Abstract
The abstracts that follow demonstrate the broad range of timely issues addressed in the contributed oral and poster presentations at ISBER's 2017 Annual Meeting & Exhibits.
ORAL ABSTRACTS
Ethical, Legal, & Social Issues
The Comparative Study of Willingness of Chinese Children and Their Guardian Towards Biospecimens Donation
Effect of Deliberation on the Public's Attitudes Toward Consent Policies for Biobank Research: A Mixed Methods Study
Center for Ethics and Humanities in the Life Sciences, Michigan State University, East Lansing, Michigan, United States,
Lab of Immunoanalysis, Faculty Hospital Pilsen, Pilsen, Czech Republic,
The special issue will be the creation of generally acceptable informed consent (IC), which vary not only among the national biobanks, but even between hospitals. The concept of IC seems to be defined closely as so-called open consent. Anonymization is another important issue to be solved in the near future. To establish the generally accepted rules in compliance with BBMRI-ERIC statement will be the necessary process for the upcoming period.
Department of Pathology, Duke University, Durham, North Carolina, United States,
Pathology & Laboratory Medicine, Boston Medical Center/Boston University, Boston, Massachusetts, United States,
Repository Management
The National Institute of Standards and Technology (NIST) has been involved in the long-term archiving of biological and environmental samples for over 35 years, first by the establishment of the National Biomonitoring Specimen Bank (NBSB) in Gaithersburg, Maryland, and more recently the Marine Environmental Specimen Bank (Marine ESB) in Charleston, South Carolina. Sample collections were originally intended for monitoring geographic and temporal contaminant trends and include marine mammal tissues, seabird egg contents and tissues, bivalve tissue, and sediment. In 2010 the Marine ESB collections expanded into the Pacific Islands region to include sea turtle tissues and coral ecosystem samples (i.e., coral, crustose corraline algae). Additionally, after the BP Deep Water Horizon oil spill in 2010, the Marine ESB became the primary repository for frozen marine mammal specimens associated with the event. Although collections were originally intended for monitoring environmental contaminant trends, NIST has been investigating alternate uses for these cryopreserved samples, including genetic analyses and metabolomic and lipidomic studies. Because of the vast collection of invaluable samples archived in the Marine ESB it is imperative that sample records and details remain traceable, well organized, and searchable. This presents numerous challenges, particularly due to the wide variety of sample types archived and the metadata associated with the samples. With the induction of an updated barcoding system and the ongoing development of an innovative searchable database, the Marine ESB continues to maintain an organized and accurate collection of samples available for a wide range of analytical applications far into the future.
DiscovEHR Browser: A Portal for Sharing Genomic Data from Geisinger MyCode® Community Health Initiative
Geisinger Health System, Danville, Pennsylvania, United States,
For the financial dimension, SBP has developed a marketing and communication plan resulting in a stakeholders' mapping analysis, success and key performance indicators to follow.
In the operational dimension, SBP will be positioned as a certification body while developing a specific biobank quality standard fragmented into modules. This module-approach has the advantage to fit to any type of biobanks covering aspects from consent to distribution of samples.
To support implementation of harmonized processes, SBP has a centralized IT strategy with the development of a specific SBP module provided to the biobanks of the network. The idea is to equip main biobanks with an IT solution at a lower price through a reliable collaboration with a LIMS provider.
In the social dimension, SBP is developing a “one-stop shop” model for samples with the ambition to deliver fair, transparent, and efficient distribution of samples. This requires, on one hand, clear access and benefit-sharing guidelines with harmonization on samples' pricing, and on the other hand, structured biobank governance models. Engagement of multiple stakeholders from academic to private companies, as well as public engagement will support these developments.
Developing a Dashboard and Balanced Scorecard as an Administrative Tool to Rapidly Assess the Overall Health of a Biobank Program
Biobanking Sustainability How a Strategic Paper Helps in Operating a Biobank
Biospecimen Research/Quality
Room Temperature Storage Solutions: An Alternative to Cold Chain Management Within Biobanks and/or Diagnostics and Research Laboratories in Africa
Haematology, University of Stellenbosch, Cape Town, Western Cape, South Africa,
NIH, Rockville, Maryland, United States,
How Important Is the Time of Cold Ischemia to Molecular Research and When Do Most Changes Secondary to Cold Ischemia Occur?
Pathology, University of Alabama at Birmingham, Birmingham, Alabama, United States,
Utilization of Mobile App for Better Implementation of GCP in Sample Collecting Process for Biorepository
Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China,
IBBL, Luxembourg, Luxembourg,
Accreditation/Standardization and High Impact Studies
Department of Surgery, Duke University, Durham, North Carolina, United States,
University of Santo Tomas Collection of Microbial Strains, Research Center for the Natural and Applied Sciences, Thomas Aquinas Research Complex, University of Santo Tomas, Espana, Manila, Philippines,
The University of Santo Tomas Collection of Microbial Strains (USTCMS) in the Philippines is committed to the systematic collection, preservation, identification, classification, and culture institutional exchange of indigenous microbial strains derived from applied and basic researches by faculty and students of the university.
Tropical Philippines straddling west of the Pacific Ocean and East of South China Sea is rich in marine and brackish oomycetes (straminopiles), particularly halophytophthoras, thraustochytrids, and labyrinthulids. These microorganisms, hitherto poorly known and unstudied in the country, were found recently by a group of our graduate and undergraduate students to be associated consistently with shed mangrove leaves. Sample leaves were collected from selected mangrove stands in three island groups in the country (Luzon, Visayas, Mindanao), and in our laboratory were gently wiped with tissue paper, cut into strips, and placed for isolation of the organisms in Petri dishes with clarified V8-seawater agar medium. Isolation plates were incubated at room temperature for 3 days or until halophytophthoras, thraustochytrids, and labyrinthulids were visible respectively as mycelial growth and clumped colonies around the leaf explants. Portions of the observed growth were cut out and purified on the same agar medium for halophytophthoras. For thraustochytrids and labyrinthulids, colonies were dispersed in sterile seawater and loopfuls therefrom were streaked for purification on the same agar medium. Pure cultures of isolates were preserved in mineral oil and coded for isobanking following the Stealth Database management system.
We have now from mangroves a diverse collection of halophytophthoras, thraustochytrids, and labyrinthulids, all linked probably to the stages of decay of shed leaves. Molecular identification (ITS and COX2) for taxonomic diversity is on the way with the end in view of a) their specific role in ecological succession in mangroves; b) their potential use in biotechnology, for example, with thraustochytrids as alternative, cost-effective source of polyunsaturated fatty acids (e.g., DHA, docosahexaenoic acid); and c) their use as models to improve further our competence in the proper handling of marine microorganisms from isolation to biobanking.
Translational Research Center, Lianyungang Municipal Hospital for Maternal and Children's Health, Lianyungang, Jiangsu, China,
Biobanking of human specimens during the entire period of pregnancy is the fundamental basis for clinical translational research on reproductive disorders, including spontaneous preterm birth (sPTB), which is a syndrome resulting from various etiological factors. sPTB is the most common cause of neonatal mortality and morbidity, representing a significant clinical problem globally. The pathogenic mechanisms underlying sPTB are not yet clear. Applying multi-center prebanked human placentas, which were delivered from sPTB, compared to full-term birth (FTB) and premature rupture of fetal membrane (PROM) at FTB, in addition to maternal bloods collected from the first, second, and third trimesters, we have employed a systems biology approach with whole-genome exome sequencing (WES), differential expression profiles (DEPs) of transcriptomics, and genome-wide methylation profiles (GMPs), and identified a certain number of pathogenic pathways for sPTB. A ubiquitin-proteasome-collagen (CUP) pathway was determined in sPTB, which could be associated with preterm premature rupture of membrane (PPROM) that accounts for 40% of sPTBs. Our WES data showed that there were 20 variants—five mutations localized at collagen genes, three at ubiquitin enzyme genes, and four at ubiquitin associated proteasome/peptidase genes—identified from peripheral bloods of women who had sPTB delivered. Finding of these variations, including mutations at CUP loci, confirmed the genetic predisposition. Upon which, the epigenetic regulation may trigger the clinical condition. Indeed, nine CUP-associated long non-coding RNAs (lncRNAs) were identified to be differentially expressed in human placentas, with extremely statistical significance at P value less than 10-6. Nine pairs of lncRNAs and lncRNA-overlapped mRNA were identified from microarray study and validated with qRT-PCR. In placenta samples, the most different expression pattern of the RNAs was found between the groups of rupture of the membrane group vs. labor without membrane rupture. When validated with human fetal membranes (the amniochoriotic membranes), the striking significance has been noticed among the sPTB cases with rupture of membrane. Further bioinformatics analysis demonstrated that the CUP-associated lncRNAs and lncRNA-overlapped mRNAs are co-expressed and formed a functional network. Our study demonstrated that to develop multi-centered biobanks has been to a crucial factor in the reproductive research.
Preparing a Large Biorepository for College of American Pathologists (CAP) Accreditation
Biospecimen Accessioning and Processing Core Laboratory, Biorepository Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States,
Biobanking, NSW Health Pathology, Sydney, New South Wales, Australia,
Certification requires the resource leader to register details of the facility and complete, with team members, up to nine pertinent education modules. As a new initiative, leaders can register as either a biobank or a pathology department that undertakes biobanking activities, and a specific education module has been developed for this. For each module attempted, there is a new requirement to pass a short test, which has been developed with the NSW Health education and training provider. The resource leader then submits a declaration of compliance to adhere to best practices and uploads key documents for auditor review. Biobanks can opt to be listed on a publically available Biobank Locator.
Center for Personalized Diagnostics, Arizona State University, Tempe, Arizona, United States,
Access to high-quality samples is critical to the future of precision medical research. Unfortunately, many biobanks go underutilized, their precious samples gathering ice. Simultaneously, researchers looking for samples often end up using the easiest samples they can find. It is too burdensome for researchers to find repositories they are unfamiliar with and too costly for biobanks to market themselves. This leads to researchers obtaining samples through existing collaborations and yet these samples are not always appropriate for the particular experiments planned. 315 papers in the literature directly demonstrate how differences in sample preparation affect experimental outcomes and reproducibility, due to the fact that all biological molecules and structures are not equally preserved under all collection protocols. Different preservations methods have different end uses. Therefore, when researchers use samples which are incompatible with the analytical test performed, they risk generating irreproducible results. Irreproducible results in biomedical research continue to waste billions of research dollars each year. Both of these issues, the underutilization of biobanks and matching researchers with the most appropriate samples, can be addressed by building a worldwide listing of all biobanks that showcases how samples were prepared and what purposes they are fit for use in.
The Global Biological Standards Institute and the Biodesign Institute of Arizona State University have developed an open and public database, called Biospecimen Commons, to store, search, and compare collections along with the SOPs used in processing samples. Directly linking each collection to the actual SOPs used during processing enables researchers to not only find new collections, which they were not aware of, but it also allows them to quickly screen collections for those most fit for their intended experiments. Differences in sample preparation can be more easily identified by listing the protocols from different repositories in one easy-to-search place, making it easier to determine what changes during sample preparation lead to different outcomes in experimental results. Biospecimen Commons is intended to be an open community resource and is currently building its foundation of repositories and collections prior to public release. Within three years, we envision this will be a widely-adopted database for finding biorepositories in order to obtain samples for research.
Innovative Technologies
School of Molecular Sciences, Arizona State University, Tempe, Arizona, United States,
Counting the Costs: The True Price of Manual and Automated Cold Storage
The benefits of automation may seem obvious but the expense often difficult to justify. A comprehensive study will be presented, which reveals the true costs of automated versus manual storage, providing insight on when it is right to automate and when it is not. A cost calculator will be demonstrated which can help users identify where automation can provide cost benefits as well as operational improvements, and can be used to build a business case for automation
Ultimate Sample Storage–The New Panasonic TwinGuard Helps Biorepositories Become More Efficient
In today's biorepositories, there is no room for poor quality, failures, or ongoing maintenance problems. A significant investment in biorepositories include cold storage for the long-term storage of samples. In regard to ultra-low temperature (ULT) freezers, the vast majority of today's ULT utilize a cascade or single refrigeration design. Unfortunately, should a compressor malfunction, the entire system comes to a halt, which can result in a catastrophic failure. The user must quickly remove samples to prevent them from warming up, possibly compromising the sample integrity.
Panasonic Healthcare's new innovative TwinGuard refrigeration design utilizes a redundant compressor system demonstrating proven 99% reliability. Not only does this system run efficiently, but should one compressor fail, the redundant system will continue to operate, keeping the interior chamber temperature at −70°C, indefinitely in a 30°C ambient.
Furthermore, the new TwinGuard design provides exceptional temperature recovery and uniformity performance across a wide temperature range that simply cannot be achieved utilizing standard cascade refrigeration system designs.
When making a ULT purchase decision, biorepositories look for several important items:
The Panasonic Healthcare's new Twin Guard is an amalgamation of 50 years of freezer design experience to meet today's biorepository requirements.
The Marketplace for Human Biospecimen Collections: Biorepositories in the Cloud to Fuel Research
Users of this technology are able to search for specimens and/or patients, view feasibility results and details about matching cases, request a quote, and track their order throughout the fulfillment process—essentially streamlining what is a very difficult and time-consuming process today. Participating biorepositories gain a single point of communication to thousands of researchers who need to the very samples they store which allows them to both more easily fulfill their research mission as well as increase their sustainability. In addition to connecting researchers and biorepositories, the free technology also manages the biospecimen fulfilment process—through a simple point-and-click interface that supports the picking, collecting, packing, and shipping of samples. Biorepositories can also use the technology to help manage their collections, making the specimens more readily visible to their own internal researchers or across a network of researchers they designate, further enabling collaborative sharing of specimens and data within and across institutions.
The promise of biorepositories—to support and fuel research—will finally be achieved through the economies of scope and scale made possible by iSpecimen's ground-breaking biospecimen marketplace.
Secure High-Density Automated Sample Storage in a Small Footprint
The number of smaller, satellite biobanks is growing, as well as the number of samples stored in these locations. These locations typically have smaller laboratory spaces to work with, and therefore have manual freezers for sample storage. However, the need for automation is increasing as labs seek to ensure sample integrity and security.
In order to meet these needs, the SAM HD was developed. SAM HD is a low-capacity automated sample management system storing samples at temperatures down to −80°C in a small footprint. The SAM HD has a capacity of up to 60,000 tubes in standard racks, or 86,250 tubes using the exclusive SBS-compliant, high-density RackWare® racks from Hamilton Storage. These racks and the ability of SAM HD to store the racks were designed to allow a higher capacity in a smaller footprint for laboratories seeking the security of automation, but needing the solution to fit into smaller spaces.
Additionally, the SAM HD provides flexibility by storing up to six different tube types with the same diameter in the same system to accommodate varying sample collection workflows while maintaining secure sample documentation and tracking. This variety of labware can also be picked without the hassle of tooling changes, and without compromising the integrity of unpicked samples.
The new technologies supported by SAM HD provide a walkaway solution for labs seeking to transition from manual to automated sample storage.
Brooks ISIDOR Portal: Bringing Efficiency and Usability to Biobanking Applications
Brooks new ISIDOR Portal is a web-based application that manages single sign on access to multiple applications, and allows users to create a personalized navigation dashboard to access specific features as quickly as possible, whilst delivering dashboarding capability across all applications.
Smartphone technologies have changed user expectations of software look and feel, navigation, and interoperability within the same environment. As new standards for web technology are adopted, it is possible to manage and navigate different web-based applications using a common user portal replicating the smartphone model.
Shortcuts to other web applications and URLs can also be configured to giving a single user experience across the range of applications needed to carry out their daily activities. Reports and interactive dashboards can extract data from multiple sources, reducing the time to find and act on important information.
User identification and application access is managed using Microsoft Identity Server functionality, simplifying access and delivering a single security model across all the applications.
BioLix™ SAB: A Novel Automated Storage Platform to Increase Biosample Utilization
Liconic Instruments, US, Woburn, Massachusetts, United States,
BioLix™ SAB has 2 features that innovate centralization and utilization processes. First, the stacked columnar infrastructure creates an estimated 30% higher density of space which maximizes storage capacity, enabling the user to integrate a larger amount of legacy collections. Second, the rack based transport shuttle mechanism (SBS and mixed formats) offers ultimate configurability for an unlimited range of storage containers with no reformatting required. The shuttle picks up columns allowing batch handling of up to thousands of samples. This enables capability to integrate both legacy and de-centralized collections in real time.
Global Specimen Solutions, Raleigh, North Carolina, United States,
POSTER ABSTRACTS
Biobank Education Tools
Clinical Pathology, National Cancer Institute, Cairo University, Cairo, Egypt,
Collaborating partners—including biobanks and biorepositories, pharma and biotech companies, and contract research organizations—have the challenge of working together to ensure effective use of tissue, blood, and other biospecimens that are donated by patients for conducting research studies in the age of precision medicine. These biospecimens along with their associated clinical/health-related data offer an invaluable resource to researchers and clinicians trying to identify biological traits that can help them select tailored treatments for each patient. Hence, sharing of these data among a network of biobanks and with clinicians is imperative. Currently, biobanks either use paper-based systems, desktop-based tools, or traditional products for managing biospecimens and the associated meta data. On one hand, paper-based systems and desktop tools are not collaborative in nature and are unable to comply with regulatory guidelines. On the other hand, traditional products are too expensive to offer a viable solution for real-time sharing of critical biospecimen data within the research community. The resulting lack of coordination among the scientific research groups hinders the progress of on-going research studies and therefore the health of individuals and the population at large.
The advances in information technology have enabled significant changes in the way research is conducted and have also provided a means to share data on a global scale. One such advancement among these is cloud technology. Cloud technology is emerging as a viable alternative to paper-based, desktop tools and traditional products. The cloud-based solutions such as laboratory information management systems offer advantages such as enhanced security, rapid scalability, and dynamic allocation of services. Most importantly, the cloud platform fosters collaboration among a network of biobanks/laboratories, even if dispersed geographically, by using a shared environment. Biobanks can now harness cloud technology to drive collaborative research by securely storing clinical data in the cloud and by following ethical sharing with collaborators.
Biodiversity/Environmental/Animal/Repositories
The “Power” Is in Collaboration: Vascularized Composite Allotransplantation Collaborative Initiative (VCAci) Biobank
The NASA Ames Life Sciences Data Archive: History, Best Practices, and Scientific Opportunities
Space Biosciences Research Branch, NASA Ames Research Center, KBRwyle, Moffett Field, California, United States,
The NASA Ames Life Sciences Data Archive (ALSDA), which includes the Biospecimen Storage Facility (BSF), is managed by the Space Biosciences Division and has been operational since 1993. ALSDA is part of the Institutional Scientific Collection at NASA Ames. The ALSDA is responsible for archiving information and animal biospecimens collected from life science spaceflight experiments and matching ground control experiments. Both fixed and frozen spaceflight and ground tissues are stored in the BSF. The ALSDA also manages a Biospecimen Sharing Program, performs curation and long-term storage operations, and makes biospecimens available to the scientific community for research purposes via the Life Science Data Archive public website (https://lsda.jsc.nasa.gov).
As part of our best practices, a viability testing plan has been developed for the ALSDA, which will assess the quality of archived samples. We expect that results from the viability testing will catalyze sample use, enable broader science community interest, and improve operational efficiency of the archives. The current viability test plan focuses on generating disposition recommendations and is based on using RNA integrity number (RIN) scores as a criteria for measurement of biospecimen viability for downstream functional analysis. The plan includes 1) sorting and identification of candidate samples, 2) conducting a statistically-based power analysis to generate representative cohorts from the population of stored biospecimens, 3) completion of RIN analysis on select samples, and 4) development of disposition recommendations based on the RIN scores. Results of this work support NASA open science initiatives and guides development of the NASA Scientific Collections Directive (a policy on best practices for curation of biological collections). Our RIN-based methodology for characterizing the quality of tissues stored in the ISC since the 1980s also creates unique scientific opportunities for temporal assessment across historical missions.
Support from the NASA Space Biology Program and the NASA Human Research Program is gratefully acknowledged.
The Microorganisms & Viruses Culture Collection Center (MVCCC) was built in 1979, relying on Wuhan Institute of Virology, Chinese Academy of Sciences. It was then registered as a member of World Federation for Culture Collections in 1989. After years of development, MVCCC has become the most comprehensive virus resource center in China for virus preservation and biotechnology research. In 2013, it was nominated as one of the six national preservation centers in China by the National Health and Family Planning Commission. MVCCC had the preservation of more than 1300 virus isolates including human and animal viruses, insect viruses, plant viruses, and phages which are involved in 6 orders, 37 families, 79 genera, and 266 species. The center also had the collection of the virus susceptible cells and related bacteria, and genetic resources as well as meta-databases. MVCCC is qualified to manipulate and preserve the highly pathogenic viruses as it is equipped with its own BSL2, BSL2+, BSL3 labs and the unique BSL4 lab in China relying on Wuhan Institute of Virology, as well as the related qualified technicians. MVCCC possesses four research groups engaged in virology research of different fields: the virus resource and biotechnology group, the systems virology group, the molecular virology and bio-engineering group, and the bioinformatics group. Under the direction of a qualified management system audited by China Quality Certification Center, MVCCC provides resources and services that are related to virus samples preservation to domestic and abroad research organizations and institutes, universities, and enterprises, including exchange and transportation, detection and identification, storage and preservation, proliferation, sequencing, and open access to virus information inquiry. MVCCC hopes to strengthen the international exchanges and cooperation with other biobanking members, and promote its own development in biological samples preservation and biobanking construction. All those will benefit the researches and industries of population and health, as well as life sciences.
Biobanking Profiles
Shanghai East Hospital has set up a large-scale, high-quality biobank, characterized by storage of stem cell with complete clinical information to support scientific and clinical research. The biobank has standard operating procedures for sample collection, transferring, storage, quality control system, cold chain, and environmental monitoring system. It was funded by government with nearly 300 million RMB. The total investment of this clinical-grade stem cell bank is about 60 million RMB. The stem cell biobank occupies an area of 550 square meters, with a total capacity of about 2.5 million samples. It has become a China stem cell resource sharing platform, public inspection service center, and regional information management center and developed clinical stem cell research information management software with independent intellectual property rights for data tracking and traceability management in the whole process of preclinical, clinical, and post-clinical as well as the cell life cycle. The hospital has led the establishment of the stem cell R&D institution and teamed up with universities, enterprises, scientific research institutes, and another 63 institutions to set up the Shanghai Stem Cell Industry Alliance, which is the national innovative research group with nearly 200 people. The stem cell R&D institution is designated as a stem cell translational medicine industry base in the Zhangjiang national innovation demonstration zone as well as “four new” economic innovation base in Shanghai, and is one of the first NHFPC- approved stem cell clinical research institutes in 2016. At present, the stem cell bank has built a three-level management system including a seed cell bank, master cell bank, and working cell bank to achieve the mirror image storage of the precious stem cell resources, and successfully built and launched the third-party storage services. The operations of the stem cell bank comply with the best practices and AABB standards. Currently, stem cells are used in clinical research involving heart disease, nervous system disease, bone arthritis, and tumors. The professional quality analysis platform achieves quality control of whole process. The platform has equipped a fully automatic liquid handling system, automatic nucleic acid extraction workstation, biomacromolecules analyzer, and other high-end equipment allowing to automatically process DNA, RNA, protein extraction, and analysis, thus guaranteeing the quality of specimen, and provide high-quality data and reliable results.
China National GeneBank as an Open Platform for Leading the New Era of Life Science
China National GeneBank (hereinafter referred as “CNGB”) is a non-profit project/organization supported by the Chinese Government since 2011. Until June 2016, CNGB has stored about 10 million bioresources in the biorepository, including human biospecimens and biodiversity resources, and the total data capacity of 20PB.
On Sept. 22, 2016, CNGB held its opening ceremony in Shenzhen after 5 years of construction, with a focus on establishing an open platform for global scientific research. In order to better serve the life science industry, CNGB endows new functions and programs that not only store bioresources and data, but set up an infrastructure from bioresource storage, data analysis, to bioresource utilization.
Platforms:
– CNGB establishes a digitalization platform configured of 150 self-developed BGI-seq500 and one fully-automatic sequencer called Revolocity. This platform could generate about 5PB data per year and has the capacity to sequence 50,000 human genomes per year.
– The synthesis and editing platform of CNGB launched five projects including the Sc2.0 project collaborated with six Countries, and set up synthesis software development and laboratory procedure. Based on this platform and technology, CNGB published 7 papers and applied for patents as well as 4 software copyrights.
– The living biobank of CNGB is committed to building a China Noah's Ark, which would protect and save the life resource of almost 300 thousand plant species, a million animal species, and 10 million microbe species.
Projects:
– CNGB launched a series of cohort studies covering cancer, birth defects, etc., as well as population-based cohort studies.
– Based on the massive data storage, CNGB established over 40 databases, such as the cancer database, millet database, covering over 7,000 species, 27 individual species, 70,000 samples, 1 million genes, 10 million mutation information, and 1 PB raw data. All these databases are open to public and could be retrieved through the official website of CNGB.
– Through the global collaboration and alliance, CNGB will digitalize all bioresources for better understanding of life, better utilization of the biological resources, and better sharing and exploration.
Biobank and Translational Medicine in China
The Guiding Significance of the ISO9001:2015 Revision for Clinical Biobank
Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China,
The First Central Hospital of Tianjin, China, is a comprehensive third-class hospital that specializes in organ transplantation, which integrates medical treatment, teaching, scientific research, and prevention. It is one of the medical centers in Tianjin. Our hospital organ transplant center was founded in 1998 by the famous organ transplant expert Professor Zhongyang Shen, who in 2002 established the Tianjin Institute of Organ Transplantation. The center is the largest organ transplantation center in Asia.
Our hospital has a biological sample library, an existing full-time technical staff of eight, five part-time guidance experts, the use of an area of 800 square meters, an under the organ transplant sample bank, a hospital-integrated biological sample bank, and a tissue organ bank. The biological sample bank adheres to the “standard management, quality assurance, scientific use, create value” concept, and develops perfect sample bank specifications, systems. and standard operating procedure files. Now, it is routine to carry out the organization, blood, urine, bile, cells, nucleic acids, and other types of samples preservation, and gradually realize the automated sample processing; besides, organ transplant samples have been fully implemented with gas phase liquid nitrogen preservation. As one of the hospital scientific research platforms, the biological sample bank carries out clinical research technical services, such as pathological slides, immunohistochemistry staining, tissue microarray preparation, apoptosis detection, tissue processing and magnetic separation, cell viability, apoptosis, cycle and detection of circulating tumor cells, PDX sorting model, program cooling, and other technical services. With the help of the rich sample resources, the biological sample bank supports more than 30 items including the National 863 project, the National Natural Science Foundation, and the provincial- and ministerial-level scientific research projects. We have published nearly 100 papers including SCI. In the future we will continue to strengthen the construction of the hospital large-scale comprehensive biological sample bank with the size of 1800m2 in our new hospital, so laying a solid foundation for the research work of the hospital.
For cooperation, please contact us at
The number of biobanks in China increased staggeringly in recent years, which brought in more and more professional biobankers to devote themselves in biobanking. These biobanker professionals are working in several categories, including biospecimens registering, handling, managing, data processing, and so on. In order to build up standardized biobanks in China, we have been working closely together.
In 2009, the Biobank Branch of the China Medical Biotechnology Association (BBCMBA) was established and held its first annual meeting. The delegates have risen from 100 to 2,000 in 7 years. Besides the annual meetings, BBCMBA organizes training classes several times a year. The biobankers from same regions were spontaneously assembled into some biobank salons occasionally. We also take advantage of on-line tools, like Wechat, which has groups for all biobankers and one for directors, so we could link up easily and communicate with each other about all aspects of biobanking.
As an active and studious group, we set up a biospecimen science team. We summarized some topics about biobanking, and after being reviewed by specialists, released them daily in the Wechat platform for the biobanker community. As of the end of 2016, we have already released more than 250 excellent references; our strict censorship system received Chinese biobankers' trust. We also compiled references and publish quarterly. In the spring of 2016, we translated Canadian Tumour Repository Network (CTRNet) standard operating procedures into Chinese and shared to the Biobankers all around China, and received much appreciation from our biobanker professionals.
Biospecimen Research and Science
The Tube Really Does Matter—An Assessment of Four Different Blood Collection Tubes for Automated RNA Extraction in a Biorepository Environment
Residual Formalin in a Tissue Processor Previously Used for FFPE Blocks Reduces Nucleic Acid Yield and Quality in PAXgene-Fixed Tissues
Developing a Genomic Big-Data Program Based on High-Quality Cancer Biobank
The Effect of Specimen Collecting and Placing Time on Cytokine Determination
Etiology Comparative Analysis of Hand, Foot, and Mouth Disease from 2013 to 2015
Beijing Key Laboratory of Emerging Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China,
Gynecology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China,
The Effect of Liquid Nitrogen Storage on ctDNA Extraction from Plasma
Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States,
Storing quality control plasma standards at −80°C produces a mean concentration of ctDNA of 0.95 ng/μl. We stored aliquots of a parallel standard in LN2 for 2 weeks and were able to extract a ctDNA concentration of 1.019 ng/μl. Additional data will be presented at the meeting. Initial results indicate that plasma storage in LN2 is at least not inferior, if not superior, to storage at −80°C. Storage at temperatures higher than −80°C is not recommended and further data will be acquired to study how time-sensitive cfDNA is with respect to “needle-to-freezer” speed and handling.
Functional Study of Differential Expression Plasma miRNAs in Patients with HBV-Related Liver Diseases
Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China,
The Molecular Virology and Bio-Engineering Lab, Wuhan Institute of Virology, China Academy of Science, Wuhan, Hubei, China,
Ticks can carry and transmit viruses that pose a threat to human health. In this study, investigations of the tick-borne viruses in the dominant tick species, B. microplus, collected in Yunan province, China, was carried out using next-generation sequencing. The transcriptome data of the tick pools revealed that B. microplus carried diversified tick-borne viruses, including novel viruses that belong to the family Bunyaviridae and Flaviviridae, and other novel viruses which are unclassified. Epidemiological investigation showed that in B. microplus ticks from Yunnan province, four of the novel unassigned tick-borne viruses were mostly found from 2015 to 2017, which are designated as YNTV1, YNTV2, YNTV3, and JMTV-YN16. The genome sequences and organizations of these novel viruses were characterized, and the phylogenetic analysis was performed. All the results will not only facilitate the better understanding of RNA viral diversity and evolution carried by ticks, but also benefit the prevention and control of tick-borne viral diseases.
Imperial College London, London, United Kingdom,
Biorefinery, IBBL, Luxembourg, Luxembourg,
Adipose-Derived Autologous Mesenchymal Stem Cells for Treatment of Deep Burns in the Hand
Cairo University, Cairo, Egypt,
Cairo University, Cairo, Egypt,
Premature ovarian failure (POF) is defined as failure of the ovary to function adequately in its role either as an endocrine organ or as a reproductive organ in a woman younger than 40 years. It is characterized by amenorrhea, hypoestrogenism, and elevated serum gonadotropin levels. This condition occurs in approximately 1% of women and it has major physical and psychological consequences/impact in those patients.
Stem cell therapy is increasingly gaining grounds in the regeneration of damaged or failed tissues and organs.
The purpose of this study is to investigate the role of the transplantation of autologous bone marrow-derived mesenchymal stem cells in amelioration of this condition.
- Primary Outcome Measures:
Cases will be followed using serum follicle-stimulating hormone (FSH), estrogen, and anti-mullarian hormone (AMH) levels.
- Secondary Outcome Measures:
Disappearance of menopausal symptoms, e.g., hot flashes, and rise in serum AMH level. Pregnancy rate within 1 year. Long-term follow-up for any adverse effect, assessed for 1 year from injection.
Subjects and Methods:
Subjects:
30 patients with POF were included:
Inclusion Criteria:
- Patients with normal karyotype spontaneous premature ovarian failure.
- Patients between 18-40 years old.
Exclusion Criteria:
- Patients with secondary ovarian failure (e.g., hypothalamic causes).
- Autoimmune diseases.
- Those with major medical problems such as malignancy, hepatitis, etc.
- Abnormal karyotyping (e.g., Turner syndrome)
This study shows that autologous MSC may improve the conditions in patients with POF. Optimization of the cell dose and route of injection needs further experimentation.
Blood for biobanking is often collected, processed, and stored for intended downstream use in nucleic acid extractions. The delay in time between the collection of the blood specimen and the time it is received at the laboratory can lead to less than optimal nucleic acid recovery. A novel method was developed for immediate lysis and stabilization of blood upon collection to optimize nucleic acid preservation prior to transportation, processing, and storage at the biobank.
Four-milliliter serum (red top) vacutainers were filled with 2 mL of lysis buffer V (LBV) by evacuation of 2-ml air with a syringe and needle, and the subsequent addition of 2mL of LBV. The vacutainers were then used to collect 2 ml of peripheral blood. The blood in LBV was held at either temperatures of 4°C or 24°C for time points of 1 hour, 1 day, 2 days, 3 days, 4 days, and 7 days. This blood was compared to blood that was drawn into an ethylenediaminetetraacetic acid (purple top) vacutainer or a heparin (green top) vacutainer prior to addition of LBV.
DNA was extracted from 200 μl of the blood and LBV mixture using a Qiagen blood DNA kit. The purity and quantity of DNA was measured using an ultraviolet spectrophotometer; DNA quality was measured by gel electrophoresis. Similar amounts of DNA were isolated from the samples after 6 days; initial quantity of DNA extracted was 29.6ng/μl while the sample held at room temperature for 6 days had a DNA quantity of 21.3ng/μl. Both results from the gel electrophoresis showed thick bands of DNA near top of the DNA ladder. These results indicated that a vacutainer prepared with DNA lysis buffer is an effective and efficient method for collection of whole blood for downstream DNA extraction. Studies are ongoing investigating the usefulness of this method in the preservation of RNA for future extraction.
A Cost-Effective Method for Temperature Mapping of Liquid Nitrogen VAPOR Storage Tanks
Freezer Temperature Excursion Effects on Biospecimen Temperatures
For all trials the sample temperature changes among sample type and volume were highly variable.
Vapor Shipper Dewars as Temporary Storage Devices at Clinical Sites
The Importance of Quality Control and Clinical Information Collection for Gastrointestinal Biobank in Shanghai Ruijin Hospital
Shanghai Institute of Digestive Surgery, Shanghai Ruijin Hospital, Shanghai, China,
Eastern Maine Medical Center, Brewer, Maine, United States,
Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,
Oral cancer (OC) is one of the most common cancers that badly affects the health and living quality of people. The surgical therapy for OC is limited by its operational area. Because of its unique anatomy and primary achievements from genetic studies, OC is an ideal model for carrying out molecular classification strategy. The tumorigenesis and development of OC is a continuous and multi-process event. Integration of description of tumorigenesis regulatory network and searching for their vital junction and regulatory factors are the most effective strategy for conducting precise medicine.
To date, the molecular study of OC is conducted in parallel by national and international researchers. We still lack a multi-level molecular standard to overwhelming by evaluating the process of OC development. The purpose of this study is mainly based on the OC tissue bank and bio-information data, to investigate the proteomics and genomics classification of OC development; the complex regulatory network and vital molecular event that drive the cancer development, diagnosis and treatment; the idea molecular targets for tumorigenesis, molecular prediction, and prevention.
We have used high throughput screening technology to describe the OC develop processing systemic and multi-divisionally. We have also developed original multi-study integration analysis technologies to draw the molecular regulator network of OC. Based on the innovative bio-informatics analysis models, many driver genes during oral oncogenesis have been obtained. The filtration and verification of gene targets and molecular markers for OC prevention and treatment have being carried out. The new system for OC molecular diagnosis and individual treatment will be built. Some diagnosis and treatment molecular markers have being evaluated using big-size clinical OC samples. This study will illustrate the molecular process of different stages of OC and help to develop the molecular classification technologies.
The study is supported by National Program on Key Research Project of China (NO. 2016YFC0902700).
Life Science, Brooks Automation, Chelmsford, Massachusetts, United States,
The objective of this study is to compare two methods of preparing, transporting and storing live T-cells at both −80°C and −190°C to demonstrate best practices to achieve the highest post-thaw viability.
The other half were prepared with a traditional home-brew cryoprotective media consisting of 95% fetal bovine serum and 5% w/v DMSO and frozen to −80°C using an isopropyl alcohol freezing device and shipped using a conventional Expanded Polystyrene dry ice shipping container to Brooks.
Upon arrival, all cryovials containing Jurkat cells were handled identically and stored in either a −80°C ultra-low-temperature freezer or the −190°C BioStore III Cryo system.
After frozen storage of one year, the cryovials were packed and shipped back to BioLife in the same containers and using the same methods as employed previously. Both groups were thawed and analyzed for viability and functionality immediately post-thaw and at 24- and 48-hr post-thaw using the identical pre-freeze assays.
CPTAC Phase III, Continuation of the Proteogenomic Analysis of Cancers
Frederick National Lab for Cancer Research, Rockville, Maryland, United States,
The Clinical Proteomics Tumor Analysis Consortium (CPTAC) is a National Cancer Institute initiative that seeks to uncover the molecular basis of cancer using a proteogenomic approach to study prospective cancer biospecimens. Leidos Biomed provides an infrastructure for supporting the collection of high-quality biospecimens and data, in addition to project and subcontract management for the program. CPTAC applies the understanding of the molecular basis of cancer to identify biomarker candidates. Phase II of CPTAC, completed in 2016, collected over 500 cases from breast, colon, and ovarian patients. Since early 2016, CPTAC Phase III has been collecting and will analyze 200 cases of each of ten additional cancers. The cancers include glioblastoma, pancreatic ductal carcinoma, lung adenocarcinoma, lung squamous cell carcinoma, sarcoma, head and neck squamous cell carcinoma, uterine corpus endometrial carcinoma, clear cell renal cell carcinoma, and acute myeloid leukemia. The goal is to collect 200 qualified cases of as many of these tumor types as feasible.
This project is funded by NCI Contract No. HHSN261200800001E.
The study entails collection and pathology evaluation of biospecimens, high-quality clinical data, and images from clinical sites around the world. A biorepository receives, evaluates and processes the biospecimens, sending nucleic acids to a sequencing center and tissues to proteomics groups. Data are combined and analyzed by translational centers. Genomic data are made available to the research community through the NCI Genomic Data Commons. Proteomic data are made available through the Data Coordinating Center. We report here on progress in collection of tissues and clinical data, and progress through biorepository, proteomics and genomics, and analysis centers.
Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada,
If blood proteins degrade during collection, processing or storage, then this degradation may confound the comparison of plasma samples across different physiological states and compromise the search for disease biomarkers. Thirty human ethylenediaminetetraacetic plasma samples from male and female subjects ranging in age from 24 to 74 were collected on ice, processed, and aliquoted ice cold, and held at −80°C prior to randomly assigning post-centrifugation treatments. Tryptic peptides from complement component 4B (C4B) were rapidly released in plasma at room temperature compared to samples on ice or ice plus inhibitors as confirmed by random and independent sampling, automated targeted analysis, and manual isotope dilution. Random and independent sampling, automatic-targeted analysis, and manual isotope dilution analysis followed by 1 point internal calibration all agreed that the tryptic peptide NGFKSHALQLNNR of C4B was a sensitive indicator of plasma degradation at room temperature in as little as 1 to 4 hours. Proteolytic peptides from complement component C4 were rarely observed with long term storage at −80°C or −196°C in liquid nitrogen, or cold vacuum drying followed by storage at −20°C or cold vacuum drying followed by storage at room temperature. We conclude plasma may be effectively preserved on ice for several days, or by vacuum drying and storage at room temperature for at least 1 year or freezing for at least 1 year with no significant proteolytic digestion of C4B by tryptic enzymes.
Effects of Pre-Analytical Variables on Thrombosis Biomarkers in Cancer Patients: Study Planning and Launch
Biospecimen Research Group, Leidos Biomedical Research, Inc., Rockville, Maryland, United States,
Thrombosis, specifically venous thromboembolism (VTE), is a major source of morbidity and is associated with increased mortality in cancer patients. Incidence of thrombosis varies widely among cancer patients with multiple factors known to impact the risk, including clinical characteristics and individual patient characteristics. To build upon the current knowledge in the field and to identify gaps and priority research areas, the National Heart, Lung, and Blood Institute and the National Cancer Institute hosted a cancer and thrombosis meeting in August 2014 (http://cancerres.aacrjournals.org/content/76/13/3671.long). One of the major unmet needs identified was the further development and validation of biomarkers and risk assessment models, to stratify cancer patients by thrombotic risk, to better enable identification of cancer patients at high risk, and to help identify patient populations that might benefit from thromboprophylaxis. Central to marker and model development, is a need to both measure and assess the impact of pre-analytical factors on the downstream marker analyses and to standardize methods for identification and measurement of markers used for diagnosis, risk assessment, and prognosis of thrombosis in defined cancer patient populations.
To address these needs, a pilot study has been designed. The overall objectives of this study are to provide guidance for standardization of methods and approaches used for measuring thrombosis biomarkers in cancer patients. In particular, the focus of this project will be to identify and evaluate the steps during biospecimen procurement, handling, processing, and storage, which are critical for optimal specimen preservation for accurate marker detection.
As part of this study, blood samples will be collected and processed from cancer patients with high risk of thrombosis using vigorous standard operating procedures. A number of pre-analytical variables, such as delay to blood processing, delay to assay, freeze-thaw cycles, etc., will be evaluated for their impact on detection of thrombosis biomarkers such as D-dimer, soluble P-selectin (sP-selectin), and prothrombin fragment 1.2 (F1.2).
The findings from this study, which will help identify the impact of selected pre-analytical variables on measurement of thrombosis biomarkers, will lay a foundation for future biomarker studies to assess thrombotic risk and predict efficacy of antithrombotics.
This project is funded by NCI Contract No. HHSN261200800001E.
Pathology, Phoenix Children's Hospital, Phoenix, Arizona, United States,
IRGB-CNR, Milan, Italy,
Isenet represents a fundamental source of highly-controlled biomaterial that fulfills the most stringent standards since it participated in several European and National Research Projects in collaboration with academic stem cell laboratories. Isenet acquires, cryopreserves, characterizes, and distributes well-documented biospecimens since it applies sequentially and systematically a high-quality management system for long-term cell cryopreservation by following a quality control stem cell pipeline. Cells are cryopreserved in culture medium containing 10% dimethyl sulfoxide (DMSO) and/or in Cryostore CS10, a Good Manufacturing Practice cryoreagent containing 10% DMSO, free of animal proteins. This DMSO-based and serum free solution gives optimal results in term of cell viability. All cell line batches are stored in liquid nitrogen containers at −196°C.
Leidos Biomedical Research, Inc., Rockville, Maryland, United States,
Precise identification and quantitation of proteins in tissue specimens is a highly desirable for accurate downstream study of systems biology, clinical diagnosis, prognosis, and personalized medicine for any disease. In this study, critical preanalytical variables, namely post-mortem interval across three different time points (0, 4, and 12 hours from time of death or clamp time) and four different preservation methods and formats (cryopreserved in LN2, cryopreserved in dry ice, PAXGene-fixed paraffin-embedded and PAXgene fixed in PAXgene stabilizer solution [PFS]) were examined. The study examined differences in total proteome and phosphoproteome expression analysis in 20 cases (organ or tissue transplant donor) for two different tissue types (skeletal muscle and thyroid). Standard protocols for total protein and phosphoprotein enrichment from cryopreserved samples were employed, while modifications needed for PAXgene-fixed samples were developed for the study. Compared to cryopreserved specimens, PAXgene-fixed samples show promising results for total proteome and phosphoproteome analysis for biomarkers discovery and analysis utilizing LC-MS analysis. This study is designed to elucidate the usefulness and potential applications of PAXgene-fixed tissues at various post-mortem intervals compared to traditional means of fixation and long storage for complex analysis of proteins and phosphopeptides for the advancement in biomarker discovery and expression analysis.
This project is funded by NCI Contract No. HHSN261200800001E.
Effects of Storage Conditions on Protein Measurements: A Biospecimen Preanalytical Variables Program Study
National Cancer Institute, Rockville, Maryland, United States,
Biospecimen Research Group, Leidos Biomedical Research, Rockville, Maryland, United States,
This project is funded by NCI Contract No. HHSN261200800001E.
Ethical, Legal, and Social Issues
In Japan, the collection, storage, and use of human specimens and their related information are conducted in different ways depending on the repository. Regarding informed consent, broad consent is becoming the standard nationwide, but no unified policy yet exists for the use of collected specimens and their related information. Since 2013, the Tissue Research Project of Kyoto University has established a unified governance system within the campus for the collection, storage, and use of human specimens and their related information. By 2015, the policy on the use of human specimens, the standard informed consent format (broad consent), and the guidelines on using human specimens for research outside of Kyoto University had been established. As we presented last year at the annual meeting of ISBER, the transfer of human specimens and their related information from Kyoto University to other institutions is performed based on the following principles:
1. The specimens and their related information are to be used only for research that the Kyoto University Ethical Committee has deemed to be scientifically significant (to prevent the waste of specimens donated by courtesy, especially specimens of rare diseases).
2. Collaborative research contracts are required for the use of specimens and their related information (to make it possible for Kyoto University to monitor the management of the transferred specimens and information, etc.).
3. Specimens remaining after the research has been completed must be returned to Kyoto University (to allow valuable specimens to be used again, or for preventing the abuse of specimens).
Since 2015, based on the above rules, we have transferred specimens and their related information to some corporations. In this presentation, we will first describe how to make a boilerplate contract and clarify the unique features of the contract procedures at Kyoto University. Then, we will introduce two examples of completed contracts and an example of a non-completed contract to demonstrate the requests of corporations and the remaining challenges. The return of specimens after research has been completed is the main point of the discussion, because transport costs represent a burden for corporations. In addition, for corporations, it is better for them to retain the leftover specimens and to reuse them for other purposes in the future. We present here our efforts in protecting specimen donors while accommodating the requests of corporations.
“Universal Patient Language”—Improving Informed Consent
In clinical trials, the collection of samples begins with the process of Informed Consent. As paradigms for obtaining informed consent continue to evolve, Bristol-Myers Squibb gathered a diverse team of study participants, caregivers, and experts across various disciplines to apply a holistic, systems approach to improving the health literacy of the informed consent document and improve the consent experience. Following a three-day intensive “co-creation event,” we utilized our Universal Patient Language (UPL) toolkit to bring the ideas from co-creation to life, delivering an informed consent document and associated tools that show great promise for improving participant understanding by eliminating complex language, bringing graphics and tables to the presentation of difficult concepts, and, in all things, putting the patient at the center of the experience. An embedded video of the creative process lets the audience hear from leaders at Bristol-Myers Squibb, as well as many workshop participants, to gain insights into the importance of the process for patients and for scientific advancement. This talk opens a dialog about the opportunities to implement this structure to enhance the patient experience; and, audience members will be provided with take-away materials to invite engagement after the meeting.
Improving Qatar Biobank Consent Comprehension
Qatar Biobank, Doha, Doha, Qatar,
Qatar Biobank (QBB) complies with the Ministry of Public Health policies, regulations, and guidelines for research in human subjects. QBB is following the different versions of Informed Consent that have been approved by the HMC Institutional Review Board (IRB) on an annual basis. QBB started in 2012 using a short simplified consent form and an information leaflet, the consent form stated that the participant read and understood the information leaflet and had the opportunity to ask questions. The participants were asked to sign only the consent form (Group 1). In March 2016, the participants were asked to read and sign two consent forms, the initial short form and an additional more detailed form which included the information leaflet (Group 2). In October 2016, the consent form was reviewed by the IRB and both short and long forms were merged into long comprehensive consent form to include all the information that should be provided to the participants (Group 3). The aims of this study are 1) to examine and assure QBB Informed Consent comprehension through the different versions, and 2) to suggest interventions to improve consent comprehension if needed.
Clinical Trials Unit, DKMS GmbH - German Bone Marrow Donor Center, Dresden, Germany,
The legal patchwork complicated the installation of the Collaborative Biobank. Beside the challenges to ensure the legal framework with an intended broad consent to use data and samples, different interests of participants, cooperation partners, and competent authorities had to be considered. This included, in particular, transparency issues concerning the ownership of samples versus the individual rights of the participant stated in the informed consent, e.g., the information on stored data and the right “not to know,” i.e., the right not to get information on critical mainly genetic findings. With regard to the protection of data integrity, privacy, and self-determination, a limitation for the use of uploaded sensible data and a process for the right of withdrawal have been developed. To support extended future research projects a re-contact option has been included in the informed consent. The listed issues must be updated constantly in accordance to the complex legal background. The different requirements for research are currently under evaluation and as a solution major stakeholders ask for a Biobank Act in Germany.
Midwestern Division, Collaborative Human Tissue Network (CHTN), Columbus, Ohio, United States,
Development of a Strategy for Personal and Public Involvement (PPI) for the Northern Ireland Biobank
In order to deliver on the Strategy, the NIB worked closely with representatives from cancer charities and other relevant parties to establish a dedicated NIB PPI Focus Group.
Cardiology, SickKids Hospital, Toronto, Ontario, Canada,
Human Specimen Repositories
High-Quality Biospecimen Collection from a Diverse Patient Population, in Collaboration with NCI's Biospecimen Preanalytical Variables Program
Pathology & Laboratory Medicine, Boston Medical Center, Boston, Massachusetts, United States,
Pathology and Laboratory Medicine, UC Davis, Sacramento, California, United States,
Long-Term Stabilities of Selected Tumor Markers in Serum
Recruiting Biospecimen Resources for the National Cancer Institute's Specimen Resource Locator
Facilitating Acceptance of an Institutional Biobanking Protocol Through an Established Research Support Model
Surgery, Duke University, Durham, North Carolina, United States,
Surgery, Duke University, Durham, North Carolina, United States,
The availability to collect well-characterized biological specimens and data is critical to support critical care treatment through innovative therapeutics and precision medicine. The Surgical Critical Care Initiative (SC2i) Biorepository is a joint effort of seven premier academic and research-focused organizations. The SC2i was developed through collaboration between military and civilian healthcare centers to increase overall sample acquisition and enable enhanced data analysis of clinical and translational studies to aid in the development of clinical decision support systems.
The SC2i biorepository is informed by a multi-site tissue and data acquisition protocol (TDAP), a standardized institutional review board protocol designed to minimize cost and regulatory effort at all sites and support a variety of research projects. To maximize specimen retrieval and data collection a standardized process was implemented across institutions. The SC2i Biorepository operates under Good Clinical Laboratory Practices (GCLP) and utilizes standardized sample collection, processing, and transfer across sites. A SC2i-specific REDCap database was implemented to collect standardized clinical data. Specimens are housed at a central location within the individual sites and data is housed within a central data repository to maintain integrity and security. The standardization of these processes allows for specimens and data acquired to establish a library representative of complex and critically injured patients derived from military and civilian healthcare centers.
Under TDAP the SC2i biorepository has collected over 30,000 clinical samples that include tissue, urine, wound effluent, cerebral spinal fluid, peritoneal fluid, peripheral blood mononuclear cells, plasma, serum, and whole blood. Over 3,000 samples have been distributed and utilized in downstream assays to support the development of precision guidance tools used to improve clinical practices and outcomes.
The SC2i TDAP and Biorepository serve as a model for comprehensive support of clinical and translational research in traumatic injury and allow for a comprehensive library of high-quality, well-characterized biological samples combined with correlated clinical data relevant to complex critical injury. The SC2i collection facilitates the development of clinical decision support tools, in support of precision medicine for the critically ill, in both military and civilian healthcare settings.
Department of Surgery, Kanagawa Cancer Center, Yokohama, Japan,
Robotic High-Volume Tissue Microarray (TMA) Construction from Lung Adenocarcinomas
Pathology, MSKCC, New York, New York, United States,
Pathology, MSKCC, New York, New York, United States,
Due to high volume and engagement of biobank personnel in various operations in a busy cancer center, it is not always possible to transfer the tissue in to liquid nitrogen immediately upon receipt. We are studying the impact of transport/storage at room temperature on fresh tissue kept at room temperature (RT) for various time points.
Department of Pathology, National Health Laboratory Services, Parow, Cape Town, Western Cape, South Africa,
To date, the rapidly expanding era of genomic, proteomic research and personalized medicine promises real and tangible solutions to help alleviate health burdens; however, it would require large-scale genomics studies which is currently lacking or limited in SA as most occur in Europe and in America despite the high burden of both communicable and non-communicable diseases. Lack of these large-scale genome wide association studies in SA is most likely attributed to a shortage of genomic scientific researchers, limited computational expertise, and lack of resources and biomedical infrastructure. Our natural biological resources is of interest to the global community and this is why consortia such as the H3Africa and B3Africa is interested in funding genomic and bioinformatics research within SA and other African countries.
Thus to ensure sustainable research, access to high-quality specimens of our unique ethnic populations in statistically relevant numbers is needed and attention should be given to infrastructures such a biobanks. It plays an integral role as these types of essential resources, if properly designed and maintained, are very important for addressing important questions on national, continental, and global health issues. To date, the value of biobanking in SA and rest of Africa has increased and has emerged as a complex science. However, this is still an emerging concept due to the myriad of complex considerations relating to ethical, legal, political, societal, religious, cultural, financial, and educational challenges. Thus an overview of the NHLS/Stellenbosch University Biobank (NSB) established in 2012 within the Division of Haematology and registered with Stellenbosch University is given as well as lessons learned over the years. NSB follows standardized ethical, social, and legal policies, procedures, and protocols frameworks governed under both an external and internal governing structure. Thus important fundamental issues such as governance, ethics, infrastructure, and bioinformatics that are important foundational prerequisites for the establishment of a successful human biobank are covered along with services that the biobank can provide to the outside research community.
Biobank, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China,
Institute of Population Research, Peking University, Beijing, China,
Pathology Biorepository Core, Van Andel Institute, Grand Rapids, Michigan, United States,
While several thousand samples were processed and analyzed as part of the BPV Program, a very large repository of samples remain in storage at the Biospecimen Core Resource at the Van Andel Research Institute in Grand Rapids, Michigan.
The collection is comprised fully of the following: H&E slides and electronic images, IHC-stained slides, frozen tissue stored at −80°C and liquid nitrogen (LN2) vapor phase, blood byproducts stored at both −80°C and LN2 vapor phase, DNA and RNA PAXgene preservative blood tubes stored at −80°C, FFPE tissue blocks, TMAs, and DNA and RNA derivatives.
Cancer Control Research, BCCA Cancer Research Centre, Vancouver, British Columbia, Canada,
Pathology Biorepository Core, Van Andel Institute, Grand Rapids, Michigan, United States,
Biospecimen Accessioning and Processing Core Laboratory, Biorepository Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States,
Midwestern Division, Collaborative Human Tissue Network (CHTN), Columbus, Ohio, United States,
Biobanking is still a young discipline. Throughout most of biobanking history since 2009 in China, we have attempted to unlock value by matching our resource in clinical practice to research resource with feasible strategies. The development of biobanks has experienced several stages with gradual realization of the important factors hallmarked with quality, associated data, and utilization of banked samples. Overall, two strategies are implemented in most hospital-based biobanks in China. One of them is to collect biological samples aiming to accomplish funded research projects; another one is to build a biobank mostly for samples available in the hospital. The drawback of the first resource would restrict the resource to the project themselves; the second one would face the challenges how to utilize the resource to meet the needs of diverse research questions. ELP (short for Early Life Plan) is such a longitudinal initiative by Xinhua Hospital, to explore the early life programming and developmental disease susceptibility for diagnosis, genetic counseling, and clinical decision-making, improve the quality of the birth population. One of the major components in ELP is to establish a population of clinical data with a biological repository designated to the ELP initiative. ELP resource is characterized by tracing back to the originating samples, analyzing disease-related factors such as environmental effects and potential epigenetic changes when clinical phenomena arises during childhood growth. ELP encourages researchers and clinicians with different kinds of expertise from different disciplines, but sharing a research focus, to explore the same groups of population. Therefore, the interdisciplinary research results can create a holistic view for researchers to give more comprehensive analysis. ELP resource strategy is characterized by: 1) minimal impact on routine clinical practice; 2) developing a strategy to complement data collection above existing data from the clinical data registry. In addition, the second step is to harmonize operation mode, workflow, and management strategy for data and sample collection and management in alignment with the alliance member hospitals. This would increase interoperability and reduce heterogeneity of collection across the hospitals. In a summary, it would be much more economical to establish a research resource. The work was supported by International S&T Cooperation Program of China (ISTCP) Funding (Grant No. 2014DFG31460).
The SEER Virtual Tissue Repository Pilot: Leveraging Population-Based Biospecimens
The Important Role of Control Population Collections in Biobanks
Integrated Biobank of Luxembourg, Luxembourg, Luxembourg,
Histology and Cell Biology, Faculty of Medicine UGM, Yogyakarta, Yogyakarta, Indonesia,
The Manchester Cancer Research Centre (MCRC) Biobank is a multi-center Biobank set-up to collect human tissue samples from cancer patients in the Greater Manchester area, with the ultimate aim of making high-quality tissue collection and retrieval easier for the researcher. The MCRC Biobank has evolved since its initial untargeted “six pack” collection model—consisting of fixed and frozen tumor and normal tissue with related blood and urine samples, to a more tailored collection style, facilitating prospective collection of fresh tissue and mining of the vast pathology archives available.
Access to biological materials is paramount for scientific research in any medical field, and in particular for research into rare cancers, such as neuroendocrine tumors (NET) and hepato-pancreato-biliary (HPB) cancers, where access to high-quality samples and associated clinical data remains limited. The MCRC Biobank has developed an infrastructure within the working model it already has in place to collect specimens from patients affected by these cancers, with associated clinical data.
Patients who are identified as suitable for sample collection are consented by the clinical team, and a standard pack of blood is collected, which includes whole blood, serum, and plasma samples, as well as plasma for cell-free DNA. The MCRC Biobank consent forms also allow additional consent for samples from patients which may have been collected in the past, surplus to clinical needs, as well as future samples. This allows researchers access to diagnostic biopsy material and tissue from surgical excisions which the patient may have had at referring hospitals across the country, as well as follow-up blood samples in clinic which can be collected in the future from each patient.
The MCRC Biobank, in collaboration with the clinical teams, has created an efficient management model with the aim of optimizing sample collection from patients with HPB and NET cancers. High-quality sample collection can be assured when executed through the MCRC Biobank infrastructure, which includes thorough training methods, robust standard operating procedures, and compliance with ethical guidelines and local approvals. A number of research projects have been approved through the MCRC Biobank using these samples, with the ultimate aim of improving understanding of the underlying mechanisms of these diseases and improved treatment options.
Surgical Critical Care Initiative: Evidence to Inform Practices of Clinical Data Standardization Across Multi-Site Consortiums
Surgery, Duke University Medical Center, Morrisville, North Carolina, United States,
Hot Topics
Marianna J. Bledsoe Consulting, LLC, Independent Research Professional/Consultant, Silver Spring, Maryland, United States,
Given the limitations of assessing demand for specimens retrospectively, approaches were also identified for assessing demand for specimens in real-time and prospectively, including establishment of mechanisms for obtaining ongoing feedback and reporting from researchers.
Analysis of Short-Term Efficacy and Pathological Outcome of Paclitaxel Plus Platinum as Neoadjuvant Chemotherapy in the Treatment of Locally Advanced Cervical Cancer
Gynecological Oncology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China,
In addition to quantifying the benefits of energy-efficient freezer technology, the study found that significant energy savings can be achieved through behavioral change. Advocates for energy efficiency in laboratories have suggested that increasing ULT freezer temperature from −80°C to −70°C can reduce energy usage while maintaining performance. This study corroborated that view, finding that such a temperature change reduces energy consumption by an average of 37%, for both standard-efficiency and energy-efficient ULT freezers, without any discernable effect on temperature stability.
Pathology and Its Recognized and Unrecognized Links to Quality Biobanking
Center for Global Health, NCI, NIH, DHHS, Bethesda, Maryland, United States,
Repository Automation Technology
One of the key issues in biobanking is sample storage and registration. Each laboratory or hospital participating in a biobank consortium is supposed to operate an efficient system which allows long term storage of big amount of samples, their recording and easy retrieval.
The Teaching Hospital in Pilsen is using a software developed by the Beckman Coulter company - Intelligent Sample Bank software—intended for liquid sample storage and recording. The software is interconnected to the preanalytical unit AutoMate and to the Laboratory Information System (LIS). Serum samples are automatically aliquoted to barcoded tubes in a microplate which is recorded and then stored in the freezer. Software allows easy and quick sample retrieval according to sample ID. The connection to laboratory and hospital information systems allow easy retrieval of clinical information for pseudoanonymized samples. Moreover, a cooperation with the Pathology Department and a connection with an existing tissue samples database will be realized in 2017.
The main advantages of the system are: an integration of two systems (for routine analysis and for biobanking) in one instrument, a complete automation minimizing human error risk, and integration of all sample information in one database.
Generic Portal to Request Access to Biobank Data and Samples
Durrer Center for Cardiovascular Research, Amsterdam, Netherlands,
In addition, we are sharing programmatic interfaces with BBMRI-ERIC towards interoperability of biobank request workflow systems.
The complexity of handling biosample information which is both required and desired has never been more challenging. The added complexity of understanding and executing effective cold chain management standard operating procedures is equally challenging. Unfortunately the problems associated with poor sample collection management include inaccurate or missed scientific results as well as added costs.
This poster will share a framework to evaluate your readiness for automated sample storage.
- Refocus manual “picking” resources, salaries
- Storage density gains (tubes per sq. meter)
- Protect innocence samples (-F/T)
- Simple inventory management, and audit trail
- Minimized human variability/error
- Laboratory information management system connectivity for enhanced query ability
- Natural collection succession plan
- Automatic collection defragmentation
- Automatic Informed Consent management–query cull list
- Ease of use, ergonomics
- Sample access security
- Documented cold chain of custody records
- Administrator defined user level controls/access
- Minimized facility heating, ventilation, and air-conditioning and infrastructure support costs
Uppsala Biobank's Model for Mimicking Automation by Using a Web-Based Application That Enables Sample Collection Everywhere
Uppsala Biobank recognized a need for a manual back up routine, so the process could be up even if the robotic system was down. The development of a backup routine that was of low cost and not space consuming was initiated.
An Efficient and Cost-Effective Silica-Based DNA Extraction from Whole Blood
IRGB-CNR, Milan, Italy,
Several DNA extraction procedures, starting from any biological source including whole blood, are commercially available. However, not all of them yield high quality of DNA reliable for genotyping using NGS and DNA array platforms; furthermore, the yield is often too low for long-term DNA banking and more rounds of extraction are necessary to obtain enough nucleic acid for storage purposes. Advances in genomic technologies have contributed to the understanding of the genetic basis of human diseases. Not enough genomes have been sequenced in order to find resilient genetic mutations. A possible avenue to address this issue is to focus the analysis on those environmental modulators that keep individuals healthy, by suppressing the effects of the disease-causing mutation. Thousands of genomes need to be sequenced along with the generation of nation-specific correlation databases. Here our contribution to this challenge is described by scaling-up previously published in house silica-based DNA extraction procedure (Malferrari G. et., al 2002) which meets the quantity and quality standards. In this context, to validate and exploit the procedure, we extracted 8,000 DNAs from the Moli-Sani Project, a population-based study in the Molise region (Italy). This procedure is cost and time-effective; the obtained DNA is pure and of high-quantity. Starting from 500 μl of whole blood or buffy-coat, previously stored in liquid nitrogen, the yield ranged from 30 μg to 50 μg of DNA, with OD ratio 280/260 = 1.9/2.0; moreover, 24 samples DNA can be obtained in less than 1h with a cost inferior to 2 euro per sample
Repository Management
Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States,
Methods:
The LILAC process for obtaining and characterizing FFPE tissue is as follows:
1. Review participant medical records to identify the healthcare facilities storing their tumor tissue.
2. Contact facilities to obtain their specimen release policies.
3. Request tissue, prioritizing acquisition of FFPE blocks first, followed by unstained slides for those facilities that do not release blocks (20% of facilities).
4. Enter received tissue into the specimen inventory database, and store in a temperature- and humidity-controlled room.
5. Submit pathology reports to the study's pathologist to identify priority tissues for H&E creation.
6. Perform pathology review of the H&E slides to document key characteristics.
Biobank, Nanjing Drum Tower Hospital, Nanjing, China,
Tohoku Medical Megabank Organization, Tohoku University, Sendal, Miyagi, Japan,
The statistical data on the whole genome sequences (WGS) of more than 2,000 people in the TMM biobank (>30 × coverage), as well as the metabolomics, proteomics, and DNA methylation data, are publicly available on our websites. The data elucidate the considerable differences in the frequency of single nucleotide variations between the Japanese and Caucasian populations, and these WGS data have been utilized for variant prioritization in dozens of studies in various institutes in Japan. Researchers can use individual data (after data cleaning) and biospecimens when the review and contracting processes are completed.
In 2013, St. Luke's Mountain States Tumor Institute, the cancer center for a nonacademic-based community hospital in southern Idaho, opened a biorepository. We recognized engaging a committed network of people was critical to maintain an active and growing bioresource. This would require sustained engagement with more than 100 people utilizing the biorepository staff of three part-time employees. We accomplished the building of the network of people by having an engagement plan; persistent communication (cheerful, dogged, and annoying); and providing regular feedback demonstrating efforts are actively contributing to ongoing research. We have learned that biorepositories have many moving parts that have to come together to produce the final product, continual and sustained maintenance is essential, and social interactions are the most important element for continued success.
Leveraging Cloud Technology to Manage Processes and Data to Maintain High-Quality Storage Services at The University of Sheffield Biorepository
CloudLIMS.com, Wilmington, Delaware, United States,
Office of Research Informatics, Duke University, Cary, North Carolina, United States,
There is a need for a centralized technology platform to support data integration and virtual sample data access to enable researchers to secure optimal sample and data assets. Data standards exist for many types of analytical, biological, and clinical data, and several standards have been proposed to normalize biobanking data. Defining a data standard makes information exchange easier to accomplish. However, without a centralized technology platform to host and mine data from multiple sources, it fails to address the researcher's fundamental challenge.
Utilizing System Engineering Methods to Support Rapid Scale Up of Biorepository Operations: The Mayo Clinic Experience
Operating a Federated Biorepository Model for the Canadian Partnership for Tomorrow Project
Cancer Control Research, BCCA Cancer Research Centre, Vancouver, British Columbia, Canada,
Biomaterials have been informally stored for centuries in one form or another, hence the concept of biobanking is not new. Recent technological advances have made it possible for human, animal and plant specimens as well as the associated data to be stored in an organized fashion. A diverse set of research purposes ranging from drug research, diagnostic as well as genetic studies are catered for by biobanking. Biorepositories enable the collection and storage of both small and large sample sizes, facilitating enhanced research outputs through readily available biomaterial. The World Health Organization recognizes the pivotal role that biobanking pays in society and has proposed a global governance framework for biobanks. The framework encompasses elements of participant confidentiality, safety, and sample and data quality that biobanks need to adhere to. The NHLS Biobank was established in response to the growing burden of communicable and non-communicable diseases not only in South Africa, but globally as well. The main purpose of the National Biobank is to manage and secure biomaterial collections and storage for research purposes. The National Biobank is unique and encompasses multiple components of biobanking, namely: cancer, cell culture, genetics, molecular biology, and nucleic acid storage. Key quality indicators that are considered in ensuring adequate preservation of specimens include an efficient transport system, availability of constant power (back-up power in cases of power failure), as well as the constant availability of dry ice. Crucial quality aspects being adhered to include enhanced temperature control by ultra-low temperature freezers interphased with a temperature monitoring system and software. In addition, there's strict biomaterial inclusion criteria such as procedure for previously thawed and or aliquoted biomaterial as well as standardized procedures for specimen storage and retrieval. The ultimate objective of biorepositories is not only enabling research studies to be carried out with statistically significant sample sizes, but also within reasonable time frames.
Unsustainable? CAP Survey of Pathology Directors Highlights Inconsistent Support for Tissue Procurement
Department of Pathology, Duke University, Durham, North Carolina, United States,
Pathology Department, Gulou Hospital, Nanjing, Jiangsu, China,
Tissue Microarrray (TMA) innovation with the introduction of digital pathology and automated TMA systems, such as the Perkin Elmer TMA Master, has allowed researchers to produce high-quality TMAs quickly, with greater histological accuracy and a lower cost than manual arrayers. The automated systems do present a few drawbacks, such as the need for donor tissue blocks with a depth of at least 0.5 cm, due to the automated coring process that is standardized to a specified depth. Nonetheless, TMAs provide researchers with a screening tool representing multiple donors for research and discovery that is more efficient and less costly compared to the single slide-single donor approach.
The Cooperative Human Tissue Network at Vanderbilt University Medical Center (CHTN-VUMC) has developed a resource for internal investigators that will allow them to view, design, and request TMA's to be constructed from tissue blocks procured under stringent standard procedures. This proof-of-concept approach utilizes the CHTN-VUMC Donor Portal, which houses all the de-identified clinical and pathologic data associated with the TMA-designated donor cases, arranged in a searchable catalog that allows the investigator to select donors based on histologic, pathologic, clinical data, or molecular data. This approach also allows the investigator to design the array to meet their specific research needs or to utilize an array-generator to randomly place cores and place the order for the build. The construction time for a TMA varies from 3 days to 5 days once cases have been selected and depends on the tissue type, core number, and design.
TMAs are gaining recognition as an important research tool, especially in studies examining molecular biomarkers for possible diagnostic and prognostic purposes. TMAs allow for the screening of several donors at once, improving the speed of research and discovery while decreasing the costs of processing. Current options for ordering a TMA either require the researcher to order a slide from a premade non-customizable TMA or require the researcher to wait a long time for a custom TMA to be built. Thus, through the use of this proof of concept approach to “Custom TMAs Build on Demand,” CHTN-VUMC continues its commitment to developing methodologies that improve the speed of production and distribution while decreasing research costs.
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. Today biobanking is a highly dynamic activity needing to deal with ever increasingly complex demands of managing data and integrations with existing databases. Therefore, having a biobank database is now more than simply a “tick box” exercise.
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's caBIG program and has continued its further evolution with industry (Krishagni) and academia partnerships. For the past 5 years, Krishagni has worked closely with its adopter community develop a robust, scalable, and highly flexible open source biobanking informatics platform. As a result, OpenSpecimen is today used in 50+ biobanks across 15 countries.
Open source software (OSS) is a very powerful and proven means to advance software development. OSS promotes collaboration, avoids single “vendor lock-in” and drives the cost of ownership down. Its openness also 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 customised 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 state of the art 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 Stanford University (USA), University of New South Wales (Sydney, Australia), Singapore General Health, SAHMRI (Adelaide, Australia) 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.
Establishing a Global Infrastructure for Clinical Trials Through Integrated Biorepository Services and Harmonized Quality Assurance Platforms
Sample Preparation Services, BioStorage Technologies, Indianapolis, Indiana, United States,
Children's Hospital Medical Center, Cincinnati, Ohio, United States,
Adding Value to Your Clinical Study Through a Successful Biobanking Strategy
Nottingham Health Science Biobank, Nottingham, United Kingdom,
Biobanking infrastructure is critical to the discovery, impact and implementation of new drugs and must be linked to high-quality biospecimens and clinical data informative of phenotype. It is therefore, essential to harmonize biobanking procedures and to develop innovative solutions supporting biobanking interoperability and specimen sharing. Such scenarios, however, bring along several challenges such as ethics, data protection, IT-implementation, quality management (QM), standardized ontology, and harmonized standard operating procedures (SOPs). In this presentation I will describe how we have achieved this by the full integration of the central biobank management system into the clinical context, an informed consent procedure starting at the central patient admission, a harmonised approach to data collection and a distinct concept for access rights and rules.
Challenges of Biobank—Sustainability, Expansion and Networking: Developing Country Prospective
A biobank fosters research by offering high-quality samples for future research. The success of a biobank management system is based on maintaining the flow of samples as well as the funds requested to run the facility. Setting a sustainability plan that addresses all dimensions of sustainability from the early phase of the biobank establishment increases the chances of success of long-term operation. Maintaining social acceptability through public engagement and willingness to participate and a challenge if the society culture does not support research. The operational sustainability as well as the financial sustainability which includes issues related to quality of service and revenue generation as well as expansion plans should be maintained and updated. Continuous expansion by opening new sections within the biobank, meanwhile, maintaining the quality and adding more services, will encourage researchers to trust and acknowledge the service provided. Encouraging researchers to request using samples from biobanks and teaching them how to keep the samples to maintain its integrity is one of the awareness outreach tasks of the biobank. Research authorities within institutions as well as within countries should run regular funding calls and encourage researchers to use samples from authorized biobanks to ensure consistent long-term financial support. There are always opportunities to network with regional biobanks for maintaining sustainability, expansion, and fostering basic, applied and translational research. We succeeded to design a sustainability plan to maintain our biobank in a budget restricted setting while maintaining the quality and increasing the service provided.
Converting a Regional Tissue Procurement Program to Enterprise Level: Implementation Challenges for Pancreatic Tumor Biorepository
Pathology, Hofstra-Northwell Health School of Medicine, Lake Success, New York, United States,
The NHLS Biobank is within the NIOH which has been accredited for ISO 15189; 17020; 17025 by the South African National accreditation System (SANAS). Furthermore, there is adherence to ISBER's Best Practices For Biorepositories as well as compliance with the National Health Act 61 of 2003 which provides a framework for a structured uniform health system within the Republic of South Africa. The model of the NHLS Biobank is designed to manage and secure biomaterial collections and storage as well as the associated data for research purposes both in the short-term as well as long-term. The Biobank encompasses multiple components of biobanking, namely: cancer, cell culture, genetics, molecular biology, and nucleic acid storage. The storage capacity is large scale for internal and external clients, can store over a million specimens with additional premises and infrastructure currently being made available and should be fully operational by the end of 2017. All stages of the quality cycle, as part of the Quality System Essentials (QSEs) are continually being assessed, namely: equipment, facilities and safety, organization and personnel, purchasing and inventory, documents and records, information management, corrective action, occurrence management. These QSEs are grouped into three categories: resource management, process management, as well as improvement management form quality indicators and ensure maintenance of QMS. Biomaterial data tracking is through specialized software and laboratory information system (LIS). To date, a substantial amount of resources and time have been invested on continued personnel development in ensuring that quality standards are maintained. Future plans of the NHLS Biobank include implementation of the ISO 9001:2015 standard, ISO/ TC 276, enhanced networks, and stakeholder involvement as well as continued technical improvements on pre-analytical specimen factors which ultimately impact on specimen quality. These future plans tie in with maintaining quality within the NHLS Biobank.
IT Architecture for Supporting Biorepository Automation
Building Biobank Network in Indonesia
Department of Anatomical Pathology, Faculty of Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia,
The sustainability of biobanking depends on the ability to utilize and adapt existing core competencies and research infrastructure. The research support model developed within the Substrate Services Core (SSC) was built utilizing existing research infrastructure and strengthened through biobanking core competencies. This model enabled the SSC to apply for status as an institutional shared resource starting fiscal year 2017.
Transitioning to the Substrate Services Core and Research Support Service (SSCRSS) allowed for the development of a standardized fee structure to support research and biobanking. The identified funding sources for cost recovery over the first 5 years included internal, industry, pharmaceutical and federal grants and contracts. The funding generated allowed the SSCRSS to absorb the majority of cost for laboratory infrastructure to include the laboratory information management system (LIMS), equipment, service contracts, maintenance and a percentage of the staff and facility.
The SSCRSS has vetted 85 study support requests for development and implementation, generating a balanced distribution of studies through internal institutional funding, federal grants and contracts, and industry and pharmaceutical entities. The SSCRSS supports 29 clinical trials and collaborative studies, including industry, National Institutes of Health (NIH), Food and Drug Administration (FDA), and Department of Defense (DoD). Eight trials have been carried through to completion and 48 new studies are awaiting initiation. These studies span 54 investigators over nine departments and 22 divisions within the institution. Enrollment in biobanking is approaching 1000 participants with more than 1350 participants enrolled in research studies through the SSCRSS. Over 63,000 samples have been banked and over 6500 samples distributed to investigators for use in research studies.
Leading challenges have been lack of research coordinator resources, biobanking visibility, and engagement of investigators and patients. Shifting the focus to providing research support alongside biobanking as a shared resource has assisted in mitigating these challenges. It has increased visibility and provided potential users education regarding biobanking initiatives. This approach allows for engagement and education of investigators to encourage participation in centralized biobanking and use of retrospective collections for future research while provide sustainability through research support.
Biobank SOPs Development as the Technique Advantages
Tissue Bank of Fudan University Shanghai Cancer Center has been established for 10 years. Standard operating procedures (SOPs) of 10 years' experience have been published in 2016. The tissue bank itself has developed from an institutional biobank toward a Shanghai government-supported consortium of malignant tumor biosamples.
The set of SOPs has been written and revised according to the technical changes in laboratory. The main changes in lab SOPs include: 1) Input of automatic liquid handler; additional SOP was added to the existing SOPs. Manual SOPs for liquid handling have to be kept for some situations such as machine maintenance or one sample arrivals. 2) Scientific study revealed that some methods were not suitable for some experiment. For example, 95% EtOH has been used for liquid-based samples such as ascites, pleural fluid, and urine. For the cell pellet part EtOH had been used to preserve the samples. However, our results showed that EtOH damaged the surface antigen in the flow cytometry test. Some media such as dimethyl sulfoxide, 1640, and fetal bovine serum showed protection for the surface antigens. 3) Change the DNA and RNA concentration measure from spectrum to fluorescent dye measure, to provide more precise results for downstream analyses.
Repository Standards
Quality Control Protocols for Documentation of Tumor Procurement and −80°C Storage of Bone Marrow Mononuclear Cells in Progress at the Medical College of Wisconsin Tissue Bank
The Medical College of Wisconsin Tissue Bank (MCW Tissue Bank) is an institutional shared research core available to MCW investigators. As a resource for future unspecified research at MCW, it is vital that banked specimens be both accurately recorded and of high quality. It is logistically difficult to maintain these high standards day to day with limited staff and diagnoses that are not necessarily available when specimens are banked. Therefore, two ongoing quality control (QC) methods are in the process of being instituted. A clinically trained pathologists' assistant (PA) is employed to procure tissue for the MCW Tissue Bank. This dedicated PA works closely with the QC Pathologist, as well as Pathology residents, to perform QC on each banked tumor tissue specimen. What is documented grossly in the Bank's organizational software is confirmed histologically during QC. The qualitative measurement of the proportion of cancer cells to both normal and non-viable cells is recorded for each malignant tumor slide. A second QC initiative seeks to assess both cell counts and viability of bone marrow mononuclear cells (BMMCs) specimens stored in −80°C for varying amounts of time. A small pilot project, optimized with help from the institutional biostatistics core, is being introduced and preliminary results are expected in the coming months. Data gathered from this BMMCs initiative will be reported and used to optimize methods for specimen processing. Both QC projects will be instrumental in helping to define the content of the Bank's collection and in designing future QC protocols. These combined efforts will ensure that specimens are accurately described for researchers to best use in future studies.
National Cancer Institute's Biospecimen Evidence-Based Practices (BEBP): The Development of Evidence-Based Guidelines for Human Biospecimen Collection, Processing, and Storage
Standard operating procedures (SOPs) used for human biospecimen collection, processing, and storage can vary greatly across institutions. This variation can affect the quality of specimens and the accuracy of downstream analytical results. In an effort to minimize the effects of preanalytical variability on biospecimens used for research, the National Cancer Institute (NCI)'s Biorepositories and Biospecimen Research Branch (BBRB) is developing a series of documents known as NCI Biospecimen Evidence-Based Practices (BEBPs) that are based upon published findings in the field of biospecimen science. To support the development of BEBPs, meta-analyses are performed on pertinent literature identified via NCI's Biospecimen Research Database (BRD; http://biospecimens.cancer.gov/brd), a free and publicly accessible online database that is continuously updated and currently houses approximately 2,500 articles meticulously curated by a team of PhD-level scientists according to type of biospecimen, technology platform used, pre-analytical factor(s) investigated, preservation method, and analyte(s) of interest. BEBPs contain step-by-step procedural guidelines annotated with literature evidence in a detailed, yet adaptable, format that facilitates the development and modification of SOPs. Their modular format also permits periodic updating to reflect the current state of Biospecimen Science. Each BEBP is reviewed by experts in the field to ensure recommendations are practical and accurate. In 2014, the NCI BEBP “Snap-freezing of Post-Surgical Tissue Biospecimens” was the first BEBP to be published and made available for public use. Additional BEBPs either completed and awaiting expert review or in progress include: Formalin Fixation and Paraffin Processing of Tissue Biospecimens; Collection and Processing of Plasma for Proteomic Analysis by Mass Spectrometry; Blood Collection and Processing for Circulating Cell-free DNA; DNA and RNA Extraction from Formalin-Fixed, Paraffin-Embedded Tissue Biospecimens; and Blood Collection and Processing for Circulating Tumor Cells. This global approach to standardization of biospecimen handling procedures can minimize the risks due to preanalytical variability, improve the quality of biospecimens, and increase research reproducibility. Contributions to the BRD in the form of article suggestions and SOP submissions are greatly appreciated and can be submitted directly through the website or via email to
Validation of the Countess™ II Automated Cell Counter for Counting Peripheral Blood Mononuclear Cell (PBMC)
Evaluation of Biobank Sample Correctness and Integrity in TMM Biobank
Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan,
Alberta Health Services, Calgary, Alberta, Canada,
CPTP recognized the need for quality and consistency in biorepository procedures across the federated model.
This committee consults Best Practice Guidelines and reviews scientific evidence when formulating biosample methodologies. A Steering Committee, responsible for the scientific and operational procedures, reviews and approves all developed procedures before implementation. A separate harmonization committee is responsible for developing a core dataset.
Public Health Sciences, Fred Hutch, Seattle, Washington, United States,
Effect of Cryostorage and Time to Processing on RNA Integrity of Biobanked Blood Samples and Derivatives
The DNA Integrity Number: A Novel Approach for Objective Integrity Classification of Genomic DNA Samples
Agilent Technologies, Waldbronn, Germany,
Genomic DNA (gDNA) is used as starting material in the experimental workflow of many applications in molecular biology. The integrity of the DNA critically affects the success of many downstream experiments like qPCR or next-generation sequencing. Initial electrophoretic analysis of the sample is highly recommended as the respective downstream applications can be expensive and time consuming. The Agilent Genomic DNA ScreenTape Assay has been primarily developed for the electrophoretic analysis of genomic DNA samples. A ScreenTape is a pre-packaged microfluidic device designed for performing electrophoretic applications in a microscale format. It is used in combination with the Agilent 4200 TapeStation instrument. Degradation of gDNA is typically a gradual process in which high-molecular-weight DNA is fragmented into smaller species. It can occur enzymatically, chemically, or mechanically. Judging the integrity of DNA by visual evaluation of the electropherogram trace is subjective and can be error-prone. In order to standardize this, a novel algorithm was developed to score gDNA samples on the 4200 TapeStation. The DNA integrity number (DIN) is calculated from several features obtained from the electrophoretic trace and ranges from 1 to 10. Here we show data demonstrating the reproducibility, scalability, and linearity of the DIN. The DIN is independent from instrument, reagent, and sample concentration variability and can be used as objective measure for determining the integrity of gDNA.
Promoting samples sharing goes in pairs with interconnectedness of Biobanks and, to exchange samples between biobanks, comparable samples are needed making the sample quality an unavoidable issue. Each laboratory has their own practices, highly diverse in terms of standard operating procedures (SOPs), preanalytical documentation, and of course in terms of quality.
The standards followed by a vast majority of biobanks in Europe are mainly the specifications edited by the European Committee for Standardization (CEN) and the Standard PREanalytical Code (SPREC) developed by ISBER combining 7 preanalytical factors that may have an impact on the integrity of samples.
The biobank practices were evaluated with surveys based on CEN specifications and SPREC requirements. This state of biobanks helped us to identify the lacks and to prioritize where biobanks should improve their practices. We are currently developing an innovative SOPs generator fit-for-purpose to harmonized practices. Moreover, a Swiss Standard for biobanks based on the future ISO TC 276, a self-assessment tool, and a quality handbook are currently in development.
An SBP coordinator is in place in each hospital to support the implementation of harmonized processes and a centralized IT strategy with the development of a specific SBP module provided to the biobanks of the network is currently in discussion.
Sample Storage Tubes as Quality-Critical Components in Biobanking
(1) Infrared spectroscopy of 10% ethanol extracts from tubes was utilized to assess if demolding reagents, occasionally used in labware production, were present.
(2) Closure of tubes from different vendors and their capability to retain sample volume was assessed in long-term storage tests in the vapor phase of liquid nitrogen.
(3) Non-specific biomarker binding was assessed based on the adsorption of radioactively labelled IGF 1 onto the surface of sterile and non-sterile cryogenic tubes from different suppliers.
(4) The quality of datamatrix codes of tubes from different manufacturers was analyzed using a barcode validation system.
In summary, cryo tubes used for biobanking differ in quality and functionality, and care should be taken to choose the optimum tube type with regard to the intended storage duration, type of sample (liquid/tissue) and method of sample tracking.
Use of Agilent TapeStation for External Quality Assurance of Genomic and cfDNA
IBBL, Luxembourg, Luxembourg,
Ontario Tumour Bank, Ontario Institute for Cancer Research, Toronto, Ontario, Canada,
Quality, Biospecimen Research Group, Leidos Biomedical, Rockville, Maryland, United States,
High-quality, well-annotated tissue specimens are in high demand for biomedical cancer research, and the establishment of Quality Management (QM) and Clinical Data Management (CDM) programs are essential to standardizing biobanking methods, documenting processes, and validating clinical data sets. Essential to the startup of an internal QM program is engaging leadership in order to ensure effective organization of internal resources. QM personnel independent of operational responsibilities should: establish control mechanisms for procedure control/training; conduct assessments to ensure compliance; gather data from many sources about non-conforming events, deviations, and customer feedback; and coordinate various internal and external resources to implement corrective/preventive actions and continual improvement efforts. CDM personnel independent of operational responsibilities should work towards ensuring high-quality and reliable data using a process whereby data are collected, validated, and confirmed to be complete and consistent. Data confirmation is generally conducted with a combination of automated real time validation rules and edit checks, independent operator verification by the source site, and manual data review for inconsistencies and other evidence of potentially discrepant data. A variety of important considerations go into the establishment of QM and CDM systems and this poster describes how to establish robust and effective QM and CDM systems to support cancer biobanking.
Late-Breaking Abstracts
Actelion Pharmaceuticals Ltd., Allschwil, Switzerland,
* The study perspective to define the protocol of the study. It helps to put the biosample back into its context and it is particularly useful for the preclinical studies, where predefined actions have to be taken (treatment, measurements, sampling).
* The biosample perspective to query and enter biosample. A configurable ontology helps to categorize the samples into living samples (human, animal), solid samples (organ, tumor), liquid samples (blood, serum, plasma), or purified samples.
* The location perspective to manage the physical sample inventory in liquid nitrogen tanks or freezer.
* The result perspective to enter and analyze results. Through this unique connection to the study, SPIRIT provides some automated analysis tool and can display line graphs for the weight increase, or box plots for the LCMS.
Effective facilitation of the translational cancer research underpins world class clinical care and is dependent on the availability of quality well-annotated biomaterials and biobanks fill the niche in this area. A risk management plan is essential to continuity and sustainable operation of a biobank. Currently there are no standard requirements or templates available for research biobanks to manage risk. Biobanking is considered a low-risk research activity when taken from the tissue donors and ethical perspective; however, the impact of a catastrophic loss of biomaterial by a biorepository presents a significant risk that goes far beyond the longevity of a biobank itself. It equates to loss of knowledge about rare diseases and, therefore, goes against the core values of the health system. Australia/New Zealand Risk Management Standard AS/NZS ISO 31000:2009 Guidelines and NSW Risk Matrix provided a general framework to the risk management process. Biobank activity was assessed within a strategic and operational context, and major risks were identified in consultation with the key internal and external stakeholders. The risk management plan was established based on the following risk treatment strategies: 1) Change the likelihood; 2) Change the consequence; 3) Increase opportunity. The strategic outcomes were achieved by sharing the risk, accepting, avoiding, or transferring the risk. Actions to treat the risk were either implemented immediately or proposed to be implemented within a specific timeframe. The effectiveness of the plan lies within ongoing monitoring and review against biobank goals and key performance indicators with the aim to downgrade the level or overall negative impact of risk. The process of establishing the risk management plan for a pediatric biobank has highlighted its strategic value as well as its operational strengths and weaknesses. This necessitated a review of standard operating procedures on tissue and data collection, storage and distribution, informed consent, and biobank-researcher interaction. We learned that availability of a well thought-out risk management plan presents excellent strategic opportunity for a biobank to place itself as an expert service provider in the area of tissue and data handling for basic science research, clinical trials and play a role in the personalized medicine model of care. This comprehensive risk management plan is specific for a pediatric research biobank with strong links to clinical operations.
A Business Model to Harness the Potential of Your Pathology Department to Drive Targeted Treatment Strategies and Improve Outcomes
Department of Pathology, University of Washington School of Medicine, Seattle, Washington, United States,
Biobanking Without Borders, LLC, Durham, North Carolina, United States,
Biobanks commonly evolve for diverse research needs with heterogeneous data representations presenting challenges to query for samples and associated clinical annotation across biobanks. A biobanking ontology is being developed and refined through engagement and collaboration with academic medical institutions, national scientific biobanking forums and standards organizations. The Ontology for BioBanking (OBIB) was created through a multi institutional collaboration and managed within the Open Biomedical Ontologies Foundry. OBIB covers data elements from the National Institutes of Health Genotype-Tissue Expression (GTEx) Project and the National Cancer Institute's Biorepositories and Biospecimen Research Branch. OBIB leverages use cases from a Health Level 7 (HL7) Domain Analysis Model related to biobanking and OBIB classes are being linked to terms in MIABIS 2.0 (Minimum Information About BIobank data Sharing version). Pre-analytical variables identified as critical for sample integrity by the College of American Pathologists are being modeled in the ontology. Major collaborators are: University of Pennsylvania, University of Arkansas for Medical Sciences, Duke University, the National Cancer Institute, University of Michigan, Medical University of South Carolina, International Society of Biological and Environmental Repositories (ISBER) and Biobanking Without Borders, LLC. The Ontology for BioBanking (OBIB) contains 738 terms (including 551 classes); 48 terms (46 classes) were created de novo. The rest were re-used from existing ontologies including 130 terms from Ontologized MIABIS (OMIABIS). The further refinement of the ontology OBIB benefits from the diverse members of the collaboration, engagement with biobanking subject matter experts, national biobanking organizations and forums, national standards organizations and alignment with international biobanking efforts.
Urine Samples Were Recommended for Rapid Detection of Mt3243 A>G Mutation
Effect of PH on the Stability of Urine Biomarkers in Diabetic Nephropathy Patients
Interuniversity Bio-Backup Project (IBBP) for Life Science
In order to realize a life sciences community resilient to natural disasters and calamities, the National Institutes for Natural Sciences (NINS) and Hokkaido University, Tohoku University, Tokyo University, Nagoya University, Kyoto University, Osaka University, and Kyushu University concluded an agreement on June 1st 2012 to launch a system to “back up” the biological resources essential to the work being done at universities and research institutions nationwide, called the Interuniversity Bio-Backup Project (IBBP). The IBBP center was established as a centralized backup and storage facility at the National Institute for Basic Biology, while IBBP member universities set up satellite hubs and work closely with the IBBP center to put in place reciprocal systems for backing up important biological resources that have been developed by researchers residing in the area for which each university satellite hub is responsible.
The IBBP center includes earthquake-proof structures capable of withstanding even very large scale quakes, cryopreservation facilities equipped with automatic liquid nitrogen feeding systems, deep freezers, and refrigerated storage, as well as all manner of automated laboratory equipment, cell culture tools, and the latest equipment necessary to back up the genetic resources in a collaborative manner. The specific methods of preservation are freezing of the sperm and eggs of animals, cultured plant and animal cells, proteins, and gene libraries. Plant seeds are frozen or refrigerated.
University satellite hubs receive preservation requests of biological resources from researchers and report to the Managing Project Committee of IBBP, where the relevance of the request is reviewed. When the request is sustained, biological resources to be preserved will be sent to the IBBP center by the requesting researcher, where they will be frozen and their particular information will be registered into a database. In the event of a disaster leading to the loss of a researcher's own biological resources, preserved samples will be promptly supplied back to the researcher so they can quickly resume their work.
Through the development of this backup system biological resources that had only been stored at individual research institutes can now be preserved at the state of the art facilities of the IBBP center, and Japan's research infrastructure has been significantly strengthened.
Biobanking Efforts of the Philippine National Collection of Microorganisms (PNCM) to Conserve the Country's Microbial Diversity
The PNCM embarks on microbial prospecting from various habitats, i.e., mangroves and the surface of fruits and flowers, to search for enzyme-, plant growth hormone-producing and antimicrobial bacteria, fungi, and algae for agro-industrial uses. Polyphasic identification is done for bacterial cultures (Vitek II, MaldiTOF and 16S rRNA gene sequencing). For some bacteria, physiological characterization, % mol G + C and fatty acid analyses are also done. For the fungi, 18S rRNA gene or ITS sequencing are conducted aside from phenotypic characterization.
The data associated with the accessions are stored in Microsoft Access database.
Some identities of the enzyme producers are Dendrophoma spp, Empedobacter brevis, Weeksella viros, and Virgibacillus dokdonensis (also anti-Vibrio). Zooshikella ganghwensis is anti-MRSA.
Enzyme-producing yeasts from banana peel include Brandoniozyma complexa, Candida wangnamkhiaonsis, and Pseudozyma hubeiensis.
Chung-Ang University Hospital, Seoul, Korea (the Republic of),
An increased emergence of human biobanks established for supporting research by encouraging and ensuring efficient storage and sharing of biomaterials and the associated data continues. Sample collections can either be small scale for study-specific projects or large scale at the national level for future and multidisciplinary research. The South African National Biobank of the National Health Laboratory Service (NHLS Human Biobank) is a human biobank with a large-scale storage capacity for human specimens ranging from biological fluids, tissues, and nucleic acids. This study aims to describe established basic guidance criteria for sampling, processing, and storage of biological materials ensuring that a targeted research population and the resultant data collection is achieved. We will also describe a number of ethical issues and limitations to consider where human research and biobanking are concerned. These include pre-collection, collection, pre-storage, storage, sharing, and post-sharing aspects. All these aspects lead to the biobanking complexity matrix which requires a full scale consideration of these aspects to optimize the utilization of the stored material. Careful consideration by human research ethics committees is crucial, especially with clear consideration of pre- and post-research deliberations. Crucial aspects including relevance of informed consent, data confidentiality and donor protection, specimen ownership, donor discrimination, post-research and futuristic utilization, material transfer benefit sharing, and results communication should be well described and declared. The NHLS biobank applies a sample coding system that promotes participant confidentiality and information protection procedures. Data and sample protection is further enhanced through the use of an electronic access control system. There is still no clear national governance and regulatory structures of human biobanks in South Africa and thus regulatory compliance in the National Biobank is maintained though compliance with the relevant national and international laws and continued collaborations with various stakeholders which involves information sharing. Lessons learned and the process established and planned national drive for human biobanks will be shared.
The Development of a Clinical Service by a Research Biobank
Financial sustainability is always an issue for biobanks. In order to increase revenue from our biobank, we've looked into income streams from different avenues. Besides the provision of various services for research purposes, we are now looking into developing clinical services for the processing of sputum from asthma patients. The clinical specimens processed are used for both clinical analysis and as well for research biobanking purposes. We will discuss the process of (1) initial biobanking of sputum from research purposes. (2) The extension of the services for clinical specimen. (3) Training, accreditation, and the eventual development of the clinical charge code of the clinical services.
A Biorepository to Support CDx Development and New Biomarker Discovery
Samples and Data Management for a Large Epidemiological and Clinical Study at the MRC/UVRI Biorepository: A Case of H3Africa Diabetes Study
The MRC/UVRI biorepository uses a sample management software that uses pre-printed 2D barcode sample labelling and tracking system to manage the storage accurately. The system uniquely identifies sites, participants, samples, and storage aliquots across all sites.
The MRC/UVRI biorepository designed SOPs that we shared across all sites. We also designed, printed, and distributed barcode labels for sample collection and storage tubes. We coordinate shipments; receive samples for storage, data entry, and management.
Advances in Biospecimen Science Technology via The Innovative Molecular Analysis Technologies (IMAT) Program of NCI
A Proactive Approach: A Clinical Program Designed to Increase Biobank Activity
The mission of the Cornell Veterinary Biobank (CVB) is to store high-quality biospecimens and associated data to accelerate biomedical research and improve animal and human health. To increase its activity, the biobank governance reached out to researchers/users of its products and services and in response created the Senior Feline Health Screening Program to expand the genomic resources available for the domestic cat. For this program, the CVB clinical team, in conjunction with several specialty services at the Cornell University Hospital for Animals, recruits healthy purebred 10-year-old cats (or older) to serve as universal controls for different genetic mapping studies. The screening consists of a general physical exam, a fasted blood sample (for complete blood count, chemistry panel, feline leukemia virus and feline immunodeficiency virus test, and thyroid panel), urinalysis, an echocardiogram, and consultation with various specialty services around the hospital, including orthopedics, ophthalmology, oncology, dentistry, and nutrition. Selected individuals qualify for a second day of screening where a full body computed tomography scan is performed to rule out orthopedic diseases or certain types of cancer. To date, the screening has been completed on 46 cats who fit the eligibility criteria for the program. Of those, 27 are good controls for hypertrophic cardiomyopathy, 36 for diabetes mellitus, 21 for hyperthyroidism, 16 for feline Factor XII deficiency, nine for chronic kidney disease, 26 for obesity, 28 for hip dysplasia, and 24 for alimentary tract lymphoma. Samples from 10 of these cats were whole genome sequenced by the “The 99 Lives” Cat Genome Sequencing Initiative, and as a result of this collaboration, three manuscripts were accepted for publication. Data collected from the controls cats is currently being used for three genome-wide association studies at Cornell University College of Veterinary Medicine and 56 feline biospecimens have been requested since the start of this program.
Sample Analysis Automation for Biorepository Quality Control
OGVFB, National Eye Institute, Bethesda, Maryland, United States,
A Laboratory Information Management System (LIMS; SampleMinded) was later integrated to automate the SCT process. CSV files are imported directly from the CE into the LIMS, and SCT profiles are attached to each sample record. Allele calls for each participant are reviewed by the LIMS, and any inconsistencies or identical profiles are reported to the user, prompting further investigation.
Establishing a Continuously Evolving Tissue Collection Program for The Cornell Veterinary Biobank
The Cornell Veterinary Biobank (CVB) was established in 2006 with the goal of banking high-quality biospecimens and associated data, to accelerate research, and improve animal and human health. Initially, the CVB began processing blood donated from patients presenting to the Cornell University Hospital for Animals (CUHA) for DNA extraction and banking. During 2011, with the cooperation of CUHA clinicians and pathologists, the CVB started collecting and banking tissue samples harvested immediately after surgical excision of tumors and from definitive surgical corrections. In the following years, the CVB augmented this tissue collection program to include tissue harvested from animals donated immediately post-mortem (warm body necropsies) with the goal of collecting as many healthy and diseased tissue samples as possible within 1 hour of euthanasia. In 2015, the CVB added targeted fresh tissue collections in conjunction with clinical trials. Additionally, the CVB began collecting tissue samples from our satellite hospital in Stamford, CT. The Cornell Veterinary Biobank currently stores over 25,000 research quality, clinically annotated biospecimens and 3,600 of these specimens are unprocessed tissue. Phenotypic information for each animal/tissue is confirmed to match the criteria defined for disease phenotypes of interest and the data is stored in a custom designed database. Standard operating procedures (SOP) for client informed consent, patient enrollment, collection procedures, storage techniques, and demographic/phenotypic data entry have evolved as new processes, technology, and downstream applications have been identified. Currently, most excised tissue collected for the biobank is stored (in liquid nitrogen, RNAlater, or formalin fixed) within 10 minutes of excision and post-mortem tissue is collected within a goal of 30 minutes following euthanasia (improved from the original goal of one hour). Timely coordination of the tissue collections between the consenting client, attending clinicians (clinician performing euthanasia or surgeon excising a tumor), biobank pathologists, and CVB collection personnel have been paramount in reducing post-mortem or post-excision intervals.