Late Breaking Abstracts.

Abstract

Biopreservation and BiobankingVol. 16, No. 3 AbstractsFree AccessLate Breaking AbstractsPublished Online:1 Jun 2018https://doi.org/10.1089/bio.2018.29038.LBabstractsAboutSectionsPDF/EPUB Permissions & CitationsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail Information Technology – LBALBP-1 The Construction and Development of Information System of Clinical BiobankGuo D., Xu Y., Fan Z., Liang Z., Zhang S.PUMCH, Beijing, ChinaBackground: Due to the rapid development of translational medicine research, the construction and application clinical biobanks have increasing attention. The information system is the core of the biobank, which plays an important role on sharing of clinical information and specimens. So the development of clinical biobank information system should based on supporting the overall process of operation, management and service.Methods: The multifunctional requirements of the clinical biobank need powerful information system to track the full life cycle of biospecimen from collection, reception, transportation, processing, storage and distribution. So, the function of information system should include management of biospecimen, clinical data, molecular data, materials, personnel, equipment finance, and so on. Biospecimen management system should take sample as center, and Clinical data management take patients as center. Besides common data element standardization is the basic point of information system, which also has characters of flexibility, openness and safety.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.Results: Compared with the traditional biobank which rely on manual input data, new generation biobank are more focused on the quality and integrity of data. The information system joining the sample and data collection process with ADT, CPOE, EMR, LIMS, AIMS, PIS, PACS and MRMS could not only acquire automatically, but also guarantee the reliability, timeliness and accuracy of the data.Conclusion: A powerful biobank information system could realize the efficient management and promote comprehensive sharing of biospecimen, clinical information and molecular data, which would take advantage of the era of big data to support biomarkers detection, individualized medical treatment, drug research and development.LBP-2 Comprehensive Paperless Biorepository ManagementThomas C., Thomas S., Lamptey J., Indibi R., Colligan L., Shao W.Preclinical Development, Regeneron Pharmaceuticals, Inc, Tarrytown, New York, United StatesBackground: Regeneron's Sample Management Group (SMG) manages sample receipts, requests, and transfers, and maintains short- and long-term storage for samples from both non-clinical studies and clinical trials. The increase in number of samples that are received daily from central Labs and the requests for sample transfers within multiple departments at Regeneron along with the rising complexity of sample tracking from acquisition through destruction have necessitated process changes and/or improvements to increase efficiency and minimize errors while maintaining compliance.Methods: Paper based sample management process is no longer sustainable for handling an ever increasing number of samples. In order to maximize efficiency and ensure that data is captured accurately in a Laboratory Information Management System (LIMS), a paperless sample receipt and sample request process was developed and implemented. The process includes the use of electronic forms in LIMS, which facilitate tracking accuracy from the time samples arrive through disposal.Results: Implementation of paperless sample receipt and request forms has allowed SMG to document and track shipments, and pull requested samples more efficiently and with fewer errors. The paperless sample receipt form prompts the user for electronic data entry of all shipment information including quantity of samples received and short-term storage location. The paperless sample request form matches each scanned barcode to the barcodes listed in the request, and ensures that the samples are in the correct order and position. The paperless sample request also facilitates the timely and automatic communication of the job status to the requestors and SMG team.Conclusion: The use of paperless sample receipt and request forms in LIMS has dramatically improved efficiency and accuracy. Through this significant process improvement sample management professionals and biobank communities have been able to streamline processes to maintain high throughput, increase sample visibility, and compliance despite increasing sample quantities.LBP-3 A Comprehensive Biobanking Ontology of the Lifecycle of the Biospecimen Made for-and-with Diverse Subject Matter ExpertsEllis H. J.1, Brochhausen M.5, Masci A.3, Manion F. J.6, Obeid J.4, Stoeckert C. J.Jr.2, Zheng J.21Biobanking Without Borders, LLC, Durham, North Carolina, United States,2University of Pennsylvania, Philadelphia, Pennsylvania, United States,3Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina, United States,4Medical School of South Carolina, Charleston, South Carolina, United States,5University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States,6University of Michigan Comprehensive Cancer Center, Ann Arbor, Michigan, United StatesProblem Statement: The field of biobanking demands data integration. Biobanks commonly evolve for diverse research needs with heterogeneous data representations presenting challenges to query for samples and associated clinical annotations across biobanks, within and across institutions. Moreover, there are ethical and regulatory requirements for the use of specimens and data, including documentation and adherence to the permissions and restrictions expressed by research participants during consent.Proposed Solution: The Ontology for BioBanking (OBIB) has been developed and refined through engagement and collaboration with several academic medical institutions, national scientific biobanking forums and national standards organizations. An ontology provides clearly defined terms and the relationships between them in a computer-interpretable way, enabling integration of disparate data into one harmonized, reusable system. OBIB was developed following principles of the Open Biomedical Ontologies Foundry, which requires re-use of existing interoperable ontologies in order to prevent multiple representations of the same entities. The scope of OBIB is the Lifecycle of the Biospecimen as defined by NCI's Biorepositories and Biospecimen Research Branch (BBRB), starting with the participant consent process. Important aspects of informed consent are addressed by cross-linking with the Informed Consent Ontology (ICO). OBIB leverages work done on data elements from biobanks at academic institutions as well as the NIH Genotype-Tissue Expression (GTEx) Project and the NCI's BBRB. The contributions from GTEx include comprehensive research authorizations related to post-mortem tissue donation, and terms from the BBRB relate to pathology staging and grading, specimen annotation and medical history. OBIB classes are being linked to terms in MIABIS (Minimum Information About BIobank data Sharing) version 2.0. OBIB currently contains 1970 terms including 1617 classes, of which 130 terms originated from Ontologized MIABIS (OMIABIS) and 1234 were imported from other ontologies.Conclusion: The continued development of OBIB benefits from the diverse members of the collaboration. OBIB provides a solution for identifying specimens for research, and effectively using the wealth of information present in biobanks by integrating data stored in those repositories, with clinical data and relevant consents. OBIB is freely available at https://bioportal.bioontology.org/ontologies/OBIB.LBP-4 Transforming Sample Creation Process for Biobanking Registration with Excel MacrosLiu Y., Shum E., DeMarte R., Ngo M., Valluzzo S., Colligan L., Shao W.Preclinical Development, Regeneron, Tarrytown, New York, United StatesStatement of the Problem: When Nautilus Laboratory Information Management System (LIMS) is used to manage study samples received from different central Labs or contract research organizations (CROs), creation of new samples in preparation for pre-registration of thousands of samples in LIMS has typically been a manual process. This is because the different systems used by CROs, which generate sample listing files in different formats, make it very challenging to automate the sample creation process. LIMS samples can be created by importing sample information in Microsoft Excel with a format required by LIMS configuration. However, the manual creation of Excel files can be time consuming and introduce human error for shipments with large quantities of samples. The repetitive operations in Excel also pose high ergonomic risk.Proposed Solution: Macros written with Excel VBA (Visual Basic for Applications) were used to automate steps during Excel file creation in order to increase efficiency and accuracy. The macros extract required sample information from multiple electronic shipping manifests and combine all the information into a single Excel worksheet. The macros then format sample information, e.g. site, subject, visit, time point, sample collection date, etc., and generate a file that can be imported into LIMS to create new samples and vials. The automated process can reduce hours of manual work into seconds without an error, depending on the size of the files, the number of samples and the number of shipments. It also replaces repetitive manual operations in Excel to lower ergonomic risk.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.Conclusions: Manual creation of new samples in LIMS can be very time consuming and is prone to human errors. Excel Macros are very efficient tools to automate the steps to create Excel files with new sample information that can be imported in LIMS. The macros with simplified interface are very helpful to harmonize the file creation process, increase efficiency, minimize human errors and lower users' ergonomic risks.LBP-5 OpenSpecimen - Experiences of Collaborative Development of an Open Source Biobanking Informatics PlatformAdiga S.Krishagni Solutions Pvt Ltd, Pune, Maharashtra, IndiaAccess 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.LBP-6 Data Quality Assessment of the Human Biobank Information System in the National Biobank of KoreaJi B.1, Lee S.1, Hyun H.1, Chu M.1, Kim D.1, Shin J.2, Jeon J.11Korea National Institute of Health, Cheongju-si, Chungcheongbuk-do, Korea,2Ministry of Health & Welfare, Sejong-si, KoreaMost 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.LBP-7 Reducing the Human Data Entry Burden of a Growing Pediatric Brain Tumor Biospecimen Banking ConsortiumFelmeister A. S.1,2, Leary S.3,4, Stevens J.4, Mason J.1, Teneralli R. E.1, Bailey C.1,5, Waanders A. J.1,51The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States,2College of Computing and Informatics, Drexel University, Philadelphia, Pennsylvania, United States,3Fred Hutchinson Cancer Research Center, University of Washington School of Medicine, Seattle, Washington, United States,4Seattle Children's Hospital, Seattle, Washington, United States,5Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United StatesBackground: Researchers at Children's Hospital of Philadelphia (CHOP) and Seattle Children's Hospital (SCH) are collaborating on a project to inform diagnostics and treatment options of pediatric supratentorial malignant cortical brain by correlating molecular results and longitudinal outcome data. The source of the tissue is the Children's Brain Tumor Tissue Consortium (CBTTC). Data from the CBTTC is manually abstracted prospectively from surgery through treatment. In this study we aim to automate the annotation of biospecimens by leveraging observations in Clinical Data Research Networks (CDRNs).Methods: We are focusing the effort of this research on the CDRN, PEDSnet, where two CBTTC specimen collection sites participate. We obtained simulated patient data in the model used by PEDSnet. We performed an exploratory data analysis of this data ran multiple algorithms to predict a specific condition in a patient based on frequencies and sequences of events. Thus creating pipelines to distinguish data-driven phenotypes of specific subsets of patients. Concurrently, a distinct list of histological conditions was mapped from the CBTTC terminology to SNOMED-CT that was preliminarily hand-validated with neuro-oncologists from both CHOP and SCH for an initial request of data from PEDSnet.Results: The observational data model lent itself to straightforward visualizations at the individual and population levels, and patient-based analyses for disease and comparison with te rest of the population. These data points successfully fit Kaplan-Meier curves for any disease qualification category. Timelines were also created at the individual patient level showing a longitudinal series of events that tie into the time of biospecimen accessioning at a surgical diagnostic event. Each event at any level of the model is tagged with time points or time ranges.Conclusion: The next steps are to receive pediatric data from PEDsnet in the same model as the simulation data inclusive of the large cohort of patients diagnosed with aggressive forms of cortical tumors as identified in our methods. The predictive models built in the exploratory analysis will be applied to the data as it is received. We intend to validate the data-driven phenotypes derived and apply their content as specimen annotations. Validation will occur by comparing well labeled data in the CBTTC with data derived from our models.Repository Management - LBALBP-8 Challenges in Integrating Automated Solutions for Biobanking Workflows: A Piece of Equipment is Not the SolutionTrapp B., Khan M., Chakrabarty R., Muppaneni H., Derrig M., Josey A., Tran T. A.Biorepository, Boston Children's Hospital, Boston, Massachusetts, United StatesThe 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.LBP-9 Strategic Implementation to Establish Biorepository Sample Processing Platform in Clinical Laboratory for a Examination Remaining Blood Genomics Biobank Without Disrupting Clinical Examination PracticeWu M.1, Qian K.1,2, Xiao Y.1,31Department of Biological Repositories, Zhongnan Hopital of Wuhan University, Wuhan, Hubei, China,2Laboratory of Precision Medicine, Zhongnan Hopital of Wuhan University, Wuhan, Hubei, China,3Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, ChinaStatement of the Problem: In the current era of individualized medicine, a large-scale genomics biorepository of human samples is essential to support clinical and translational research. Clinical laboratory collected and analyzed huge amounts of clinical blood, urine, fecal and clinical microorganism from health populations and patients. However, there are hurdles in the field of clinical laboratory and biobank, including workflow of examination remaining sample processing, safety and ethical issues.Proposed Solution: To be familiar with the clinical laboratory workflow and management system, biobankers have a pre-job training in clinical laboratory. Standard operating procedures (SOPs) were drawn for examination remaining sample administration, sample collection, reception, temporary storage, processing, and shipping the samples to the Biorepository in accordance with the standards of ISO15189, ISO17025 and the ISBER Best Practices. With the goal of guaranteeing all the clinical waste should be safely disposed of in the clinical laboratory, a sample processing platform was established directly in clinical laboratory to support ethical issues counseling and sample processing. To ensure the examination remaining clinical sample should be temporarily stored at the cold storage for nearly 7 days to prevent re-examination without influence sample genomics quality, the examination remaining EDTA blood cell samples were processed in the clinical laboratory directly, then transported and stored at the Department of Biological Repositories (Zhongnan Biobank) according to the established SOPs under obtaining informed consents from individuals.Conclusion: The implementation of establishing a biorepository sample processing platform in clinical laboratory has enabled us to validate a large amount of clinical laboratory examination remaining blood genomics biobank, and provide reliable strategy of cooperation with clinical and medical departments particularly in large population based disease cohort studies.LBP-10 The Biospecimen Research Database: An Online Literature Repository and SOP Library to Improve Specimen QualityCampbell L. D., Engel K., Greytak S., Casas-Silva E., Guan P., Moore H. M.Biorepositories and Biospecimen Research Branch, National Cancer Institute, Bethesda, Maryland, United StatesThis 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.LBP-11 A Unique Approach to Rare Disease Specimen CollectionMann M., Chery G., Greenberg B.Neurology & Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, Texas, United StatesBackground: Researchers in rare diseases face multiple challenges, including the availability of adequate numbers of quality biospecimens for study. Developing a method to collect research samples outside the clinic setting offers a way to increase numbers and promote diversity of the sample pool. To address this need for the University of Texas Southwestern Medical Center's open access biorepository for neuromyelitis optica (NMO), we established a staff position for a traveling research nurse whose focus is longitudinal collection of samples and data from patients with NMO.Methods: The biorepository protocol was amended to allow collection and shipping of biospecimens outside the clinic setting. The travel nurse received certification in phlebotomy and IATA hazardous goods shipping. Biorepository lab personnel helped develop a protocol to standardize the collection, processing, and shipping of blood samples to be comparable to those collected on site. It was determined that the travel nurse could collect the same tube set as collected in clinic visits: ACDs shipped ambient, EDTAs and PaxGenes shipped refrigerated, and SSTs to be spun in a mobile centrifuge, aliquoted, and shipped on dry ice. The samples are shipped via FedEx to arrive at the lab within 24 hours of collection. The nurse recruited 40 subjects in 8 US locations to be visited 3 times per year. Visits are held in a private setting and take about 1 hour to collect, process, and pack each sample. Multiple visits may be scheduled in a day.Results: Since 2014 we collected 266 samples from 45 research subjects with NMO outside our clinic. This compares to 285 samples from 58 subjects collected during clinic visits since 2010. Remote patients express appreciation that they may easily participate in research opportunities they might not otherwise have had. Quality and viability of the remotely collected samples are comparable to those collected in clinic. We have also been able to provide specialized collections for research collaborators including sharing DNA samples to understand the genetic underpinnings of this rare disease.Conclusion: Use of traveling research personnel can augment the size and diversity of the biospecimen pool available for researchers in rare diseases. Also, the quality of the specimens is maintained through the shipping process. Lastly, patients feel more engaged in the research and are more likely to continuously contribute longitudinally.Biobanking Profiles - LBALBP-12 Setting & Maintaining a Biobank with a Training Perspective in Laboratoire La Grace, Yaounde – CameroonNana J. M.Diagnostic Medicine, Laboratoire d'Analyses Biomedicales La Grace, Yaoundé, Centre, CameroonBiobanks 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.LBP-13 National Liver Disease Biobank in India: Fostering Research Collaboration across India and AbroadYadav B. K.1, Bihari C.1,2, Sarin S. K.2, Sarin S.31Biobank, National Liver Disease Biobank, New Delhi, India,2Hepatology, Institute of Liver and Biliary Sciences, New Delhi, India,3Department of Biotechnology, Government of India, New Delhi, IndiaBackground: High Liver disease burden and diverse population in India provides an excellent opportunity to researchers. As per the World Health Organization liver disease is the tenth most common cause of death in India. The major causes of liver cirrhosis are Hepatitis B, C, alcohol abuse and non alcoholic fatty liver disease. There is very little progress has been done in this Field. Major obstruction in the translational research is unavailability of quality biosamples with standardized clinical annotations. Having a national level biobank and good research facility is the only solution to evade the problem. Institute of Liver and Biliary Sciences being a premier liver institute has established the National Liver Disease Biobank.Methods: National Liver Disease Biobank proposal was submitted to central government agency for initial funding. The biobank was established in the area of 464.61 square meter at ILBS with a $3,531,713 five-year grant from the Department of Biotechnology, Government of India. We have adopted decentralised sample collection, centralised storage and centralised informatics model for our national biobank facility. We sensitized the biobanking in different hospitals and research in