Abstract
Information Technology – LBA
The Construction and Development of Information System of Clinical Biobank
To construct the information system, the sample/data collection flow should be considered firstly. When the patient enter the hospital through the ADT (Admission, Discharge, Transfer System), doctors recruit them to different research projects according to clinical phenotype and diagnosis, sign informed consent, and begin the sample collecting procedure with CPOE (Computerized Physician Order Entry). With the acquiring of clinical data and diagnosis from AIMS(Anesthesia Information Management System), EMR(Electronic Medical Record), PIS (Pathology Information System), clinical biobank could access the quality of the biospecimen, then judge whether would be archive.
Comprehensive Paperless Biorepository Management
A Comprehensive Biobanking Ontology of the Lifecycle of the Biospecimen Made for-and-with Diverse Subject Matter Experts
Biobanking Without Borders, LLC, Durham, North Carolina, United States,
The macros also enable flags that require users' attention and provide the flexibility of manual updates if there are errors or discrepancies in the manifests. The macros were designed with user friendly interface that simplifies the training process.
OpenSpecimen - Experiences of Collaborative Development of an Open Source Biobanking Informatics Platform
Access to high-quality biospecimens with associated data annotations is crucial for research. Recent advances in molecular biology and genetics have resulted in a concomitant increase in the demand for well-annotated, properly preserved specimens. Today biobanking is a highly dynamic activity which faces many challenges, including the need to deal with ever increasingly complex demands of managing data and integrations with existing databases.
The available informatics solutions will not have an “out of the box” support or sufficient data elements set up appropriately. The informatics platform will need to support the complex sample management workflows and data collection needs which are of diverse nature and specific to each collaborator, disease, or even geographic location.
OpenSpecimen is the result of the collaborative efforts of NCI and has continued its further evolution with industry and academic partnership. For the past eight years, Krishagni has worked closely with its biobanking community to develop a robust, scalable and highly flexible open source biobanking informatics platform.
As a result, OpenSpecimen is today used in 65+ biobanks across 15 countries.
Open source software (OSS) promotes collaboration, avoids single “vendor lock-in” and drives the cost of ownership down. It ensures a higher level of security since the source code is publicly available for audit. In comparison, proprietary software is highly secretive, can only be customized or enhanced by the vendor, usually at a prohibitive cost. In many instances, adopters are left with no option when the vendor ceases operation or decides to focus on some other product or business.
In this poster, we will demonstrate how collaboration with biobanks across the globe has allowed OpenSpecimen to expand and meet the ever-increasing needs of this domain. We will present examples of collaboration with Johns Hopkins, Memorial Sloan Kettering, Children's Hospital (Dallas), UT Southwestern (USA), University of New South Wales, SAHMRI (Australia), Singapore General Health and University of Leicester (United Kingdom). The poster will also highlight the open source methodology and the enhancements developed in OpenSpecimen as part of these collaborations.
In summary, this poster will highlight an increased need for informatics systems to stay apace with the changes being experienced by biobanking societies and how OpenSpecimen uses open source to achieve collaboration amongst biobanks across the globe.
Data Quality Assessment of the Human Biobank Information System in the National Biobank of Korea
Korea National Institute of Health, Cheongju-si, Chungcheongbuk-do, Korea,
Most biobanks are manipulating biospecimen-related inventory data by manual into the informatics system, which may generate various errors in the database.
The National Biobank of Korea (NBK) has operated the self-developed Human Biobank Informatics System (HuBIS) which maintains the storage and dissemination information of biological samples. This HuBIS handles various biobank inventory data generated from a central biobank and 17 regional biobanks which comprised of the Korea Biobank Network (KBN). Here, we report the analysis results of the data quality and database structure of the HuBIS in order to improve the database quality and reliability. The HuBIS database was analyzed for pattern of data errors in terms of 12 assessment areas including uniqueness and column consistency according to the Database Quality Certification-Value (DQC-V) of the Korea Data Agency. As the assessment result, the uniqueness was 0.17% and column consistency was 3.3%. The error rate of the total evaluation standard was 3.04%, which is equivalent to 3.2 of a Sigma level and the Silver class of the DQC-V standard. In addition, we analyzed the Entity Relationship Diagram (ERD) of the database structure, showing that it is possible to increase the data quality efficiently by improving data normalization.
Based on the assessment results of database quality, we will apply for a data quality certification of the Korea Data Agency, and will implement the 5-year roadmap of data quality management of the HuBIS.
The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States,
Repository Management - LBA
The institutional biorepository at Boston Children's Hospital (BCH) has applied instrumentation and informatics solutions to automate standard workflows. The challenges of implementing automation are not exclusive to the instrument, but in reality are multifaceted. A great deal of time, effort, and collaboration from all groups within the core is required, including informatics, management, research, and laboratory staff. Research and laboratory staff must standardize many procedures before a specimen can reach an instrument. Additionally, the informatics team must implement enhancements to the laboratory information management system (LIMS) to streamline the lab processes. The ability to overcome these challenges is the key to enabling innovation.
Strategic Implementation to Establish Biorepository Sample Processing Platform in Clinical Laboratory for a Examination Remaining Blood Genomics Biobank Without Disrupting Clinical Examination Practice
Department of Biological Repositories, Zhongnan Hopital of Wuhan University, Wuhan, Hubei, China,
This interactive demonstration will detail how to use the Biospecimen Research Database (BRD; biospecimens.cancer.gov/brd) to locate standard operating procedures (SOPs) from a wide range of private, academic, and government institutions and to identify literature relevant to individual steps in preanalytical handling for specific analytes of interest. The BRD is a free and publicly accessible online tool from the National Cancer Institute (NCI)'s Biorepositories and Biospecimen Research Branch (BBRB) that contains more than 430 SOP documents submitted by over 60 participating sources and over 2700 peer-reviewed articles covering a broad range of topics spanning the biospecimen lifecycle, each with an original summary by a Ph.D.-level scientist. The presentation will demonstrate how to search the BRD's SOP library by keyword or curated fields (source organization, applicable biospecimens, and topic). Guidance will be provided on the creation of a session-specific compendium of SOP documents, allowing a user to view and download multiple SOPs as a zip-file rather than individually. The presentation will also include a demonstration on how to browse and submit tailored queries of literature entries for specific biomarkers or genes as well as preanalytical factors pertaining to biospecimen acquisition (collection method, timing, warm ischemia, etc.), preservation (type, duration, delivery method, etc.), storage (duration, temperature, freeze-thaw cycling, etc.), analyte isolation (method, washing, removal of protein, RNA or DNA, etc.), analytical methodology, and patient characteristics (age, gender, diagnosis, etc.). In addition, guidance for submitting article suggestions and SOP contributions through the website will be presented.
A Unique Approach to Rare Disease Specimen Collection
Biobanking Profiles - LBA
Setting & Maintaining a Biobank with a Training Perspective in Laboratoire La Grace, Yaounde – Cameroon
Biobanks have been heralded as essential tools for translating biomedical research into practice, driving precision medicine to improve pathways for global healthcare treatment and services. There has been considerable investment in biobanking and research infrastructure in scientifically advanced countries. This is because of the perceived research benefits they provide. Setting, maintaining and managing biobanks is still a serious challenge in Cameroon. Virtually, no coherent strategy has been put in place to handle the challenges that the biobanking community has to handle. Biobanks present the interest of collecting both data and samples. Due to the advanced research in the field of HIV/AIDS and the emergence of antimicrobials resistance in Cameroon, many laboratories have started to constitute large biological collections, which unfortunately are more or less well preserved. The value of biological sample collection lies in the quality of the biological resources, their collection condition and also their preservation. The quality of the information associated with the samples being also very important. Yet, very few students, researchers or professionals are trained to the norms, the criteria and the processes of biobanks.
National Liver Disease Biobank in India: Fostering Research Collaboration across India and Abroad
Biobank, National Liver Disease Biobank, New Delhi, India,
Chung-Ang University College of Medicine Seoul, Korea,
The Human Cancer Biobank at St. Luke's Medical Center (SLMC) was conceived in 2014 by a team of oncologists, surgeons, pathologists and basic scientists with a goal of improving medical research in the country. It aims to provide scientists appropriate and adequate materials to study cancer as a prevailing health problem of the country. The team conceptualized the organizational structure, formulated the goals and policies, identified key partners in the hospital and worked for ethics approval of the project. In the beginning, four key challenges/needs were identified: (1) a considerable budget to cover purchase of necessary equipment, a software support for databanking, system of coding specimen, storage and retrieval of samples and salaries of the laboratory staff; (2) a committed group of clinicians and scientists who are willing to enrol subjects to the project; (3) well trained staff who will do data and sample collection as well as sample processing and storage; (4) a continuing system of improvement to make the whole project a sustainable. It was fortunate that SLMC one of the leading private tertiary hospitals in the country has a well-established research and biotechnology laboratory facilities; an accredited ethics and institutional review boards and seasoned researchers and clinicians who believe in the project. With the strong support from the hospital administration, the Human Cancer Biobank (HCB) of SLMC officially started its operation in January 2016 and has been marked the first functional cancer biobank in the country. At present, we have a total of 802 patients enrolled, from which the following samples were collected: liquid biopsies, fresh-frozen tissues, formalin-fixed paraffin embedded tissues as well as DNA and RNA derivatives. Top three cancer tissues collected are: breast, colon and thyroid. Problems and challenges continue to arise and we address these as best as we can. We look into improving our protocols, strengthen our translational research unit and build a research culture within our medical community. We hope that in the near future we can develop into a cross-sectional structure that will be able to work with other biobanks both locally and internationally. We are one in our belief that the establishment of this human cancer biobank is a major step towards establishing a national genomics research in the Philippines that will ultimately impact disease diagnosis, treatment and management.
Management Mechanism of Clinical Specimen Bank in Large Comprehensive Hospital
As one of the largest comprehensive and first-class modern research-based hospital in China, Chinese People's Liberation Army General Hospital (PLAGH) has a great demand of clinical sample collection and storage in scientific research. Therefore, Clinical Specimen Bank (CSB) of PLAGH formulates a management mechanism to guide effective collection and rational usage of sample resources.
There are three sections in CSB, consisting of samples repository, data bank and resources sharing platform. samples repository stores and governs clinical samples. Data bank stores clinical information. Resources sharing platform releases information on sample description, disease categories, available quantity of storage and so on. Academic Committee, composed of professors and experts from laboratories or clinical departments of PLAGH, makes evaluation and verifies that the specimens are scientifically collected and used. Ethics Committee is responsible for the ethical examination of sample collection and usage. It also has the duty to supervise the informed consents signed and the right of privacy of patients protected.
As for the samples management, researchers who intend to collect and store specimens should submit an Application of Admission to CSB. Academic committee verifies the application materials and give permission. Then researchers sign an agreement with CSB on sample storage and administration. After the specimens are taken into the repository, all the related clinical information should be delivered to the Data Management System, to which different account numbers and authorities are set up and allocated. When the samples are required for using, researchers submit an Application of Releasing for permission and gain the samples conforming to the SOPs.
In order to assure sample quality, CSB tracks the procedure of sample collection and treatment by electronic information system. By consulting with patients, doctors obtain informed consent and give advices, which would be input to the Electronic Medical Record (EMR) and Health Information System (HIS). These processes make sure that the specimen information is correct and intact, and moreover the specimens are collected with normalization and legality.
With the working and development of the management mechanism, Clinical Specimen Bank of PLAGH plays an important role in promoting the achievements in scientific research and greatly improving the academic level and influence of PLAGH.
China Biobank Profile
China National GeneBank (CNGB) is a non-profit organization supported by the Chinese Government.
CNGB is committed to develop a global biobank consortium to provide a platform for information sharing, Biobank materials exchanging, omics data acquisition, and Trans-omics scientific research. In order to contribute to the life science industry, CNGB has built an integrated infrastructure of “Three banks and Two platforms,” that not only for bioresources and data storage, but also for data analysis and bioresources utilization.
The CNGB living biobank is committed to build China Noah's ark, which will protect and save life resources up to 300 thousand plant species, 1 million animal species, and 10 million microbe species.
Based on the massive data storage, CNGB has established over 48 databases, such as cancer database, millet database, covering over 7 thousand species, 27 individual species, 70,000 samples, 1 million genes, 10 million mutation information and 6 PB raw data. All these databases are free accessible to public, and all data can be retrieved from the CNGB website.
PUMCH Biobank and National Rare Disease Registry System of China (NRDRS)
Biospecimen Research and Science - LBA
Pin1 Promotes Regulated Necrosis Induced by Glutamate in Rat Retinal Neurons via CAST/calpain2 Pathway
The purpose of the current study was to investigate whether peptidyl-prolyl cis/trans isomerase NIMA-interacting 1 (Pin1) can interact with calpastatin (CAST) and regulate CAST/calpain2, under excessive glutamate conditions, and subsequently regulate necrosis in rat retinal neurons. Glutamate triggered CAST/calpain2-mediated necrosis regulation in primary cultured retinal neurons, as demonstrated by propidium iodide-staining and lactate dehydrogenase assay. Co-IP results and a computer simulation suggested that Pin1 could bind to CAST. Western blot, real-time quantitative polymerase chain reaction, immunofluorescence, and phosphorylation analysis results demonstrated that CAST was regulated by Pin1, as proven by the application of juglone (i.e., a Pin1 specific inhibitor). The retinal ganglion cell 5 cell line, combined with siRNA approach and flow cytometry, was then used to verify the regulatory pathway of Pin1 in CAST/calpain2-modulated neuronal necrosis that was induced by glutamate. Finally, in vivo studies further confirmed the role of Pin1 in CAST/calpain2-modulated necrosis following glutamate excitation, in the rat retinal ganglion cell and inner nuclear layers. In addition, a flash electroretinogram study provided evidence for the recovery of impaired visual function, which was induced by glutamate, with juglone treatment. Our work aims to investigate the involvement of the Pin1-CAST/calpain2 pathway in glutamate-mediated excitotoxicity.
Immune-Checkpoints Screening in Tumor Specimens of Gastric Cancer from Hospital Biobank in Shanghai
Shanghai Institute of Digestive Surgery, Shanghai Ruijin Hospital, Shanghai, China,
Neuromyelitis Optica (NMO) is a rare, autoimmune, inflammatory demyelinating disease that affects both the spinal cord and optic nerves. Although there is no cure, immunosuppressive drugs such as Rituximab and Mycophenolate Mofetil (MMF) are well-known management strategies used to treat this disorder. Rituximab is an antibody that specifically targets CD20 proteins expressed on the surface of B cells which are a cell type of the immune system that contributes to the pathology associated with NMO. MMF is also used to treat NMO, but was originally used as an immunosuppressant drug to reduce the immune response towards the transplanted organs. However, there have been no studies to determine whether the immune cell profiles are altered in response to MMF in NMO patients. The aim of this study is to compare the concentration of PBMCs in the NMO patient cohort on Rituximab and the NMO patient cohort on MMF. The second comparison was between each patient cohort and the age- and sex-matched healthy donor cohort. Blood was obtained in Acid Citrate Dextrose (ACD) tubes from 12 NMO patients on Rituximab, 12 patients on MMF and 12 age- and sex-matched healthy controls. ACD tubes were spun in a centrifuge at 1400 revolutions per minute (RPM) for 10 minutes with the break off. Upon completion of the spin, plasma was extracted from the samples which was aliquoted and stored for future research. To obtain isolated peripheral blood mononuclear cells (PBMCs), the remaining blood was diluted at a 1:1 ratio with room temperature 1X Phosphate Buffered Saline (PBS), layered over Ficoll-Hypaque and then spun at 1900 RPM for 25 minutes with the break off. The first gradient containing plasma/PBS was discarded while the second layer containing the PBMCs was extracted and was later used to determine the concentration of PBMCs per mL of blood. This study is currently on going, however, the data obtained will be presented during the ISBER conference this spring
Clinicopathological Significance and Prognostic Role of EZH2 Expression in Pulmonary Adenocarcinoma with a Micropapillary Pattern
High-Quality Samples for Biobanking – Biobank Graz Concept for Quality Assurance and Quality Control
Biobank Graz, Medical University Graz, Graz, Austria,
In biobanking, the preanalytical phase (including sample collection and transportation) is the most critical and error-prone part. When samples are finally stored in a biorepository, mainly storage conditions and duration have a huge impact on sample quality.
First, it is important to define activities that ensure the maintenance of biospecimen quality (quality assurance; QA). This includes the implementation of the CEN standards. In the second step, biobanks need to implement reliable techniques and tools to evaluate their actual sample quality (quality control; QC).
For the latter, a wide range of standardized and validated sample analysis methods are available. QC tools can focus on morphology, on data quality or on biomolecules. The latter comprises nucleic acids (DNA, RNA), proteins and metabolites. Histologic quality control involves morphological validation of tissue. For biomedical research, also access to high-quality sample-associated data is crucial. Finally, QC activities depend on the material (e.g. tissue or blood) and on the analyte of interest.
a) Biomolecules: different methods/assays and quality biomarkers b) Morphology: morphological validation of tissue samples c) Data: high-quality pathological and clinical data required
In biobanking it is not always possible to control all variables (especially in the preanalytical phase), but their documentation is important. Finally, the overall goal of QA and QC in biobanking is to provide fit-for-purpose biospecimens for researchers.
Study of the Potential Tumor Markers of Renal Clear Cell Carcinoma with Proteomic
The Results of Peripheral Blood Mononuclear Cells Isolated from Liver Disease and HIV-1 Infected Individuals from Hepatitis/AIDS Biobank
Role of Aldehyde Dehydrogenase 1A2 in Ovarian Cancer
Obstetrics and Gynecology, Gangnam Severance Hospital, Biomedical Research Center, Seoul, Korea,
Aldehyde dehydrogenase (ALDH), retinoic acid synthesis gene, is an enzymes for detoxification of endogenous and exogenous aldehyde substrates through NAD(P)+-dependent oxidation. Recent evidence suggests that enhanced ALDH activity is a measurable hallmark of cancer stem cells. However, we found the expression of aldehyde dehydrogenase 1 family, member A2 (ALDH1A2), is significantly decreased in ovarian cancer tissues compared to normal ovarian tissues. Low ALDH1A2 expression was implicated with an unfavorable prognosis of ovarian cancer patients, suggesting the possibility that ALDH1A2 have a critical role as a tumor suppressor gene in ovarian cancer. Furthermore, we observed that the forced expression of ALDHA2 gene impaired significantly cell proliferation and invasive activity via time-dependent manner in ovarian cancer. A small interfering RNA (siRNA) targeted against ALDH1A2 resulted in accelerate colony formation in soft agar in human ovarian surface epithelial (HOSE) cells. Collectively, our findings reveal that ALDH1A2 is a candidate tumor suppressor, further suggesting that the enhanced ALDH1A2-linked pathway might provide new opportunities for therapeutic intervention in ovarian cancer.
The cryopreservation of human peripheral blood mononuclear cells (PBMCs) is a critical issue left non-elucidated thoroughly in the field of bio-preservation. Many factors remain to be examined about their impacts on the quality of PBMC cryopreservation. To address this issue, we carried out a systematic investigation of relevant factors involved in every step of cryopreservation from the initial leuko-apheresis, subsequent traffic, freezing and thawing of PBMCs.
Upon the leuko-apheresis, the contamination of red blood cells (RBCs) other than platelets was likely to adversely affect the cell viability and cell recovery of frozen PBMCs when its concentration was more than 0.5x10e12 cell/L. Gentle vibration rates lower than 200 rpm/min resulting from traffic didn't influence the subsequent cryopreservation of PBMCs, while the vibration of more than 1500 rpm/min led to a dramatic reduction of cell viability and cell recovery. After that, fresh PBMCs can be stored at 4-8 °C for at least 48 h without any loss of cell viability for subsequent cryopreservation. Then, we investigated the optimal cell concentration verse volume of cryomedium in each vial, formulation of cyromedium in the presence of DMSO as the cryoprotectant, as well the operational fashions. For a cryovial of 2.0 ml, 1x10e7 cells in 1.5 ml cryomedium was the best option, having near 95% cell viability while the number reduced to less than 90% when the concentrations were higher than 5X10e7. By developing a cyromedium, we obtained the better quality of frozen PBMCs than those by using commercial cyromedium. And thawing cells at 42 °C or 65 °C contributed to an increasing improvement of cell viability and cell recovery than 37 °C. In conclusion, newly defined key factors here not only improved our understanding of PBMC cryopreservation, but also would significantly contribute to the standardization of PBMC bio-banking worldwide.
Optimizing Thawing Temperature to Improve the Quality of Cryopreserved Human Peripheral Blood Mononuclear Cells
Thawing is an important step in cryopreservation, the conversion of cells from a frozen, glassy state where they exist in a stasis, to a viable temperature where on recovery they are able to proliferate. However, literature regarding the thawing of cryopreserved human peripheral blood mononuclear cells is surprisingly limited and therefore an apparent lack of understanding remains. Protocols usually advise rapid warming in a 37 °C water bath. Nevertheless, it is essential for more definition of the critical parameters in thawing process, especially for the temperature used to de-freeze frozen PBMCs.
Our present findings uncovered the fact that using 42 °C or 65 °C as alternative thawing temperature instead of regular 37 °C led to an increasing improvement of cell viability and cell recovery for PBMCs and two cell lines, i.e. 7721 and McAb. Then, we performed the phenotypic and functional analysis to further assess the consequence of thawing at elevating temperature. It turned out that elevating thawing temperature did not impair the population of T, B, NK cells in PBMCs, and PHA-induced T cell responses including the cell surface expression of activation marker CD69 and CD25 as well as the expansion capacity in LPA assay. Nevertheless, PHA-triggered release of IFNγ and IL-2 was much higher in 65 °C-thawed PBMCs than those in 42 °C and 37 °C. These data strongly demonstrated the most protective capacity of using 65 °C as thawing temperature for PBMC instead of 37 °C.
Molecular Biological Characterization of Newly Established Epithelial Ovarian Cancer (EOC) Cell Lines
Obstetrics and Gynecology, Gangnam Severance Hospital, Biomedical Research Center, Seoul, Korea,
Human biospecimens, such as tissue, blood, urine and saliva have emerged as critical resources for basic and translational research in gynecologic cancer because they are the direct sources of molecular mechanism research used in the initiation of a tumor, and its progression for metastatic disease and resistance for treatment. However, its application for research use has been limited. Recently immortalized cell lines are widely used in further personalized medicine customized to the study. Experimental models such as immortalized cancer cell lines are very useful tools because they can serve as substitutes for in vivo human body conditions through in vitro experiments.
So we report the characterization of 5 immortalized cell lines (designated YDOV-13, YDOV-139, YDOV-151, YDOV-157 and YDOV-161) established from primary tumor samples of Korean patients.
The newly derived immortalized cell lines may be an important research resource for studying cancer cell biology and should also be very useful for developing new strategies that inhibit cancer cell growth and progression.
Ames Life Science Data Archive, NASA, Moffett Field, California, United States,
The purpose of this study is to assess the quality of NASA spaceflight tissues stored in Ames Life Science Data Archive (ALSDA) −80C freezers. Garnering information – for downstream functional analysis such as generation of omics datasets – from tissues is, in part, dependent on the state of sample preservation. To assess the viability of a select group of tissues, RNA integrity number (RIN) values were calculated for RNA extracted from rodent livers. Rat livers from Spacelab Life Sciences 1 (SLS-1) and mouse livers from Commercial Biomedical Test Module 3 (CBTM-3), Rodent Research 1 (RR1), and Rodent Research 3 (RR3) were tested. It was found that mean RIN values from CBTM3, RR1, and RR3 were suitable for downstream functional analysis (RIN >5) while the mean RIN value for SLS-1 was not (RIN = 2.5 ± 0.1). Information from this study could lay the foundation for future efforts in determining the types of assays that are most appropriate for different tissues stored in ALSDA −80C freezers, therefore maximizing the scientific return on rare spaceflight samples.
In the past years, genome-wide single nucleotide polymorphisms (SNPs) have become increasingly popular as a marker of choice in population genetic studies. Genetic sampling methods, which includes hair, tissue, and blood samples among others, has increased the scope and efficiency of genomic studies in livestock populations such as cattle, sheep, goats, and pigs. Many previously banked biomaterials have been unsuitable for DNA analyses due to the extensive degradation (Der Sarkissian et al., 2015) due to poor sampling and storage conditions. Environmental exposure to moisture and ultraviolet radiation, along with collection and storage methods, can degrade DNA in biological samples, whereas cool and dry conditions are known to minimize degradation (Stetz et al., 2015). Sequences of DNA can be easily broken as DNA is a fragile molecule (Lindahl 1993), which in turn can affect SNP genotyping. As genotyping is still expensive in most developing countries, lower call rate and failed genotyping can be a challenge since repeated genotyping is costly. Therefore, limiting exposure to DNA degradation on collected samples is important component for genomic study design. This study shows the effect of using previously banked cattle hair samples on SNP genotyping, and how the sampling and storage methods can be improved for better quality DNA. Twenty-four cattle hair samples, collected between the years 1997 and 2012 were retrieved form the ARC Biobank. Several hair roots were cut to extract DNA using phenol and chloroform protocol. Samples were genotyped using bovine 150K assay on an Illumina platform. DNA quantification showed the ratio of UV absorbance ranging from 1.5 to 2, showing the quality of DNA. From the total genotyping, approximately only 58% of samples were successfully genotyped with a lower proportion of sample with low genotyping call rate. This shows that there was a notable level of degradation on selected samples. This could be due to the condition from which samples were collected, part of the animal body from which hair samples were plucked, or the storage condition after collection. Therefore, proper sampling and storage methods for hair samples must be considered to preserve high quality DNA sufficient for genomic studies.
Characterizing Freezing Responses of Human iPS Cells Using Low-Temperature Raman Spectroscopy
Mechanical Engineering, University of Minnesota, Saint Paul, Minnesota, United States,
Cell aggregates cryopreserved in the osmolytes solution at seeding temperature of −4°C and cooling rate of 1°C/min showed similar amount of IIF compared to those frozen in DMSO solution, suggesting effective IIF prevention of these osmolytes. However, there was a larger gradient of osmolytes concentration across the aggregates than that of DMSO concentration, indicating greater transport limitations of osmolytes in aggregates.
Integrated Biobank of Luxembourg, Luxembourg,
Integrated BioBank of Luxembourg, Dudelange, Luxembourg,
In a collaboration project between the Integrated Biobank of Luxembourg (IBBL) and the Jena University Hospital (Germany), we evaluated (1) the fitness-for-purpose of a new blood collection tube, for demanding metabolomics analyses, and (2) the plasma pre-analytical quality control tools, which have been developed by IBBL and by Jena University Hospital to check for pre- and post-centrifugation delays.
The study was designed to compare the Barricor tube to the classical K2-EDTA tube, assessing three pre-centrifugation delays at room temperature (1h, 23h, 53h), and three post-centrifugation delays, also at room temperature (0h, 24h and 48h). For all of these testing conditions, blood was collected from 5 volunteer donors and the obtained plasma samples were distributed in 8 aliquots to perform the QC tests, each time on a separate aliquot.
The Barricor blood collection tube contains a plastic separator which isolates the plasma from the other blood components upon centrifugation. According to the manufacturer, centrifugation can be done at 4000 g for 3 min only, and post-centrifugation shipment of pure plasma samples in the original tube is feasible. This saves time and resources.
To evaluate the fitness for-purpose of the Barricor tube for isolation of cfDNA, we spiked cfDNA mimics for the 1h pre-centrifugation delay conditions, and then extracted cfDNA from isolated plasma and finally analysed the cfDNA content and profile of these samples.
Several quality control tests were performed on the collected samples: platelet count on the blood sample and platelet count (by CASY counting) on the isolated plasma samples after the imposed pre- and post-centrifugaton delays. The following QC tests were performed:
sCD40L measurement by ELISA to assess the performance of this tool in the “diagnosis” of room temperature exposure of plasma or serum samples; IL-16 and IL-8 measurement to assess the performance of these tools in the “diagnosis” of pre-centrifugation of more than 24h at RT; metabolites testing by LacaScore (lactate/ascorbate) and by LC-MS/MS at Jena University Hospital.
A comparative table with results obtained with these seven different tests will be presented as well as a summary table with the evaluation outcome.
Biospecimen Research and Science – LUX
National Research Center for Preventive Medicine of the Ministry of Healthcare of Russia, Moscow, Russian Federation,
Initial testing at LMA involved screening field collected swabs for the presence of OPXV according to published qPCR protocols (Li et al. 2007). This is a generic assay designed to detect all OPXV species except Variola virus. In this way, will be recovered any additional new isolates or other species of OPXV that may be circulating in the region. Any positive samples will be further characterized to establish species identification and marked for genome sequencing.
Training and educational outreach will result in improved capacity for efficient identification and diagnosis of emerging OPXV, and will as well improve bio-surveillance capacity for OPXV in both human and animal populations.
The improved surveillance activities and understanding of OPXV disease burden in the agricultural sector will promote further research collaborations with local and international partners.
Evaluating the Utility of Necropsied Marine Animal Tissues in Genomics
The NIST Marine Environmental Specimen Bank is a useful tool for long term and retrospective studies relating to environmental health and the health of marine animals with respect to environmental contaminants. Focus on research relating to genetics, metabolomics and proteomics can support measured contaminant data by adding layers to our understanding of the effect contaminants have on animal health, life history, and the environment. The strict protocols established by NIST for the banking of animal tissues and fluid for environmental contaminants have also preserved sensitive biological molecules for many samples. Research materials banked at the Marine ESB are obtained from live and expired (through necropsy) marine animals. Many of these samples are from federal and state protected marine species and can be difficult for researchers to obtain due to permitting and sampling logistics, especially from live animals, and may be limited in the number and quantity of sample available. Expired animals however can provide larger quantities of tissues from internal organs that cannot be obtained from a live animal, which can also aid in understanding metabolism, genetic expression, and overall health. This research examines how RNA degradation and gene expression is altered in necropsied tissues stored at the Marine ESB for the National Marine Mammal Tissue Bank. It will explore the limitations of these tissues and provide a framework for researchers studying marine animals to determine if more accessible and abundant tissues from expired marine animals can be utilized for their studies.
Biospecimen Research and Science - Quality - LBA
The Biobanking of Human Peripheral Blood Mononuclear Cells
Human peripheral blood mononuclear cells (PBMCs) are required in multiple prospective and functional analyses in infectious diseases and clinical vaccine studies, as well as serving as precursors for potential immunotherapy development in translational medicine. Therefore, the biobanking of PBMCs is of growing importance. High quality of biobanked PBMCs positively contributes to their efficiently exploratory and future applications.
According to our findings here, age other than gender is a major autologous factor affecting PBMC cryopreservation. Upon thawing, PBMCs from people older than 60 years showed significantly less cell viability and cell recovery than those from younger ones. Besides determining the cell viability and recovery, we also developed multiple platforms to do phenotypic and functional evaluation of bio-banked PBMCs, which include the analysis of TBNK population, lymphocyte proliferation assay (LPA), T cell activation and subsequent effector cytokine secretion, NK expansion as well as dendritic cell differentiation. Consequently, here we showed a stable and durative good performance of PBMC cryopreservation strategy, with more than 90% of cell viability and 80% of cell recovery in average after their thawing, which provide strong basis for the construction of PBMC bio-bank.
Three Methods for Leukocytes Separation and RNA Quality Control
The Proficiency Testing Program in National Biobank of Korea
In 2013, the proficiency testing program was introduced to improve the accuracy and precision for quality management of biospecimens. From 2013 to 2015, we assessed the proficiency of DNA concentration and purity, RNA integrity, bacteria contamination in human genomic DNA and cell viability of 17 regional biobanks of the Korea Biobank Network (KBN) and clinical lab testing service organizations. In 2016, the proficiency testing (PT) was opened to all government-licensed biobanks across the country. The PT results were statistically evaluated according to ISO 13528:2005 Robust analysis or Q/Hampel method. In the first year of the PT program, in 2013, the conformance ratio of the participants was 95.5% (DNA concentration), 100% (DNA purity, RNA integrity and cell viability) and 86.4% (bacteria contamination in human genomic DNA). Since then, the conformance ratio of all PT schemes remained in a stable state more than 90% except for 2016. In addition, educational training courses for practical QC/QA were regularly conducted for various biobanks including KBN-member and non-member biobanks by the National Biobank of Korea, which contributed to improve the measurement capability and laboratory skills of participants.
Determining Quality of BioBank Tissue Samples
The quality of nucleic acids and proteins from the punch samples were analyzed quantitatively. Gross and histologic assessment was used to compare frozen tissue versus tissue submerged in a preservation buffer.
Biospecimen Research and Science - Quality – LUX
Stability of Total and Free Prostate Specific Antigen After Ten Years Storage
Department of Immunochemistry, University Hospital Pilsen, Pilsen, Czechia,
Many factors have an influence on nucleic acid quality, such as sample source, handling, extraction method and storage condition. The responsibility of the biobanks to collect, store and ship samples makes it essential to determine sample quality at the point of receipt and release. Sample quality includes concentration and integrity which are both important parameters to ensure that nucleic acid samples are fit for purpose. Nucleic acid quality can be assessed using conventional gel or automated electrophoresis systems.
The DNA Integrity Number (DIN) has been established for genomic DNA (gDNA) qualification with automated electrophoresis systems. It provides an assessment of gDNA sample quality by assigning a numerical score from 1 to 10. A high DIN indicates intact gDNA, and a low DIN degraded gDNA. The DIN enables comparison of samples and allows defining a DIN quality threshold for specific types of samples or preparation. This poster shows examples of DNA sample patterns and correlating DIN across a wide quality range for DNA originating from blood, fresh frozen tissue and formalin fixed paraffin embedded (FFPE) material.
The RNA integrity number equivalent (RINe) delivers an objective assessment of total RNA degradation for samples from eukaryotic or prokaryotic origin. The RIN is independent of sample concentration and analyst and allows unbiased confirmation of RNA sample quality. RNA samples extracted from FFPE tissue are typically highly degraded. Many tailored FFPE RNA library protocols use an additional quality metric DV200 to define the optimal RNA input amount for successful NGS library preparation. The DV200 represents the percentage of RNA fragments above 200 nucleotides. This poster exhibits sample patterns and corresponding quality scores of intact and degraded RNA including FFPE RNA samples.
OPTIMARK Project: Preliminary Results on Antigenicity and Integrity in Non-Tumor Tissue Samples
Pulmonary Biobank Consortium, CIBER of Respiratory Diseases (CIBERES) - ISCIII (Madrid), Instituto de Investigación Sanitaria de Baleares (IdISBA) - Hospital Universitario Son Espases, Mallorca,
Ethical, Legal, and Societal Issues – LBA
Tackling Compliance Challenges for Use of Biological Assets in Drug Discovery
Biological assets play a vital role in drug discovery and development. Maintaining compliance with third party agreement and licensing terms for biological materials sourced from academic and government institutions, as well as from well-established repositories, can prove to be a challenge for large international pharmaceutical companies. This challenge is magnified due to increasing third party interactions with external collaborators and contract research organizations. ABS compliance for the Nagoya Protocol adds an additional layer of governance required for biological research materials used in R&D. This poster discusses these challenges and the approach taken by GlaxoSmithKline to centralize license and agreement acquisition, enforce data registration, and implement tracking measures to improve and strengthen the compliance framework surrounding our biological assets.
Implementing Electronic Consent in an Academic Biorepository
The Cooperative Human Tissue Network at Vanderbilt University Medical Center (CHTN-VUMC) is a federally funded academic biorepository that is dedicated to providing high quality biospecimens and services to the research community. For 15 years, CHTN-VUMC has been obtaining broad consent from patients to collect samples for a wide variety of research studies. Due to the complexity and regulatory requirements, the consent process is inherently time-consuming and a multi-step process, which utilizes staff time and money. CHTN-VUMC routinely implements process improvements and the adoption of Lean Six Sigma (LSS) principles within our biorepository, which has driven the decision to implement digital consent documentation. Wastes that could be reduced were defined as inventory, motion, defects, and extra processing. According to CHTN-VUMC's error-reporting software, 25% of consenting errors in 2017 were categorized as major or critical. In an effort to address these wastes, the current paper process was evaluated against the digital consent proposal through SIPOC and Fishbone diagrams to identify all relevant elements of the process improvement before a commitment was made to implement digital workflows.
Through the use of LSS diagrams, the root cause of waste was determined to be the sizable number of steps in the consenting process. CHTN-VUMC's goal for implementing electronic consent (eConsent) is to save around $2600 that was previously spent on printing costs and staff time, as well as reduce the percentage of major or critical consenting errors to less than 15%. The launch of CHTN-VUMC's eConsent will be through Research Electronic Data Capture (REDCap), VUMC's secure web-based application for surveys and databases. REDCap will allow patients to be consented using an iPad to capture a “wet signature” using a finger or stylus rather than by traditional paper consent. Following LSS principles has allowed CHTN-VUMC to operate efficiently using limited resources. Putting these ideals into practice via eConsent will allow the lab to significantly reduce waste and allow for more focus to be on providing the highest quality biospecimen to researchers.
Parental Attitudes and Willingness to Donate Children's Biospecimens for Congenital Heart Disease Research
Keywords: Congenital heart disease, biospecimen donation, parents' willingness
The Re-Consenting Hurdles of a Pediatric Biorepository
Reflexivity and Ethics for ABS of the CBD: Empirical Analysis by Network of Scientific Articles with NLP
Graduate School of Environmental Studies, Tohoku University, Sendai, Miyagi, Japan,
ABS has global challenge for decades, particularly since the birth of CBD. Analysis have largely been conducted separately at various disciplines (ecology, biology, pharmaceutics, law, ethics) and the interlinkages, despite their importance, remain unexplored.
We have selected 176 papers from the database of the PubMed and the Web of Science by using the keyword “Access and Benefit Sharing.” We have focused on disciplines, regions and relationships between the academic papers that discuss ABS issues. The relationships of the academic discourse can be analyzed by focusing on the citations between the papers. We scanned all papers in the reference lists of the 176 selected papers and detected cited papers in the selected papers.
As first step, we identified disciplines where ABS related publications are found and referred to. We also identified regional specific trends, where focus in Africa was on bioprospecting while the discourse in Asia was linked to culture. For example, frequently mentioned terms in the research of Asia include taro, horticulture, ornamental, and cultivar. In the research of Africa, the terms that include bioprospecting, medicine, industry are relatively frequently mentioned. On the other hand, in the research of Europe, the terms that include conservative, achievement, leadership, performance and objective are frequently mentioned and the related research topics are discussed. As the second step, we grouped the references networks and found that the discourses are fragmented into three groups and others.
These results, limited to the scope of academic papers, suggest that it is necessary to share the multi-and trans-disciplinary approaches. There are clusters of the papers from the similar disciplines. The journals, including this journal, Biopreservation and Biobanking, are identified as a hub for different discipline and play a role as catalysis. Because the issues of ABS need to be addressed by the multi-and trans-disciplinary approaches, the catalyst that can connect the approaches from different disciplines is indispensable, and the research focusing on the science policy interface and participatory approached of various stakeholders need to be implemented with international collaboration including academia, industry and local communities.
Hot Topics - LBA
Anatomy and Neurobiology, Basic Medical School, Central South University, Changsha, Hunan, China,
The Annual Biobank China (ABC) Conference is as an interactive and innovative conference experience which promotes the development of the Chinese biobanking system and offers a great platform to provide further education to Chinese biobankers. Six ABC conferences have established a global network of professionals, providing the opportunity and momentum for major progress in the development of biobanking and related medical research.
The Annual Biobank China 2017 & International Symposium on Precision Medicine, (ABC2017), is the latest ABC meeting. ABC2017 was successfully held in Changsha, China on December 1st–2nd, 2017, organized by the Central South University (CSU), with invaluable assistance from the Shanghai Clinical Research Center (SCRC) and the Shanghai Engineering Research Center of Biobank (SERCB).
ABC2017 succeeded in inviting more than 100 leading biobanking researchers as speakers. It also attracted more than 1000 participants from 8 countries who were mainly biobankers, academics, other top scientists, manufacturers, and policy makers. Comprising 5 plenary symposia, 5 parallel sessions, 2 seminars and 2 special programs, ABC2017 promoted consensus on quality control and standardization system, ethical and regulation issues, sustainable development strategy and application of big data, automation and artificial intelligence(AI) in biobanking construction and management. ABC2017 also promoted a broad discussion on precision medicine and next-generation biobank construction between biobankers operating under different laws and ethical regulations, different networks, different business models, variable development status and different governmental strategies. During this meeting, the Hunan Industry Technology Innovation Strategic Alliance was founded, an AI specimen storage system from Genepoint Biological Technology (Shanghai) was released. In particular, ABC2017 was the first ABC meeting which held a photographic exhibition, showing the history of biobanking in China and interesting stories from biobankers across the world.
Sincerely, we would like to thank Prof. Jim Vaught and other chairpersons, professionals, volunteers for their efforts during this meeting, which not only contributed to the success of this inter-disciplinary, multi-field conference, but also will promote worldwide cooperation among country-based health and technology programs.
This work was funded by the National Key Research and Development Program of China (2016YFC1201800).
The National Repository of Bacteria and Viruses (NRB&V) is a part of National Center for Disease Control and Public Heath(NCDC) of Georgia. There are kept collection of Especially Dangerous Pathogens - obtained from humans and environment, other pathogenic and potentially pathogenic microorganisms that are of a scientific or practical value and reference strains; The Pathogen Asset Control System (PACS) is implemented and successfully used for biological agent stocks accounting and control, that is a secure, comprehensive information system developed under Cooperative Biological Engagement Program that is implemented by the Defense Thread Reduction Agency (DTRA) to track biological materials. In order to increase Biosafety/Biosecurity capacity at biological laboratories, a pilot project was made to integrate PACS radiofrequency identification (RFID) technology. The goal of the integration was not only to allow enhanced security of storage but also to simplify tracking and improve effectiveness of laboratory operations. Pilot Project was implemented in the NRB&V located at the Lugar Center. PACS-RFID System included following components: Standalone workstation with PACS database and application; Barcode printer; Barcode scanner; RFID reader and desktop antenna; RFID plate reader; RFID-enabled −80C freezer (manufacturer – Terso Solutions); RFID printer; Plastic vials with embedded RFID tags; Variety of RFID tags to be used with existing vials. Each component was used for specific purposes. Methods included: New material registration, Material transfer, Material subculturing, Material aliquoting, Material destruction, Inventory Audit, Freezer Operations. Pilot Project showed that not all RFID technology enabled equipment provides benefits of the same level, some equipment tested during the project was not deemed reliable (e.g. RFID-enabled non-sterile vials). Project participants identified that RFID technology increased security of biological materials storage and tracking but to a limited level (e.g. box-level tracking by Terso Freezer), generally increased efficiency of operations (e.g. fast inventory), as well as improved accuracy. It was identified that RFID technology increased convenience and speed of operations with PACS, especially inventory audit, as well as enhanced general accuracy. At the same time, it provided limited benefits to the security as the technology still requires further improvement – e.g. vial-level tracking by Terso Freezer.
ACMG Incidental Findings at the CLIA-Certified Colorado Center for Personalized Medicine Biobank
Biobanks Managing Specimen and Annotations Associated with Patient Derived Xenografts (PDX)
Human Specimen Repositories – LBA
MW CHTN Researcher Requested Tissue Sample Sizes (Weight) Distributed, 2015–2017: Supporting Data for Biorepository Research Tissue Sample Weights for Storage
CHTN-MW Division, Columbus, Ohio, United States,
Texas Children's Hospital, Houston, Texas, USA,
Congenital heart disease (CHD) is associated with life-long morbidities, premature mortality, and high health care costs. Atrio ventricular canal defects (AVSD) account for about 5 percent of all congenital heart disease, and are most common in infants with Down syndrome and is associated with variable outcomes. The genetic etiology of atrioventricular septal defect remains unknown in 40% cases. To overcome the lack of suitable number of samples sets, a multicenter approach was utilized. This study is the first project of an international initiative called CHSS Registry of Biobanks, created to engage in genomic research and foster collaborations among networks of biobanks of congenital heart diseases. A group of 7 centers in the US and Canada currently participate by sharing data and samples. In this project, we defined the genetic landscape of AVSD using next-generation whole exome sequencing in a cohort of 230 unrelated AVSD probands, syndromic and non-syndromic, collected from biobanks of four different collaborative groups. Variant filtering analysis revealed a complex genetic landscape with 78,644 rare variants identified in the cohort that are being further analyzed. Though the analysis is still in process, the Registry has enabled a collaborative project that received Federal grant support and has now completed sequencing. It establishes a new paradigm for the broad sharing of genomic resources and information in congenital heart disease.
Utilization Performance of Bioresources Distributed by the National Biobank of Korea
National Biobank of Korea (NBK) has supported biorepositories of national cohorts and surveys including the Korea Genome and Epidemiology Study (KoGES), the Korea National Health and Nutrition Examination Survey (KNHANES). NBK has also distributed biospecimens and related genetic and epidemiological data sets to research projects approved by the distribution review committee. Here, we reports distribution statistics and bioresource utilization performance. From 2003 to 2017, a total of 616 research projects was approved for access to NBK bioresources. The distributed bioresources were 475,675 vials of biospecimens, 614 sets of epidemiological data, and 483 sets of genetic data. Using these NBK bioresources, 374 research papers and 28 patents were published. Regarding publication quality, the average impact factor (IF) of research papers was 5.0. The studies with both biospecimens and related data of epidemiological and genetic data produced research papers of the IF average of 8.7 whereas the studies with genetic data was 6.1 (biospecimens 5.4 / epidemiological data 5.5). Based on these results, it is necessary to collect and provide more genetic data in order to improve bioresource utilization performance. On the other hand, as NBK recently opened biofluid distribution of serum and plasma samples, it is expected that NBK bioresources will contribute to the development of diagnostic methods and new drugs.
Enabling Detailed & Operator-Independent Plasma QC by an Innovative Spectrophotometric Approach
Blood plasma and serum, as a biomaterials for both molecular and functional analysis, have become increasingly important as an important analytical resource in both research and diagnostics. As these bio-molecules are present in limited amounts and are sensitive to degradation as a function of collection, processing, and storage (i.e., freeze-thaw), it is of utmost importance to qualify and quantify the quality of plasma prior to any analyses. Plasma quality is currently assessed by a rough visual inspection being imprecise, labor-intensive and operator-subjective. Moreover, many current QC tools lack the ability to predict downstream performance of the sample. This study presents the development of a novel plasma quality control approach utilizing a micro-volume UV/Vis spectrometric approach (Lunatic - Unchained Labs). This technological approach extends the capabilities of standard UV/Vis by dissecting the measured absorbance spectrum into its relevant constituents. As a result, the typical color and clarity grading are decomposed and quantified into its biologically relevant contributors: protein as major component, heme (hemolysis), bilirubin (icteric serum) and turbidity (lipidity). Using this approach, the 4 plasma QC parameters can be objectively quantified in a batch-wise method while consuming only 2 μl of plasma. In this study the correlation between the visual inspection and UV/Vis approach is demonstrated, showing not only good correlation between the two methods but also the more robust, operator independent and in-depth analysis of the UV\Vis method. Lastly, the study demonstrates the correlative value of relating quantitative measurements of plasma, using this new approach, with downstream analyses of both cell free nucleic acid and functional measurement quality. The implementation of this approach is the basis of a global standardization for plasma quality that can help assess the effects of pre-analytical and processing variables.