forensics. The ARC, a consortium member of BioBankSA, collects, processes, banks and distributes a representative range of value-enhanced biomaterials from key wildlife and indigenous livestock species for research and biotechnology development.
Methods: Tissue and blood specimens are submitted by the owners of animals, DNA extracted and an aliquot banked for future use.
Results: Samples held include 65 wildlife species, 10 livestock species, including different breeds and a number of avian and fish species. The National Animal DNA Bank has about 13,000 samples, each uniquely identified by a barcode ID number. Information pertaining to the samples is stored in a database and allows for easy access and value adding. Dynamic operational policy ensures protection of ownership on the one hand while promoting availability and access of samples for research purposes. Access and release of sub-samples to beneficiaries is mediated though a peer-reviewed evaluation process.
Conclusion: A number of projects have culminated from samples originating from the National Animal DNA bank and includes technology development for forensic identification of a range of wildlife species, including rhino, impala, kudu, sable antelope and buffalo. DNA samples, representative of the species diversity of southern Africa, will be added to the collection, so increasing its value and use, to the benefit of society.
National Zoological Gardens of SA, NRF, Pretoria, North West Province, South Africa
Introduction: Biomaterials play a pivotal role in biodiversity conservation and biotechnology development. A unique, one of a kind wildlife/indigenous livestock Biological Resource Bank (BRB) has been established in South Africa.
Method: Biomaterials are collected from a variety of species, processed and banked in the BRB. Different tissue-types making up the BRB include fibroblast cell cultures, gametes, embryos, skin, DNA, hair, feathers, shells, blood and muscle. Tissue is stored under different conditions, including room temperature, refrigeration, mechanical freezers and Liquid Nitrogen freezers. The BRB represents a knowledge-hub and is expanding to meet the growing biodiversity communities' needs of biomaterial access, processing, curation, research (Science of Collections) and distribution for trans-disciplinary research, including molecular genetics, reproduction, epidemiology, health, forensics, species discovery (Barcode of Life) and environmental pollution. The knowledge-hub further engages stakeholders in technology transfer, knowledge generation, human resource development and access and benefit sharing (ABS) practices. The BRB is the custodian of the biomaterials, on behalf of the legal owners of the animals, from which the biomaterials were collected.
Results: The BRB has 45,000 samples from more than 450 species and together with the samples banked at the BioBankSA consortium partners, represents a significant resource for the national, regional and global research communities.
Conclusion: Biomaterials are national assets and the BRB plays a pivotal role in the securing of such assets and the use thereof for ethical research, to the benefit of society.
Biospecimen Science
U.S. National Cancer Institute, NIH, Bethesda, MD, USA
The US National Cancer Institute's Program for Innovative Molecular Analysis Technologies (IMAT) offers several funding opportunities to support those innovators who are developing novel technologies that have the potential for making a high impact in cancer research and patient care. As an investigator-initiated program, the research community has the burden of identifying the unmet need and pairing it with an innovative technological solution that has the potential for broad impact. There is one targeted area that IMAT has a very specific solicitation and it is in the area of biospecimen science. The overall goal of these solicitations is to develop technologies capable of interrogating and/or maximizing the quality and utility of biospecimens or their derived samples for downstream molecular analyses. These opportunities will support the development of tools, devices, instrumentation, and associated methods to assess sample quality, preserve/protect sample integrity, and establish verification criteria for quality assessment/quality control and handling under diverse conditions. Supported technologies are expected to have a potential to accelerate and/or enhance the research in cancer biology, prevention, diagnosis, treatment, epidemiology, and cancer health disparities, by reducing pre-analytical variations that affect biospecimen and/or sample quality.
Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
Background: Participation rates in population studies might be enhanced by offering saliva as an alternative to blood collection but there may be low DNA yield, high costs, and alcohol-based mouthwash which is offensive to some populations. Our method yields high-quality genomic DNA from buccal cells that is non-invasive, cost-effective, and acceptable to individuals who abstain from alcohol.
Methods: We compared five DNA isolation kits using saliva, and evaluated quality for alcohol-free mouthwash vs. passive collection in 70% ethanol. We also tested temperature and prolonged storage effects on yield by UV spectrophotometry, agarose gel electrophoresis, and RT-PCR.
Results: Mean DNA yields varied among test kits. Oragene and EpiCentre kits yielded the most DNA followed by EZNA, Norgen and Qiagen. EpiCentre, Qiagen and Norgen kits all produced DNAs with high purity, while Oragene and EZNA DNAs contained protein impurities. Norgen failed in RT-PCR. Immediate saliva sample processing collected in alcohol-free mouthwash yielded the most DNA; time delay in processing and temperature did not significantly alter DNA yield or purity.
Conclusions: The best method for DNA isolation from saliva with respect to DNA yield, quality, and cost is “swish and spit” with 10 ml Crest Pro-Health alcohol-free mouthwash and DNA isolation with the EpiCentre Master Pure DNA kit. This method is cost effective compared to the Oragene kit. This method yields repeated success in our current NIH-funded study of gender differences in bladder cancer risk factors in Egypt, where many recruited subjects abstain from alcohol use.
University of Alabama at Birmingham, Birmingham, AL, USA
Background: Idiopathic pulmonary hypertension (IPH) is characterized by elevated pulmonary arterial pressure culminating in right ventricular failure. The pathophysiology has not been elucidated and research has been frustrated by a lack of quality, well-characterized tissue samples. The Pulmonary Hypertension Breakthrough Initiative (PHBI) was established to characterize the genotype, cellular basis, and biomolecular pathways of IPH and to fund a network of ten lung transplantation centers, two tissue processing centers and a coordinating center.
Methods: As one of the tissue processing centers, our laboratory operates the PHBI Biobank. This is a disease-specific biobank for IPH tissues. Standard operating procedures were designed for the collection, processing, and storage of samples. Lung transplantation centers enroll and obtain consent for the collection of tissues, and clinical histories from participants prior to transplantation. Blood is obtained for genotyping or processing prior to banking. Following lung explantation, fresh samples are shipped immediately. Execution of the standard operating protocol yields over 100 aliquots of tissue that are frozen or preserved using multiple techniques to accommodate analysis of cells, protein, DNA, and RNA. All fixed and/or frozen samples are sent to the Biobank where they are bar-coded, linking them to annotated clinical data.
Results: To date, tissue has been obtained from 51 lung transplants and >1000 samples have been distributed.
Conclusion: This biobank, which collects and distributes specimens from transplant sites across the United States, has increased the opportunity for a generation of new information about pulmonary hypertension. Similar models could be established for other rare diseases.
Cincinnati Children's Hospital, Cincinnati, OH, USA
Background: Storage of RNA can be problematic with temperature fluctuations, freeze-thaw cycles, and shipping potentially causing degradation of samples. We tested a new technology for the ability to stabilize RNA at 22°C or 56°C for extended time periods.
Methods: RNA (n = 4) was prepared from peripheral blood mononuclear cells (PBMCs). Samples were stored at 22°C and 56°C in GenVault's GenTegra RNA matrix or −80°C, 22°C or 56°C in water. After storage, RNA integrity numbers (RIN) were determined using the Agilent Bioanalyzer 2100. Samples were labeled using NuGEN WT-Ovation Pico and assayed on Affymetrix Human Exon 1.0 ST Array to assess matrix interference in this downstream application.
Results: RNA stored in water at −80°C for two weeks, had a RIN of 9.6 compared to decreased quality in RNAs stored in water at either 22°C or at 56°C (RIN: 7.2 and 3.1, respectively). By comparison, RNA samples stored with matrix at 22°C or 56°C were protected (RINs of 9.6 and 8.6, respectively). Finally, transcriptome profiling indicated that RNA stored in matrix at 56°C performed as well as RNA stored in water at −80°C as demonstrated by similar present calls (59% and 60%) and background values (115 and 130) measured by microarray.
Conclusions: The GenTegra matrix offered significant protection of RNA integrity when compared to RNAs stored in water. Further, matrix did not interfere with the performance of downstream applications such as NuGEN labeling and subsequent profiling on Affymetrix exon arrays. Technologies for room temperature storage hold promise for improved sample preservation.
Integrated Biobank of Luxembourg, Luxembourg, Luxembourg
Management and traceability of biospecimen preanalytical variations are necessary to provide effective and efficient interconnectivity and interoperability between Biobanks. Therefore, the ISBER Biospecimen Science Working Group developed a “Standard PREanalytical Code” (SPREC) which identifies the main preanalytical factors of clinical fluid and solid biospecimens and their simple derivatives. Implementation of the SPREC is expected to facilitate and consolidate international multicenter biomarker identification research and biospecimen research in the clinical Biobank environment. The SPREC is easy to implement and can be integrated into Biobank quality management systems and databases. Its flexibility allows integration of new novel technological developments in future versions. The SPREC is simple, straightforward and easy to implement, even for Biobanks in developing countries and those with limited resources since it can be hand-written or incorporated into a linear or two-dimensional barcode. The SPREC is flexible, making it possible to add new elements and/or new preanalytical options and corresponding coding characters. The value of SPREC-01 is also being proposed for use in non-human biorepository sectors with a view to encouraging a wider debate as to its value across different thematic biobanking sectors.
Integrated Biobank of Luxembourg, Luxembourg
An immunoenzymatic serum fingerprinting method was developed which allows researchers to establish a serum sample fingerprint through determination of IgG titres of three different specificities. Three widespread antigens were selected for their capacity to induce long lasting humoral immune responses. This fingerprinting method can be used to differentiate between two serum samples and allows to assess if two serum samples come from the same primary blood specimen or not. The precision of the method was sufficient to confer it a 99.5% specificity. This method can be used as a quality control method for biobanked serum samples. The serum fingerprinting method does not allow discrimination between individual donors of serum samples as the same donor may have different IgG titres against a specific antigen over time. The method allows discrimination either between individual donors at a given time or between primary blood specimens.This method offers a novel, easy to implement and specific tool to overcome one of the rarely recognized challenges of biobanks, in terms of quality control and quality assurance.
Doctorate School of Molecular Medicine; Biorep srl, Milano, Italy
Background: Genomics, transcriptomics, and proteomics have increased the importance of tissues in the discovery and validation of prognostic, diagnostic and therapeutic biomarkers. Human tissue has become a strategic and unavoidable tool for all –omics technologies including high-throughput in situ proteomics to study signal transduction and protein-protein interactions. Tissue microarray (TMA) systems allow for the study of hundreds of samples (paraffin embedded tissues or cells) on a single slide for hystochemical analysis. The “Galileo CK4500” (www.isenet.it) is a high-throughput semiautomatic and computer-assisted TMA platform with the unique feature of picking cores of interest in a tissue or cell block and extract nucleic acids for subsequent molecular biology analysis.
Methods: Harvested and agarose re-suspended Neural Stem Cells (NSCs) were fixed in PFA (4%) and treated like the human glioblastoma xenografts tissue donor block selected for the specific study. Cores of cells or tissues (previously selected) from the donor blocks were placed by the arrayer either in a second paraffin block or in appropriate vessels to be processed for nucleic acid extraction.
Results: TMA and CLMA (Cell Line Microarray) technology were used to analyze glioblastoma xenografts and NSCs, to verify stemness and tripotency. From the cores DNA, RNA and microRNAs were successfully extracted.
Conclusions: The Galileo CK4500 platform is a powerful pathology tool to simultaneously screen a huge number of tissues or cell lines treated in different conditions or with different phenotypes. This technique will be particularly useful to obtain immunophenotypical information and to perform epigenetic studies in specific selected areas of a biological sample.
Translational Genomics Research Institute, Phoenix, AZ, USA
Background: Formalin-fixed paraffin-embedded (FFPE) tissues offer a valuable resource in cancer research for both biomarker discovery and clinical validation. In reality, existing sample procurement methods have been collected tissue under less than optimal conditions with uneven documentation of collection parameters, contributing to the ‘pre-analytic variable’ phase of a given research sample. In our experience, FFPE-extracted DNA possesses remarkable stability and sample processing permits successful application to high resolution CGH microarrays. The epigenome encompasses DNA modifications that though reversible can be stably transmitted. Epigenetic changes in cancer are poorly understood.
Methods: Twelve CRC samples and matched normal tissues were collected in 2006 and obtained from an established commercial vendor. Time to preservation was reported <25 minutes. DNA extractions for all samples were performed by the Maxell 16 automated DNA extraction system. Sample DNA integrity was determined by gel electrophoresis, 260/280 spectrophotometer and sample baseline integrity by RIN value. Sample DNAs underwent bisulfite conversion and were applied to the Infinium HumanMethylation27 BeadChip array.
Results: FFPE tissues showed variable DNA fragmentation with several samples showing significant bands above 12 kb. Mirror frozen sample DNAs were of high quality. RIN values ranged from 5.5 to 8.7 and >30% were <7 suggesting sub-optimal collection and cautionary for potential transcriptome analyses. FFPE/frozen tumor pairs showed high concordance on the Infinium methylation array.
Conclusions: High density assays to determine DNA methylation patterns using FFPE samples are highly concordant to fresh frozen counterparts and supports the use of archival specimens for use in high density methylation arrays.
IRCCS San Raffaele Pisana, Rome, Italy
Background: Standard operating procedure (SOP) optimization for DNA extraction from stored samples is of crucial importance in a biological repository, considering the large number of collected samples and because their future application may not be known.
Methods: Whole blood was collected into different Vacutainer tubes (EDTA, Lithium-heparin, NaCit, CTAD and Fluorure-Oxalate) and stored at different times and temperatures to optimize SOP of the BioBIM. DNA extraction was performed using an automated method, a commercial (Qiagen) and an in-house kit. After quantification, DNA quality was tested evaluating different PCR length products and qRT-PCR.
Results: No significant differences were observed among DNA recovery in samples collected into different anticoagulants with respect to the three selected extraction methods. Conversely, DNA recovery tended to decrease over blood storage time at RT and 4°C, whereas blood storage at −80°C preserved DNA integrity for all anticoagulants used with results comparable to those of a freshly drawn sample. PCR amplifications testing were all satisfactory regardless of the fragment length, samples time storage and anticoagulant used, with the exception of reactions carried out in the presence of Lithium-Heparin. DNA quality was investigated performing qRT-PCR, which showed a progressive decrease over time with a slight improvement after 24 h sample storage. Strikingly, using qRT-PCR on Lithium-Heparin samples were amplifiable even though with a lower efficiency.
Conclusions: DNA extraction from stored blood samples requires that all efforts should be made to prevent degradation, preserve molecular integrity and to avoid the presence of any possible inhibitor. Partially supported by Grant ACC-WP 3/1b.
Biomatrica, San Diego, CA, USA
Background: Current methods for storing and shipping human and animal blood, tissue or cells for clinical, forensic and biomedical research needs are costly and can be insufficient for reliable molecular diagnostics requiring preservation of high-quality genomic DNA. Mammalian tissues are commonly shipped on dry-ice or in liquid nitrogen which are costly and often not practical for the collection of samples in the field.
Method: We have applied synthetic chemistry to create a formulation that stabilizes genomic DNA in mammalian blood, tissue and cultured cells at room temperature. The recovered DNA stored at room temperature in this medium (called DNAgard™) was then subjected to different downstream applications such as PCR, qPCR and sequencing analysis.
Results: We will present data demonstrating that DNAgard™ preserves the integrity of genomic DNA in tissue and cells stored for over 60 days at room temperature, and provides DNA yields comparable to frozen controls. Genomic DNA integrity is also preserved in samples stabilized with DNAgard™ during extended exposure to extreme heat (45–50°C), with DNA remaining intact for 1 month in tissue samples and for two months in cultured cell samples. Tests exploring the capacity of this product as a shipping application demonstrate that DNAgard™ preserves the integrity of genomic DNA in human and animal blood, tissue and cell samples when exposed to extreme fluctuations in temperature.
Conclusion: In conclusion, the recovered DNA stored at room temperature in DNAgard™ is perfectly suitable for numerous downstream applications including qPCR, as well as techniques requiring intact DNA, such as sequencing and long-fragment PCR.
DNASU Plasmid Repository, Tempe, AZ, USA
The Protein Structure Initiative Material Repository (PSI-MR; http://psimr.asu.edu) provides centralized storage and distribution of information and samples for the 80,000 protein expression plasmids created by PSI researchers. These plasmids are an invaluable resource that allows the research community to dissect the biological function of proteins whose structures have been identified by the PSI. Researchers can search for and request plasmids from the PSI collection through the repository's distribution website, DNASU (http://dnasu.asu.edu). Each PSI plasmid is linked to the PSI Structural Genomic Knowledgebase (PSI-SGKB; http://kb.psi-structuralgenomics.org/) and numerous other biological databases, which facilitates cross-referencing of a particular plasmid to protein annotations and experimental data. Thus far over 25,000 PSI plasmids are in the process of full-length sequence validation and annotation at the MR, and nearly 17,000 are already available from DNASU. In addition to distributing materials, the MR has sought to simplify the material transfer agreement (MTA) process in order to decrease the time it takes for institutions to deposit or receive plasmids. To achieve this goal, the MR pioneered two documents, the depositor's agreement, which sets forth the terms enabling the MR to distribute deposited plasmids from outside institutions, and the expedited process MTA, which eliminates the need for researchers to wait for their institutions to sign an MTA. In the future, the MR will continue to make PSI plasmids and data available to researchers and will expand its expedited MTA network so that researchers can receive PSI plasmids without delay.
BioinfoExperts Consultants, Thibodaux, LA, USA
Background: The NCI-funded AIDS and Cancer Specimen Resource (ACSR) has stored HIV-infected human biospecimens from HIV-related or associated diseases from 1992–2010. These preserved tissues are an underutilized resource, particularly for the computational biologist who requires laboratory space, skills, and experienced personnel to generate genetic data from unprocessed tissues. The objective of our study was to use ACSR specimens to quickly develop a wide-ranging bioinformatic study focused on disease evolution.
Methods: Seven multisite tissue autopsies from the ACSR were identified that correlated to HIV-associated disease pathologies, including lymphoma, dementia, cardiovascular disease and mycobacterium avium complex. All 55 tissues sampled were of sufficient quality for DNA extraction. Because the experimental protocols used to generate HIV sequence data were straightforward and well-defined, these were outsourced to commercial facilities.
Results: High-quality DNA was extracted from all tissues; however, due to the varied nature of HIV infection in specific tissue types, HIV copy number varied. We generated 1731 3.3 kb HIV sequences and demonstrated the intact nature of the stored specimens. The data was subsequently analyzed by experts in the field of bioinformatics without the need for in-house DNA isolation, PCR, cloning or sequencing. Genetic data were used to study HIV genetic evolution, HIV micro RNAs, and in three-dimensional structural modeling of HIV proteins. In all three studies, specific findings were linked to HIV disease pathology.
Conclusions: At a minimal cost, the data enabled a series of independent bioinformatic studies, formed the foundation for multiple future projects, and provided public data for other researchers.
IRCCS San Raffaele Pisana, Rome, Italy
Background: Pre-analytical procedures may have a profound influence on Low Molecular Weight (LMW) proteome profiling.
Methods: Blood samples were obtained from six consenting donors and collected in eight 4-mL Vacutainer CAT tubes. Four samples (from each donor) were immediately treated with protease inhibitor (PI). Blood was allowed to clot for different times at RT, thereafter, serum samples were divided into six aliquots (three of which added with PI 80 μL) and immediately stored at RT, +4°C (1, 2, 3, 6, 12, and 24 h) or −80°C (up to 1 year) for subsequent analysis. Serum samples were fractionated using manual and automated functionalized magnetic beads (RP C18) for the capture of LMW proteins and analyzed by MALDI/MS system. Resulted mass spectra profiles were processed and CV values for each corresponding peak were calculated.
Results: Automation allowed an increased LMW peak recovery of 16.2%, as well as a better reproducibility compared to manual procedure; clotting times up to 2 hours resulted in minimal changes in serum LMW profiling; serum samples (with or without PI), obtained from PI-free whole blood, were stable up to 1-hour storage at 4°C, but PI addition was required for RT storage; addition of PI on whole blood and/or serum samples had relatively minimal effects on serum proteome profiles up to 1-year storage at −80°C.
Conclusions: Our study outlines the influence of pre-analytical factors on serum LMW proteome profiling, thus contributing to standardize methods for serum pre-analytical procedures and collection for future proteomics studies. Partially supported by Grant ACC-WP 3/1b.
Erasmus MC, Rotterdam, South-Holland, Netherlands
Background: The EC FP7 project SPIDIA aims to standardize the pre-analytical phase of diagnostic procedures, according to the principles of evidence based biobanking. To contribute in providing guidelines and protocols for optimal collecting, handling and storage of tissue samples one of the dogmas in biobanking is investigated. With this initial study we investigated if RNA quality decreases faster in small biopsies than in larger samples.
Methods: Small (<10 mm3), medium (±100mm3) and large tissue fragments (±500 mm3) of pig liver were frozen with 0, 5 and 15 minutes time-lag after harvesting. Samples were snap-frozen using cooled isopentane in liquid nitrogen. Sections were cut for RNA isolation using the Tel-test RNA Bee kit. RIN values were obtained using Agilent Bioanalyzer 2100 RNA nano chips.
Results: Large samples were frozen immediately after preparation showed an average RIN value of 7.4 (5.2-8.6, n = 6), medium samples 7.2 (6.6-7.5, n = 3) and small samples 6.8 (5.5-8.2, n = 5). Large samples frozen after 5 minutes of ischemia showed an average RIN value of 5.4 (3.4-8, n = 6), medium samples 6.1 (4.3-7.5, n = 5) and small samples 5.1 (3.3-6.2, n = 4). Large samples frozen after 15 minutes of ischemia showed an average RIN value of 6.8 (6-7.5, n = 2), medium samples 6.8 (6-7.8, n = 4) and small samples 6.2 (5.8-6.9, n = 3).
Conclusions: Data from this initial study indicate no correlation between sample size, ischemia and decrease in RIN value. For allowing final conclusions, larger studies will be performed and other RNA quality parameters (PCR performance, other tissue types, profiles, procedures) will be investigated.
PPD, Wayne, PA, USA
Background: Peripheral Blood Mononuclear Cells (PBMC) used in clinical assays are temperature-sensitive, and their integrity during inventory and retrieval is critical for quality results in functional assays. The current PBMC inventory and retrieval procedures were compared to modified procedures using the MVE Cryo Cart, through evaluation of temperature stability, processing time, ergonomics and cost savings.
Methods: Aluminum, stainless steel, and plastic freezer boxes were filled with vials of serum, which represented the PBMC sample matrix. Freezer boxes were placed in a LN2 unit and temperature profiles were continuously monitored with various sample retrieval and handling conditions.
Results: Samples evaluated in any freezer box type with the current vial retrieval practice, demonstrated >121°C temperature (warming) profiles during the 15 minute retrieval time. Samples evaluated with the modified procedure using the MVE Cryo Cart demonstrated a temperature (warming) profile of 9°C, 11°C and 15°C in aluminum, stainless steel and plastic boxes respectively. Additionally, the MVE Cryo Cart maintained acceptable sample temperature ranges with the various freezer boxes for up to 11 hours.
Conclusions: Sample temperature stability during the retrieval process was improved with the MVE Cryo Cart compared to current retrieval methods and the aluminum storage box was evaluated as most suitable for maintaining temperature, improving ergonomics and cost savings. Modifying the current PBMC retrieval methods to include using aluminum storage boxes and the MVE Cryo Cart will ensure sample integrity for downstream testing.
PPD, Wayne, PA, USA
Background: The need for establishing a more consistent, effective method for collecting functional Peripheral Blood Mononuclear Cells (PBMC) for the analysis of T cell responses has been recognized within the vaccine research community. A PBMC Network service was created with Esoterix Inc, a LabCorp Company to coordinate activities across select clinical programs for the acquisition of viable, high quality PBMCs.
Methods: The PBMC Network evaluated the practice of collecting PBMC such that isolation, processing and freezing are completed within 6–12 hours. All processing laboratories used a consensus SOP, which defined these major steps:
Isolating PBMC using Accuspin™ tubes, wash, lyse RBC Counting total cell number and determining number of vials to freeze Freezing at 1 × 107 cells per vial (maximum 20 vials) at −70°C in StrataCooler™ Storing >24 hours at −70°C, and shipping weekly overnight on dry ice Ensuring optimal temperature during handling, storage and shipping.
Individual processing laboratory technicians participated in a two day workshop which included classroom lectures, lab demonstrations and finally hands-on preparation. Labs were qualified based on assessment of PBMC samples for cell quality parameters as well as functionality in the IFN-gamma ELISPOT assay.
Results and Conclusions: Laboratories located in the vicinity of various clinical sites have been successfully trained and qualified to process PBMCs within 6-12 hours of blood collection using a consensus SOP. Further evidence with clinical samples supports the superiority of using a consensus SOP and PBMC Network compared to non-Network processing.
Cryogenics and Cell Preservation
SeraCare Life Sciences, Frederick, MD, USA
Background: Reliable results for PBMC isolation from whole blood are dependent on careful separation techniques performed by experienced laboratory technicians. The most employed method is density gradient centrifugation. Preparation tubes containing porous polyethylene barriers have been recently developed to facilitate efficient, reproducible results while decreasing labor and skill level requirements.
Methods: PBMCs were isolated from whole blood using three density gradient centrifugation methods: Ficoll-Paque™ underlay, Leucosep® and Lymphoprep™ tubes. Isolated PBMCs were counted by Hemacytometer using ACK lysing buffer and Trypan blue to calculate total cell yield. PBMCs were cryopreserved, thawed seven days post-cryopreservation, and counted for calculation of percent recovery.
Results: PBMCs isolated from preparation tubes were more sensitive to ACK lysing buffer compared to Ficoll-Paque™ underlay, resulting in under-representation of the total cell yield; cell counts were most accurate using Trypan blue only. The average cell yield (millions) was: Ficoll-Paque™ 11.9, Leucosep® 14.3, Lymphoprep™ 12.8, while the post-thaw recovery yield was: Ficoll-Paque™ 9.4 (79%), Leucosep®10.2 (71%), and Lymphoprep™ 9.2 (72%). Total processing time per sample (minutes) was recorded at: Ficoll-Paque™ 89, Leucosep® 70 and Lymphoprep™ 62.
Conclusion: The Leucosep® tube produced comparable to superior results requiring less processing time and technician skill-set than the traditional Ficoll-Paque™ method. The Lymphoprep™ tube yielded the lowest post-thaw cell count; percent recovery was similar for the preparation tube methods. Completion of cell proliferation analysis is in process to compare cell functionality.
Health Protection Agency, Salisbury, Wiltshire, UK
Background: The conversion of a blood sample from an individual participant in a biobank to a lymphoblastoid cell line ensures a permanent, expandable and renewable supply of genetic and other cellular material, including DNA, without any requirement to return to the donor. However, the current method, involving the separation and cryopreservation of peripheral blood lymphocytes (PBLs) can be considered expensive and time consuming and relies on relatively large volumes of blood. We describe here the development of a simple technique for the Epstein Barr virus (EBV) transformation of small volumes of cyropreserved whole blood.
Methods: Aliquots of whole blood (cryopreserved in 10% v/v Dimethyl sulphoxide ( DMSO)) were exposed to EBV, and the resulting transformed cells expanded and cryopreserved. No separation steps were carried out. Bench top flow cytometry was used to assess cell viability and transformation where conventional microscopy techniques proved difficult.
Results: A total of 48/50 cryopreseved blood samples were successfully transformed at the first attempt giving a transformation success rate of 96%. Aliquots of 1.5 ml and 800μl of blood transformed with equal success and flow cytometry proved critical to the assessment of transformation.
Conclusions: We have developed a robust, efficient and cost effective technique, suitable for high throughput generation of lymphoblastoid cell lines from small volumes of cryopreserved whole blood without the requirement to pre-isolate PBL's. This presents biobanks with the opportunity for storing small amounts of blood for the future generation of material representing important disease collections.
Biorep srl, Milano, Italy
Background: In general, cells including stem cells are frozen in medium containing high concentration of cryoprotective molecules such as Dimethyl Sulphoxide (DMSO) in addition to animal proteins. An important consideration should be taken in using non-toxic levels of DMSO on stem cells during preservation processes since several reports have underscored that in hESC the pluripotency capacity diminished in a reversible manner (Katkov LL et al., 2006; Adler S. et al., 2006) in addition to cell quiescence induction in a dose dependent and reversible manner (Sahgal. et al.2005). It has been reported that DMSO affects the epigenetic system by acting on the three DNA methyltransferases (Dnmts) and on five wide DNA methylation profile, the ES and embryonic bodies undergo changes in their phenotypic behavior (Iwatani M. et al.,2006). A non-toxic alternative protectant is Trehalose, proven to stabilize stem cells during freezing, the challenge is to find a way to introduce this big glucose disaccharide in the cells.
Materials and Methods: We used the HEK293 and NSC46 (murine neuronal derived stem cell) and different methods to internalize trehalose in the cells.
Results: It is possible to vehicle trehalose in these cells using the pore channelling capacity of ATP and appropriate extra/intracellular trehalose concentration ratio. Good cell recovery was obtained in both cell lines.
Conclusion: We show that it is possible to use trehalose as cryoprotectant reagent.
Biorep srl, Milano, Italy
Background: Stem cells have acquired a great deal of attention as they promise to be new vehicles for gene therapy. It is then important to optimize culture conditions, cryostorage protocols and monitoring systems to obtain ready-to-use cells for clinical applications. BioRep is a partner in two European Financed projects (FP6 and FP7) with the aim to establish a cell bank hosting neural derived stem cells and define the proper procedures to limit the unreproducibility of their use.
Methods: BioRep regularly performs a series of tests to assess the presence of contaminants in the cultures including the presence of viral particles. Cells are cryopreserved and banked in liquid nitrogen tanks connected to a central monitoring alarm system. Routinely, the cells are assessed for their pluripotency status and differentiation capabilities, chromosomal stability and viability.
Results: A set of standard operating procedures (SOP) have been generated relating to each step of stem cell culturing, processing and storage with the objective to guarantee the freezing of cells with highly reproducible characteristics. Using GMP freezing medium free of animal proteins (Cryostor CS10) in addition to a controlled rate cooling system, it is possible to achieve remarkable cell viability and low apoptotic level.
Conclusions: Joining the stem cell biology expertise of the academy with the technology standards of the industry has allowed the development of reagents and processes to generate safe and effective stem cell lines. In this way, several neural stem cell lines have been established and made available to the scientific community.
Istituto Zooprofilattico Sperimentale di Brescia, Brescia, Italy
Background: Optimization of cryopreservation protocols to maintain the quality of mesenchymal stem cells (MSCs) is an important task for stem cells banks. To allow long-term storage, MSCs are slowly cooled and stored at −196°C in liquid nitrogen. Unfortunately, despite the use of well standardized protocols, the percentage of living cells after thawing is low. In order to use MSCs for regenerative medicine, it is important to find a cryopreservation solution able not only to reduce cell death but also free of animal proteins, in order to reduce zoonoses risk.
Materials and Methods: Rat, sheep (models) and horses MSCs were isolated from bone marrow and adipose tissue and in vitro cultured. Each MSCs sample was frozen in three different cryoprotectant solutions (BioLife Solutions). After thawing and re-seeding, cell viability was assessed for three consecutive days and cell counts were performed at 24-h intervals.
Results: Cell viability differences were observed not only among the three different cryopreservation reagents used but also according to the species from which the MSCs were derived. Equine MSCs were much more sensitive to the freezing process than rat and sheep derived cells.
Conclusions: The possibility for long-term storage for MSCs and other types of cells in a frozen state which are suitable for immediate clinical application could provide immense benefit in regenerative medicine. Moreover, identification of more effective cryoprotectant solutions deprived of animal proteins could improve the quality of the freeze/thaw process and reduce cost/benefit ratio.
Singapore Health Services Pte Ltd, Singapore
Background: Due to shortage of storage space, we have been exploring the possibility of storing 3 fragments of tissue per cryovial. The main problem with such a move is that frozen tissue fragments tend to stick together, making it difficult to separate during tissue withdrawal and raising the fear of unwanted thawing. To prevent tissue fragments from adhering to each other, we consider wrapping each fragment in aluminium foil prior to cryopreservation. In this study, we consider the processing time during tissue acquisition and withdrawal with and without wrapping tissue fragments in aluminium foil.
Method: 60 fragments (3–5 mm3) of non-neoplastic breast tissues were divided into two study groups, 30 in each group. 3 fragments were placed into one cryovial, with and without aluminium foil wrapping. The time taken for tissue acquisition and tissue withdrawal using 1 to 10 cryovials was recorded.
Results: The average time taken at tissue acquisition to process tissues wrapped in aluminium foil is 780 secs (range: 92 to 1825 secs) compared to an average time of 402 secs (range: 38 to 903 secs) without aluminium foil wrap. The average time taken for tissue retrieval is 4 secs per fragment (range: 3 to 5 secs) with aluminium foil wrapping compared to an average time of 6 secs (range: 5 to 7 secs) without aluminium foil wrap.
Conclusion: Our preliminary data show that wrapping tissue fragments in aluminium foil prior to cryopreservation doubles the processing time with 8 or more cryovials (p < 0.001) but with only modest reduction in tissue retrieval time.
University of Bedfordshire, Luton, Bedfordshire, UK
Background: Specimen cryo-banking can ensure a record of species genome and proteome, and in the case of future extinctions this may be the only source of such information. A major determinant of value of any such cryo-bank is the quality of the material held, which in turn is determined by the protocols used in their processing. Cryopreservation protocols exploiting cryoprotectants and storage below glass transition temperature, enables long-term preservation of molecular components and viable cells from tissue explants.
Methods: A biological resource bank of freshwater (FW) and marine fish from UK waters is being established. For all species banked - three tissue treatments are performed:
(i) muscle tissue, cryopreserved using protocols to ensure long-chain DNA protection; (ii) fin clippings, cryopreserved to give viable cell retention for cell line culture; (iii) blood samples, held on Whatman FTA cards.
Results: Following a series of collection surveys in 2009, from lowland rivers in England, and the Irish and Celtic Seas, tissue samples were processed from 122 species, 19 freshwater and 103 marine. Cell line cultures have already been established for 20 species and cryobanked. Cell lines from the remaining species will be established during 2010.
Conclusions: Cryobanking of bulk tissue and viable cell lines, provides for future genomic and proteomic applications, and also ensures that withdrawals do not deplete the resources bank. Protocols for cryopreservation and cell culture have been established and will be reported.
Biosapling Systems, Saint Ouen l'Aumône, France
The revolutionary ICE® tube system integrates both a datamatrix code and an RFID tag that remains active in liquid nitrogen and −80°C freezers. Dual security tabs on the cap of the ICE® tube guarantee the integrity of the contents. The first ensures the container was not opened before being filled, and the second ensures it was not opened after being filled. With this system, we can configure lab software to store reliable sample information in the RFID tag of each tube.We have developed a unique plastic insert which facilitates the storage and retrieval of several separate, very small tissue sample biopsies in a single ICE® tube.81 ICE® cryotubes are stored in a unique, custom designed cryobox with industry standard dimensions: no need to change your −80°C freezer and nitrogen cryobank infrastructure.
Disaster Recovery
University Hospital of Verona, Verona, Italy
Background: Biobanking is the cornerstone of research and requires a Disaster Recovery (DR) plan to protect its assets, biological material and associated data. DR is made of processes, policies and procedures for recovery or continuation of infrastructures after a natural or human-induced disaster and must include planning for key personnel, facilities and data recovery. To date, no comprehensive data exist on which to base a biobank DR plan. The aim was to evaluate acceptable down-time, loss, feasibility and cost to create a DR plan specific for biobanks.
Methods: First, risk analysis was carried out, based on biobank specific parameters, to identify potential natural and man-made disasters affecting both biological material and data banks. Then, a set of experiments was designed to emulate these disasters, monitoring the resulting effects on the material and data contained in the bank.
Results: The disaster emulations provided maximum response times for the biobank analyzed. These times varied according to both container type and material type. Of note, the data also showed anomalies to generally considered maxims, e.g. material generally considered more sensitive, i.e. RNA, resisted to disaster conditions better than tissue.
Conclusion: Our study showed that specific risk analysis parameters must be identified for biobanks. Furthermore, a biobank DR plan is not a one size fits all solution, as these parameters differ according to variables such as environment, materials and objectives. Disaster simulations and tests should be carried out to evaluate their effect and design a biobank specific functioning DR plan.
Environmental Repositories
National Zoological Garden of S.A, Gauteng, South Africa
A survey was conducted in the National Zoological Garden of South Africa during the month of September 2009 to January 2010 to assess the transportation of fish in the Aquarium. The purpose was to collect baseline information between the zoo keepers and educators on how to transport or move fish in the Aquarium. Details about the movement and transportation of fish were shared for the well-being of fishes being transported, including transportation within institution premises and transfers from one institution to another. Skills, training and experience were shared among the keepers to ensure the well-being of fish such as medical requirements, container size, size of the tanks, temperature and life support system. The other changes in an animal's normal behavior could be expected as a result of being moved and transported, and every precaution was taken to ensure the safety of the animals such as recognizing the territorial behavior, ages, sex and health. The implications of these appropriate steps (such as use of tranquillizers), which is taken to reduce the stress levels of fish and water quality is discussed. The major handicap in the development of transporting or moving fish in the Aquarium is skill shortage among workers. In conclusion this paper will discuss how staff interact and share experience and knowledge within the community of zoo keepers, aquarist and zoo educators. Key words: fish, keepers, stress, transportation, skills transfer.
“Green” Repository Solutions
Société IMAGENE, EVRY Cedex, France
Background: One of the challenges regarding DNA repositories is the exponentially increasing number of samples to be preserved making classical freezer storage unreliable and prohibitively costly. An appealing solution is room temperature storage of dehydrated DNA but we recently showed that storage in air is inadequate for optimal DNA conservation at room temperature. Indeed, we showed that solid-state DNA degradation is greatly affected by atmospheric water and oxygen and that these conditions generally lead to DNA loss by aggregation after a few weeks storage. We also confirmed that there is no airtight plastic ware. However, we found that, protected from water and oxygen, DNA primary structure is extremely stable and that the secondary structure is preserved or fully restored upon rehydration, except possibly for small fragments.
Methods: DNA chain breaks were quantitated by plasmid relaxation or denaturing electrophoresis. DNA denaturation was estimated by hyper-chromicity measurements.
Results: From the above observations, we developed a high throughput fully automated process where DNA samples are desiccated in glass inserts which are then enclosed into small laser-sealed capsules under anoxic and anhydrous atmosphere. Traceability is insured by engraving a 2D data matrix code on the capsules. This process has been applied to DNA samples prepared by different techniques from various organisms. Accelerated aging studies established the high stability of these samples.
Conclusion: We developed an original procedure which, by ensuring a full and permanent protection of DNA from water and oxygen, allows safe and autonomous room temperature storage with no maintenance and energetic cost.
Baylor College of Medicine, Houston, TX, USA
Background: Biorepositories, especially of pediatric subjects, must look to the future when developing collection and storage protocols. Establishing a sustainable biobank, maintaining high rates of donation, and ensuring that sufficient material is collected for future analyses are essential to creating a successful, robust repository.
Methods: Samples were collected using Oragene® DNA or Scope mouthwash protocols. Two types of dry-state, room temperature storage technologies were then evaluated. Aliquots of saliva or buccal cells were applied to GenPlates, which consist of FTA paper arranged in a 384-well format, and stored for 2 weeks prior to DNA extraction. Purified DNA or whole-genome-amplified DNA was applied to GenTegra DNA tubes, which contain an inert chemical matrix that stabilizes DNA. Collection and storage protocols were evaluated by examining recovery yield, DNA quality, and performance in allelic discrimination PCR.
Results: High quality DNA was recovered using Scope mouthwash and Oragene® DNA protocols, with increased yields obtained with Oragene®. Storage of saliva or buccal cells in GenPlates; or purified or whole-genome-amplified DNA in GenTegra tubes did not alter DNA quality. Samples stored at room temperature using GenPlates or GenTegra exhibited equivalent performance to samples prepared immediately and stored at 4°C until allelic discrimination by PCR was performed.
Conclusions: Non-invasive collection methods, such as mouthwash and Oragene®, are good sources of quality DNA. Whole genome amplification can be used to maximize DNA yield from these samples. Room temperature storage technology is a sustainable alternative to freezers and does not alter DNA quality or performance in downstream analysis.
QIAGEN GmbH, Hilden, Germany
Background: Conventional storage and shipment of biospecimens poses space, cost and energy problems. Biomatrica, Inc. has developed sample matrix technology to store, ship and archive samples at room temperature based on the natural principles of anhydrobiosis (“life without water”). QIAsafe DNA Blood, a product co-developed by QIAGEN and Biomatrica, allows the dry storage and shipment of whole blood at room temperature preserving DNA.
Methods: Blood was stored for up to 9 months at room temperature or 45°C (equivalent to approx. 3 years of room temperature storage) in QIAsafe DNA Blood alongside frozen and unprotected controls. After storage DNA from blood was purified according to manufacturer's instructions followed by downstream applications to demonstrate integrity, yield and performance (e.g. agarose gels, PCR, and sequencing).
Results: DNA yields and integrity from blood-stored with this technology are comparable to frozen controls (−20°C or −80°C) and superior to those samples collected on dry filter paper. Isolated DNA can be used in many downstream applications including PCR, qPCR, genotyping, and DNA sequencing, giving equivalent results to DNA which has been isolated from frozen blood.
Conclusions: QIAsafe DNA Blood allows ambient temperature transport and storage of blood samples for subsequent DNA purification. DNA is of high quality and yield which will enable biobankers to perform downstream applications from archived samples. This technology does not require cold storage and thereby eliminates the risk of freezer breakdown, and at the same time reduces energy costs and carbon emissions.
Biomatrica, San Diego, CA, USA
Background: Biological sample preservation and integrity is of concern to every biological scientist. Samples and reagent quality determines the quality of our research results. New technologies have evolved to study systems biology and high through-put discovery, while our ability to manage bio-specimens has not evolved as much over the past hundred years. Scientists are required to protect their biological samples and reagents from degradation in a cold chain that can be unreliable. The costs for maintaining these cold chains are growing as well as their deleterious impact on the environment due to the large amounts of CO2 emissions from the fluorohydrocarbons in the refrigerants in these cold freezers. The future of biobanking and bio-repositories of biological specimens will require the adoption of novel technologies that addresses all of these known deficiencies.
Method: We will present technologies and methods that are derived from extremophile biology, organisms that can survive stasis for >100 years, while applying these molecular stabilization principles towards transporting and storing a wide range of biological samples, from purified gDNA and RNA, to more complex mixtures in blood, tissue and cell lines at ambient room temperature.
Results: Long-term stability data for DNA of 30 years and RNA of 12 years (accelerated stability) will be presented as well as the progress into complex samples and protein stabilization at room temperature.
Conclusion: Room temperature technology has a tremendous impact on the future of biobanking in relation to sample quality and economics of scale for sustainable sample management.
Human Specimen Repositories
University of California Davis, Sacramento, CA, USA
Background: The Cancer Center Biorepository (CCB) at UCD was created in 2004 for the procurement and storage of fresh, frozen specimens. Responding to researcher interest in fresh (unfrozen, unfixed) specimens, to allow cell culture and gene expression studies, we have developed a protocol to disperse specimens between 20 min - 3 hours after resection. Additionally, we developed a protocol to obtain research blood samples via the clinical laboratory, thereby eliminating the need for a dedicated phlebotomist.
Method: We employ three means to facilitate collection and dispersal of fresh specimens:
List surgeons and other clinicians on CCB protocol to allow patient pre-op consent and order subsequent blood draws. Add previously approved CCB paragraph for research tissue collection to clinician's protocol-specific consent form. Researcher obtains exempt IRB protocol that allows acquisition of coded specimens via the CCB.
After consent is obtained, CCB orchestrates notification of interested researchers, preparation of coded vials and patient information, and notification of grossing room and pathologist. On arrival from surgery, the pathologist determines the suitability of tissue for research, these are stored in RPMI media, and researcher contacted for pickup.
Results: To date, we have dispersed >170 fresh specimens (breast, brain, kidney, bladder, lung, prostate, colon and pancreas) and increased our serum/plasma collection from 33 specimens in 2008 to >900 specimens in 2009.
Conclusions: We have developed effective means to obtain fresh tissues for rapid dispersal to researchers. We continue to refine methods to increase volume, improve efficiency and logistics.
Hospital A C Camargo, Sao Paulo, Brazil
Background: The A C Camargo Hospital Tumor Bank (ACCHTB) was established in 1997 to provide human tissue samples for the Human Cancer Genome Project, an initiative by the Sao Paulo Research Foundation and the Ludwig Institute for Cancer Research. It culminated with the identification of a million gene sequences of the most frequent tumors in Brazil. Since then, it has accelerated the improvement of cancer research done at A C Camargo Hospital (ACCH). In 2009, it provided biological samples for twenty-seven research projects and contributed to 15% of the theses and dissertations of our Postgraduate Program.
Methods: We analyzed, from 1997 to 2009, the number of publications by ACCH's authors and collaborators, the average impact factor of publications for each year, the sort of publication (regional versus international journals), and the contribution of the ACCHTB for each factor.
Results: Along with a significant increase in the number of publications (from 107 in 1997 to 200 in 2009), there has been an increase in the average impact factor of publications (from 2.08 to 4.187) and a shift from predominantly regional to predominantly international publications (90% of publications in international journals in 2009).
Conclusion: The possibility of using high-quality biological human samples, provided by ACCHTB, has made possible for scientists and collaborators to have access to state-of-the-art equipment for genomic analyses, which had an impact in the quality of cancer research done at our Institution. The development of such initiatives by other institutions can improve cancer research in Brazil.
Indiana University School of Medicine, Indianapolis, IN, USA
Background: Our efforts to prevent and treat breast cancer are significantly impeded by a lack of knowledge of the biology and developmental genetics of the normal mammary gland. This ignorance has been the consequence of the lack of access to richly annotated, high quality normal breast specimens. To provide the specimens that will enable the study of normal mammary development and to provide normal controls for breast cancer research, the Susan G. Komen for the Cure® Tissue Bank at the IU Simon Cancer Center (KTB) was established. The KTB is a repository of specimens from volunteer donors with no clinical evidence of breast malignancy.
Methods: Donors are recruited from the general population of the State of Indiana. The KTB banks fresh frozen and formalin-fixed, paraffin-embedded (FFPE) breast tissue, DNA, whole blood, serum, plasma and cell lines derived from the tissue. These specimens are richly annotated with detailed information regarding the donors' reproductive history, medical history, family history, and medications. All of this information is recorded in an Oracle-based, searchable database. Specimen data is linked to image data, e.g. mammograms and H & E sections, and to molecular data.
Results: As of 1/1/2010, the KTB and its predecessor, Mary Ellen's Bank, have available fresh frozen breast tissue (10 gauge cores) from 807 individual donors and FFPE from 408, DNA from 6752, serum from 1642 and plasma from 3079 donors.
Conclusions: The KTB is a unique and invaluable research resource which is now open for business and accessible to researchers across the globe.
Affiliated to the Tel-Aviv University, Sackler School of Medicine, Tel Hashomer, Ramat Gan, Israel
Background: Sheba Medical Center (SMC) is the largest medical center in the Middle East. Our patients present with significant demographic diversity including ethnicity, socio-economic condition and religion, which provides an opportunity for the collection of a wide variety of biosamples.Vision: Our goal is to establish an Institutional Tissue Bank (ITB) in order to provide researchers with high-quality and well-annotated biospecimens. The ITB will enable SMC to be at the front of the translational-research field, building a foundation for the 'Translational-Research & Personalized Medicine Program'.
Methods: Collection and preservation of human tissues from patients with cancer and other diseases. Following Institutional Review Board (IRB) approval and signing an Informed Consent Form (ICF), the specimens are collected by a designated pathologist, at the operating room. Tumor and tumor-free specimens are collected, only when there is sufficient amount of tumor, in excess of the routine needs. Blood samples are collected prior to surgery/procedure. Specimens are processed immediately (10–30 minutes for tissues and up to a few hours for blood) and preserved in small aliquots. Clinical/pathological/follow-up data is collected in a designated database. All ITB activities are according to well established & validated procedures.
Results: Since activation on January 2009, we have obtained biosamples, from over 450 patients (colon/rectum n = 40, pancreas n = 25, brain n = 155, liver n = 30, stomach n = 20, thoracic n = 20, kidney n = 65, bladder n = 15, Gynecology n = 20, orthopedics n = 10, children n = 50, Head & Neck n = 20). These building-block samples are soon to be used in research for the development of ‘targeted therapy’, facilitating pharmacogenetic studies.
ECOGENE-21 Clinical Trial Center, Chicouitmi, Quebec, Canada
Background: Managing investigational products (drugs or biodrugs) in conformity with Good Clinical Practice (GCP) requirements is a challenge that the sites participating in clinical trials with the pharmaceutical industry are not necessarily prepared to assume.
Methods: The Ecogene-21 clinical research center along with the Genome-Quebec/Chicoutimi Hospital Biobank are developing a GCP toolbox for the management of investigational products and biological samples. The toolbox is adapted to the scale and the needs of the clinical sites participating in clinical trials and includes:
(1) the technologies and standard operating procedures from reception of the investigational product to distribution and use by the participant, storage conditions (temperature, humidity, security, access), drug accounting, return or destruction procedures if required; (2) samples management (from sample collection to shipping or use); (3) training of qualified personnel and coordination by a pharmacist; (4) development of technologies and automated storage systems.
Results: In the last year, the toolbox has been tested in 12 clinical trials (phase I to III). A transdisciplinary, GCP-trained, team with experience in biobanking, technology development/assessment and clinical trials accompanies the process. All deviations to storage conditions, procedures or study protocols were noticed and rapidly solved, thus facilitating the monitoring of the studies and improving the site capacity to follow the audit trail.
Conclusions: Clinical sites conducting clinical trials require reliable GCP systems to manage investigational products and biological samples. We have developed, evaluated and implemented an adapted biobanking approach and new technologies to cover these needs.
Mayo Clinic, Rochester, MN, USA
The Mayo Clinic Biobank serves as a source of non-disease controls for numerous research projects having the goal of improving disease outcomes. Participants in the biobank complete a health questionnaire, allow access to medical records, and provide blood samples from which DNA, serum, and plasma are prepared and archived. Within the Biospecimens Accessioning and Processing (BAP) Laboratory, blood samples are accessioned into Mayo's Research Laboratory Information System (RLIMS), a custom LIMS built on the Sapphire platform (LabVantage). RLIMS will track the progress of the sample thru the laboratory and drive the process of preparing derivative material per a specific IRB protocol. RLIMS is interfaced with the Electronic Medical Record in a prospective and HIPPA compliant manner to couple the biospecimen with the participant's medical record, maximizing the sample's utility for biomedical research. BAP utilizes a combination of effective staffing levels at peak times and automation to provide high quality processing and sample storage services to the Biobank and other research customers. With its current automation and information technology, the BAP laboratory accessioned 43,000 samples in 2009, extracted DNA via the AutoGenFlex STAR platform from almost 33,000 samples, and plated over 45,000 samples in 96 well-plate format for downstream analyses. BAP monitors its efficiency using process workflow modeling to identify workflow bottlenecks with current and projected volumes. This modeling process also enables modeling of future states of the laboratory, including introduction of additional automated equipment to assess the need for increased automated equipment, staffing, and/or space to meet anticipated demand.
QIAGEN GmbH, Hilden, NRW, Germany
Background: The RNA content and profile of unstabilized blood specimens are altered post-phlebotomy due to RNA degradation and gene induction. The need for stabilization of cellular RNA for accurate gene expression profiling in blood is widely accepted, and the PAXgene® Blood RNA System is commonly used to address this problem. This system was designed to isolate high molecular weight RNA species, such as mRNA. We have now developed a chemistry that maximizes yields of small RNAs like miRNAs from PAXgene Blood RNA Tubes as well.
Methods: Blood was collected into PAXgene Blood RNA Tubes from consented healthy adults, and miRNA was isolated using the PAXgene Blood miRNA Kit. Yield and quality of small RNA species were determined using an Agilent 2100 Bioanalyzer and gel electrophoresis. Purified RNA was analyzed for genomic DNA contamination and PCR-inhibition. miRNAs were quantified by qRT-PCR as well as in a low-density array format.
Results: Using miRNA protocols enrichment of small RNAs in total RNA was demonstrated by electrophoretic analysis. Higher miRNA contents could be confirmed with qRT-PCR assays detecting miR-10a, 16, 30b, 192 and let7a. Little gDNA (<1%) was present in eluates which showed no RT-PCR inhibition. There was no interference with assays for the mRNA transcripts FOS and IL1B.
Conclusions: The PAXgene Blood miRNA Kit produced high quality enrichment of these RNA species from the PAXgene Blood RNA Tube. miRNAs isolated by this method are ready for direct use. The PAXgene Blood miRNA Kit is intended for research use only. Not for use in diagnostic procedures.
Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
Background: Scientists at TGen perform genomics and proteomics research to understand the molecular mechanisms of a variety of human diseases. As TGen is a research institute that does not directly treat patients, partnering with clinical sites is essential for obtaining high quality biospecimens and clinical data. A model has been implemented to streamline the development of collaborations with local healthcare entities, which serve as TGen collection sites. A cornerstone of this model is the presence of jointly-hired clinical research coordinators (CRCs) at several collection sites.
Methods: As the logistics of working with multiple healthcare systems can be challenging, more efficient processes have been developed for ethics review and contracting. Hiring, training and monitoring the work of the joint CRCs is coordinated between staff at TGen and the clinical site. To facilitate clinical and biospecimen data collection, a custom, online biospecimen management system (BIOMAP) has been implemented.
Results: Two joint TGen CRCs perform collections at one large medical center and two more will be hired in Spring 2010. Active biospecimen collection studies are ongoing at six additional healthcare sites. To date, 3,013 samples have been collected from all clinical sites, with 1,367 samples collected at the site with joint CRCs. The new BIOMAP system has been instituted, which facilitates specimen tracking and QC reporting across all collection sites.
Conclusions: The combination of streamlining administrative processes, joint CRCs at collection sites, and the use of an online biospecimen management system has significantly improved the collection and tracking of biospecimens at TGen.
University of Sydney at Westmead Millennium Institute, Westmead, NSW, Australia
Background: The Breast Cancer Tissue Bank (BCTB, www.abctb.org.au) is a repository of biospecimens and information, designed to support breast cancer research. Material is collected and stored at multiple sites and the project is co-ordinated by a central management team. Diagnostic pathology reports are an important source of data for the BCTB. In addition, a standardized pathology dataset is being collected through a process of centralized pathology review. A third level of pathology data is derived from content review of individual tissue samples provided to researchers.
Methods: Strategies employed to collect pathology data include:
Collection of diagnostic pathology reports from many different pathology services/companies, with extraction of data into BCTB designed database fields. Establishment of a digital image library including a high resolution image of a representative H&E stained section from each BCTB case. Review of these images is performed by a single experienced breast Pathologist to establish a standardized central pathology review dataset which again is captured in the database. Pathologist review of individual frozen and formalin-fixed paraffin embedded tissue blocks for tissue content prior to dispatch to researchers.
Results and Conclusion: Pathology data forms a substantial component of clinical and specimen inventory information collected by the BCTB. In addition, centralized pathology review is providing an image library and standardized dataset that enhance the research resource. A combination of data extraction and dedicated pathology review processes is used by the BCTB to optimize research use of breast cancer tissue samples.
Affiliated to the Tel-Aviv University, Sackler School of Medicine, Tel Hashomer, Ramat Gan, Israel
Background: Our newly established ITB at Sheba Medical Center (SMC) was launched in January 2009, to provide researchers with high-quality and well-annotated biospecimens, essential for accelerating biomedical research and medical-product-development. Since its initiation, we encountered and overcame major challenges:
Institutional Review Board (IRB) approval- Israeli genetic regulations require the submission of separate applications to each field. Accordingly, our ITB is divided into sub-banks controlled by one central-administration. Surgeons' collaboration- In order to improve the willingness of surgeons to collaborate with the ITB, each sub-bank is represented by the head of the relevant department, as a Principal Investigator. Patient recruitment- Since SMC is a general hospital and most patients are not oncological, the sorting of relevant patients is complex. We mainly depend on departmental-secretaries. Signing Informed Consent Form (ICF)- Only M.D.s are allowed to conduct genetic studies and to have patients sign an ICF. Therefore ICFs are signed at the pre-operation-clinic, few days prior to surgery. Proper infrastructure & designated manpower - Our preservation tanks can accommodate ∼30,000 biosamples. A sterile biological-hood is located in the operating-room for various uses. Current staff includes: a pathologist, a technician, a database-manager and a scientific-director. Intelligent database- We are currently building a database integrating clinical/demographic/other data from many sources. In addition, Israel is building a national-program for tissue banking of biosamples from all cancer patients. A National-Tissue-Bank would facilitate pharmacogenetic studies and the development of ‘targeted therapy’.
Conclusions: The establishment of an ITB requires a concentrated effort of a multi-disciplinary team composed of para-medical, medical & scientific professionals.
AstraZeneca, Macclesfield, Cheshire, UK
Background: As part of its global biobanking infrastructure, the AstraZeneca (AZ) R&D site at Alderley Park (AP) expanded its already established human cancer bank to include samples from all R&D areas on site. The new site biobank was fully commissioned in November 2009 and stores human biological samples (HBS) collected principally from AZ clinical trials, but also samples from AZ sponsored research collaborations and commercial suppliers.
Methods: The facility was designed to provide safe, secure storage primarily for frozen samples together with sample reception and preparation laboratory space and a small office. Risk assessment and analysis included the following factors dictated by legislation, regulation and AZ policies and procedures:
Health and safety - laboratory design and user requirements—ultra low temperature (−80°C) samples storage and sample preparation Legal Compliance - Good Clinical Practice and UK Human Tissue Act (2004)—licensing and ethical approvals Governance - Quality systems for laboratory and sample management—HBS life cycle management.
Results: Budget approval to full commissioning was completed in one year within which time we were able to transfer existing on site samples for long term storage and receive samples stored externally from two clinical studies. Transfers of additional clinical samples are underway and at the time of writing 5 out of 14 freezers are full. The laboratories are fully functional.
Conclusion: Risk identification and management underpins regulated storage of human tissue in a centralized site biobank established to increase the utility of samples collected in AZ clinical trials.
Fudan University Cancer Center, Shanghai, China
Background: The Institutional Tissue Bank (ITB) of Fudan University Shanghai Cancer Center was established in 2006 as central repository of human tissue samples for cancer research. Variant samples including blood, tumor tissue, and body fluids are collected. It is important to keep undeniable high quality samples and reliable tracking.
Methods: Altogether 17,000 samples have been banked in the ITB by the end of 2009. From the whole bank, 41 samples including tumor and normal tissue were randomly chosen for RNA quality control. Total RNA was extracted from RNALater reserved tissue using Trizol or Qiagen RNA extraction kit. Thirty-four RNALater reserved tissue samples were extracted using Trizol and the other 7 using Qiagen Kit. RNA qualification and quantification was performed using GE Nano Vue (classic) and Agilent 2100 Bioanalyzer (Chip).
Results: Twenty-one out of 34 samples showed satisfactory RNA quality and quantity in the cases using Trizol. Seven out of seven samples showed satisfactory RNA quality and quantity in the cases using Qiagen kit. All 41 RNA samples were checked using Chips and 12 with dual methods.
Conclusion: RNA was well preserved in our bank. There was good consistency between two readings using dual Chip and classic systems. However, it is of important to observe the peaks for 18s and 28s obtained from Chips. It might be possible that some factors would influence the report of Chip by cutting off some qualified samples eligible for further study.
Mental Health Research Institute, Parkville, Victoria, Australia
Background: The Australian Brain Bank Network (ABBN) www.nnf.com.au/abbn was formed in 2003. Building on previous grants, an Australian National Health and Medical Research Council (NHRMC) Enabling grant scheme (2004–2009) transformed a group of Australian brain banks into a truly national and comprehensive network supporting neuroscience research. Our aim has been to achieve long-term financial sustainability.
Method: A review of the income as total grant money and the costs for collection, processing, characterization, storage and distribution of tissue, was performed, on the basis of 192 brains per annum.
Results: The ABBN (2004–2009) has been successful in receiving a number of: 14 Australian, 6 NHRMC and 3 international grants of which all or part of the funding has been directed towards infrastructure and operational costs. The introduction in 2006 of a cost recovery policy for services associated with tissue requests resulted in AU$16,951 per annum. The total income was AU$1,017,000 per annum. Real costs for collection, processing, characterization, storage and distribution of tissue was AU$20,000 per brain. The difference between income and costs was AU$2,823,000 per annum shortfall.
Conclusion: Despite some financial success this represents a fraction of the total cost needed to maintain the infrastructure of the ABBN. A recent submission to the NHMRC resulted in securing partial funding until 2014. We face an ongoing challenge along with increasing costs to achieve long-term financial sustainability.
Oral Cancer Research & Coordinating Centre (OCRCC), Kuala Lumpur, Federal Territory, Malaysia
Background: An oral cancer biobank was developed where collections of tumor and normal tissues were done and DNA, RNA were extracted for molecular studies. This report is to highlight the benefit and usage of a high quality biobank.
Method: Tissues obtained from tumors and normal sites were processed for extraction of DNA and RNA. Only samples with high tumor cell content (>75%) and high-quality mRNA (RIN > 7) were selected and subjected to transcriptome sequencing.
Result: Since 2004, we have collected specimens from 390 cases and 55 controls. To date, we processed 137 cancer and 33 normal samples. Of the 170 samples, 108 were processed for RNA extraction while 62 were not processed as they were either connective tissue, adipose/muscle, salivary gland, no tumor or <10% tumour cells. RNA was found to be of good quality with an average RIN > 7. DNA was only extracted from 89 tissues as there were insufficient tissues after RNA extraction. RNA from 15 samples were used for Next Generation Sequencing transcriptome profiling. This high throughput sequencing showed that 48 genes were differentially expressed between cancer and non-cancer samples, where 17 were found to be down regulated while 31 were highly expressed. Meanwhile 36 SNPs were observed to be common in all tumor but not in normal samples where 13 were found to be novel.
Conclusion: Good practice of specimen collection and processing leads to high quality nucleic acid content which enable us to carry out high throughput research which translates into novel knowledge in oral cancer research.
The Univerity of Sydney, Sydney, New South Wales, Australia
Background: The Australian Brain Bank Network (ABBN) www.nnf.com.au/abbn was formed in 2003 to coordinate the collection of post-mortem human brains and related information across Australia. The Network now consists of eight banks located in five Australian states with a centralized management structure. The ABBN facilitates research into neurological and psychiatric disorders, and normal aging. The ABBN aims to standardize across sites the tissue collection, processing, storage and distribution protocols.
Methods: A national survey was conducted to examine four major components of brain banking: Donor recruitment; brain retrieval; diagnostic procedures and tissue storage to ensure that tissues are of the highest quality and can be used in current and prospective studies.
Results: The survey resulted in 33 recommendations, 17 criteria warranting immediate review and 16 for future review. All were minor adjustments to existing protocols to standardize and maximize tissue quality across brain banks. A set of recommended guidelines for enhancing brain banking were developed in line with State and National ethics and legislation and which were compliant with international standards of brain banking.
Conclusion: With declining autopsy rates, it is imperative that the ABBN ensures that the stored consented brain tissue available for research is of highest quality. Implementation of National guidelines for banking of brain tissue, across the Network, is imperative in achieving this aim.
Oral Cancer Research & Coordinating Centre (OCRCC), UM, Kuala Lumpur, Federal Territory, Malaysia
Background: To facilitate research through sharing of limited resources, an oral cancer biobank and databank was developed. The aim of this report is to highlight problems faced in managing an oral cancer biobank/databank.
Method: Specimens and data were obtained from participating referral centres. These were stored temporarily at each respective centre before being centralized at Oral Cancer Research & Coordinating Centre (OCRCC), University of Malaya.
Results: Since 2004, data was collected from 620 cases and 280 controls along with 390 tumor and 55 normal tissues. Blood samples were also collected from 266 cases and 266 controls. DNA/RNA was extracted from some specimens to facilitate molecular/genetic research. A major challenge in data collection is the ability to randomly check accuracy of data. The main problem identified in managing the bank is the lack of a formal body to vet application for usage of data/specimen. Lack of policy on authorships and acknowledgements evokes unfairness for original parties involved in the development of the bank. Lack of funding to carry out specimen collection and processing cast doubt on the continuity of the biobank. The establishment of a Central Advisory Committee (CAC) to govern policies related to data/specimen usage was proposed, while a minimal fee for specimen processing for research was suggested.
Conclusion: A check and balance system is needed to ensure accuracy of data. There is a need for a standard operating procedure for request to use data/specimen and a formally structured governing body to make decisions to avoid dissatisfaction and dispute among researchers.
Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Canton de Vaud, Switzerland
Human biobanks are a valuable source of biospecimens and personal data to be used for research. Little is known of how many biobanks exist at a given Swiss University Hospital. The purpose of this survey conducted at the CHUV hospital (>40,000 patients hospitalized per year) and the faculty of biology and medicine (FBM) at the University in Lausanne, Switzerland was a) to provide an overview of the number of biobanks, b) to assess their purpose and size, c) to determine the kinds of biospecimens collected and d) to analyse the extent to which the biobanks follow the Swiss Academy of Medical Sciences (SAMS) guidelines on biobanks. Eighty-three services (FBM: 15, CHUV: 68) were contacted. Twenty did not respond, 35 had no collection of human biospecimens. 28 services had 37 research biobanks and 6 collections for diagnosis and treatment; the latter were excluded from further analysis. Fifty-seven % of biobanks store >1,000 biospecimens. One third of biobanks stored tissue (92% fresh frozen, 46% FFPE, 31% DNA, 23% RNA, and 23% frozen cells), 65% stored blood components (58% serum, 63% plasma, 46% frozen cells, 38% DNA, 17% RNA, and 4% whole blood). The majority of biobanks have accepted the SAMS guidelines. Forty-one % of biobanks used the biospecimens and data only for their own research, almost half share biospecimens and data, but only a quarter use a material transfer agreement. The data collected in this survey will allow biobank infrastructure optimization at the CHUV and will improve research support.
Royal Brompton & Harefield NHS Foundation Trust, London, UK
Background: The Royal Brompton & Harefield NHS Foundation Trust (RBHT), in partnership with Imperial College London, was awarded NIHR Biomedical Research Unit (BRU) status for both Respiratory and Cardiac research programmes. The Respiratory BRU incorporates clinical research facilities for advanced lung diseases. The Cardiovascular BRU encompasses advanced facilities for cardiac imaging, interventional cardiology and genetics.
Methods: A research Biobank has been established across both BRUs. The Biobank prospectively collects, processes, and stores specimens, together with clinical data, consented for donation to research by patients undergoing treatment at RBHT. A dedicated collection team ensures all possible samples are procured. Access to samples is done equitably, based on prioritization and availability and is open to all researchers.
Results: Each year, RBHT serves >90,000 outpatients and >26,000 inpatients representing specialized cardiovascular and respiratory disease cohorts. The Cardiovascular BRU has stored >2100 samples in the Biobank since August 2009. The Respiratory BRU will store multiple samples from an estimated 8,000 patients annually. Access to the Biobank is governed by recognized leaders in cardiovascular and respiratory research who form the core of each BRU.
Conclusions: The Biobank facilitates access to an extensive range of specimens from highly unique patient populations. As a shared core facility between the Respiratory and Cardiovascular BRUs, operations are harmonized providing a well-organized, proficient resource to enhance research opportunities between both academic and clinical institutions and thus, stimulate development of novel treatments for respiratory and cardiovascular disease. The processes and infrastructure created enable increased access, efficiency, and collaboration within a transparent, equitable and ethical framework.
BioStorage Technologies, Inc., Indianapolis, IN, USA
As clinical research trends towards globalization, the process of transporting human biospecimens has become increasingly complex. Regulatory requirements, quality control concerns, import and export guidelines and maintaining the visibility of temperature-sensitive biomaterials pose distinct challenges to organizations collecting biospecimens on an international scale. Without careful consideration for cold chain logistics, compliant storage, information management and audit trails, researchers risk specimen degradation and losing valuable clinical information. As a result, information provided will impart attendees with invaluable insight into logistical strategies and highlight in-depth measures that help ensure the on time, compliant transportation of valuable biospecimens. Specific topics that will be addressed, include:
Maintaining Regulatory Compliance Adhering to Custom Regulations Specific Aspects of Maintaining Visibility of the Cold Chain The Role of Validated Packaging for Extended Transit Times Standards for Labeling and Documentation.
The presenter will also address the process of developing a comprehensive cold chain strategy, taking into account best practices for the labeling and handling of specimens.
Addressing the Challenges of a Complex Disease through a Repository-Centered Strategy: The Design and Implementation of the Accelerated Cure Project Multiple Sclerosis Repository
Despite decades of research, the etiology and pathophysiology of multiple sclerosis remain very poorly understood. This lack of progress and understanding is due primarily to MS being a complex, heterogeneous disease. A multitude of factors contribute to initiating and driving the disease, and the specific factors involved vary from person to person. Determining how to prevent, treat, and cure MS requires strategies specifically tailored to the challenges of investigating a complex, heterogeneous disease. The Accelerated Cure Project MS Repository is the cornerstone of such a strategy. It collects longitudinal blood samples (RNA, DNA, plasma, serum, and lymphocytes) from MS subjects and controls, characterized with over 40 pages of information about each subject. Samples and data are shared with scientists in many disciplines investigating the causes and mechanisms of MS—who in return provide their experimental data to the Repository to be incorporated in the database. Combining clinical and epidemiological information with genetic, gene expression, proteomic, and other types of experimental results creates a rich and multifaceted dataset that can yield new insights into the biology of MS. The Repository currently has 2,000 sets of samples and data collected through a network of nine clinical sites across the US, has supported over 30 research projects, has recovered several experimental data sets, and is now developing an informatics and data analysis plan for extracting new findings from the Repository database. This presentation will describe the design, status, and future directions of the MS Repository.
The University of Sydney, Sydney, New South Wales, Australia
Background: The New South Wales Tissue Resource Centre (TRC) of Australia, collects human brains from forensic institutes and associated pre-consented donor programs. The primary focus is supporting research of substance abuse of alcohol and schizophrenia. Recent tissue requests for genetic research projects have indicated the requirement of large cohorts to substantiate findings. The challenge for this bank is the ability to meet these needs while working within finite financial and infrastructure support.
Aim: The goal of this study was to evaluate the collection process and assess the acquisition rates, the current research cohorts and to identify the cases that are under utilised or do not meet criteria for research.
Results: There have been 660 brains collected since 1994. Of these, 510 cases are assigned to the research cohort while 150 cases have not met inclusion criteria due to pathological or clinical measures. The research cohorts are further subclassed by DSMIV, alcoholic liver disease and smoking history. The female gender is under represented in each group; control - 27%, schizophrenia-36% and substance abuse of alcohol-23%. The yearly collection rate average has increased from the first 5-year period of 38 cases to 60 cases for 2008–2009.
Conclusion: Strict inclusion criteria and insufficient clinical information has excluded a number of cases from the research cohort. A review of collection protocols has indicated access to medical records in a shorter timeframe and a more rigorous review of available information is warranted to reduce the limitation of usage.
Royal Dutch Academy of Arts and Sciences, Amstelveen, noord Holland, Netherlands
Background: The diagnosis of most neurological disorders is severely hampered by the absence of reliable biomarkers that can be measured in body fluids such as blood, urine and cerebro-spinal fluid (CSF). Biomarkers search strongly depends on specimens collected from living donors as well as autopsy material collected and stored by Biobanks and tissue banks.
Methods: Biomarkers validation copes with data fluctuation due to the huge variability in biomarkers between individuals and the rapid post-mortem changes. We are currently using amyloid and Tau as early diagnostic markers in the pathology of dementia and in differential involvement in Alzheimer's disease (AD), Lewy Body dementia (DLBD), Vascular dementia, fronto-temporal lobar degeneration (FTLD) and non-neurological controls.
Results: Due to the overlap in pathophysiological hallmarks of the various disorders syndromes, we identify common markers in blood and CSF. We also determine CSF-total and phosphorylated tau and CSF- Aß42 in blood and CSF, both in living donors and in rapid autopsy material, in combination with imaging techniques to assist in differential diagnostic procedures.
Conclusions: Although it is clear that no single biomarker can discriminate between AD and other dementias, a judicious combination of several biological markers may substantially increase the sensitivity and specificity of the diagnosis. If the results from a panel of biomarkers are added to the findings derived from a classical work-up, diagnostic accuracy can be further increased. Biobanks using internationally accepted SOPs, play a major role in the collection of large numbers of high quality specimens for Biomarker identification.
Victorian Cancer Biobank, Carlton, Victoria, Australia
Background: The Victorian Cancer Biobank (Biobank) is a consortium formed in 2006 by five parties including 4 pre-existing tissue banks. Each member agreed to a centralised application process to streamline the access to specimens, this required the introduction of a structure that gave custodianship of all biospecimens to the Consortium whilst retaining a sense of shared management and decision making over their allocation for research.
Methods: During 2007, the Consortium Committee developed terms of reference for an Access Committee to oversee access to samples. The Committee includes representatives from the Consortium members and independent members with expertise in research and human ethics. An Applications Manager was appointed to work with researchers and support the committee.
Results: Initial challenges were encountered when “rolling over” existing projects from local to central management and supporting different types of research. The application process was revised and developed further to cater for such challenges. Since the formation of the Access Committee the Victorian Cancer Biobank has processed 47 new applications. After implementing this process the Biobank has distributed approximately 1100 biospecimens to these new and rolled over projects.
Conclusion: Overcoming the sense of ownership of tissue samples has probably been the most significant challenge associated with a centralised access policy. The successful centralisation process has streamlined access to biospecimens and reduces the duplication of resources required for approving applications and distributing biospecimens. The adaptability of the model has enabled us to move forward with supporting clinical and translational research by providing both services and products.
Flinders University, Bedford Park, South Australia, Australia
Background: Established in 1986, the South Australian Brain Bank collects and stores post-mortem human neurological tissues for use in research. In 1993, with the development of the Australian Brain Bank Network, a modified methodology was needed, to ensure flexibility in line with changing technologies.
Methods: Whole brain perfusion fixation via cerebral arteries is ideal when histological and immunohistochemical studies are the primary research goal. With careful storage in buffered formaldehyde, these tissues remain useful decades after collection. Evolving technologies required tissue that had not been chemically treated, so we modified a method(1) whereby one half of each brain (chosen randomly or according to case specific pathology) is immersion- or perfusion-fixed for diagnostic studies. The contralateral hemisphere is dissected into 10 mm coronal slices that are rapidly frozen and stored at −80°C.
Results: The completion of the Human Genome Project in 2003 resulted in a propensity for genetic studies, increasing the demand for fresh frozen tissue. The modification to our protocol ten years earlier has enabled us to facilitate a variety of new national and international research studies.
Conclusions: Careful preservation and storage of human tissues ensures its viability for both current and prospective research. This is particularly important when storing rare or inherited neuropathologies. Flexibility in this process is crucial to keep ahead of emerging technologies.Reference:1. Vonsattel, et al, An improved approach to prepare human brains for research, J Neuropath Exp Neurology 54 (1): 42–56, 1995.
Norwegian Institute of Public Health, Oslo, Norway
Background: The MoBa study is a nationwide population-based pregnancy cohort where biological samples from mothers, their partners and newborns have been collected from more than 100 000 pregnancies. The samples were collected at participating hospitals, and sent by mail to the central biobank where DNA was extracted and stored at −20 °C. From 1999 to 2003 some blood samples were stored at −20 °C without processing. DNA is now extracted from these samples, and the quality will be compared to fresh samples. In some of the samples, incomplete protein digestion during the extraction process resulted in protein contaminated DNA. These samples have been re-extracted (to a maximum of 3× per sample) and ongoing studies are performed to see how the re-extraction procedure affects the quality of DNA.
Methods: DNA was extracted using a commercial kit. After extraction, DNA was diluted to 100 ng/μl and 12.5 % of DNA samples were subjected to the quality control program which consists of DNA concentration measurements (NanoDrop ND 8000), DNA fragmentation measured by agarose gel analysis and PCR success on a 1.2 kb PCR fragment.
Results: The average DNA yield of fresh blood samples compared to long-term frozen blood samples was 30 and 20 μg DNA pr ml blood, respectively. Both frozen and freshly drawn blood samples showed marginal DNA fragmentation and PCR has a success rate of 100 %.
Conclusion: According to the QC testing performed in our laboratory, the DNA quality from both freshly drawn and frozen blood samples are satisfactory.
Norwegian Institute of Public Health, Oslo, Norway
Background: The Biobank at NIPH collects and stores cord blood samples in Tempus™ blood RNA tubes (∼52,000 tubes have been collected). Long-term storage of samples before extraction may affect the quality and integrity of RNA contributing to artifacts in gene expression (GE) analysis. We have evaluated the effects of storage on the stability of RNA in blood in Tempus tubes.
Methods: Cord blood from three placentas (3 ml blood/tube, 45 tubes) and whole blood from three healthy adults (3 ml/tube, 172 tubes) were drawn in Tempus tubes and stored overnight at −20 °C and then at −80 °C during long-term storage. RNA was extracted and analyzed after 0, 1 and 2 years. RNA quantity and quality were examined using Nanodrop™ spectrophotometer and Agilent Bioanalyzer. The stability of the GE profile of seven genes (18S rRNA, FOS, IL-1ß, IL-8, MYC, TP53, and CDKN1A), was analyzed by qRT-PCR (7500 Fast, Applied Biosystems).
Results: In general, long-term storage had no significant effects on RNA yield and quality. The expression levels of the seven genes were not altered by storage, except some differences in MYC expression levels. We are now conducting analysis of data from four-year stored samples.
Conclusions: Our results suggest that the storage of blood in Tempus tubes for up to two years has no significant effects on the RNA quality and yield. This suggests that blood samples in large biobanks—frozen in suitable collection tubes for RNA stabilization—can be used for GE studies even after years of storage.
IRCCS San Raffaele Pisana, Rome, Italy
The Interinstitutional Multidisciplinary BioBank (BioBIM) is an organized collection of biological samples, which operates under the auspices of the IRCCS San Raffaele Pisana, Rome, a private Scientific Institution certified by the Italian Minister of Health. Biological samples are obtained from individuals referring to several Italian Institutions. Each Institution has identified at least two medical doctors, one clinician and one pathologist who are in charge of supervising the project. The BioBIM primary objective is to provide a service for development of interdisciplinary research lines and exchanges among different working groups, through the centralized and automated collection of human biological samples belonging to subjects with particular characteristics or specific diseases. The BioBank is organized so as to ensure the storage of samples for 20 years, the quality and the correct use of the stored material and to protect the donors' privacy. The BioBIM is organized in 5 pathology-based biobanks (cardiovascular and respiratory diseases; neurodegenerative disorders; cancer; developmental disabilities and rare diseases) and a healthy donors collection. Each biological sample is associated with the donor data, and all information obtained is treated in accordance with the current Italian and European regulations. The BioBIM has obtained the Quality Certification according to standard UNI EN ISO 9001:2000 with the explicit purpose and scope of certification activities as an independent and autonomous unit. In synthesis, the BioBIM is organized as to ensure: the long-term preservation of samples in a high quality fashion, the correct use of biological samples and the safeguard of donor privacy.
Second University of Naples, Naples, Italy
Background: Naples Human Mutation Biobank (NHMB) is active since 1991 at the University Hospital of the Second Naples University, as a part of the Cardiomyology and Medical Genetics Service.The specificity of the Bank is to store biological samples of patients affected with primary myopathies, such as X-linked and Autosomal Muscular Dystrophies (DMD, BMD, LGMDs, DM1 and DM2, channelopathies, spinal muscular atrophies)—and cardiomyopathies, and to make samples available to the scientific community worldwide. The aim of the bank is to provide in the near future a personalized therapy for each patient.
Methods: NHMGB is a partner of EuroBioBank, a European network of biobanks concerned with storage of biological samples from patients affected by rare diseases, the Italian Telethon network for neuromuscular diseases and Treat-NMD. DNA and/or RNA from blood, skeletal and heart muscle are extracted with conventional methods, according to legal and standard operating procedures (SOPs) developed in agreement with EuroBioBank.
Results: The actual number of samples stored in the bank regards 6220 blood/DNA and 500 muscle specimens and 130 sera. The bank also contains DNA samples from 451 normal individuals, to both study the occurrence of polymorphisms in our population and to confirm new molecular variations.
Conclusions: The Bank serves as a worldwide available scientific source, so that all scientists, including those who do not have routine contacts with clinicians, may have access to a vast number of well-diagnosed specimens regarding their research field, so that they can be facilitated in their studies.
University of Calgary, Calgary, Alberta, Canada
Background: Colorectal cancer (CRC) is the second most common cause of cancer deaths in North America. Biomarkers hold the promise to transform CRC screening, replacing stool-based tests as a more effective method of identifying those at high risk for CRC neoplasia, while being more acceptable to the target population. It is crucial that potential biomarkers be subjected to critical and rapid evaluation in a screening-relevant population so that those that are inaccurate can be abandoned and those that remain promising can be evaluated in clinical trials. To support the development and validation of novel non-invasive CRC screening tests, a biorepository of blood, urine and tissue linked to comprehensive risk factor and outcome data is being developed.
Methods: The biorepository is located at the Forzani & MacPhail Colon Cancer Screening Centre (Calgary, Canada), an endoscopy unit providing colon cancer screening colonoscopies. Biorepository participants complete comprehensive questionnaires on their health and life-style, family history, diet, use of medications and nutritional supplements and provide blood and urine samples. Blood is fractionated into serum, plasma, whole blood and buffy coat and stored at −80°C. Participants undergo colonoscopy with removal of all polyps. Normal colonic biopsies are obtained on a subset. Formalin-fixed tissue is available from all polyps removed. Subsequent linkage to the provincial cancer registry will identify interval cancers. Samples can be obtained based on specific participant characteristics or neoplasia status. The goal is to recruit 1,000 asymptomatic, average risk participants annually.
Results: Over 650 individuals have been recruited to date.
Feist Weiller Cancer Center, LSU Medical Center, Shreveport, LA, USA
Background: In this emerging genomic research era, availability of tissue samples is an essential key for the success of basic translational research, hence the establishment of biorepository units for tissue and serum banking. However, the success of the biobanks is largely dependent upon the goodwill of the public. Therefore we carried out this study to evaluate the support of an American general public for tissue banking for biomedical research; and to assess the willingness of patients to donate their tissue samples for future research.
Method: The study consists of patients who underwent surgical resection of a tumor at an American public university medical center between October 2006 to December 2009. The patients were solicited to donate their tissue samples to be banked for unspecified future biomedical research. They were also provided with the options to opt-out of the program whenever they choose to do so, with no questions asked (opt-out plus consent method).
Results: In all, 2191 patients were solicited to participate in the study and 2116 (97%) of them signed up to donate their tissue samples. Only 75 patients (3%) of the patients refused to participate. From the consented population, tissue samples were backed from 882 patients (40%) and so far, only 1 patient (0.1%) had withdrawn from the study.
Conclusion: There is an overwhelming public support for tissue banking with the majority (97%) willing to donate tissue samples to be banked for future academic biomedical research—even when approached to do so in the immediate pre-operative period.
Genome Quebec and Chicoutimi Hospital/Ecogene-21 Biobank, Chicoutimi, Quebec, Canada
Background: Implementing a biobank represents an important challenge and many elements need to be addressed, among which personnel, governance, technologies, automation, workflows, versatility, throughput, redundancy and capacity. The GQ Biobank is an infrastructure comprising different off-the-shelf systems operated by highly qualified personnel using standardized procedures.
Methods: The GQ Biobank includes technological platforms implemented to process and store a variety of sample types in various conditions and on different sites. Refrigerators and freezers: Primarily used for temporary to mid-term storage, this platform accommodates a wide range of needs for many different specimen types at temperatures ranging from −80°C to 4°C. Cryopreservation: Comprised of several liquid nitrogen cryocontainers, it is primarily used for long-term storage of several sample types within straws or cryovials. Controlled ambient temperature storage: Fully automated, this platform is suitable for long-term storage of a variety of samples such as DNA, RNA and proteins. Sample processing: Diverse sample handler systems and validated manual procedures were implemented to process and track hundreds of samples every day. R&D: Development of new technologies, robotics, information systems and procedures.
Training: Development and maintenance of qualifications of highly qualified personnel.
Results: The GQ Biobank provides short and long-term storage solutions with flexibility regarding storage conditions and sample types, and a capacity of tens of millions of samples.
Conclusion: By selecting or developing a combination of storage technologies that minimize operating costs and maximize versatility, the GQ Biobank constitutes a sustainable infrastructure having the potential to grow according to the needs of users of today and tomorrow.
BC Cancer Agency, Victoria, BC, Canada
Founded in 2003 through funding from the Canadian Institute for Health Research, CTRNet's mission is to improve capacity and quality of cancer biospecimens and associated data through standardization and improvement of biobanking processes. CTRNet does not fund or direct tumor banks but seeks to leverage its expertise and effort in creating national standards and harmonization mechanisms to increase the ability of cancer researchers to utlize these resources. Specific achievements include developing a comprehensive set of policies and SOPs; creating a database to support all aspects of cancer biospecimen annotation and biobank operations (Advanced Tissue Information Management-ATiM); and launching a web-based biospecimen catalogue to enhance access. CTRNet has also contributed to harmonization of international biobanking and benefited from linkage to similar initiatives in the international community. CTRNet is entering the next phase of its development. Plans include:
1) Expanding its scope and size through broader membership of existing biobanks and assisting development of new Canadian biobanks; 2) Maintaining and improving existing policies/SOPs and developing new ones; 3) Facilitation of purpose-designed prospective collection including developing a densely annotated Biospecimen Science Research cohort to enable future analyses on influences of pre-analytic variables on biospecimen quality; 4) Developing Certification, Training and Education programs in conjunction with ongoing centralized sample quality assurance services for all member banks; and 5) Refining ATiM and the biospecimen catalogue to enhance capabilities for tracking specimen release, utilization and costs. CTRNet continues to focus on developing the necessary infrastructure for high-quality and high-capacity biobanking in support of cancer researchers' changing biospecimen needs.
BC Cancer Agency, Victoria, BC, Canada
Background: Cancer biospecimens hold the key to unlocking the mechanisms of cancer development and progression. The demand for tissue biospecimens has increased threefold over the last 20 years, with the most significant demand for formalin-fixed paraffin-embedded tissues (FFPE). We set out to address the hypothesis that emerging research techniques drive these observed biospecimen trends.
Methods: We analyzed 262 publications encompassing papers published at five-year intervals (2008, 2003, 1998, 1993, and 1988) in the journal, Cancer Research. We categorized publications for tissue biospecimen utilization, biospecimen format type (Frozen, FFPE and fresh), extract type (RNA, DNA, protein and cells) and assay techniques.
Results: We observed that the mean number of techniques performed per publication did not change over the last 20 years. However, significant changes in the proportions of techniques using a specific extract type were observed. These changes correlated with the proportion of techniques which require FFPE tissue. Significant changes were also observed in types of techniques. Further analyses will be performed to look at the relationship between trends in techniques and biospecimen format.
Conclusions: Techniques such as the TMA, PCR, RT-PCR and increased use of cell lines are likely driving the observed shifts in tissue biospecimen formatting. Conclusions from this report are intended to assist biobanks in understanding historical trends and to project future trends in biospecimen needs that will materialize as a result of emerging technologies. Consideration of research trends and emerging technologies will aid biobanks in decisions around priorities for biospecimen accrual and optimal preservation format.
Feist Weiller Cancer Center, LSU Medical Center, Shreveport, LA, USA
The need for high quality human tissue and serum samples for translational research is increasing, but access to such samples continues to elude many researchers. Therefore, FWCC established a Tissue and Serum Repository (TSR) that provides for all interested investigators, equal access to human tissue and serum samples.
Method: The following factors were put in place:
A full-time pathologist dedicated to tissue banking program. Personnel for recruiting and consenting patients. Couriers for timely transportation of surgical specimens from operating rooms to pathology dissection suites. Interdepartmental cooperation between FWCC, Department of Pathology, and surgeons. Active involvement of surgery and operative room nurses. Reliable computer-based tissue inventory system. A histopathology laboratory. Funding underwritten by the FWCC.
Results:
Co-operation between all stakeholders. High recruitment rate: 97% (2,116 of 2,191 patients) assented to donate their tissue sample for future biomedical research. Timely transportation of surgical resection specimens from operating room to pathology dissection suite. Expert handling of specimens to ensure diagnostic workup of the specimens is not compromised. Not a single complaint received from pathologists—with more than 2,000 specimens examined for potential tissue banking over a 40 month period. Free access of the TSR personnel to surgical resection specimen. Prodigious banking of tissue samples for future biomedical research with 16,430 pieces of frozen tissue samples banked.
Conclusion: The FWCC tissue and serum banking model is an efficient and workable model for successful establishment of a Tumor and Serum Repository.
ECOGENE-21 Clinical Trial Center, Chicouitmi, Quebec, Canada
Background: The term “biodrug” refers to bioactive substances used for disease prevention or treatment. Biodrugs include vaccines and monoclonal antibodies against microorganisms or complex diseases (cancer, diabetes, …), transgene products (gene replacement therapy), viral capsids or bio-shuttles used for drug delivery, SiRNA (anti-sense therapy), protein transcription factors, nutrients and other bio-particles. The number of trials assessing the innocuity and efficacy of biodrugs is exponentially increasing. The storage and management of biodrugs, from pharmaceutical production to clinical sites and patients' delivery raise very specific challenges.
Methods and results: The Ecogene-21 clinical trial center and the Genome-Quebec/Chicoutimi Hospital Biobank are developing a good-clinical practice (GCP)-certified toolbox for the management of biodrugs in clinical trials (from Proof of concept to phase I-III studies). The toolbox covers the critical path from shipment by the pharmaceutical industry to the clinical site and from the site to the patient: handling and transportation, storage conditions, bio-sample preparation and administration, drug excess recovery and bio-wasting. Standard operating procedures (SOPs) covering the audit trail, automated biobanking technologies and information systems were developed by a transdisciplinary, GCP-trained team with experience in clinical trials, technology development and biobanking. The toolbox has been tested in phase I/II and II/III gene therapy (associated adenoviral capsid), anti-sense therapy and nutritional trials. This allowed the step-by-step improvement of the SOPs and the development of adapted technologies.
Conclusions: To assess the efficacy and innocuity of transgene products or biodrugs require strict and specific storage procedures and adapted technologies.
Rutgers University Cell and DNA Repository, Piscataway, NJ, USA
Background: The Netherlands Twin Register is a longitudinal study of adult twins and their family members, started in 1987 by Prof. Boomsma and colleagues, to provide biological specimens for a variety of behavioral and epidemiological genetic analyses. Over 22,000 participants were enrolled through the 1990's. From 2004 through 2008 blood samples were collected from over 8,400 participants for DNA and RNA extraction, plasma isolation, and cryopreservation of lymphocytes. In 2009 the NIMH awarded funding to the Rutgers University Cell and DNA Repository to convert the CPLs into lymphoblastoid cell lines, extract genomic DNA, extract RNA from stored frozen PaxGene blood tubes, and amplify cDNA in order to establish shared biological resources.
Methods: CPLs were thawed and transformed into culture on a layer of irradiated MRC5 cells and expanded for cryopreservation of LCL stocks and DNA extraction. Cultured cells were extracted on a Qiagen AutoPure LS DNA extractor. Total RNA was isolated on a Qiagen Universal liquid handling system utilizing solid phase extraction chemistry. A new protocol was developed and validated to simultaneously isolate miRNA in a separate fraction using a modified Qiagen RNAeasy protocol. The total RNA and miRNA fractions are stored independently in a Micronic 2D tube storage system. A small amount of total RNA was utilized to linearly amplify cDNA that will be distributed for qPCR, microarray, RNAseq and other gene expression applications.
Conclusion: These biological resources and extensive phenotypic data will provide an invaluable resource for the investigation of genetic determinants in mental and physical health.
University of New Mexico, Albuquerque, NM, USA
Background: The EBCR began recruiting breast cancer patients in 2006 from the UNM CC. Clinically annotated sera, plasma and DNA at baseline and 1 and 5-years thereafter, as well as excess fresh frozen tumor and normal breast tissue at surgery are collected.
Methods: Eligibility criteria include diagnosis within 1 year of definitive surgery at any stage, 18 years old or older, and expected follow-up at UNM CC. All eligible patients have at least 24 hours to consider participation. We reviewed race/ethnicity and zip code from all eligible patients in the UNM CC eVelos system.
Results: From 2006 to 2009, 429 eligible patients were approached. Within race/ethnic group 12.6% non-Hispanic white, 14.0% Hispanic, 37.0% Native American refused participation. Patients who refused were more likely to live in the Albuquerque metro area (77.1%) and northeastern New Mexico/northwestern Arizona (17.2%). The latter region corresponds with a large Native American population. Reasons for refusal: not interested (51.4%), passive refusal (15.7%), 'too overwhelmed' (10.0%), confidentiality concerns (4.2%), and other (18.7%). Response rates fluctuated by year and recruiter: 2006 = 93.2% (A), 2007 = 84.5% (A,B), 2008 = 69.1% (B,C), 2009 = 72.2% (C,D,E). Most recruiters were Hispanic and fluent in both Spanish and English. All were female, and of similar age, experience and training.
Conclusion: Our analysis confirms previous literature that Native Americans are more likely to refuse participation in research than other race/ethnic groups. Differences in a recruiter's style affect the response rate. We plan to investigate new ways to train recruiters, encourage more active physician involvement, and follow-up with the Native American community.
BioStorage Technologies, Indianapolis, IN, USA
There are now over 250 biobanks in Europe, which represents a dramatic increase over the last decade. This has been driven by the realization that well annotated and properly consented samples can give significant insights into the etiology of diseases and their treatment. Such samples can only retain their value if their integrity is uncompromised and since they may be kept for many years, temperature sensitive samples must be maintained in specialized environments. The curator of these collections is responsible for the implementation of standardized best practices and procedures, and should embrace advances in cold chain and monitoring technologies. Such Good Storage Practice will be highlighted in the poster presentation, including:
Excellence in cold chain logistics with correct packaging and temperature monitoring. Assurance of adequate equipment temperature mapping and maintenance. Well defined data collection policies and appropriate sample annotation. A fully scalable inventory management system with an automated auditable history in compliance with 21 CFR Part 11. Aliquoting of samples that are likely to be examined repeatedly. Digitized temperature monitoring that links temperature history immediately to the sample. Internal inventory audits by QA department. Business continuity planning ranging from redundant equipment to emergency backup power. Full attention to all aspects of health and safety in the repository.
Ultimately the conclusions drawn from the analysis of stored samples will have impact on patient treatment and safety. It is therefore an ethical responsibility to ensure standards of excellence are maintained in storage practice.
Monash University, Melbourne, Victoria, Australia
Background: The ASPREE Healthy Ageing Biobank aims to collect biospecimens from up to 10,000 healthy Australians who are 70 years of age or older and who have agreed to participate in the ASPREE study. ASPREE (ASPirin in Reducing Events in the Elderly) is a double-blind, placebo-controlled clinical trial of low dose aspirin for primary prevention of major disease in the elderly. The biospecimens will provide the opportunity to evaluate new preventative biomarkers associated with outcomes of interest, over time. This is the only Biobank in the world to be focussing on older persons. To obtain samples of the highest quality bloods need to be collected, processed and stored within 4 hrs. If Biobank participants are not willing to come to a specialist laboratory, we need to take the laboratory to the people. This is particularly an issue for older persons. A mobile laboratory (the ‘BIOBUS’) is to be commissioned that will also serve as a mobile assessment clinic in both metropolitan and rural areas.
Methods: A Mercedes Benz Sprinter van will be outfitted with non-porous bench tops and flooring, refrigerated centrifuge, mobile LN2 vapor phase storage tank which is safe to transport, back-up generator, clinical examination table and many other laboratory features and equipment.
Conclusion: The BIOBUS will provide the necessary link between the research laboratory and the community for ASPREE and further community-based trials. This is particularly advantageous for studies involving older people who do not have the mobility or confidence of younger people to attend new environments.
Other Hot Topics
Brady Corporation, Milwaukee, WI, USA
Background: Do more with less … gain efficiency in your lab through automation, labeling and lean transformation. The healthcare community is in the process of adopting barcode technologies and lean practices at an increasing rate to replace the use of manual data entry and wasteful practices.
Methods: Learn how labs can save time, improve efficiency and reduce errors to meet biobanking best practices, improve patient safety and track chain of custody by using visual clues, bar coding, sample labeling and quality improvements. There is a simple way to navigate through the challenges of setting up a barcode system. In addition to these implementation challenges, we will cover solutions to lab labeling for processing and storage environments that are extreme and can create real obstacles. Highlights from NCI Best Practice Whitepaper on Specimen Tracking will be covered. Beyond automation, labs can use lean tools and methodology to increase productivity by streamlining the flow and reducing waste through understanding waste, process mapping and 5S techniques.
Results: Using hands on exercises and examples of labs you will see how they have made improvements to their work-flow and sample tracking that will provide real benefits back to your constituents such as physicians, hospitals and to the patient community. We will highlight these rewards by implementing a coherent process for labeling samples in the laboratory.
Conclusion: By focusing on the overall picture, turn around time or cycle length is immensely reduced and the results are increased quality and worker optimization in the lab.
Genetic Alliance, Washington, DC, USA
Background: Disease advocacy organizations (DAO) are actively involved in establishing and managing biorepositories and registries.
Methods: To gain a better understanding of their roles and to assess training needs, Genetic Alliance BioBank conducted an exploratory survey in December 2009, and 37 DAOs responded.
Results: Approximately one-third have biorepositories (33%) or registries (41%), and many have been in operation for more than 5 years (50% biorepositories, 75% registries). These resources are DAO-established (67%) and owned (53%). DAOs are involved in recruiting participants (94%), obtaining informed consent (61%), providing financial support (56%), and fundraising for financial support (56%). DAO-initiated biorepositories collect a variety of sample types, including blood (72%), frozen tissue (56%), formalin-fixed tissue (50%), cell blocks (28%), and cell lines (22%), while 81% would like to collect additional sample types. Samples are primarily used for DNA/genomics analysis (64%) compared to protein/immunohistochemistry studies (14%) or RNA expression studies (7%). Most samples are stored in university labs (57%), but some are stored in commercial labs (21%), non-profit organizations (21%), or government labs (7%). DAOs who do not currently have these resources are interested in creating biorepositories (65%) or registries (86%). When asked about training needs, fundraising strategies (79%), public relations strategies (65%), and examples of successful advocacy-initiated registries and biorepositories (62%) were among the most requested.
Conclusions: DAOs are playing integral roles in biorepositories and registries. It is important to understand these roles and provide training opportunities to assist DAOs in navigating the scientific landscape.
Biobusiness Consulting Inc, Lowell, MA, USA
Post mortem tissue procurement has been well utilized for a number of applications including brain related research, medical education, tissue allograft for transplantation, ocular therapies, and other biomedical innovations. Tissue provided through post mortem procurement offers substantive options for a range of biomedical research applications. Normal & diseased post mortem tissues suitably supplement sometimes scarce surgical tissue collections for organs i.e. prostate, breast, and metastatic bone and offer opportunities for biomarker as well as biospecimen science related research. It is, however, vital that there are controls for post mortem interval related ischemia and other acquisition variables, and that the samples are assessed for quality, and annotated appropriately. Careful orchestration is required to support fresh, frozen and fixed tissue collection. Tissue recovery, both arduous and challenging, requires recovery technicians ideally certified tissue banking specialists (CTBS) on 24-hour call to manage prerequisite logistical hurdles. Constant communication is required with recovery team partners' i.e. health care institutions, medical examiners and funeral facility personnel to 1) minimize recovery times 2) assure due diligence from consent through procurement and preservation, and 3) respect the funeral and closure needs of donor families. Experience demonstrates that staff responds best by understanding the value proposition behind the beneficence of donation for research. While the future appears bright for post mortem research applications, collaborative studies are still needed to define and validate tissue quality parameters. This role would be complimented via industry and academic partnerships allowing for shared expertise of lessons learned from cadaveric recovery, dissection and processing.
University of Michigan, Ann Arbor, MI, USA
Purpose: This poster presents results from a study that seeks to develop research models that allow for the comparative use of similar biomedical indicators across multiple data sets. While an increasing number of studies collect and release biomarker and biometric information in the form of secondary data it is often unclear if measures can be compared across studies due to differences in protocols, essays performed and results reported. This project attempts to introduce some structure within the existing body or research data.
Methods: We perform a thorough review of existing secondary data sets in the public domain and categorize them according to how they are organized and presented as analysis variables. We examine the related published research literature using these studies to offer additional insight into the protocols and procedures that were used to collect and apply these variables in health research.
Results: The National Archive of Computerized Data on Aging (NACDA) Program examined over 500 studies and developed a four level classification system for biomedical indicators in secondary data collections which allows us to accurately assign research data in a hierarchy driven by the level of detail and the potential comparability of specific variables for research across data sets looking at similar health outcomes.
Conclusion: This approach represents the first attempt to systematically organize and catalog the inventory of biomedical indicators in the public domain to facilitate their use in original research.
University of Michigan, Ann Arbor, MI, USA
This paper builds on work presented at the 2009 ISBER Meetings on the efforts by the National Archive of Computerized Data on Aging (NACDA) to build an understanding of the science underling organization and preservation within a formal specimen repository. NACDA, the nation's largest repository of secondary research data on aging and health is currently building a registry system to identify studies that use biomeasures and biospecimen data in their research design. Within our existing collection of 1,600+ studies we have identified studies utilizing biospecimen collection in over 500 individual surveys. With the growing number of federally funded social science based surveys now collecting biospecimens as part of their research design NACDA is actively building relationships with formal bio-repositories and building an understanding of how our methods intersect with traditional approaches to the archival sciences. Our core finding is that this process of understanding has only just begun and interacting with biospecimen researchers is central to our continued growth. The paper addresses our growing understanding of the commonalities that exist in our common approach to information and data management. Both bio-repository and data-repository researchers face similar challenges and objectives; working to strengthen these intersections among preservation specialists in serving our respective user communities will continue to strengthen multidisciplinary research on biomedical and biosocial issues. The growing collaborations between the biomedical and the social scientists argues that the preservation specialists who protect and maintain the product of these joint research efforts for future generations likewise need to strengthen their relationships.
University opf Cape Town, Observatory, Western Cape, South Africa
Introduction: A component of BioBank SA is a collection of mammalian skin fibroblast cultures secured in liquid nitrogen for trans-disciplinary use. Most of the specimens were collected from animals caught in the wild from various localities, predominantly in southern Africa, over the last 30 years.
Method: Skin biopsies were cleaned, chopped into small pieces and placed into petri-dishes containing culture media, covered with a glass cover slip and cultured to confluence in a CO2 incubator. Cells were placed into cryovials and frozen at −80 °C before being stored in liquid nitrogen.
Results: Samples held include 20 different species of bovid, 7 different cetacean species, 5 felids, black and white rhinoceros, African Elephant, Hippopotamos, Hyaena, Plains and Mountain zebra, Small and large spotted genet, common molerat and chacma baboon.
Conclusion: Uses include: molecular systematic studies (e.g. Science 317 (2007) 519–523.); molecular population genetic analyses where there are sufficient numbers of individuals stored (e.g. Molecular Ecology 14 (2005) 2981–2990) - the value of wild-caught animals of known provenance being essential here; comparative metabolism (e.g. Comp. Biochem. Physiol. 110B (1995) 37–46); and hybrid identification using karyotyping and/or microsatellites (e.g. Conservation Genetics, 6 (2005) 141–145). Examples in each of these categories will be given. Of special relevance to conservation of endangered species is the potential of using cloning technologies on previously banked cells to retrieve different individuals from a population or species which has become recently extinct or is close to extinction.
Legal and Ethical Issues Related to Repositories
Netherlands Institute for Neurosciences/KNAW, Amstelveen, noord Holland, Netherlands
Background: International research codes require researchers to obtain the informed consent of subjects before starting a study. This requirement poses special challenges in conducting dementia research. The cognitive capacities of the patients vary widely; individuals in early stage of the disease can make their own choices whereas individuals with severe impairment will be incapable of making the informed choice.
Methods: Genetic research, e.g. linkage analysis studies, raise serious ethical problems and complexities; the collection of patient-related data for the researchers is often in conflict with the use and implications of this information for the providers, the families and the patients involved.
Results: The links we find between genes and neurological diseases, create a heavy burden on physicians, health care workers, Bio-bankers and researchers. The outcome of studies in Huntington's diseases, the Apo-E genotyping in AD and chromosome 17-Frontal temporal Dementia (17-FTD) pose a heavy load on the afflicted individuals and their families.
Conclusions: Genetic testing often has a limited predictive value and should be accompanied by counseling for the families. It can be psychologically incapacitating, especially because currently there is no treatment or cure for most cases. Early diagnostic tests may prove extremely useful when treatment becomes available which makes the information obtained by genetic testing essential for the scientific effort to develop the right therapeutic strategies. As many of the molecular genetic studies are performed by international collaborative efforts, it would be advisable to have a global concensus on the legal/ethical codes of conduct.
Foundation Biobank-Suisse, Bern, Switzerland
Different types of biobanks located in or linked to hospitals store a great number of human biological materials. These specimens are of immense value for research, especially when linked to patient data. A major barrier to research involving these biospecimens is that often consent for the use of these biospecimens is not obtained when the specimen is taken or the consent is limited. A working group including all major stakeholders in Switzerland developed a standardized general consent form to be used routinely at admission or during hospitalization, in Swiss hospitals. It seems ethically sound and feasible to discuss with all patients whether they agree that their reversibly anonymised biospecimens and data may be used for future medical research, and without having to contact them again for any new research project. In our standard consent form we have deliberately not addressed the “right to know or not to know”. We will present arguments for this decision (i.e. non-predictability of research results generated with genome-wide array chips, questionable clinical “relevance” of novel findings, medical qualification of researchers, etc.) and we will discuss the potential role of IRBs and of the treating physicians in this complex scenario. The proposed informed consent form underwent an extensive review by major stakeholders in Switzerland including the medical, legal and administrative departments of the University hospitals. Implementation of this consent form will start in 2010. We will follow this process to identify possible barriers to this type of general consent research involving human biospecimens and data.
AstraZeneca, Macclesfield, Cheshire, UK
Background: Predicting the impact of intestinal absorption on overall fraction absorbed (Fabs) following oral dosing is a significant challenge in the drug discovery setting, given variability in commonly used pre-clinical species. Access to human intestinal tissue for laboratory investigations would allow direct assessment of gut absorption in man prior to clinical dosing. The challenge is logistical but preliminary laboratory results indicate that the endeavour is worthwhile.
Methods: Whipples (pancreatoduodenectomy) surgery was identified as the most likely source of tissue suitable for study. The processes required to collect fresh intestinal tissue from resected samples in the operating theatre were not covered by existing procedures. Consent procedures were established, governance requirements were agreed with the hospital's (Pennine Acute Trust) research and development (R&D) department and independent study specific ethical approval was obtained. Intestinal tissue was collected in a physiological preservation solution and couriered to the research laboratory for immediate Ussing Chamber investigations into drug permeability.
Results: The study took approximately 15 months to establish from initial enquiries to receipt of first sample. Subsequently 12 samples were obtained within a 5 month time frame. The tissue was assessed to be functionally viable with maintained integrity during transport and over the experimental time-course. Results have yielded strong correlations to equivalent results generated in rat small intestine.
Conclusions: The study successfully established a method for acquiring and utilizing fresh human intestinal tissue for drug absorption investigations. Future studies will aim to expand on the uses for the excised tissue to investigate other intestinal processes.
University of Calgary, Alberta, Canada
Background: Project reviews by Research Ethics Boards (REBs) can significantly delay research studies. Reviews by our REB can take up to 5 months, often requiring revisions. Our aim was to develop a strategy to reduce delays associated with ethics approval and enhance the function of our Intestinal Inflammation Tissue Bank (IITB).
Methods: A model was developed in which the REB allowed patients to be consented and have their tissue directly entered into the IITB. We then developed three broad projects that encompass all foreseeable studies by our affiliated researchers. In short the projects were; 1) inflammatory regulators, 2) apoptosis-tight junctions and, 3) host-microbial interactions. REB approval was obtained for these projects. To initiate a new proposal, investigators are only required to submit a 1 page addendum to one of the above studies to the REB.
Results: Since instituting this model, 29 projects were submitted in 2.5 years, all of were approved without revision with an average time of 19 days. This marked reduction (versus 5 months with a 20% revision rate) was favorably accepted by both the REB and the researchers.
Conclusions: This model has been highly successful, allowing consent and collection from over 850 patients and providing tissue for the above projects, resulting in numerous high level publications and successful grant applications over the last two years. Efficiency of the IITB played a key role in securing an interdisciplinary team grant from the Alberta Heritage Foundation for Medical Research for the development of the Alberta Inflammatory Bowel Disease Consortium.
World BioBank, Memphis, TN, USA
Background: Archival clinical formalin-fixed paraffin embedded tissue blocks (FFPE blocks, or paraffin blocks) are a vast potential resource for medical research. In the U.S., a main impediment to accessing clinical FFPE blocks for research are sample retention rules imposed on clinical pathology laboratories by CLIA and CAP, requiring block retention for specified periods (2 and 10 years respectively). Pathology laboratories often, and justifiably, point to these rules when choosing not to participate in research projects requesting clinical FFPE blocks. The question: Are there reported, non-anecdotal, studies demonstrating usage rates of archival clinical FFPE blocks for subsequent clinical care, for which ostensibly the regulations exist?
Methods: Three sources were examined:
(1) CLIA, (2) CAP regulations, and (3) existing medical literature (Pubmed).
Results: CLIA provides no rationale for its retention requirements. CAP regulations, differing substantially from CLIA, provide no clues about usage rates or rationale for retention requirements. There are no studies in the medical literature reporting usage rates of archival clinical FFPE blocks.
Conclusions: No published data exists regarding usage rates of archival clinical FFPE blocks. The rules requiring pathology laboratories to retain these were implemented decades ago, long before many current FFPE-based research methodologies existed. It is perhaps time to examine the benefit v. risk of releasing archival clinical blocks for research. First steps should include examination of current usage rates of archival blocks for subsequent clinical care and a subsequent reassessment of CLIA and CAP rules pertaining to retention requirements.
Inserm, Toulouse, France
Exchanging (import/export) human biological samples is an important step for collaborative medical research within and outside Europe. Such exchanges must comply with heterogeneous National, European and International regulations. In this context, hSERN, “human Sample Exchange Regulation Navigator”, is a web based tool providing theoretical and practical information on legal and ethical requirements for transnational exchange of human samples for research uses. Initiated within the European GA2LEN network of excellence (FP6) it is now further developed in connection with BBMRI (Biobanks and BioMolecular European Research Infrastructure). The beta version of hSERN is available online at http://www.hsern.eu/. This tool is dedicated to research institutions, researchers, and anyone interested in the regulation of such exchanges. hSERN is based on the analysis of the relevant texts, namely: International regulation issued by several organizations (WHO, Council of Europe…), European Union's regulation (such as Directive 2004/23/EC …) and national legal frameworks on medical research of the 27 Member States of European Union; 4 countries are fully documented so far (Belgium, France, Spain and UK) and 7 others partially. Legal experts in each country are validating the information presented in a systematic way. The structure and functionalities of this tool and the issues encountered will be described. This tool is provided freely to the scientific community; it is oriented towards offering clear information on heterogeneous regulation and its systematic and transparent organization, as a first step of the global harmonization that is difficult to reach with so many variable regulations.
Museum Repositories
The Natural History Museum London, London, UK
Background: Molecular research at the NHM plays a major role in resolving questions on the diversity of life. Plants and animals are collected for traditional dry or alcohol preservation, and as a long term resource for molecular analysis. Molecular products are also extracted from ‘traditional’ collections. The NHM is developing new ‘molecular collections’ (in parallel to the ‘traditional’ collections) for future use beyond its own research programmes, making them accessible to the wider community and ensuring their long term value to science. Developments in the techniques of molecular biology, including next generation DNA sequencing, create exciting research opportunities and drive forward the need to preserve biological samples for study by future generations.
Results: The NHM molecular collections have been managed by individual scientists and their research teams. New infrastructure, management and curation is now planned to accommodate existing and future collections and to integrate their development and management with the traditional collections. To ensure this, the NHM will build a central specialized storage facility within easy access of the NHM's research teams and the traditional collections.
Conclusions: Future-proofing the facility requires international legal compliance, identification of optimal storage methods, global standards, best practice and incorporation of new science and IT technologies. Exchange of knowledge in all these areas among partner institutions is vital to promote global sharing of genetic data. Our poster attempts to contextualize the current position of the molecular collections at NHM London within existing global networks of molecular initiatives.
National & International Biobanking Networks
Federal Office for Radiation Protection, Neuherberg, Germany
The sharing of data and biomaterials from publicly funded experimental radiation science will yield substantial scientific rewards through re-analysis and new investigations. To that end, the STORE Consortium will create a platform for the storage and dissemination of both data and biological materials from past, present and future radiobiological research. The project will be completed by an assessment of viable financial models for long term support of a bioresource and Data Warehouse for radiobiology. The strategy to achieve these goals is multi-level:
1) To provide a “one-stop-shop” portal integrating international databases and other repositories currently active, such that the user can find material and data held remotely. 2) To archive primary (raw) data or pointers to data in public databases, from radiobiological experiments and studies. This resource will be open to individual investigators and to funding agencies as a potential central repository for data sharing. 3) To physically archive threatened material resources which are considered to be a valuable resource to the Community, and whose state of preservation is consistent with STORE benchmarks. 4) To provide a single point of access to the integrated biomaterial resources through standardized request procedures.
STORE will provide a single online portal to radiobiological information that is presently distributed over scientific centres worldwide, and it will provide the necessary SOPs for the evaluation of archived tissue usability.
Federal Office for Radiation Protection, Neuherberg, Germany
Today's research is providing us more and more with the opportunity to quantify radiation risks at the individual level. New approaches allow the re-analysis of old data using new techniques. Thus, the retrospective analysis of earlier studies is an important resource for modelling and evaluating risk parameters. The European Radiobiology Archives (ERA), together with corresponding Japanese and American databases, hold data from nearly all experimental animal radiation studies carried out between the 1950s and the 1990s, performed on different species and involving more than 400,000 animals. The concept and preliminary work on a computerized database to store and index this huge amount of data was started by G. Gerber and has now been transferred to a web-based database to maximize its usefulness to the scientific community and achieve compliance of data coding and structure with currently accepted semantic standards for anatomy and pathology. The accuracy of the primary data input was assessed and improved, thereby detected errors were corrected with a low mean-systematic error rate of only 1.7%. The majority of the original rodent pathology nomenclature was recoded to Mouse Pathology (MPATH) and Mouse Anatomy (MA) ontology terms or a combination of both.The database is accessible online at https://era.bfs.de, and has the potential of becoming a world-wide radiobiological research tool for numerous applications, such as the re-analysis of existing data and as an information resource for planning future animal studies.
Westmead Millennium Institute, Westmead, Australia
Background: Personnel involved in the operation of tissue banks in Australia and New Zealand recognized that their relatively small population coupled with large geographical distance would benefit from the formation of a national alliance1. Due to limited funding, such networks are often project- or clinical trial driven. As the Australasian tissue banking network expands, the need for a more formalized structure became apparent and an autonomous networking structure was established to ensure continuity, independent of funding or project goals.
Methods: A voluntary informal network of tissue banks was established in 2002: The Australasian Biospecimens Network. Successful annual meetings; recommended SOPs; and involvement in several Federal and State government review papers have contributed to the biomedical research landscape in Australasia. With the value of the network apparent, the decision was taken to formally constitute the network into an association.
Results: The Australasian Biospecimen Network Association (ABNA) was incorporated in July 2009. To date it has attracted 80+ subscribed Australian and New Zealand members from diverse biorepository backgrounds. ABNA allows tissue banking professionals to come together to share relevant non-confidential information to assist improvement of operational efficiencies, provide education and technical assistance to individuals establishing biorepositories and provide a structure and focus within the broad biobanking community of Australasia.
Conclusion: The evolution of an informal network of tissue banking professionals to a formal association reflects the development and maturation of tissue banking in Australasia. ABNA provides the stability of an independent association underpinning an international network of biobanks. 1 AJMS 2007; 28, 1, 16–20.
BioRep s.r.l., Milano, Italy
Background: Biobanks or biorepositories are increasingly seen as an essential tool in translating biomedical research into real improvements in healthcare. The CHDI Foundation has established a secure, global biorepository that stores and distributes quality-controlled and reliable biomaterials to support Huntington's disease (HD) research in a broad spectrum of research endeavours.
Methods: The Coriell Institute for Medical Research in USA and BioRep in Italy have joined their biobanking expertise and together constitute a “Global Biorepository” to serve biomedical research and worldwide clinical trials. HD collections at Coriell include the HD Community BioRepository, COHORT, and MITO-HD with specimens from United States, Canada and Australia. BioRep houses Registry (EHDN, European Huntington's Disease Network) and TRACK-HD samples. For the Registry network, Biorep collects and processes samples from 16 European countries and will soon include samples from Korea, Singapore, Russia and Turkey.
Results: Together Coriell and BioRep have banked samples from more than 5000 different individuals for HD research. These collections include: lymphoblastoid cell lines (LCL), genomic DNA samples extracted from whole blood and from LCL, RNAs, urine samples, plasmids containing HTT cDNA with CAG repeats of known lengths, antibodies that react with HD-relevant antigens, and striatal or PC12-based cell lines. BioRep has also started the distribution of DNA samples to any researchers that request the material through the EHDN portal.
Conclusions: The Global Biorepository for HD Research facilitates international collection of biospecimens. This effort aims to accelerate discovery of biomarkers and new therapeutic agents to slow or delay onset of the disease.
Botanic Garden and Botanical Museum Berlin-Dahlem, Berlin, Germany
The partner institutions of the DNA Bank Network share their DNA data via a central webportal (www.dnabank-network.org). Scientific customers can search for and order DNA samples. The webportal provides full online documentation of each record. For this purpose multiple databases are connected live. Thereby dealing with redundancy and copies to be updated can be avoided and verifications or metadata analyses can easily be accomplished. Whereas data like taxon information, collection details and voucher images of the organism from which DNA or tissue was taken are contributed from specimen databases. DNA data such as extraction method, DNA purity and quality are provided by DNA databases. Additionally, links to inferred molecular data are placed if those are published in sequence databases. Here, the structure of the webportal's underling data architecture is presented. GBIF's wrapper software DiGIR/DarwinCore and BioCASE/ABCD is used to transfer specimen data from multiple sources. The DNA Module was newly developed as an open source software to enter and manage DNA sample data by the partner DNA banks. Using unique identifiers DNA and specimen datasets can be referenced. To transfer DNA data via BioCASE a DNA extension of ABCD schema (ABCDDNA) was developed. The webportal currently offers data of four DNA banks associated to major biological research collections such as the Bavarian State Collection of Zoology (Munich), the German Collection of Microorganisms and Cell Cultures (Braunschweig), Zoologisches Forschungsmuseum Alexander Koenig (Bonn) and the Botanic Garden and Botanical Museum Berlin-Dahlem. The webportal is open for cooperation with further DNA banks worldwide.
Spanish Respiratory Research Network (CIBERES), Palma de Mallorca, Baleares, Spain
Background: In 2008 the Spanish Respiratory Research Network (CIBERES) promoted the creation of a network structure for the systematic collection of lung tissue samples and clinical information to facilitate respiratory research. Ten tertiary spanish hospitals joined the initiative. The objective of this platform is to standardize the methodology to obtain and preserve lung tissue, to assure that tissue samples are linked to full clinical, functional and imaging information of the patient and to create a bridge between hospitals and researchers.
Methods: The first step was to agree with all participating hospitals the common management and methodology to be used. After the standard operating procedures were agreed, common database software was launched and the persons involved were trained. At each hospital thoracic surgeons, pathologists, pulmonologists and local biobanks participate in the activity of the platform.
Results: One year after its launching, the CIBERES Pulmonary Biobank Consortium includes 4,700 aliquots from 250 patients. All of them required thoracic surgery for clinical reasons, mostly lung cancer. Samples are available to the entire scientific community (www.ciberes.org), provided that samples are used in a specific research project approved by an ethics committee, and that investigators agree in returning their raw data to the platform. In this way, it will not only be a repository of tissue but a source of information for future investigations.
Conclusions: The CIBERES Pulmonary Biobank Consortium has established a hospital-based network for the systematic collection and preservation of lung tissue samples coupled to relevant clinical information under strict quality control criteria.
Trans-Hit Biomarkers, Montreal, Quebec, Canada
Academic research laboratories and their Offices of Technology Transfer (OTTs) along with private research laboratories from pharmaceutical and diagnostic companies have the pressing need to get easy access to retrospective clinical sample collections to facilitate the discovery and to accelerate the validation of new biomarkers. A survey indicated that identification and selection of biobanks can be “challenging” for those seeking quality biospecimen collections. On the other hand, biobanks have the critical need to find new resources. Establishing a partnership with scientists who are developing new biomarkers is one option for biobanks who also wish to establish scientific collaborations. Therefore, expanding their ability to get international visibility becomes important. A new communication tool has been developed to offer keys players in the biomarker field an easy way to interface with each other. A website has been built offering a variety of services such as: regulatory requirements for biomarker development, appropriate animal models from reputed preclinical CROs, biomarker licensing opportunities offered by worldwide OTTs. This new website is visited by private and public scientists. It is an interactive web based tool to facilitate networking and connection between “seekers” of sample collections and biobanks. Functionalities of this free website service will be presented as well as results of our experience. The usefulness of this tool for biobanks to gain exposure and international appeal for their collection and to introduce their expertise by utilizing web based technology will be discussed.
Plant/Seed Repositories
Chungnam National University, Daejeon, South Korea
The genus Brassica, phylogenetically related to Arabidopsis thaliana, is one of the economically important crops and a botanical model of plant polyploidization and rapid phenotypic evolution. We established the Brassica Resource Bank(BRB) in order to supply basic plant materials for structural/functional genomics and breeding of Brassica. BRB has served various Brassica species, especially, general germplasm, inbred lines, and DNA stocks including BAC libraries and cDNA libraries. All germplasms of BRB have been propagated and maintained. Currently, BRB has collected 9,689 accessions for Brassica species, 91,446 clones for cDNA libraries, and 277,440 clones for BAC libraries, and 1,398 genetic markers. BRB has served more than 621,345 clones, 280 genetic markers and 4,023 lines to researchers in 10 countries since 2003. Information and other requests for genomic resources of Brassica are accessible at http://www.brassica-resource.org.
University of the Witwatersrand, Johannesburg, South Africa
Introduction: South Africa has a rich flora but many species are under major threat. Many of the plant species are either poor seeders or produce recalcitrant (desiccation-sensitive) seeds and cannot be stored conventionally. There are particular problems associated with successful germplasm cryostorage of tropical and sub-tropical plants.
Method: Excised embryonic axes, somatic embryos and excised shoot tips of several species were subjected to various cryopreservation protocols.
Results: Variable success has been achieved, and currently, cryopreservation protocols have to be optimized on a per species basis; no generic methods can yet be presented. Our criterion for successful cryopreservation is >50% production of both roots and shoots. Success has been achieved with the poor-seeding important African food crops cassava (Manihot esculenta) and yam (Dioscorea rotundata), using somatic embryos and excised shoot tips, respectively. Of the vulnerable medicinal species, successful cryopreservation has been achieved with globular stage somatic embryos of two poor-seeding Haworthia species, and whole seeds of Warburgia salutaris. Embryos of a number of species of the Amaryllidacea, and the palm Phoenix reclinata (all monocots) have survived cryopreservation. A common feature among excised embryonic axes of tropical/subtropical dicotyledonous species is the lack of shoot development; this is ascribed to excision damage involving a burst of reactive oxygen species.
Conclusion: Cryobanking can contribute to the conservation of indigenous recalcitrant-seeded and poor-seeding plant specie, although much development work remains to be done. The ultimate aim is to cryopreserve a representative sample of such germplasm for future ecological restoration.
Quality Assurance and Control
SeraCare Life Sciences, Inc., Frederick, MD, USA
Background: Biorepositories are not regulated to a single specific standard, yet customers operate in highly regulated industries and expect systems in place that control each process performed. The scope of repository processes varies for different customers. Understanding customers' project-specific requirements and their regulatory compliance needs, are essential to developing a Quality Management System (QMS) to meet these needs.
Methods: Elective standards applicable to biorepository activities include International Organization for Standardization (ISO) standards 9001, 13485, 14971, and 15189. Guidelines (i.e., ICH) and Best Practices (i.e., ISBER and NCI) may also apply. Applicable US regulatory standards could include cGLP, cGMP, cGCP, cGTP and CLIA. Once customer requirements are known, an analysis of these requirements against the applicable parameters is performed.
Results: Establishing targets based on customer requirements, and monitoring and trending performance to these targets, leads to a continuous improvement environment. Frequently used indicators include customer feedback, specimen condition, data error rates, turnaround time for specimen receipt, processing, evaluation and shipment, and measurement of first time quality for key tasks.
Conclusions: An effective QMS ensures the flexibility and capability of an organization to meet customers' specific needs and their distinct regulatory requirements. Whether specimens are stored for custodial purposes or services such as processing, testing, aliquoting, storage and distribution of blood and tissue are provided, the application of specific quality management tools to maintain and control biorepository processes is essential.
Veriteq Instruments, Inc., Richmond, British Columbia, Canada
Background: Monitoring and controlling temperature with independent systems is, in general, the best approach for maintaining the specifications of controlled environments. However, a closer look at the stability and accuracy of these systems may tell another story. Automated systems in particular provide real-time digital display of temperatures and send alarms when out of range. Why then do we still hear about losing thousands, or even millions of dollars in specimens, for example, despite everything seeming to be normal? It stems from a belief that temperature measurement accuracy equates to certainty, when it is no more than a probability.
Methods: Understanding what measurement accuracy means and what it does not mean in terms of maintaining desired temperatures. Using simple statistics, we can show how the accuracy of a measuring device determines the degree of confidence that an environment will be within its acceptable range.
Results: Systems that rely on the temperature accuracy of measuring devices alone can be shown to have varying degrees of probability that an environment will be within specification.
Conclusions: This session provides an understanding of how to ensure that system display temperature and ‘real’ temperature read the same.
Veriteq Instruments, Inc., Richmond, British Columbia, Canada
Background: Today, protecting temperature-sensitive goods in controlled environments is accomplished using three strategies: distributed, centralized and hybrid systems. Each method solves a variety of problems, either by themselves or in conjunction with other resources.
Methods: Understanding how each of these strategies align with the objectives of protecting valuable products and maintaining continuous records.
Results: The pros and cons of temperature monitoring with different approaches for protecting product quality and maintaining records needed for meeting regulations.
Conclusions: This session provides an understanding of the best-fit strategy for different types of monitored environments.
SeraCare Life Sciences, Inc., Gaithersburg, MD, USA
Background: The National Heart, Lung, and Blood Institute (NHLBI) Repository contains 4.6M biospecimens from over 70 collections conducted by 46 research programs over 40 years. The NHLBI has focused on increasing the utility of this national resource by making collections information available via BioLINCC (https://biolincc.nhlbi.nih.gov/home/). Collections were compiled and managed by multiple groups with varying levels of quality control (QC) and many of the older collections have high discrepancy rates. A QC effort is underway to assess the accuracy of data and identify any visible quality indicators.
Methods: A top-down approach to collections QC was used. Collections with the highest scientific value were targeted. A container-level reconciliation was performed to identify major gaps between the physical and the virtual inventories. A random sampling of the physical inventory was conducted and the criticality of observed discrepancies was analyzed. A determination of clinical data and informed consent availability that could allow broad research use was conducted.
Results: Collections error rates have ranged from 0% to 100%, with varying levels of criticality. Collections with a high probability for future use are being further reconciled and collections with a low probability of future use will be discarded.
Conclusions: This systematic approach to quality control allows for efficient review of large archived collections. This effort will ensure accuracy of data for the physical inventory, a reduction in custodial repository costs, and informed utilization of the collections. These efforts increase the overall value of the collections to the NHLBI and to the research community as a whole.
BioStorage Technologies, Inc., Indianapolis, IN, USA
Quality assurance (QA) procedures are fundamental to the successful operation of the biospecimen repository. It is necessary to have a fully integrated quality assurance system and comprehensive standard operating procedures to ensure the handling, processing, annotation, storage, and transportation of biospecimens occur at a consistently high level. The presenter will provide an illustrated overview of the GxP regulatory compliance requirements and expectations for computerized systems that produce, distribute and archive biospecimens. The presenter will also put emphasis on the management of electronic data and documents associated with biospecimen collection. Additional QA components that will be highlighted, include:
An overview of the regulatory framework for biorepositories How to integrate quality assurance processes as an ongoing component of standard operating procedures The role of quality assured and validated methods for specimen security and data confidentiality Best practices for ensuring business continuity with data back up systems How to establish a chain of custody for your samples to guarantee quality.
Asterand, Inc., Detroit, MI, USA
Background: Properly verified biospecimens are initial resources critical for identifying biomarkers in molecular-based biomedical research. Unfortunately, limited availability of adequately robust clinically annotated biospecimens as well as inconsistencies in clinical data that contradict pathology diagnosis can cause ambiguity in differentiating protein biomarkers in tumor and non-tumor tissues. In this study, candidate renal cell carcinoma protein biomarkers in blood were identified by determining what proteins are present and up-regulated only in tumor compared to normal human tissue and then determining which of these were also detected in blood plasma/serum samples.
Methods: Quality-controlled and independent pathologist-verified fresh frozen moderately differentiated kidney adenocarcinoma tissue, adjacent normal kidney tissue, and plasma/serum from the same patient were analyzed by GeLC-MS/MS proteomics platform. Protein identification profiles were obtained with Scaffold algorithm using files generated by Mascot. To assess quantitation, Venn diagrams illustrated overlap and correlation coefficients were calculated for each of the sample types.
Results: 3237 total proteins were detected in normal and/or tumor kidney tissue. 771 proteins (p < 0.05) were differentially expressed between normal and tumor. Of the 771 proteins, 120 were also detected in plasma and/or serum. Of the 120 proteins, 28 were ≥2-fold increased in tumor, 55 were ≥2-fold decreased and 37 had fold changes <2-fold.
Conclusions: Differentially expressed, up-regulated plasma/serum proteins (28) were identified and linked to glycolysis, rennin-angiotensin system, glutathione metabolism and Ras signaling pathways. Independently verified and quality controlled biospecimens enable integration of clinical and downstream proteomic pathway data for identification of biomarkers in human blood.
National Institute of Health, KCDC, Seoul, South Korea
Following the rapid progression of genomic research in humans, the discovery of critical genes and pathways as well as the follow up analysis of their impact and significance will depend on the quality of biological specimens. For quality control of blood samples, National Biobank of Korea performed experiments to assess the effect on the delay of blood processing time on the quality of serum and plasma. Statistically significant variation of biochemical measurements was determined using the repeated-measures ANOVA. The significant change limit (SCL) was used to determine the clinically significant changes of the measured analytes. In spite of many conflicting previous reports, the levels of seven analytes (AST, GGT, LDH, CRP, BUN, Creatinine and Glucose) were different in the serum according to the time delay before or after separation. In addition, the repeated freeze/thaw cycles affected the levels of LDH and ALT both in serum and plasma, whereas the level of TG was varied in only the serum sample. These results showed that the level of some biochemical analytes depended on the pre-analytical conditions such as the delayed time or freeze-thaw cycles.
Zoologische Staatssammlung München, Munich, Germany
Background: In current biological research, enormous amounts of DNA samples are being processed. Whether the purpose is to verify published results, to extend and complement previous investigations or to conduct new studies, high-quality long-term storage of the DNA samples is always essential. While DNA isolation methods, sequencing technologies and data analysis methods improve continually, the influence of various storage conditions on DNA quality is still insufficiently investigated.
Methods: As part of the DNA Bank Network Project (www.dnabank-network.org) funded by the German Science Foundation (DFG) we investigated DNA degradation in sample storage at five temperatures (room temperature, +4°C, −20°C, −80°C, −196°C), and in three different agents (buffer, water, QIAsafe DNA Tubes). The influence of sample dehydration, protective additives (trehalose) as well as of repeated freezing and thawing was also examined. DNA degradation was measured by a quantitative real-time polymerase chain reaction (qPCR) method. Here we present the results of our experiments after 13 months of storage.
Results and Conclusions: DNA preservation in water led to dramatic degradation after a few months of storage at the higher temperatures (RT and 4°C). With the other storage agents there was only a weak influence of the storage temperature on DNA quality. Sample dehydration had a positive effect on DNA quality, whereas the influence of trehalose was practically negligible. For large DNA fragments preservation was best in QiaSafe DNA Tubes. Surprisingly, we found no influence of repeated freezing and thawing of the samples on DNA quality.
Saint Louis University, Saint Louis, MO, USA
Background: The foundation of research is the availability and use of donated de-identified patient samples. This abstract reports a lack of awareness of proper transport of samples and appropriate use of consent forms.
Methods: Retrospective review for quality assurance of tissue donations revealed problems obtaining appropriate consent and maintaining the integrity of specimens (through monitoring time intervals for transport from the OR to the frozen section lab then the TRL).
Results: Patients(n = 879) resulted in 3001 specimens for the TRL from 6/29/05-1/28/10. Concerns emerged: potential contamination from prior tissue processing; time span for transport of specimens to TRL (75% received <30 minutes); not notified specimens were available; not enough residual tissue after pathology's processing (38 patients/4.3%); tissue released to TRL directly by the surgeon before diagnosis (2 patients,0.2%/3 aliquots(0.1%). Consenting problems: not consented (5 patients,0.5%/72 aliquots(2.4%); 2 patients consented with non-TRL forms (0.2%)/22 aliquots(0.7%). Approximately 23 patients consented using TRL consents and tissue kept by surgeon for own use.
Conclusion: In our institution, consenting problems represent approximately 3% of specimens; these specimens cannot be used for research. It's disconcerting, if the diagnosis of these 94 (3%) specimens is rare. Tissue degradation due to prolonged time from surgery to TRL adds to this number. Specimens not properly consented are ‘quarantined for an undetermined time’. Non-consented specimens (typically discarded) which cannot be released to researchers could be used to validate new lab methods. Researchers are notified annually of protocol/consent renewal, that the TRL has a specific consent form; using it requires tissue be stored in the TRL.
Istituto Zooprofilattico Sperimentale della Sicilia, Palermo, Italy
Istituto Zooprofilattico Sperimentale is a research laboratory working for human and veterinary health according to a quality system regulated by UNI CEI EN ISO/IEC 17025:2005 norms. Among research activities there is cell isolation, amplification and banking. MSCs, primary and stabilized cells are banked. Equine and canine MSCs are collected from Bone Marrow (BM) and Adipose Tissue (AT). MSCs are used in order to study tissue remodelling both autologus and allogeneic implantation. Quality controls and safety testing methods are applied to assure cell biosafety. Biosafety controls are applied to donors, reagents, growth media, bone marrow and adipose tissue samples and MSCs. Microbiological controls are:
bacteria and fungi detection: samples are inoculated into liquid and solid specific media; mycoplasma detection: culture in solid and liquid media, indirect DNA staining (Hoechst 33258), Polymerase Chain Reaction (PCR); virus detection: a panel of tests to detect pathogens, endogenous and adventitious viruses (culture in permissive monolayer cultured cells, PCR, electronic microscopy, immunoenzymatic tests).
MSCs characterization: colony forming unit, differentiation assays and molecular biology. Oncogenicity and tests: evaluation of capacity of the produced MSCs to induce tumor in vitro and in vivo in nu/nu mice. Stem cell banks have to assure the quality, traceability and MSCs safety. These aims are particularly important in the avoidance of transmissible diseases. A safety testing regime ensures the availability of MSCs for clinical and experimental use. Our certified quality system is also a guarantee for shared activities with other research groups.
AIDS and Cancer Specimen Resource (ACSR), San Francisco, CA, USA
Background: The US National Cancer Institute (NCI)-supported AIDS and Cancer Specimen Resource (ACSR) is composed of three regional biorepositories. Such multisite operations are challenged by constraints of distance and different physical facilities, access to resources, personnel and organization. Quality performance of ACSR is facilitated by a Central Operations Data Coordinating Center (CODCC).
Methods: The ACSR CODCC developed an audit tool based on NCI/ISBER Best Practices for Biorepositories that includes evaluation of: administration, internal and external guidelines, safety, inventory, marketing and informatics. Yearly audit events include
1) self audit with remediation of deficiencies, 2) onsite audit by a CODCC/NCI team with exit discussion followed by an audit report and 3) remediation of any deficiencies with documentation and 4) discussion of audit results with the ACSR executive committee.
Results: Application of this auditing format in 2009 allowed the ACSR to identify areas affecting quality of biorepository samples, opportunities for process improvement, documentation of adherence to good practices as prescribed by approved SOPs and opportunities for continuing improvement. 2009 audit findings have been translated into improved audit tools for our 2010 audit, updating of SOPs and a better understanding of practice issues across the enterprise.
Conclusions: The repeated use over time of a universally applicable auditing tool for assessment of multisite biorepository enterprises provides a format for biorepository continuing quality improvement. This process is expected to assure a consistent or more predictable biorepository product and thereby provide better service to our research community.
NUH-NUS Tissue Repository, Singapore
Sample preparation of solid tissue specimens is one of the key factors for effective extraction of DNA and RNA. The tissue needs to be broken down into fine particles for cell lysis and to maximize biomolecules yield. Effective homogenization is thus vital. Currently, there are various methods of tissue homogenization such as beads mills, rotor-stator, mortar/pestle, vortex and sonication. Our lab has evaluated a prototype unit developed for tissue homogenization through the use of abrasive materials in conjunction with cavitations. DNA and RNA yields as well as the quality of the biomolecules are evaluated. We analyzed the RNA quality by 18S/28S rRNA ratio and used PCR and gel electrophoresis for DNA quality assessment. Results showed that this method of tissue homogenization is comparable to rotor-stator which is routinely performed in our lab.
National Cancer Institute, Bethesda, MD, USA
Background: The amount of detail reported concerning biospecimen characteristics and handling varies widely in scientific publications. We addressed this by compiling reporting recommendations for biospecimens.
Methods: A workshop was held at the 2009 Biospecimen Research Network Symposium to form biospecimen reporting recommendations. The resultant list was refined at monthly teleconferences by a committee of workshop attendees and other experts.
Results: The committee composed a three-tiered list of biospecimen data that should be reported, if known and applicable, for all biospecimens or patients in the study. The first tier, items necessary to report, includes biospecimen type; relevant clinical characteristics; collection, stabilization, and preservation mechanism; type and composition of long-term preservative; storage temperature and duration; shipping temperature(s); and composition assessment and selection. Items advisable to report form the second tier: patient demographics; accrual scheme; time and temperature between acquisition and stabilization; type of collection container; time and temperature in preservation solution; aliquot volume; shipping duration(s); gross and microscopic review; proximity to relevant anatomical lesion; and details of enrichment for relevant component(s). Additional items to report, or third-tier items, include agonal state and cause of death for postmortem biospecimens; relevant exposures; reproductive status; nature of biobank; time from blood flow cessation to acquisition; specimen size; type of storage container/slide and shipping vessel; shipping conditions; number, time, and temperature of any freeze-thaw events; embedding medium; and quality assurance measures.
Conclusions: If followed, these recommendations will provide readers with comparable method information to evaluate, interpret, compare, and reproduce the results of experiments that employ human specimens.
Kyungpook National University Hospital, DaeGu, South Korea
Every year, over one hundred thousand paraffin-embedded tissue blocks (PETs) are made for making final diagnosis in the departments of pathology in general hospitals. The PETs should be used for biological research experiments if genetic materials in the PETs are well preserved. We tested the quality of RNA and DNA when fixed in 10% buffered formalin (FF-PETs), methacarn(MF-PETs) or the fresh frozen tissue(FFT) of endoscopically mucosal resected (EMR) or submucosal dissected (ESD) gastric adenocarcinomas. Three groups consisted of 20 patients. RNA and DNA integrities and stabilities are measured by Analytic Bioanalyzer (Agilent Ltd., USA) and performed GAPDH PCR. MF-PETs were satisfactory (70% success rate in GAPDH RT-PCR). Even though the FFT are the best method for preservation of genetic materials, MF-PETs of EMR or ESD tissue are necessary, because invasion depth of the cancer cells is important for diagnosis and treatment evaluation of EMR- or ESD-treated gastric adenocarcinomas. Because the genetic materials are fragile, the PETs should be stored at room temperature (−20 °C in the case of MF-PETs) and improvements of tissue fixation, processing and storage methods are necessary for long term storage of the tissue and genetic material. The standardization and quality control of RNA and DNA extraction methods with reliable verification are important. A registry integration program for multi-institutional quality assurance might consist of annotation (especially, for banking of tissue microarray blocks), quality control, search and distribution portion of the proper resources.
Genome Quebec and Chicoutimi Hospital/Ecogene-21 Biobank, Chicoutimi, Quebec, Canada
Background: Preserving and monitoring the quality, integrity and security of stored biological samples is a huge biobanking challenge. At each step, the way a procedure is applied has an effect on the status of the sample. An integrated, systematic and comprehensive quality system is required to assure the security, prevent the deterioration and estimate the duration and quality of life (DAQOL) of each biospecimen.
Methods: The Genome Québec and Chicoutimi hospital/Ecogene-21 Biobank (GQ Biobank) has developed and implemented a robust multi-level quality system to monitor the integrity, DAQOL and security of stored biological samples. This system is inspired from the pharmaceutical industry standards and includes an operating and a documentation structure established to prevent and anticipate problematic situations. Central monitoring allows the supervision of samples processing and storage, physical access, technical aspects and to trigger alarms when required. DAQOL control system evaluates the effect of time, storage conditions and sample handling on selected biomarkers such as proteins, hormones, lipids or electrolytes. A set of quality control (QC) indicators facilitates the longitudinal follow-up of the samples, technologies and methods, from sample collection to downstream analyses.
Results: The system, along with its standard operating procedures, access policies and monitoring tools, has been tested in clinical trails and in community and population genomic projects. This allowed to improve the QC tools and algorithms.
Conclusions: Reliable QC systems are absolutely required to monitor the quality of stored biological samples. The needs are huge and evolve over time. The GQ Biobank is committed to cover the unmet needs.
Rutgers University, Piscataway, NJ, USA
The quality of genomic DNA is a core component for most biorepository programs. To date many different approaches have been used for both the quantitative and qualitative appraisal of gDNA, however, there is no standardization for the functional assessment of DNA quality for downstream applications. Currently, most gDNA quality measurements use non-specific assays which demonstrate the global quality of nucleic acid but provide little or no information on gender mismatches, potential sample contamination or ethnicity which are important metrics for any lab reposing or managing samples in a repository setting. We have developed a rapid, cost effective means for assessing the quality of gDNA while capturing critical information on each sample tested. A panel of 96 SNPs (Single Nucleotide Polymorphisms) has been developed and validated using the Fluidigm 96.96 dynamic array for the efficient and cost effective processing of samples using this panel. This study describes a panel of SNPs that have been validated to determine sample contamination, decipher reported gender mismatches for genotyping studies, as well as determine ethnicity information for each gDNA. The correlation of our approach to standard QPCR validation of all assays utilized is 100%. The correlation to SNP data from DNA microarray and capillary electrophoresis analysis is 100%. This approach allows the repository to easily quality control over 10,000 samples per month while reducing operating costs and generating essential information that is used for accurate sample and study management.
Center for Genome Science, Korea National Institute of Health, Seoul, South Korea
Human genetic studies have used an increasing number of biobanked DNA samples which requires the consistency of DNA quantity and purity between multi-centers or multi-laboratories. In an attempt to standardize DNA quantitation protocols, we performed the DNA quantitation project in which 16 technicians from 11 laboratories participated in measuring optical density (A260, A280, A230) of multiple DNA samples (n = 35) of known concentrations in order to analyze variations of DNA quantity and purity indexes. The mean inter-individual coefficients of variation were 21.9%, 7.4% and 24.7% for A260, A260/A280 and A260/A230 ratios, respectively. The mean intra-individual coefficients of variation were 9.9, 1.7 and 8.3 for A260, A260/A280 and A260/A230 ratios, respectively. We identified that more than 100 ng/ul DNA concentration reduced the variability of DNA quantity (A260) and purity (A260/A280 and A260/A230 ratios) indexes. This work would help standardize DNA quantitation protocols of obtaining multi-center collaborated biobanked DNA samples.
University of New Mexico School of Medicine, Albuquerque, NM, USA
Background: Cytology smears assessed at the time of tumor collection can provide information on cell intactness (percent complete cells versus nuclei stripped of cytoplasm) and percent necrosis. This study evaluated whether cytology morphologic parameters predict DNA quality and quantity.
Methods: Thirty cases of five tumor types (sarcomas, gynecologic epithelial carcinomas, renal cell carcinomas, thyroid carcinomas and miscellaneous other) were evaluated by DNA concentration and A260 to A280 ratio. Histology assessment of paired formalin-fixed paraffin embedded tissues were compared with cytology findings and DNA quality/quantity data. Cytology parameters included percent intact cells, percent stripped nuclei, and percent necrosis (semiquantitative assessment by one cytopathologist). The same pathologist reviewed H&E sections for percent tumor volume and percent tumor necrosis (cellular intactness could only be assessed on the smears). DNA concentration and ratios were obtained using standard methodology.
Results and Comparisons: In general, cytology smear assessment of necrosis versus non-necrosis matched the H&E stained sections of tumor sampled adjacent to tumor taken for frozen storage. Five specimens with >90% cellular necrosis exhibited low DNA concentrations relative to specimens with stripped nuclei or entirely intact cells. DNA quantity and quality data showed no relationship to the estimated percent of cells with stripped nuclei. Gynecologic epithelial tumors averaged the highest concentrations of DNA (mg/ml).
Conclusions: In this pilot study, cytology estimates of necrosis predicted DNA concentration but not quality. Immediate smears may be useful in selecting tumor samples most likely to yield significant amounts of DNA.
BioStorage Technologies, Indianapolis, IN, USA
This session will review the structure and strategic benefits of implementing proven process improvement methodologies (i.e. Six Sigma) to combat rising development cost, cycle times and quality concerns. Although the information will be applicable for many operations, the presenters will focus on the role these strategies play in sample management for the pharmaceutical and biotech industries. Co-presented by two Six Sigma certified professionals, who have collectively spent 35 years in the industry, the presentations will highlight how these strategic management processes can lead to a 30 percent increase in operational efficiency. It is well documented that time is critical in pharmaceutical development, as one day lost in R&D could cost a company millions of dollars. Conversely, if a drug developer abandons a product after Phase II testing, it could have a great financial impact on the organization. Therefore, it is crucial that organizations understand the linkage between systematic, comprehensive processes and the positive effects these processes have on operational effectiveness. As such, the presenters will examine these challenges, provide practical design guidelines and use real-world case studies that help improve the success of this approach, while looking at sample management from an operational planning perspective. Topics covered include:
- How end-to-end process improvements help streamline operational activity, such as sample preparation, storage and transportation - How to use metrics as the basis for a comprehensive sample management plan - Process improvement methodologies that can add additional quality control measures to day-to-day systems and processes for managing samples and associated data.
Repository Automation Technologies
National Cancer Institute, Bethesda, MD, USA
Background: The Division of Cancer Epidemiology and Genetics (DCEG) within the U.S. National Cancer Institute (NCI) has collected approximately 12 million specimens in support of 500 studies aimed at understanding the etiology of cancer. Most specimens (68%) are stored at −80°C and many were collected prior to the routine use of printed labels and barcodes. Several other challenges exist with the storage and handling of specimens such as the use of inconsistent containers, inefficient use of containers due to partial withdrawal of biospecimens, and storage of specimens that have lost volume due to evaporation as well as other challenges all leading to higher labor costs for specimen handling, storage and retrieval.
Methods: To address these challenges, we are using automation to re-format, re-label, and re-organize material types to the extent possible without compromising specimen integrity. DNA specimens from the same subject are being combined and transferred into automation-friendly, space-efficient containers bearing 2-D barcodes. Other material types are being re-labeled (as needed) and re-grouped so that they can be stored densely in a manner that allows for more cost-efficient storage and labor saving retrieval practices.
Results and Conclusions: Initial efforts to automate the handling of DNA specimens have led to significant decreases in specimen processing time and storage space requirements. Pilot efforts to reorganize all specimens indicate that automation has the potential to lead to greater efficiencies in storage and handling and consequently will result in significantly lower overall costs for program management.
RTS Life Science, Manchester, Lancashire, UK
Background: In 2006 RTS worked with UK Biobank to produce a fully automated system capable of processing their blood samples. A strong market requirement has now led to the production of a smaller, cheaper and more versatile system to suit the needs of smaller sample processing laboratories. The new Automated Blood Fractionation system now employs a modified buffy coat recovery process that enhances yield to approach the very best manual recoveries.
Methods: Manual buffy coat extraction was compared to automated buffy coat extraction using the new RTS buffy coat recovery protocol. Buffy coat volume was measured in primary tubes and then, following aliquoting, in secondary tubes. DNA extraction was performed on harvested buffy coat and also from post fractionation remnants, i.e. remaining red blood cells, and compared for manual versus automated processing.
Results: Analysis of buffy coat volumes show that we are recovering up to 90% of the volume measured in the primary tube, with recovery being matched between manual and automated processing. However, following DNA extraction on these samples, DNA yield was found to be 80% of that achieved from manually extracted samples.
Conclusions: DNA extraction results indicate we are currently achieving 80% of the DNA yield accomplished from manually processed buffy coat samples. Manual processing allows constant alteration of movements and analysis of buffy coat recovery, which is impossible to achieve during automated recovery. However, the reproducibility of automated recovery means that we can guarantee this yield on a consistent basis and will not be subject to the variability inherent in manual processing.
Brazilian National Cancer Institute, Rio de Janeiro, Brazil
Background: The sample processing is the most technically demanding part of a biobank service, especially because of the large number of samples and protocols, which requires special attention to avoid operational mistakes. Due to the crescent number of sample collection and processing needs, in 2008 we started the implementation of automation of the BNT Laboratory.
Methods: To automate fluid aliquoting, we used MAPI System (CryoBio System, CBSTM) platform to process primary samples (plasma, serum) into multiple aliquots. Steps included the filling, sealing and bar-code identification of straws of 0.3 or 0.5 mL. We introduced the automatic platform MagNA Pure LC 2.0 (Roche Diagnostics) for both automated nucleic acid isolation and PCR set-up. Using the magnetic bead technology, the instrument processes blood and tissues samples. Steps included sample uptake, lysis, binding to magnetic beads, washing and elution.
Results: The MAPI system has been successfully set up at BNT for the preparation of fluids. To date, 1,300 blood samples from 550 donors were processed using MAPI. MagNA Pure proved to be very efficient for mid scale capacity of extracting a hundred samples per day. Also, 450 blood and 250 tissue samples were processed into DNA and/or RNA with MagNA Pure.
Conclusions: Both MAPI system and MagNA Pure platforms proved to be flexible and efficient tools. The automation of specimen processing in our biobank laboratory represented clear advantages: it increased sample processing productivity, optimized lab spaces, and reduced costs. Additionally, MAPI increased the capacity of freezer storage.
National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
Background: The US National Cancer Institute's Division of Cancer Epidemiology and Genetics (DCEG) conducts population-based and interdisciplinary research to discover the genetic and environmental determinants of cancer. DCEG has over 500 studies representing approximately 12 million collected specimens. These specimens have been or will be processed for DNA extraction, quantitation and aliquoted in an automation friendly manner for genomic testing. In close collaboration with SAIC-Frederick, DCEG initiated an aggressive plan to address the growing utilization of its DNA collection by implementing lean manufacturing and TQM practices into its specimen processing. The challenges in handling legacy specimens were identified; lack of barcodes, evolving labeling algorithms, multiple container sizes/types and inconsistent aliquoting schemes. The goal became to successfully overcome these challenges while increasing throughput at a lower cost per sample.
Methods: Addressing these challenges, DCEG began integrating automation to create pre-qualified, extracted DNA from biofluids for downstream applications. Pre-qualified samples are arrayed and tracked to allow for automated requesting, retrieval and production of run-ready plates for high throughput genomic testing. The automation allows for continuity of operations and short-term storage that is integrated within the robotic processing line.
Results: Initial efforts to automate the processing and handling of DNA specimens has led to the promise of significantly reduced costs, processing time and storage space requirements for the pre-qualified DNA. Additional components to the assembly line are being considered to expand the utility and throughput of the laboratory. The initial results indicate that greater efficiencies in biospecimen program management are attainable with automation.
Hamilton Storage Technologies, Hopkinton, MA, USA
Background: This project shows the advantages of distributed small scale biobanks that are shared between a common IT network to build a secure, cost effective, flexible, and reliable approach to large scale biobanking.
Methods: The approach will be addressed by using multiple compact, localized ambient to −80°C automated sample management systems. Each automated system will have access to a secure and compliant web service interface that will be integrated into a common Bio laboratory information management system.
Results: It is expected that allowing satellite laboratories to store and maintain their own samples locally helps facilitate a common process and approach to flexible biobanking but also increases the quality of biological research programs.
Conclusion: By introducing a unique and simple approach to satellite biobanking laboratories and combining a common top level interface that is integrated into a Bio LIMS results in a comprehensive, secure, efficient, and flexible solution for distributed biobanks.
Daedalus Software, Inc., Cambridge, MA, USA
Rich histopathologic annotation enhances the value of tissue biorepository samples. Currently, no automated, accurate annotation processes exist. Manual data entry underlies most current approaches. To solve this deficiency, we developed a novel automated process to extract standardized histopathology data from sections of the finalized pathology report (PowerPath) to download the information to our biorepository database (BTM™) for accurate sample annotation. Customized synoptic reports (SynR), based on College of American Pathologists recommendations, were developed for each gastrointestinal (GI) system organ. SynR are imported into the microscopic description section. Standardized language includes tumor types, grades and staging information. Non-productive text is deleted. Free text is limited to one field. The microscopic section text is imported from PowerPath into BTM. Then, synoptic report text is extracted, parsed and converted into annotations. These are entered into the Lucene text search engine as indices pointing to the surgical pathology case number. Each of these annotations can be used to search for samples from the relevant surgical pathology case. GI SynRs, introduced in 2007, are used routinely by all UCLA GI pathologists. We permit personalized language in the final diagnosis section as SynR in the microscopic description section ensure standardized language. Using pancreas as the test case, histopathologic data was imported successfully from the final PowerPath report into BTM and correctly associated with tissue samples. Samples with detailed histopathologic criteria are retrieved easily; for example, mixed acinar-endocrine + uncinate process + pT2. Complex searches using both SynR and other data fields elsewhere in BTM (i.e., demographics) are possible.
IRCCS San Raffaele Pisana, Rome, Italy
Traditional and innovative laboratory procedures are used for biomarker discovery studies and for the appraisal of biomolecular markers correlated to possible determinants of clinical outcome. This objective is easily achievable in our Institution thanks to the availability of a Multidisciplinary InterInstitutional BioBank (BioBIM) fully equipped for the automation of sampling, processing, storage and tracking of biological samples and completely integrated with the diagnostic section through an informatics platform connecting the laboratory informatics with a pre-analytical robotic system. Biological samples and tube racks are identified by a linear bar code and then the tube rack is scanned on a 2D reader, since each tube is assigned a unique 2D identifier. After this procedure, the aliquoting is carried out on a robotic platform by using the previously identified tubes. Finally the tube racks are stored at −80°C. A Sample Tracking Software is utilized to track all the sample identification and physical storage information. A tracking of plates and boxes handling is performed by means of RFID technology. All samples are automatically recorded in databases with encoded identification. Decoding can only be done by the biobank responsible, investigator or other authorized members of the research team. The entire process from bleeding to sample storage is controlled by an IT integrated platform. All personnel is using Standard Operating Procedures defined by international guidelines when available or internal standardized protocols. Partially supported by Grant ACC-WP 3/1b.
Genome Quebec and Chicoutimi Hospital/Ecogene-21 Biobank, Chicoutimi, Quebec, Canada
Background: Large-scale, high-throughput and cost-effective sample preparation is a must for today's state-of-the-art biorepositories. Combining reliable automated liquid handling protocols achieving complex processes with error-proof manual procedures to produce high-quality endpoint material is a considerable challenge for biobank process developers. Versatile automated workstations and robust protocols are key-components of such an integrated system.
Methods: We developed standard protocols to accurately dispense 10 uL aliquots of raw material samples to 384-well GenPlates using liquid handlers equipped with 1 mL disposable tips. Procedures were optimized for various sample types. GenPlates stored in the GenVault dynamic archive can be further processed to obtain high-quality DNA. Protocols were developed to extract DNA from GenPlate elements using an automated workstation mounted with a thermoshaker and specialized labwares. Extracted DNA is further purified with a magnetic bead-based technology and quantified by fluorescence on the same robotic platform equipped with a gripper arm, a 96-well magnet and a plate reader. Workflow among robotic workstations is ensured by normalized manual procedures.
Results: Automated workstations along with manual steps can be configured to accurately dispense small blood aliquots to 384-well GenPlates. Highly-complex, thoroughly-tested protocols ensure no contamination and sample homogeneity with a throughput of hundreds GenPlates per day. Downstream extraction, purification and quantification of 96 high-quality samples can be achieved in 3 hours using this integrated system.
Conclusions: We developed, validated and implemented protocols and procedures to maximize off-the-shelf technologies' versatility which we combined with accurate manual steps to achieve outstanding simplicity, quality and efficacy in DNA sample management.
The Charles Stark Draper Laboratory, Inc, Cambridge, MA, USA
Background: Traditionally, biological samples are frozen to protect their biochemical composition, preserve proteins and prolong cell life. All current methods of processing frozen samples require thawing before aliquots are prepared. However, repeated freeze-thaw cycling can damage samples in unpredictable ways and is labor intensive. Thus, biorepositories face a dilemma when building biospecimen inventories: freeze samples in multiple small volumes, consuming significant freezer storage space and increasing costs; or freeze in fewer large volumes, reducing initial processing time and storage space at the expense of freeze-thaw cycling later.
Methods: We developed a high-throughput robot capable of retrieving multiple frozen aliquots from a frozen biospecimen. The prototype extracts multiple frozen 0.10 ml aliquots from a single 1.8 ml cryovial of serum or plasma and deposits them into a separate cryovial for downstream analysis. The Rhode Island BioBank at Brown University independently evaluated the robot for reproducibility, variability and homogeneity using human plasma. Samples were analyzed for cholesterol, triglyceride, IgG and glucose at Children's Hospital Boston.
Results: The robot demonstrated it can extract multiple frozen, uniformly-sized and homogeneous portions of plasma which, when analyzed for 4 common analytes, give reproducible results with very low variability. The system maintains samples at −40 °C before, during and after coring.
Conclusions: The high-throughput robot supports the needs of modern biobanking. It provides a tool to distribute serum and plasma samples without exposing them to freeze-thaw cycling; protecting sample integrity and delivering critical space, time and labor savings. Uses might include serum, plasma, cells, small molecule compounds in DMSO and frozen tissues.
Repository Informatics
Baker IDI Heart and Diabetes Institute, Melbourne, Victoria, Australia
Background: The Alfred Hospital Heart Centre and Baker IDI Heart and Diabetes Institute maintain several large databases containing detailed cardiovascular records, however without linkage searching across databases was difficult and time consuming. This projects aim was to introduce a “platform” to link these records; and to access the de-identified data in a secure manner to facilitate research.
Methods: An experienced database administrator conducted an audit of the data sources and linking interfaces available. Adherence to current privacy laws and ethics was considered in choosing the platform to utilize.
Results: The Health Data Integration (HDI) system, developed by the Australian e-Health Research Centre, was selected and a ‘virtual data repository’ was created linking >41,000 Cardiac Catheter Laboratory, >11,500 Echocardiography Laboratory, >1,300 Heart Failure Clinic, >13,500 Healthy Hearts Clinic and >5,900 Biobank records. Inclusion of the Baker IDI Biobank database provides scientists with access to additional detailed clinical data relating to Biobank samples which are also available for approved research. The system has successfully assisted two research projects; (1) linking the Echocardiography and Biobank databases to identify specific valve disease patients with Biobank samples for genotyping, and (2) linking the Heart Failure and Echocardiography databases for a retrospective study of valve disease and renal dysfunction in heart failure patients.
Conclusion: We have established a centralized access point for our clinical and research databases. This will enable clinicians and researchers to retrieve a broad range of de-identified patient information using a secure and user-friendly interface.
University of Pennsylvania/CHTN-Eastern Division, Philadelphia, PA, USA
Background: The internet allows for sharing of data, speeding the exchange and transfer of data. Within healthcare/scientific research environments, protection of patient information is crucial. The needs for swift information access versus protection of patient information are not necessarily opposite dictums and can be synched in order to advance scientific research.
Method: The Cooperative Human Tissue Network Eastern Division (CHTN-ED), an NCI sponsored biorepository that prospectively procures human biosamples, has developed a three-tiered informatics approach to tracking and disseminating human biospecimens data while simultaneously ensuring HIPPA level compliance and patient anonymity. This schema employs a three-tiered approach utilizing:
1) database technology on multiple secure data-servers with functional record level encryption and unique identification numbering for data position tracking reference and de-encryption. 2) Programmatic Regular Expression Matching of patient clinical and pathological documentation prior to storage and dissemination. 3) Network layer using multiple computer industry protocols.
While the structure of database, application and network has been used historically, CHTN-ED's synergy of these constituent factors along with cross-platform internet controls speeds intellectual exchange while still ensuring clinical anonymity.
Results: The CHTN-ED has developed and implemented this structure. This demonstrates a proven record of success in providing real-time access to biosamples and the analogous, comprehensive and sensitive data, while protecting all patient clinical information.
Conclusion: Using the integration and interaction of the programmatic informatics components in a novel approach allows the distribution of biomaterials and corresponding data across the internet to advance the interests of the scientific community.
Foundation biobank-suisse, Bern, Switzerland
Biobank-suisse (BBS) is a collaborative network of Swiss biobanks running a web-based database combining information about biospecimens and patient data from participating biobanks. One major issue is interoperability which would ensure that the maximum amount of data from different sources could be collected into a single patient record to be used for research. BBS investigated the situation in Switzerland to propose a concept to ensure better use of resources and increase patient privacy. We set up a server to test the integration of applications such as CAISIS, TMAj, and SINATRAS. We analyzed the IT infrastructures in place at 6 different hospitals, where biospecimens are collected. We determined the functionality of the applications mentioned above and compared the underlying data structures. This allowed us to propose practical solutions for the collection and use of biospecimens in research. At the 6th hospital we found that the collection for biomedical research is little automated. Most data is collected manually. Automated data transfer from medical IT systems to IT systems used in research does not exist. The hospitals use different IT systems in their biobanks. None of the local biobanks exchange data with the local cancer register. We compiled a list with all IT systems in use and defined interfaces to better integrate with medical IT systems, other biobanks, and IT systems used in research. In the federated Swiss health care system, optimizing the interoperability of the IT systems could save money that is better spent for specific research projects.
AstraZeneca, Macclesfield, UK
Background: Demonstration of spatial molecular expression in human tissue micro arrays (TMA) by immunohistochemistry (IHC) and insitu (ISH) hybridization is a key part of oncology drug development (R&D). TMAs are miniature biorepositories of formalin fixed paraffin embedded tissue. Their composition should be determined statistically in advance to ensure meaningful research results.
Methods: To test expression of molecular targets in a range of human cancer samples, we have established a tiered cascade of TMAs. These enable IHC and ISH screening of multiple tissue cores across multiple cancer sub types. We used statistical methods to ensure that the composition of individual TMAs would enable the research question to be confidently answered. Different methods are appropriate depending upon whether the aim is to determine frequency of expression, differentiate clinical cohorts or compare follow-up amongst IHC-defined groups.
Results: The three tiers of the TMA cascade each required different compositions for statistical powering. For example, in a general cancer multitumour TMA, cores from 22 donors delivers a 90% chance of detecting a positive result if the frequency in the population is greater than 10%. Cancer specific TMAs in tier two and three require 30–40 donors per group to recognize statistical differences between cancer subtypes, while comparison of clinical follow-up can require several hundred individuals.
Conclusions: Establishing what is effectively a high throughput cascade of TMAs to investigate potential target expression in oncology requires considerable resource. It is important that the composition of the TMAs are at the outset appropriate to answer specific research questions.
Brazilian National Cancer Institute, Rio de Janeiro, Brazil
Background: To date (Jan 29th, 2010), the Brazilian National Tumor and DNA (BNT) has stored 14,312 samples from 3720 donors. Samples collected at the Brazilian National Cancer Institute are included in SISBNT after double de-identification, integrated with clinical, pathological, laboratory, and epidemiological data. Tissue aliquots can be either stored in −80 °C freezers or processed into DNA, RNA, protein, micro-dissected tissues, and other derivates. Fluids, including blood, pleural and ascite, are immediately processed into liquid phases (plasma, serum, other), cell phase, DNA, etc.
Methods: Due to the increasing demand of our biobank laboratory in order to attend to research projects, we needed to develop an IT solution to control a number of derivates that should be linked in the processing chain from the electronic informed consent samples collected at different times, and their multiple primary and secondary derivates.
Results: We developed a user-friendly tool for the SISBNT Oracle platform with a processing screen to select a particular aliquot and to register their derivates identified by 2D barcodes. Additionally, an electronic agenda was created to optimize human resources and equipment for activities related to a specific distribution project in the biobanking laboratory. Interestingly, the system checks resources and equipment available in the requested period, avoiding overlap.
Conclusions: This tool facilitated the routine workflow, which allowed us to organize shipping times, and the online derivate request traced by the customer. With the implementation of this new feature, it was possible to increase the efficiency of our service, organize internal processes and improve customer service.
World BioBank, Memphis, TN, USA
Background: Automated assignment of storage locations for biospecimens promotes efficiencies in accuracy and time management. We present a novel integration of two software platforms, both designed specifically for the management of biospecimens to achieve this goal:
(1) StrawIt™, the platform storage location program utilized with the MAPI storage system (both by Cryo Bio System, Groupe I.M.V. Technologies, France), and (2) caTissue Suite, the NCI's biostorage program. StrawIt™ nicely manages a cylindrical storage system (a liquid nitrogen [LN2] tank).
CaTissue manages grid/box-like storage configurations (such as mechanical freezers). We have successfully integrated the two systems in a semi-automated fashion.
Methods: Properly managing the output data files from the StrawIt™ system, containing assigned locations of cryostraws in our LN2 tank, allows us to routinely map locations to correct data fields in caTissue. Output files from StrawIt™ are CSV files. CSV files are automatically and routinely imported into correct Storage Position data fields in caTissue.
Results: Unique storage locations for our cylindrical LN2 tank (e.g. T01.Q1.C.03.L2) are mapped automatically to appropriate caTissue storage fields.
Conclusions: StrawIt™ can successfully integrate with caTissue to automatically populate storage locations assigned by StrawIt™ into caTissue. Management of output storage files allows the apparent limitation of caTissue to grid/box-like containers to be overcome. It also saves time and reduces error.
University Hospital of Verona, Verona, Italy
Background: Biobanking best practices suggest methods to improve quality of biological materials collected. Current information systems registering biorepository data are static. While they hold varying amount of data and provide varying degrees of search criteria, they do not make use of the data themselves. These systems could be used to provide quality monitoring and evidence based data analysis thus improving best practice methods.
Methods: A relational database infrastructure was created based on the analysis of biobank specimen annotation data-sets in cancer research projects. Collection and conservation protocols also provided data-set information. Specimens considered were tissue, blood and blood derivatives, DNA, RNA and cell lines. Quality test data were then added as additional related tables. This infrastructure was then developed on a management control software platform. Key performance indexes were identified based on quantative and qualitative analysis of sample and data.
Results: We have developed a specimen data management system that provides quantitative and qualitative analysis for sample selection. This allows only completely homogeneous samples to be selected. The comparative key performance indexes act as a quality control marker when applied to certain collection parameters. As such, it provides an indication on where to improve collection times to improve quality.
Conclusions: The information stored in a biobank is crucial to add value to biological specimens. However it also provides a data source to improve best practice methods. The application of business performance index tools to biobanking specimen registration software provides a means of improving biobanking using evidence-based analysis on data collected.
National Institute for Health and Welfare, Helsinki, Finland
Background: National Institute for Health and Welfare, Public Health Genomics Unit administers an extensive number of biological samples collected in various epidemiological and population based cohorts in Finland. Currently the biobank houses over 700 000 blood, DNA or RNA samples from more than 200 000 individuals. The biobank is focused on centralized DNA-extraction, quality control, storage and sample logistics. It is managed by a tailor-made laboratory information management system, SamWise. Over the past years, three different database systems have been in service in the biobank, but the need for more sophisticated and flexible LIMS has gradually emerged. Functionalities for sample management and DNA-extraction in SamWise started to operate in 2008 after one year of development. Since then the system has been built towards a more comprehensive, easily modifiable and user-friendly LIMS. Laboratory Information Management System, SamWise is designed to govern all steps of the sample flow within the biobank; data entry, recording of the samples, DNA-extraction results, quality and quantity measures, aliquoting data, sample locations and distribution of the samples. Data management is handled by versatile queries. Inventory elements, sample flow and logistics rely heavily on unique barcodes. SamWise is an in-house developed system combining database functions and LIMS. It is implemented using ASP NET and C++. It is currently using Microsoft SQL server database as a data warehouse. SamWise can be operated by several parallel users using any AJAX enabled Web-browser. Strict data confidentiality rules are followed in processes and all operations in the database are recorded into a transaction log.
IMS, Inc., Silver Spring, MD, USA
Background: BioLINCC is an NHLBI research resource which provides a single point-of-access to an aggregate of clinical data from more than 70 historical research studies and more than 4.6 million banked biospecimens dating from more than 30 years ago to the present. To establish and maintain this centralized shared resource, data must be prepared for sharing with qualified researchers and the linkage between data and biospecimens must be determined.
Methods: Standard approaches are utilized to prepare the submitted clinical data for sharing. Variables and accompanying documentation are reviewed for data sharing suitability. Personally identifiable information is removed and frequencies of data variables are compared with the study's published findings to confirm data accuracy. Data dictionaries prepared from submitted data are created. Variables regarding patient informed consent are analyzed and compared with the study's associated informed consent template documents. Biorepository inventory data are compared to submitted study data to link the two research resources. Unlinked specimens, specimens for subjects with insufficient consent, and questionable data values are investigated and corrections are made to the database upon confirmation from the original study coordinating center or study researchers.
Results: Since BioLINCC program inception in September 2008, over 70 research studies including 38 with a stored biospecimen component have been reviewed and posted to the BioLINCC website. 4.2 million biospecimens, representing more than 1.1 million study participants have been successfully linked to their research data.
Conclusions: The creation of a shared data and biospecimen research resource is feasible when standard operating processes are established and consistently applied.
TGen, Phoenix, AZ, USA
Background: As biospecimen science and sample processing technologies are evolving, software solutions do not provide sufficient flexibility to handle the variations in protocols that occur across projects. The Biospecimen Material Accessioning and Processing (BIOMAP) system was developed to support the Integrated Biobank of Luxembourg (IBBL) and address the data management challenges in the fledgling biobanking space with the intent of increasing operational efficiencies, storing complete biospecimen data and ultimately promoting scientific discovery.
Methods: BIOMAP addresses two shortfalls associated with software solutions in the biobanking space. Firstly, both biospecimen and sample/clinical data tracking are managed in a single system. The system is workflow driven and allows annotations to be compiled throughout the sample lifecycle providing a single access point to view their complete profiles. Secondly, the system is designed with the ability of all sample collection activities to be project driven. That is, the types of samples expected to be collected, the sites involved, and the data collection forms for the project are governed by user defined templates.
Results: BIOMAP has been configured and deployed for a number of different projects with varying sample and data collection requirements. Users have lauded the system for its ability to manage donor and sample identifiers, extensive data collection opportunities, standardized clinical vocabularies for online data collection, in-depth reporting and user friendly experience.
Conclusion: BIOMAP's adaptability and features have demonstrated that it can accommodate a variety of biobanking projects by providing a single data management portal and serves as a robust, stable foundation for eventual research and discovery pursuits.
A C Camargo Hospital, Sao Paulo, Brazil
Background: The A C Camargo Hospital Tumor Bank (ACCHTB) was established in 1997 to provide human tissue samples for the Human Cancer Genome Project, an initiative by the Sao Paulo Research Foundation and the Ludwig Institute for Cancer Research. To ensure the proper management of information associated with the collection of tissue, a database has been continuously developed by the Laboratory of Biotechnology (LBHC), with the help of members of the ACCHTB.
Methods: Since the establishment of the ACCHTB, regular meetings between members of the LBHC and the AACHTB have led to the refinement of the database, which has been implemented in new versions of the ACCHTB management system.
Results: The management system has evolved from a first version with basic solutions to the version currently in use, which has an interface for the management of the samples collected (e.g., fresh frozen or FFPE tissue, blood), the molecules extracted (e.g., DNA and RNA), the associated clinicopathological information and also of the research projects requiring access to samples stored by ACCHTB.
Conclusions: The experience gained has been used for the development of new solutions useful in tumor banking and cancer research. All software developed is freely available and is currently being translated into English and Spanish.
Washington University School of Medicine, Saint Louis, MO, USA
Background: Advances in molecular technologies and clinical trial design have mandated new requirements for the operation of biorepostories. caTissue Suite is a caBIG™ application designed to manage the associated complexities of biospecimen annotation data.
Methods: caTissue Suite is a software application developed with requirements gathering and acceptability testing by multiple institutions. The application uses a web browser to store and retrieve data from a relational database. Its open program interface (API) permits customized access to all of the application's features, and data integration or migration from other data systems. Using caGrid, multiple installations of caTissue Suite can connect to facilitate data and biospecimen sharing across institutions. The application supports role-based access to administrative functions (container and protocol management), biospecimen accessioning, and investigator queries. An interface allows for import and coding of textual pathology reports. Discrete pathology and clinical data entry is also supported through customized data form creation.
Results: caTissue Suite is sufficiently scalable and configurable for broad deployment across biorepositories of varying size and function. Numerous institutions have adopted the application and are using it in their daily operations. A caBIG™ supported, web-based “Knowledge Center” (https://cabig-kc.nci.nih.gov/Biospecimen/KC) provides on-going application support via discussion forums, technical and user guides, training tools, and webinars.
Conclusions: caTissue Suite is a freely available, fully supported, open-access software application for biospecimen data management. Use of caTissue Suite by several NCI Cancer Centers and other biospecimen resource groups is providing a rapid and facilitated path toward standardizing biospecimen informatics and promoting biospecimen data sharing both nationally and globally.
University of Copenhagen, Frederiksberg, Copenhagen, Denmark
Background: Copenhagen University Biobank for Explorative research (CUBE) stores biological specimens (human and animal) from experimental research projects associated with the University of Copenhagen. Experimental research materials could potentially generate more research output than initially planned. With novel information technologies, organizations can further utilize the collected samples to spur future explorative research and boost breakthrough research results. CUBE sought out for a biobanking informatics software which provides centralized data management, security, and control, in an effort to maximize data visibility, reduce manual efforts, and ensure regulatory compliance.
Methods: CUBE identified comprehensive requirements to establish its informatics backbone. The software needed to allow easy data entry on information associated with researcher, freezer, sample type, project, on any unique sample. Role-based access control was needed to provide complete data security. Moreover, extensive data accessibility was a critical requirement to take the collaborative efforts to the next level.
Results: By leveraging the informatics software, information on projects, plans, and operational procedures can be stored with associated individual samples or sample batches. Sample identities can be generated in batch with printed barcode labels and assigned to the designated researcher prior to receipt of actual samples. In the later phase of the implementation project, real-time information will be shared via web-browser among multiple researchers, both internal & external.
Conclusion: Consolidating user requirements on critical operation areas to select the best-suited informatics solution and establishing a solid implementation methodology are key to ensure success of a biobank's IT project, enabling a collaborative approach to enhance research efforts.
Massachusetts General Hospital, Boston, MA, USA
Background: MGH is one of the largest academic hospitals in the world, with over $500 million in sponsored clinical and translational research per anum. Last year, MGH Pathology built a combined clinical research testing/tissue banking facility known as “the CLR” to support this research community. Rather than using a LIMS or a banking specific IT system, the CLR was built on the department's existing, clinical laboratory information system (LIS). Reasons for the decision included the need to support a large research clinical testing flow, the ability to leverage existing infrastructure and personnel and the system's proven ability to manage the hospital's clinical specimen flow.
Methods: MGH runs a Sunquest LIS with the Shared Application Module (SAM) (Sunquest Information Systems, Tuscon AZ USA). The CLR was created as a new laboratory in SAM with controlled dictionary, data and specimen sharing with the main clinical lab including access to enterprise interfaces. Tissue banking was implemented as a set of tests under the LIS test menu that drove specimen and data collection, custom requisitions, automated processing, aliquoting and archiving under nitrogen.
Results: The CLR went live in December 2009 as a consented repository. It has clean operational and financial separation from the main clinical lab with complete, controlled access to hospital billing, ADT, results, specimen routing and patient safety systems.
Conclusions: The use of the LIS allowed rapid deployment of the CLR and should make it stable and scalable. The system is tested to support millions of specimen each year.
IT Strategy and Management Consulting, LLC, Chatham, NJ, USA
Personalized approaches to drug discovery, drug development and clinical care promise a new generation of preventive and preemptive health care. But countless data and knowledge 'disconnects' continue to result in delays, dysfunction, and poor clinical outcomes. To address these challenges organizations are beginning to look to interoperable software tools, standards, databases, and computing infrastructure to accelerate the shift to a personalized medicine paradigm. But what are the risks involved in integrating these interoperable components across processes in discovery research, biobanking, imaging, and clinical research—and how might these risks be mitigated? This paper discusses the efforts involved in identifying and addressing these risks in the establishment of a biobank and collaborative discovery environment to facilitate research in a rare disease—Neurofibromatosis (NF). Specific attention is given to outlining the “key” components of an integrated collaborative research process and how the components are used for collecting and leveraging results and findings within and across the NF research community. The paper discusses the risks associated with data and knowledge integration and how best to manage these risks to facilitate interoperability and collaboration. Finally, the paper discusses how adhering to “best practice” in data and knowledge integration can facilitate the collection and leveraging of research results and findings across a scientific community; allowing new hypotheses to be surfaced, discussed, and tested, data and biospecimens to be more effectively leveraged, and most importantly, research results and findings to be surfaced and reviewed in a more timely manner.
Sapient Government Services, Rockville, MD, USA
Background: Last year, we introduced the National Cancer Institute's initiative to create a Common Biorepository Model for biobanks and biorepository management systems vendors to use to broadcast searchable summary-level data about the available specimen collections that researchers could gain access to.
Methods: We report from an informatics perspective on the advances over the last year to augment the number of Biorepository management system vendors and the Biorepository communities interested in joining in the 'CBM Challenge' to share non-cancer and cancer-related specimen data.
Results: We have collaboratively assembled vocabulary lists from the Specimen Resource Community across additional NIH institutes that have biorepositories, as well as reached to key biorepository management software vendors to participate in testing early Model, database, and associated caBIG® (Cancer Bioinformatics Grid) caGrid service to connect repositories together to publish searchable summary level de-identified information about their biobank specimen inventory. We will demonstrate the progress-to-date of the early CBM Grid service and how we are able to obtain specimen data from several test data sites.
Conclusions: The CBM initiative has drawn participation across fourteen biorepository software vendors and steps are in progress to share summary-level biorepository data across the participants using semantically integrated and syntactically interoperable methods developed for the NCI caBIG® program. Through use of the caBIG® infrastructure and the NCI Specimen Resource Locator (SRL) initiative, there is a plan to make specimen information available to researchers and institutes looking to quickly identify locations of specimens and availability to advance their research.
National Cancer Institute, Rockville, MD, USA
Background: As advances in biotechnology have increased and the role of biospecimens in clinical discovery, it becomes essential that bioinformatics tools support the reporting and exchange of biospecimen information.
Methods: Through the caBIG® (cancer Bioinformatics Grid) program, the US National Cancer Institute focuses on developing common vocabulary, data standards, and technology grid interfaces to enable interoperable solutions across tools required for biomedical research (clinical trials, biobanks, imaging, etc). caBIG® caTissue Suite is an open-source example that employs these standards and continually evolves to meet the biorepositories' and researchers' needs.
Results: caTissue Suite is a caBIG® biorepository management tool designed for biospecimen inventory, tracking, and annotation. The software capabilities include data migration, pathology and clinical data entry, and customization through an application programmers interface (API). caTissue is in full production or pilot testing at several institutes inside the US and abroad, including Canada, UK, the Netherlands, and Australia. Using caGrid, multiple caTissue instances can connect to facilitate data and biospecimen sharing.
Conclusions: The growing caTissue Suite community and their requests for connecting to tools within their institutes support the move towards a service-oriented architecture. NCI will define and use the Service Aware Enterprise Architecture Framework (SAEAF) to provide secure and updated enterprise-access to clinical trial data, pathology images, and molecular analyses associated with the specimen. Other tools (including non-caBIG®) could also access the information through the service specifications and caGrid. The interoperability and re-use of data through services can save scientists' research time; improve their efficiency, and reduce institution and government costs.