Connect and Collaborate through Biobanking: Powering Innovation and Discovery May 10-14, 2021 - ISBER
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BIOPRESERVATION AND BIOBANKING Volume 0, Number 0, 2021 ª Mary Ann Liebert, Inc. DOI: 10.1089/bio.2021.29084.abstracts The International Society for Biological and Environmental Repositories Presents Abstracts from Its 2021 Annual Meeting Connect and Collaborate through Biobanking: Powering Innovation and Discovery May 10–14, 2021 The abstracts that follow demonstrate the broad range of timely issues addressed in the contributed oral and poster presentations at ISBER’s virtual 2021 Annual Meeting.
ORAL ABSTRACTS O-01 Effect of Ascorbic Acid on Metabolic Status, Lipid Conclusions: It is concluded that ascorbic acid 2.0 mM in Peroxidation, Antioxidant Activity and Quality extender improve motility, viability, metabolic status and fer- of Frozen Indian Red Jungle Fowl (Gallus gallus tility of frozen Indian red jungle fowl semen through enriching murghi) Semen antioxidant activity and ameliorating lipid peroxidation. B. A. Rakha1, M. S. Ansari2, S. Akhter3, E. Blesbois5, J. Santiago-Moreno4 O-02 Biobanking in the Era of COVID-19: Ethical 1 and Governance Challenges Department of Wildlife Management, Pir Mehr Ali Shah Arid Agriculture University Rawalpindi, Rawalpindi, Punjab, A. J. Goldenberg1, K. Brothers2, H. Morrin3, J. Cadigan5, Pakistan, 2Department of Zoology, Division of Science and M. Bledsoe4 Technology, University of Education, Lahore, Punjab, Pakistan, 3 1 Department of Zoology, Pir Mehr Ali Shah Arid Agriculture Department of Bioethics, Case Western Reserve University, University Rawalpindi, Rawalpindi, Punjab, Pakistan, Cleveland, Ohio, United States, 2Department of Pediatrics, 4 Department of Animal Reproduction, INIA, Madrid, Spain, University of Louisville, Louisville, Kentucky, United States, 5 3 INRA, UMR85 Physiologie de la Reproduction et des University of Otago, Dunedin, New Zealand, 4ISBER Science Comportements, Nouzilly, Tours, France Policy Committee, Colorado Springs, Colorado, United States, 5 Social Medicine, University of North Carolina at Chapel Hill, Background: Ascorbic acid is a natural antioxidant found in Chapel Hill, North Carolina, United States semen to balance the oxidative stress and improves the semen quality and fertility in various species. It has been noted that Biobanking is likely to be a crucial element of the medical concentration of vitamin C for optimum semen quality greatly and public health response to COVID-19 and future pandemics. varies among species. To our knowledge, ascorbic acid has The storage and distribution of samples and data are vital for 1) never been evaluated in extender for improving semen quality collecting and analyzing biospecimens from patients for and fertility of Indian red jungle fowl. The study was designed COVID-19 related research and 2) may become increasingly to elucidate the effect of ascorbic acid on freezability of Indian important as a resource to maintain other kinds of biomedical red jungle fowl (Gallus gallus murghi) sperm. research as regular recruitment for clinical studies becomes Methods: Semen was collected from eight cocks and qual- more difficult during a pandemic. Nevertheless, biobanks face a ified semen ejaculates having motility >80% were pooled and number of unique ethical, social, and governance challenges divided in five aliquots and diluted with red fowl extender (1:5) during COVID-19 that may require new practices and policies at 37C having ascorbic acid 0.0 mM (control), 2.0 mM and to maintain their work and meet the needs of researchers, do- 4.0 mM. Diluted semen was cooled to 4C @ -0.275C, nors, and other biobank stakeholders. These challenges may be equilibrated for 10 minutes after the addition of 20% glycerol, experienced by both new biobanks created explicitly for filled in 0.5 mL French straws, kept over LN2 vapors for 10 min- COVID-19 related research, and existing biobanks. Ad- utes and plunged into LN2 and stored at (-196C). Sperm motility ditionally, these challenges may be further complicated by the and viability were assessed at post dilution, cooling, equilibration, need to balance public health surveillance uses of samples and and freeze-thawing stage. Sperm metabolic status, antioxidant data and the clinical research uses of biobank resources. potential, free radical scavenging activity and lipid peroxidation To address these issues researchers at Case Western Reserve were studied at post dilution and freeze-thawing stage. University, University of Louisville, and University of North Results: Sperm motility did not differ (P > 0.05) in extenders Carolina in partnership with International Society of Biological having different concentrations of ascorbic acid and control at and Environmental Repositories (ISBER) Ethics and COVID19 post dilution and cooling stage. Nevertheless, higher (P < 0.05) TaskForce created a survey to assess the ethical/governance sperm motility was recorded in extender having ascorbic acid challenges of biobanking during the COVID-19 pandemic, ex- 2.0 mM compared to 1.0 mM and 4.0 mM ascorbic acid and plore the ethical challanges associated with creating new control. Sperm viability was recorded higher (P < 0.05) in ex- COVID-19 biobanks, and address needed resources for ad- tender having 2.0 mM ascorbic acid compared to 1.0 mM and dressing the ethical challenges of COVID-19 biobanking. This 4.0 mM ascorbic acid at post dilution, cooling, equilibration and talk will present the findings from our COVID19 ELSI survey freeze-thawing. Sperm metabolic status, total antioxidant po- and discuss how the results may better inform biobanking tential and free radical scavenging capacity were recorded practices and policies. We believe that a better understanding of higher (P < 0.05) with ascorbic acid 2.0 mM compared to 1.0, the experiences and needs of biobanks will help inform the 4.0 mM ascorbic acid and control at post dilution and freeze- development of best practices/policies for maintaining biobank thawing stages. Lipid peroxidation in sperm and seminal plasma operations and address the needs of existing biobanks and new were recorded lowest (P < 0.05) in extender with 2.0 mM COVID-19 related research resources. Overall, we will discuss ascorbic acid. Fertility rates were recorded higher (P < 0.05) how our findings will inform ISBER policies and guidance re- with extender 2.0 mM ascorbic acid compared to control. garding biobanking best practices, identify areas of need for A-1
A-2 ABSTRACTS maintaining biobanks during a pandemic, and benefit ISBER shown to be associated with several infectious and autoimmune members and the broader biobanking community by providing diseases, cancer and vaccine response. In clinical settings, HLA practical strategies for addressing emerging ELSI issues related is used for matching donors and recipients in transplantation. to the pandemic. EDTA blood is considered to be the most appropriate sample type for HLA typing. Blood samples require infrastructure for processing and maintaining the cold chain, however, that is O-03 Consenting Trends During a Pandemic: How often lacking in lower income countries. Dried blood spots COVID-19 has Affected Clinical Research (DBS) are an attractive alternative. DNA can be extracted from L. Radziszewski, A. L. Schild, A. Pendse DBS and used for genomic analysis such as HLA typing. The aim of this study was to evaluate the use of DBS as an alter- Department of Pathology, Duke University Health System, native sample type for HLA genotyping. Durham, North Carolina, United States Methodology: Samples were received for typing from a study based in Zimbabwe approved by the Medical Research Background: Hospitals worldwide have been severely im- council of Zimbabwe (MRCZ/A/2282) . DNA was extracted pacted by the COVID-19 pandemic resulting in adjustments to from the DBS using the QIA & DNA Mini Kit and quantified clinical and research endeavors such as postponement of elec- using the NanodropTM 2000 spectrophotometer. HLA class II tive surgical procedures and remote working for non-essential DQA/B, DRB1,3,4 and 5 alleles were amplified using Lifecodes staff members. The BioRepository and Precision Pathology SSO typing kit. Center (BRPC) plays a vital role in clinical research at Duke Results: Large variation was observed in both DNA quantity University by biobanking tissue and facilitating biospecimen & purity (260/280 ratio, 1.01-2.31) of the extracted DNA. De- collections from eligible patients. spite this, the extracted DNA concentrations ranged from 4.3 - Methods: Data were retrospectively analyzed in order to 159.2 ng/ml; in most cases, this was sufficient for HLA typing. understand the impact of COVID-19 on clinical research. Two Successful typing of 54 DBS was achieved for HLA DQA/B, separate time periods were evaluated during COVID-19 (2020) DRB1,3,4 and 5 using low concentration of DNA obtained from and pre-COVID-19 (2019) and consent events were compared one 3 mm disc of DBS. to evaluate the effects of COVID-19 on clinical research. Conclusion: This is the first study that utilized DBS as a po- Results: A total of 103 consenting events were recorded in tential sample for HLA typing. Although concentrations and the pre-COVID-19 group from 03/16/2019 to 05/14/2019, with quality varied amongst the samples, 54 samples were successfully an overall success rate of 95.1%. The same dates in 2020 with typed at all Class II HLA alleles. DBS can be shipped at ambient peak COVID-19 impact recorded 6 consenting events with an temperature and can also be stored at ambient temperature. overall consent success rate of 100%. A total of 369 consenting events were recorded in the pre-COVID-19 group from 05/15/ 2019 to 10/31/2019 with an overall success rate of 94.3%. The O-05 Coordinating COVID-19 Tissue Procurement from same dates in 2020 representing an adjusted workflow yielded Autopsy: Challenges and Lessons Learned 297 consent events with 91.2% success rate. There was a 94.2% A. L. Schild, A. M. Golowiejko, M. H. Schild, W. R. Jeck and 19.5% decrease respectively in patients consented for par- ticipation in tissue biobanking and clinical trials during the peak Department of Pathology, Duke University, Durham, North COVID-19 and adjusted workflow COVID-19 period. Carolina, United States Conclusion: Postponement of elective surgeries from mid- March to May resulted in a precipitous decline in consenting Background: The SARS-CoV-2 pandemic has, according to events, the long-term impact of which needs to be investigated the CDC, infected over 12 million patients in the United States, further. BRPC effectively changed the workflow and im- and over 250,000 in the United States have died of COVID-19. plemented new consenting procedures accommodating the In response to a need for clinically isolated samples, the Duke COVID-19 restrictions, and staff and patients’ safety needs. University Health System (DUHS) BioRepository and Precision These changes include electronic consent via REDCap software Pathology Center (BRPC) collaborated with the Duke Autopsy and ‘‘Cold Call Approval’’ policy which allows us to contact service to acquire and release tissue samples to investigators. patients except those who have opted out of research partici- Methods: Ten weeks prior to COVID-19 positive autopsies, pation. The ability to contact patients via electronic media and meetings were held to establish standard operating procedures telephone significantly increased the efficiency of patient re- (SOPs) with DUHS researchers, BRPC leadership, pathologists, cruitment. This has enabled us to continue the mission of our surgeons, and decedent care regarding safety, tissue procure- biospecimen repository by successfully mitigating the impact of ment methods, and the collection and transportation of speci- the COVID-19. mens. BRPC provided consultative services to all labs receiving tissue to amend IRB protocols, obtain approval from the school of medicine, and ensure compliance with BSL2+ enhancements. O-04 HLA Typing From Dried Blood Spots Using Autopsies were performed with two procurement personnel in Lifecodes SSO Typing Kit the autopsy suite under an approved SOP specific to these M. Gededzha1, E. Sibanda2, B. G. Chiloane1, N. Mampeule1, autopsies. E. Mayne1 Results: Three COVID-19 positive autopsies, and 4 normal control autopsies were performed. While prior non-COVID 1 Immunology, University of the Witwatersrand Faculty of autopsies yielded approximately 20 pieces of tissue, the average Health Sciences, Johannesburg, Gauteng, South Africa, COVID-19 autopsy produced over 500. Several procedural 2 National University of Science and Technology, adjustments were critical for safety and efficiency. Bulawayo, Zimbabwe Initially, investigators altered tissue procurement requests up until the start of the autopsy. A procedural change to lock the Introduction: The Human Leukocyte Antigen (HLA) genes procurement request list one-week prior to a case allowed time play a key role in the adaptive immune response and have been to assemble a labeled procurement kit prior to an autopsy.
ABSTRACTS A-3 Extensive spatial and time planning was required to ac- eration of an automated, weekly report from the EHR that commodate increased personnel and materials required. Among alerts us to any autopsies from COVID-19 positive patients for these, an otolaryngologist collected olfactory and neural tissue potential remnant tissue samples. endoscopically. Additionally, to meet CDC guidelines for Results: From March to November, over 11,700 biospeci- specimen transport, a ‘‘clean’’ technician was required to open mens have been collected from 1,300 unique patients, consist- and close containers to limit contamination. Furthermore, ing of whole blood, DNA, PaxGene, PBMC, plasma, serum, and communication regarding the timing of each portion of the various tissue samples. Over 2,370 biospecimens have been autopsy was key to limiting personnel entering and exiting the released to approved study teams. suite, decreasing risks of contamination of clean spaces. Conclusions: We have successfully established a semi- Conclusion: In comparison to a typical autopsy collection, automated infrastructure and workflow to capture annotated COVID-19 autopsies require extensive procedural alterations, specimens from patients infected with SARS-CoV-2 that sig- but yield diverse tissue samples for research that may otherwise nificantly reduces the chance that specimens may be missed. be impossible to acquire. Knowledge of the limitations, material This allows for the efficient generation of a large number of and personnel required, and time expectations prior to per- specimens that researchers can rapidly obtain for study. forming COVID-19 positive autopsies for tissue procurement is imperative for success. O-07 A Paradigm Shift - Re-purposing Resources and Infrastructure During a Pandemic to Ensure O-06 Establishment, Implementation and Utilization Sustainability of a Human COVID-19 Biospecimen Biorepository at UCLA S. Paul, A. L. Bolanos, M. Kenk, S. Nguyen, A. Bhimani, H. Wagner, N. Fleshner C. E. Magyar1, D. Flores1, C. Denny2, A. Naeim3, C. Lajonchere4, D. Ward1, S. French1 UHN Biospecimen Services, University Health Network, Toronto, Ontario, Canada 1 Department of Pathology & Laboratory Medicine, University of California Los Angeles, David Geffen School of Medicine, Problem: The COVID-19 pandemic has disrupted practi- Los Angeles, California, United States, 2Department of cally all human activities around the world, including, the Pediatrics, Hematology/Oncology, University of California Los biobanking research community. In March 2020, in response to Angeles, David Geffen School of Medicine, Los Angeles, the COVID-19 pandemic, all non-essential research activity California, United States, 3Department of Geriatric Medicine, was halted within the University Health Network (UHN) and in Hematology/Oncology, University of California Los Angeles, Canada, to protect the community and flatten the curve. David Geffen School of Medicine, Los Angeles, California, As a core facility at UHN, UHN Biospecimen Services, a United States, 4Neurology, University of California Los biospecimen storage and sample information management group, Angeles, David Geffen School of Medicine, Los Angeles, was deemed essential to expedite COVID-19 research and assist California, United States in sustaining essential research operations. UHN Biospecimen Services had to re-purpose existing biobank infrastructure and Background: We have developed a semiautomated infra- available assets to centralize resources and answer an institutional structure to identify remnant clinical fluid samples to support call for help in the battle against COVID-19. specimen collection for UCLA Institute of Precision Health Solution: In close collaboration with Infectious Disease, from patients who have opted in through the UCLA institutional Occupational Health and other departments, resources, infra- Universal Consent. This system has allowed us to collect unique structure and skill-sets were repurposed to fit the organization’s remnant fluid biosamples for subsequent DNA extraction and current needs. For example, a dedicated, Biosafety Level 2 genotyping on over 30,000 patients to date. Here we describe COVID-19 processing laboratory was established. Amidst the the modification of this system to efficiently capture specimens clinical and research shutdown, staff were re-deployed across from patients with SARS-CoV-2 causing coronavirus disease the organization to critical areas, where assistance was in high (COVID-19). demand. Over 50 staff have been re-deployed to assist in the Methods: We utilized a COVID-19 patient registry to newly formed COVID-19 Biobank facility, since May 2020. identify potential sources of remnant biospecimens. This dy- Processing COVID-19 samples involves compliance and namically linked registry to UCLA Healthcare’s electronic adherence to established organization’s COVID-19 safety pro- health record system includes all patients who have had at tocols, biobank best practices and high-quality standard oper- least one resulted COVID-19 PCR or Antibody IgG test. ating procedures (SOP) to yield prime biospecimens. New SOPs A COVID-19 remnant specimen report is generated three and guidance documents were developed encompassing such times each week by cross-referencing the COVID-19 patient standards. Additional training has been provided to clinic and registry to a listing of all clinical biospecimens scheduled for laboratory staff to ensure they are well equipped with COVID- disposal for the next three days. This report is refined by se- 19 safety procedures during sample collection, transportation, lecting patients who have had a positive PCR or IgG test result processing and storage. Emergency Response procedures were and compared to our current inventory to identify specimens adapted to fit current and ongoing infection control measures. from previously unsampled patients. Additional filtering is Conclusion: The implementation of complex and creative performed to track the interval between positive test date and strategies to: reduce costs, allocate available resources efficiently and sample collection date, allowing for the collection of longi- optimize operations to guarantee sustainability, yielded the setup and tudinal plasma/serum samples. Through our Biomaterial establishment of a biorepository for COVID-19 research. Adapt- Tracking and Management System (BTM, Daedalus Software ability of a biorepository is key to remain fit-for-purpose, sustainable Inc.), reports are generated daily to detect sample collection and enable innovation and discovery amidst uncertain climates. from onsite and offsite labs, to pull and courier samples to our UHN Biospecimen Services is able to remain sustainable during this repository. Whole blood samples are retrieved for DNA, se- unprecedented time by implementing a visionary approach and rum, plasma and PBMC isolation. We also initiated the gen- balancing financial, operational and social dimensions.
A-4 ABSTRACTS O-08 QCBio-AF: Qatar Cardiovascular Biorepository COVID-19 Biorepository is Qatar’s National project aiming to for Familial Atrial Fibrillation support the extraordinary demand on high-quality, curated clinical data and biological samples contributing to research F. M. Qafoud1, 2, N. Asaad3, J. Al Suwaidi3, M. Saad4, related to the understanding of, and response to, the COVID-19 M. Al Asmakh2, A. Salam3, K. El Izzi3, D. Darbar5 pandemic and its impacts in Qatar and worldwide. 1 Methods: COVID-19 diagnosed patients, who were Qatar Qatar Biobank, Qatar Foundation Research and Development, Doha, Qatar, 2Qatar University, Doha, Ad Dawhah, Qatar, residents and they could communicate in Arabic, English, Hindi 3 and Urdu, were eligible to participate in the study. Participants Hamad Medical Corporation, Doha, Ad Dawhah, Qatar, 4 were recruited from the main three COVID-19 public hospitals Qatar Computing Research Institute, Doha, Ad-Dawhah, Qatar, 5University of Illinois at Chicago College of Medicine, and isolation facilities in Doha, Qatar for a 7-month period Chicago, Illinois, United States (March-September 2020). Consented participants were fol- lowed up on a weekly basis until recovery, and then monthly for Background: Atrial fibrillation (AF), the most common a year. Sociodemographic and clinical data were collected in abnormal heart rhythm requiring therapy, is associated with electronic questionnaires via a face-to-face interview by trained increased risk for stroke, heart failure, dementia and death. QBB staff together with biological samples. COVID-19 Rapid There is increasing evidence supporting the concept that sus- Antibodies tests together with Anti- SARS-COV-2- ser- ceptibility to AF is related to race/ethnicity. The Qatar oprevalence tests are in place to investigate the development Cardiovascular Biorepository for Familial Atrial Fibrillation and durability of antibodies against SARS-CoV-2 infection. (QCBio-AF) overall goal is to identify and phenotypically Results: A total of 2097 consented participants were recruited characterize Middle Eastern families with early onset AF. This up to September 2020. The population is multinational (n = 45 study is to present the study design, methodology and prelim- different nationalities) with males (N = 1050; 50.07%) and females inary results of QCBio-AF. (N = 1047; 49.93%) and a mean age of 41 years (SD, 15.5). 61.0% Methodology: QCBio-AF is a familial genetic association of the participants had at least one follow up while 27% adhered to study aiming to recruit families with early-onset AF members monthly follow up visits. Data have been collected for 99.7% of (n = 500 subjects). The recruitment was through the Hamad Net- the participants, while the follow up process is ongoing. In total work hospitals in Doha, Qatar which covers 95% of the population there are 107,171 high quality specimens in the biorepository in- in Qatar. All early-onset AF patients (probands) in HMC were cluding plasma, erythrocytes, buffy coat, serum, PAXgene Whole identified. The potential participants were asked to book an ap- Blood, Nasopharyngeal secretions and DNA. 61.6% of the par- pointment at Qatar Biobank where consent, data and sample col- ticipants were asymptomatic or with mild symptoms, 12.4% de- lection were completed by trained staff. The relatives to these veloped moderate symptoms, 15.1% developed severe symptoms probands were grouped according to proband-relation: offspring and 11.0% were reported as critical. The 5.7% (n = 121) of the from either maternal or paternal proband, and siblings to proband participants were deceased after hospitalization. using PhenoTips software. The recruitment is ongoing. Conclusion: COVID-19 biorepository is a National asset for Results: At present, QCBio-AF has enrolled 18 participants Qatar. It is expected to provide high quality data and biological both males (n = 9, 50%) and females (n = 9, 50%) with a median samples to the scientific community that can be used to illu- age of 52.5 years (38, 76). Completed data have been collected minate the pathophysiology of and to identify markers of dis- for 95% of the participants, while all participants provided bi- ease prognosis of COVID-19 in Qatar and worldwide. ological samples for both viable cells and DNA, following Qatar Biobank standards. In total 15 families were identified encountered to 6 different nationalities from Middle East region O-10 European Biobanks in the Coronavirus Environment and the relevant extended pedigrees were collected. The first J. Kinkorova individual in a family diagnosed with early-onset AF, was de- fined as the proband, while the first-degree relatives (children Department of Immunochemistry, University Hospital in Pilsen, and siblings) were defined as associated relatives. The average Pilsen, Czech Republic number of siblings was 7 (SD, 2.8). Probands (n = 15) were identified, offspring from maternal proband (n = 24) and from Statement of the Problem: Europe and the whole world paternal proband (n = 40) and siblings to proband (n = 78). have been facing the COVID-19 pandemic. This is a new sit- Conclusion: The present study, with geographical focus in the uation that nobody was prepared or ready to face. Middle East provides a valuable resource of information to the Proposed Solution: The reactions to the new situation were wider scientific community allowing the formulation of effective solved at different levels from very locally, regionally at the precision medicine intervention for the management of AF. level of member states of EU, international societies and as- sociations and finally coordinated by European Commission (EC), and also with regards the rest of the world, e.g. China, O-09 COVID-19 Biorepository - Qatar USA, Canada. New COVID-19 biobanks were created as parts N. Afifi1, E. Fthenou1, M. El Deeb1, L. J. Abu-Raddad2, of just existing biobanks not well coordinated with each other M. Frenneaux3, A. Al Thani4, 1, A. Al Khal3 and harmonized. BBMRI-ERIC (Biobanking and BioMolecular resources 1 Qatar Biobank for Medical Research, Doha, Qatar, 2Qatar Research Infrastructure - European Research Infrastructure Weill Cornell Medical College, Doha, Qatar, 3Hamad Medical Consortium) immediately organized coordinated approach and Corporation, Doha, Ad Dawhah, Qatar, 4Qatar University sharing experience in COVID-19 patient samples and harmo- College of Arts and Sciences, Doha, Ad Dawhah, Qatar nized its activities resulting in joint action sharing COVID-19 databases with ISBER. The European Commission started to Background: The unpresented global spread of the severe coordinate research activities supporting 18 projects with spe- acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and cial attendance to following aspects: improving epidemiology its resulting disease (COVID-19) is characterized as one of the and public health, including European preparedness and response greatest global public health crises of the recent decades. The to outbreaks. Rapid point-of-care diagnostic tests to reduce the
ABSTRACTS A-5 risk of further spread of the virus. New treatments, in which a tation, operating procedures, infrastructure building, training, and dual approach: accelerating the development of new treatments study conduct. Local storage of banked samples and data will be and screening and identifying molecules that could work against managed within the FIB sites, which will also participate in de- the virus, using advanced modelling and computing techniques, cision making regarding the use of samples collected at their site. and development of new vaccines. A COVID-19 data portal was To enhance the visibility of existing biological resources, created. COVID-19 industrial cluster response portal was estab- FIND created the VBD, a searchable directory of information lished. SMEs portal involved in COVID-19 was supported. Re- on collections either hosted by FIND or by other organizations search infrastructure services to support the fight against COVID- or networks. The VBD is an open-access, free-of-charge tool 19 were originated under umbrella of European Commission. allowing users and sample custodians to interact on sample The most important activities and actions will be presented. transfers without FIND’s intervention. Conclusions: The pandemic has changed all aspects of Conclusion: Both the FIB and VBD are currently being biobanking life and science, accelerated new techniques and piloted to support FIND’s COVID-19 work. technologies how to collect, process and store COVID-19 FIND plans to expand the model to respond to needs within samples, basic research, research in the field of new vaccines, its disease programmes, such as neglected tropical diseases, therapeutic procedures, implementation of IT solutions. Pan- tuberculosis, malaria, fever, HIV/HCV, and pandemic pre- demic supports the international collaboration and samples and paredness. data sharing, and creation of new types of virtual biobanks. O-12 Application of Natural Language Processing O-11 FIND Integrated Biobanks (FIB) and Virtual for Biorepositories Biobank Directory (VBD): A Framework for Sample Access and Sharing to Facilitate Diagnostic P. Castro1, H. Dowst2, J. Wang3, N. Zarrin-Khameh1, Development and Evaluation and Pandemic B. Musher4, S. Hilsenbeck2, O. Kampagianni1, M. Scheurer5 Preparedness 1 Pathology & Immunology, Baylor College of Medicine, 1 2 1 A. Mantsoki , D. Emperador , A. Albertini , C. Ugarte-Gil , 3 Houston, Texas, United States, 2Dan L Duncan Cancer Center, N. Ntusi4, D. Allen1, F. Betsou1, P. Quinlan5, S. Ongarello1 Baylor College of Medicine, Houston, Texas, United States, 3 Biomedical Informatics, The University of Texas Health 1 Data Services and Biobanking, FIND, Geneva, Switzerland, Science Center at Houston, Houston, Texas, United States, 2 4 Pandemic Preparedness Programme, FIND, Geneva, Medicine, Hematology & Oncology, Baylor College of Switzerland, 3Facultad de Medicina Alberto Hurtado, Medicine, Houston, Texas, United States, 5Pediatrics, Universidad Peruana Cayetano Heredia, Lima, Peru, Oncology, Baylor College of Medicine, Houston, Texas, 4 University of Cape Town Department of Medicine, United States Observatory, Western Cape, South Africa, 5Computer Science, University of Nottingham, Nottingham, Nottinghamshire, Statement of the Problem: Biorepositories have been col- United Kingdom lecting specimen at Baylor College of Medicine (BCM) for over 30 years. Over time, a concerted effort has been made to enhance Problem: Diagnostic development and validation require the annotations of the specimen. BCM biorepositories function in consistent availability of well-characterized, high-quality bios- multiple clinical affiliates which have separate pathology and pecimens. electronic health record software. None of these systems function There is a great disconnect between biobanks and industry or together and pathology reports are provided in a text format developers’ needs, leading to slow reaction to outbreaks and which is not optimal for automated data collection. The challenge missed opportunities for sample access and sharing. is to review, read and extract useful information which would be Long-term sustainability and fit-for-purpose collections are pertinent for research and then make them accessible in a still unresolved biobank issues, even more relevant when activ- searchable format. The BCM biorepositories decided to imple- ities are performed in LMICs (low- and middle-income coun- ment natural language processing (NLP) technologies to extract tries) who are often reticent to distribute samples due to structured pathology data from standard reports. legal/ethical barriers and mistrust of research and use of samples. Proposed Solution: Our proposed solution was to train an Proposed Solution: Building on its biobank experience fo- NLP pipeline to pick up the files and extract a specific set of cused on infectious diseases in LMICs, FIND has established a data elements which are required elements of a pathology report strategy for a disease-agnostic, network-based biobank model, and are commonly used criteria for selecting research cohorts. adapted to industry needs. The model focuses on: We partnered with the University of Texas-Health Science 1) increasing sample visibility and access and Center who developed the CLAMP NLP tool. This tool provi- des multiple methods of text analysis in a pipeline for concept 2) empowering research and capacity building in LMICs mapping, assertion classification, named entity recognition, The two main components of the model are the FIND In- machine learning, and more. We began by establishing a target tegrated Biobanks (FIB) and the Virtual Biobank Directory data set, creating definitions, and identifying data relationships (VBD). within the varied pathology report formats. This information The FIB is a network of biobanks for pandemic preparedness was used to build a human annotated corpus. Agreement of this that work under FIND’s coordination to conduct collection corpus to the data pipeline results had to be achieved to es- activities to support diagnostic research, development, and tablish a gold standard for training the machine learning model. evaluation. Once trained, the machine learning model became one of the Due to the FIB structure, network sites based in LMICs will elements in the NLP pipeline. Iterative refinement of the results be able to rapidly scale-up activities to support both outbreaks from the pipeline improved the subsequent data set. Once the and local clinical and research needs. FIND serves as the central final pipeline reached over 95% agreement with the human coordinator, managing sample requests from external users, and annotated data set, the pipeline was built into a Java application ensures standardization among FIB sites in terms of documen- and the structured data loaded into a relational database.
A-6 ABSTRACTS Conclusions: An NLP pipeline was established for extract- of a biobank’s operation and ability to provide biological material ing data from BCM pathology reports. The NLP system gives and associated data for research and development. Biobank ac- the biorepositories an automated process for extracting and creditation is a formal recognition by an authoritative third party populating pathological information attached to a specific event of the competence of a laboratory to perform specific biobanking record in the database. The application of NLP can produce activities including acquisition, collection, preparation, preser- accurate and useful data. The pipeline is run at regular intervals vation, storage, testing, analysis, and distribution. Much has been to produce searchable data fields and frees up valuable human learned over the past year after conducting 3 assessments to ISO time for other tasks. 20387, especially from the deficiencies cited. Deficiencies cited by A2LA assessors are where a biobank’s quality management system or adherence to requirements are not O-13 Data Management Tools in the NIST Biorepository being followed and a finding requires corrective action. Defi- J. M. Ragland, A. J. Moors, R. S. Pugh ciencies include objective evidence that a biobank is not meeting a clause in the ISO 20387 standard, A2LA policies, or specific Chemical Sciences Division, National Institute of Standards and methods used for biobank activities. The corrective action pro- Technology, Charleston, South Carolina, United States cess should aim to prevent the deficiency from recurring by implementing actions. Those actions are to be recorded, and Asset management in biorepositories has historically been under A2LA policy, submitted with objective evidence that those focused on capital assets such as facilities, staff, and freezers. As actions have been executed. From the past two years, the defi- technical data management tools have improved, data have in- ciencies cited against currently accredited biobanks range from creasingly become considered an asset to the same degree. Such procedures missing specific items called out in ISO 20387 to data can describe the facility, a collection, or any downstream technical requirements from specific methods. data produced. Breadth and focus can range from pass-through Before assessments occur the biobank will need to apply for facilities holding minimal data describing samples and their accreditation. So why accreditation? storage, to facilities attached to clinical laboratories where ana- Benefits of Accreditation for the Biobank: lytical tests are ordered and the results stored. Regardless of the -Accreditation by a third party provides credibility to the type of data associated with physical collections, ensuring the users of biobanks and establishes a level playing field. highest possible data quality is of utmost importance to achieving -Use of Accreditation Bodies that are signatories to the ILAC operational excellence. Commercial software targeting bior- Mutual Recognition Arrangement (MRA) provides a high level epositories helps tremendously and is generally flexible enough of confidence in the Accreditation Body’s competence. This to fit the broad array of biorepositories. It cannot, however, fully confidence is based on the requirement for the Accreditation substitute for robust data quality management and practices; there Body to undergo routine and rigorous peer evaluations against will always be a gap between data management tool designs and long-standing international standards for assessing quality. the practical needs of, and direct implementation within, any Attendees during this session will gain an understanding of given repository. Over the last few years, the NIST Biorepository the A2LA process for conducting an assessment, but more in Charleston, SC, has developed several data-first tools and formally understand the deficiency process with A2LA and approaches to specifically address this gap with regard to data what is expected from a biobank according to ISO 20387. At- quality management. These include (1) data collection tools that tendees will also have an opportunity to review some defi- capture data more stringently from field or collaborator collection ciencies cited so far and how they could be resolved to prevent events; (2) workflow curation tools to ensure each process occurs recurrence to obtain a positive accreditation council vote. in the same way every time regardless of how much time has passed since the last event needing that workflow; (3) data quality audit practices; (4) data visualization tools to manage capital O-15 In Extraordinary Times: Resetting the Bar assets such as freezers; and (5) a tool to conduct physical position of Sustainability and Opportunity - Observability audits in a rapid manner. Combined, these tools and associated of Value for Biobanks approaches have greatly reduced data entry errors, accelerated D. Simeon Dubach1, M. K. Henderson2 time-intense data quality activities, and provided at-a-glance in- 1 sights into the function and status of the biorepository. The medservice Daniel Simeon Dubach, Walchwil, ZG, general approach, as well as discrete benefits and reasons for the Switzerland, 2National Institutes of Health, Bethesda, creation of five specific tools, will be discussed. Custom data Maryland, United States tools such as these are currently saving the NIST Biorepository over 1,000 hours of staff time annually and highlight the ne- Statement of the Problem: COVID-19 has been a crisis of cessity of a technical data manager in modern day bior- extraordinary proportions, causing serious impacts on human epositories. This presentation is targeted toward repository health and research. Biobanks are in a key role in facilitating the managers, data managers, and those interested in improving data understanding the SARS-CoV-2 disease and the public health re- quality practices and streamlining biorepository operations. sponse. This crisis, while highlighting the necessity of biobanks, has exposed the existing and new sustainability challenges, in operational, financial, and social aspects. Also, there have been O-14 ISO 20387 Accreditation, Corrective Actions, valuable opportunities for biobanks in research, vaccine, diagnostic and Deficiencies So Far and drug development for COVID-19. Being ready and able to C. D. Arant adapt to new opportunities is at the heart of a professional biobank. Proposed Solution: Biobanks must maintain their focus on Life Sciences, A2LA, Frederick, Maryland, United States the basics of their business plan, including vision, mission, strengths, weaknesses, opportunities and threats (SWOT) and The A2LA Biobanking Accreditation Program uses the ISO risk analysis, and performance metrics. Clarity, of mission, 20387 standard to promote confidence in biobanking. ISO 20387 stakeholders, and abilities, allow for the addition of realistic contains requirements designed to demonstrate the competence opportunities to their portfolio. The pandemic has presented
ABSTRACTS A-7 opportunities to find innovation in operations, in new stake- Background: The SARS-CoV-2 virus and the outbreak of holders, and in new observability of their value. Taking on new COVID-19 disease has been one of the most important global collections in COVID-19 public health responses is occurring crises on public health. Qatar Biobank (QBB) had to convert globally and may change utilization metrics for the biobank in and respond to this crisis by providing its services for the col- the short and longer term. Automation of processes and human lection, processing and storage of high-quality data and speci- capital management may have been forced to evolve during the mens for the better understanding and the response to the crisis, and these changes could bring further evolution to the therapy and survival of COVID-19 disease. In this study we will biobank post-pandemic. The availability of vaccines and tests to highlight the challenges, risks and opportunities of QBB during control the pandemic will likely not decrease the demand for this transformation period. COVID-19 samples for additional research in monitoring of Methods: QBB is CAP accredited and holds ISO certifica- safety, effectiveness, and durability not only for the vaccines tion for Quality Management Systems 9001:2105 and In- and tests but also for drugs to treat COVID-19 disease. In ad- formation Security Management Systems 27001: 2013. These dition, the availability of COVID-19 products will not be uni- standards helped QBB management to rabidly adapt by fol- form across all continents/countries. These factors may create lowing rigorous processes to effectively convert its operations an unbalanced situation, such that the need for samples and data and facilitate the COVID-19 National project. from different parts of the world will be variable. Results: Within 5 weeks QBB transformed to accommodate Conclusions: The COVID-19 pandemic has been a disruptive a disease/virus-based biorepository. Multi-adjustments had to and unprecedented event but, nevertheless, the crisis has been an be implemented at operational level such as: i) QBB IT de- opportunity for biobanks to show observable value to research partment developed a highly secured electronic system for the communities. This presentation will provide the key focus of sus- data collection and specimen traceability ii) Clinically trained tainability and planning that has provided the ability for successful staff (n = 17) were transferred to different healthcare facilities in biobanks to pivot during the pandemic. Discussion will include order to recruit COVID-19 positive patients; iii) QBB Labora- actual and potential impacts of the pandemic on biobanking, which tory designed special collection kit, iv) QBB Medical Review highlight its observable value to the research community. Office (n = 4) and Scientific and Education (n = 2) departments managed the recruitment process, set up the study and provided training to the staff; v) the Communications and Participants Recruitment Department (n = 7) transformed its operations to fit O-16 QBB Rapid Transformation into COVID-19 the needs of the COVID-19 initiative. The Research Access Biorepository: A Showcase Office (n = 6) designed the COVID-19 access portal and sup- E. Fthenou1, M. El Deeb1, A. Al Emadi1, E. Al Khayat1, ported the project from the purchasing of PPE and other ad- M. Al Dosari1, S. Al Fadalah1, A. Salau1, L. Hannigan1, ministrative works needed. W. Lobo1, M. Frenneaux,2, A. Al Khal2, A. Al Thani1,3, Conclusion: It is now time to consider lessons learned, as N. Afifi1 many countries have been affected by COVID-19 outbreak, and to understand that biobanks are an asset for a country and in- 1 Qatar Biobank for Medical Research, Doha, Qatar, 2Hamad tegrate them into a new standard with their sustainability in Medical Corporation, Doha, Ad Dawhah, Qatar, 3Qatar mind. Qatar Biobank and its network with academic, research University, Doha, Ad Dawhah, Qatar and governmental entities is a good showcase.
A-8 ABSTRACTS POSTER ABSTRACTS Biobank Tools ated by international organizations (ISBER, ISO and IARC) and provide scientific, operational, ethical, and legal guidelines and standards, taking into account complexities within specific geographical areas or further technical advances such as clinical PA-01 Development and Use of a Mouse Tissue Collection imaging banks. Each one of these guidelines carries its own Request and Documentation System inherent background , focus and emphasis. These differences in A. Zago1, K. Rodriques2, R. Aeran1, J. Aguilar1, C. Schwietert1 background (however slight) have the potential to manifest 1 themselves as differences in terminologies, definitions and the Encoded Therapeutics, Inc., South San Francisco, California, emphasis on the advice provided. Thus these areas of diver- United States, 2Iseehear Inc. Life Sciences, Toronto, gence are highlighted, explained and codified. Ontario, Canada, In this article we have compared three crucial interna- tional documents in the field of biobanking published within the Proper management of animal sample collection is critical last three years. As opposed to a whole text to text comparison, for preclinical testing performance, quality and reproducibility the observations described relate to structural comparisons of of data. Sample quality in toxicology studies requires a well- the texts, as well as the comparisons of the glossaries and the designed tissue collection protocol, robust documentation and definitions therein. Such a mapping is crucial in understanding an efficient sample traceability method. We describe here our which document is most appropriate for each biobanking con- successful implementation of a system to request and document text, especially as these guidelines are already starting to be tissue sample collection for in-house mouse toxicology studies adopted by the biobanking community. and preclinical research projects. We leveraged our existing use of the SoftMouse.NET database and software to implement this Biobanking Profiles system. SoftMouse.NET has supported colony management in our vivarium for four years and is specifically used to manage our mouse breeding, mouse study allocation, treatments and necropsies. We decided to extend usage of the SoftMouse.NET PB-01 Biobank Profile: China National GeneBank platform to also generate and track sample requests, registra- Y. Shao tion, labeling and collection, with the goal of allowing for greater data transparency and business continuity. To accom- China National GeneBank, Shenzhen, China plish this, our in vivo tissue collection workflow was mapped out and isolated into individual tasks. These tasks were then As the first integrated national gene bank in China, CNGB built into SoftMouse.NET as configurable experiment building is committed to support scientific research, public welfare, blocks. In practice, the scientists arrange these blocks to cus- innovation, and industrial infrastructure construction. Based tomize their study tissue collection. Once the study is built on the abilities to ‘‘read, write and store’’ genetic informa- virtually in SoftMouse.NET, the biorepository is able to pre- tion, CNGB serves as an open platform that provides access to register the samples and track their generation, and the vi- and enables exchange and sharing of genetic data and re- varium operators can document sample status at all phases of sources to advance the development of the life sciences and the project. The software seamlessly assigns a timestamp to bio-economy. each necropsy and each sample collected, thereby enhancing China National GeneBank (‘‘CNGB’’) is a non-profit orga- the quality of the animal tissue annotations. We demonstrate nization supported by the Chinese Government. CNGB has built that this system has streamlined and optimized our tissue an integrated infrastructure of ‘‘Three Banks and Two Plat- collection process from design to execution to sample storage forms’’. ’’Three Banks’’ represent the Biorepository, Bio- and distribution, which has guaranteed a well annotated tissue informatics Data Center and Biological Resource Center of collection. Plants, Animals and Micro-organisms. ‘‘Two Platforms’’ include Digitalization Platform and Synthesis and Editing Platform. Reading: An automated, informatized platform with peta- PA-02 Mapping of Biobanking Guidance Documents bytes throughput each year, the Digitalization Platform is ded- Based on Table of Contents and Glossary Analyses icated to supporting research projects in precision medicine, Z. Kozlakidis1, K. Furuta2 agricultural breeding, marine development, biodiversity con- servation, etc. 1 Laboratory Services and Biobanking, International Agency for Writing: CNGB is building a world-leading writing plat- Research on Cancer, Lyon, France, 21. Urayasu Warakuen form that is capable of synthesizing 10 million base pairs per Clinic, Urayasu, Japan year. The platform enhances application of synthetic biology and gene editing technologies in natural product biosynthesis, Biobanks have developed in great numbers throughout the disease diagnosis and treatment, modern agriculture, environ- world, reflecting the need for growth in clinical discovery, ment protection and other areas. understanding and implementation of translational research. Storing: China National GeneBank DataBase (CNGBdb) is Documents aiming to harmonize biobanking practices and an integrated platform built for biological data sharing and ap- create a much more aligned, professional field have been cre- plication. Based on big data and cloud computing technologies,
ABSTRACTS A-9 it provides data services such as archive, analysis, search, data PB-03 Adult and Pediatric COVID 19 Mississippi Biobank management and scientific databases to researchers around the Collection world. G. J. Mahajan EBB (E-Biobank): EBB bridges the gap between bio- sample holders and users by aggregating bio-sample and bio- Biobank, University of Mississippi Medical Center, Jackson, bank information at home and abroad in a standardized method. Mississippi, United States It aims to create an equal and open environment for sample sharing and enhance reasonable utilization of bio-samples. Background: At the University of Mississippi Medical Public Service Platform: Opening up its scientific infra- Center (UMMC) has been prepared to take care of patients di- structure to the public, CNGB provides public services based on its agnosed with COVID-19. There are a few studies investigating powerful abilities to ‘‘read, write and store’’ genetic information to different aspects of COVID-19. We aim to collect blood samples support the development of life science research and industry. from adult and pediatric patients with diagnosis of COVID-19 to build the UMMC COVID-19 –Biobank collection. Methods: This is an IRB approved research study to build the PB-02 Supporting Cancer Research through first Mississippi biobank of COVID-19 in adult and pediatric a Cooperative Human Tissue Network (CHTN): subjects. Biological samples and medical information are ex- Impact of Collaborative Effort 2019 tracted from hospitalized SARS-CoV-2 participants in Epic. The L. W. Ayers1, R. Mandt1, D. G. Nohle1, M. E. Couce2, invitation to participate in this research study is presented to pa- A. Parwani1 tients who express interest to their treating physician who then 1 request patient approval to be contacted by biobank research CHTN-MW Division, Columbus, Ohio, United States, personnel. Informed consent is obtained either via eConsent 2 Pathology, UH Cleveland Medical Center, Cleveland, Ohio, through REDcap or a phone call service may be used to talk to the United States patients regarding obtaining the consent or if the patient is unable to make or communicate an informed decision due to mental or Background: CHTN is an NCI-sponsored prospective hu- physical impairment, by talking to a legally authorized represen- man tissue procurement program that provides quality human tative during the hospital admission. The consent process is fol- tissue and clinical data to approved investigators. A great va- lowed with procedures to minimize exposure to SARS-CoV-2 for riety of anatomic sites, diseases, and standard/custom prepara- research personnel. Collection of blood samples occurs on day 1 tions are procured by six CHTN Divisions to meet investigator after confirmed COVID positive test, and then subsequently on day requests. Requests that a division cannot completely fulfil 7, day 14 and day 21 in SST, EDTA, heparin PST and PAXGene quickly enough are networked to the other divisions to get in- DNA and PAXGene RNA tubes. All the blood samples are pro- vestigators the needed samples in a timely fashion. The Mid- cessed within 2 hours to create aliquots of serum, plasma, buffy western Division (MWD), based at OSU, assists the other coat, PBMCs and whole blood. Each biospecimen is labeled with a divisions in serving the investigators in their territories. unique ID that is created by a biospecimen inventory software. Methods: Counts of samples shipped in 2019 by anatomic site Results: Till date we have over 3,000 specimens from 300+ and tissue type (malignant, benign, etc.) and the number of in- enrolled patients along with their clinical and biological data. vestigators they supported were obtained from the CHTN Tissue We have disbursed about 120 specimens till now to UMMC and Quest investigator management system and Annual Report. industry researchers. Each specimen request undergoes the re- Results: The CHTN shipped 16,395 malignant samples to view from biospecimen access committee in UMMC. This investigators in 2019. This represented 46.4% of 35,361 total biobank collection is ongoing and we are continuously enrolling samples shipped in 2019 to 623 investigators and does not in- during the pandemic. clude other specimen types (disease, normal, benign, in- Conclusions: We expect to use these samples for future re- determinant, or pre-invasive neoplasia). Malignant samples search including studies on the pathophysiology of COVID-19 such were from 52 different anatomic sites with soft tissue as the as diagnostic test validation, biomarker discovery, genomic testing, most common (2,289, 14.0% of malignant) followed by colon pilot projects, grant submissions in the adult and pediatric popula- (2,058, 12.6%), breast (2,016, 12.3%), kidney (1,732, 10.6%), tion. In addition, we plan to share these samples with the scientific lung (1,391, 8.5%), oral cavity (1,064, 6.5%), bone marrow community interested in advancing the knowledge on this disease. (950, 5.8%), bone (656, 4.0%), ovary (570, 3.5%), pancreas (432, 2.6%), prostate (405, 2.5%), liver (392, 2.4%), bladder (348, 2.1%), blood (339, 2.1%). 1,753 shipped malignant PB-04 Spaceflight Biospecimen Sharing in Support samples were from 38 other sites (10.7%). of Science Discovery and Exploration MWD shipped 5,472 total samples in 2019 in support of 157 R. T. Scott1, A. French2, A. Wood1, D. Lopez1, M. Del Alto3 investigators, 97 of which were in other division’s territories. 1 3,438 (21% of the CHTN’s) malignant samples were supplied NASA Ames Life Sciences Data Archive and Institutional by MWD and were from 43 anatomic sites with colon as most Scientific Collection at ARC, KBR, NASA Ames Research common (1,130, 32.9% of malignant) followed by lung (467, Center, Moffett Field, California, United States, 2NASA Ames 13.6%), oral cavity (358, 10.4%), kidney (350, 10.2%), ovary Life Sciences Data Archive and Institutional Scientific (200, 5.8%), breast (182 , 5.3%), skin (124, 5.3%), brain (87, Collection at ARC, Bionetics, NASA Ames Research Center, 2.5%). 540 were from 35 others (15.7%). Moffett Field, California, United States, 3NASA Ames Life Conclusions: The CHTN is supporting cancer research with Sciences Data Archive and Institutional Scientific Collection at nearly half of 2019 shipped samples being malignant. Addi- ARC, NASA, NASA Ames Research Center, Moffett Field, tional non-malignant samples are used as controls, etc. in cancer California, United States research studies. The availability of MWD-procured samples from various anatomic sites differs from other divisions. In- For decades, NASA and international partners have flown vestigations benefit by other divisions procuring when the home non-human biological experiments in space to understand the division cannot procure enough of the requested tissue. effects of spaceflight and address potential biological hazards.
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