BIOPRESERVATION AND BIOBANKING Volume 9, Number 1, 2011 ª Mary Ann Liebert, Inc. DOI: 10.1089=bio.2011.9120
ABSTRACTS
The International Society of Biological and Environmental Repositories present Abstracts from their Annual Meeting
Impact and Public Benefits of Biorepositories May 15–18, 2011 Arlington, Virginia The abstracts that follow demonstrate the broad range of timely issues addressed in the contributed oral and poster presentations at ISBER’s 12th Annual meeting.
ISBER Abstracts HOT TOPICS/OTHER HOT OPERATIONS TOPICS HT 01.
BreastScreen Victoria (BSV) is part of the national breast cancer screening program in Australia and a key collaborator in lifepool. Using established BSV contact protocols, women are invited to consider joining lifepool. Primary aim: To recruit participants while ensuring no negative impact on screening participation rates. Secondary aim: To determine the recruitment protocol maximizing participation in lifepool. Methods: lifepool, in partnership with the BSV Consumer Advisory Committee and Health Issues Centre, conducted a series of consultation workshops to test participant information and consent forms (PICF) and recruitment protocols. Potential impact on participation in the BSV program and clarity of information were explored with women from urban and regional communities. Amended protocols were tested in pilot recruitment projects. The lifepool project undertakes to inform individual participants about research data of significance to their health, after expert review. The challenge of providing accurate risk disclosure to a healthy population is being addressed with input from a range of legal, insurance and health ethics experts. Results and Conclusion:
Cost Recovery—Researcher Expectations versus Funding Agency Requirements
J. Edgar1, A. Thompson1 1
Victorian Cancer Biobank, Carlton, Victoria, Australia
Background: In 2006 the Victorian Government funded the establishment of the Victorian Cancer Biobank (VCB) Consortium from four pre-existing tissue banks. As a requirement of the funding, the Consortium agreed to implement a cost recovery schedule to subsidize operational costs, by cost recovering approximately 10% of the grant funding in the first 3 years. Methods: A modular format, used by other international biobanks, was adapted to suit our operations and fees. The fees were determined by considering the pre-consortium fees, researcher’s expectations and the operational cost incurred. A two-tier model was proposed, charging a higher rate for the commercial sector to subsidize the cost of collecting and supplying biospecimens to the academic sector. Results: The Consortium Committee approved the proposed cost recovery schedule in 2007. From this time the income from cost recovery has increased steadily. However, as 90% of the cost recovery income is generated from biospecimens provided to the academic sector, cost recovery income for 2010 was only 8% of the funding received. Conclusion: The implementation of a cost recovery schedule did not meet the expectations of all researchers as some previously paid only minimal fees. However, over time, most academic researchers have accepted the need to cost recover. The cost recovery income is nearing the target agreed to in the Business Plan. The VCB is now increasing collaboration with the industry=commercial sector, which should increase the income and exceed the target. This will therefore reduce the dependency on government funding.
No significant impact on screening participation Uptake of invitation varies significantly with timing of invitation Bullet point delivery of key consent elements, backed up by further detail, improves clarity and is more acceptable to participants Consumer input during protocol development is vital to this collaboration
HOT TOPICS/OTHER HOT REPOSITORY TOPICS HT 03. Novartis Translational Research Initiative: Taking Biobanking to Early Pharmaceutical Research D. Mikhailov1
HT 02.
1
lifepool: A Collaboration between Women and Researchers
Novartis, Cambridge, MA
Background: Use of high quality, well-annotated human biological material will improve understanding of disease mechanisms, validate biomarkers, and identify novel drug targets. It is also a way to de-risk drug discovery projects by testing early hypotheses in relevant disease context. The Novartis Translational Research Initiative was recently launched to facilitate access to strategically valuable human biosamples, to support early research projects and translational research studies. Methods: Achieving this objective will require a multi-year approach to build capacity and establish processes on specifics of working with human samples. This strategic initiative provides framework and answers to questions such as:
L. Devereux1, I. Campbell1, M.T. Dawson2, S. Fox1, J. Hopper3, A. Kavanagh3, B. Mann4, G. Mitchell1, M. Otlowski5, V. Pridmore6, S. Timbs7, S. Viney6 1
Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Health Issues Centre, Melbourne, Victoria, Australia; 3University of Melbourne, Melbourne, Victoria, Australia; 4The Royal Melbourne Hospital, Melbourne, Victoria, Australia; 5University of Tasmania, Hobart, Tasmania, Australia; 6BreastScreen Victoria, Melbourne, Victoria, Australia; 7Breast Cancer Network Australia, Melbourne, Victoria, Australia 2
Background: lifepool is a large prospective cohort of women on whom health and lifestyle information, mammogram results and health outcome data will be gathered. A subset of participants will provide biospecimens. lifepool will support research into breast cancer and aims to recruit 100,000 women.
-How can research teams propose and implement actionable projects? -How to take advantage of established clinical study processes and apply them for research studies?
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ABSTRACTS -How to build searchable informatics systems for sample tracking and patient annotation and integrate them with existing clinical databases and analytical results? -How to ensure international regulatory compliance and informed consent obligations while maximizing flexibility for research? Conclusion: This presentation outlines some of the operational, informatics and organizational measures the Novartis team has taken to establish best practices for using human bio-specimens in a multinational pharmaceutical research organization. HT 04. TELETHON Network of Genetic Biobanks (TGBN) M. Filocamo1, C. Baldo2, S. Goldwurm3, A. Renieri4, C. Angelini5, M. Moggio6, M. Mora7, G. Merla8, L. POLITANO9, B. Garavaglia10 1
IRCSS - Gaslini - Genova, Genova, Italy; 2S.C.LAB. DI GENETICA, GENOVA, Italy; 3Centro Parkinson e Disturbi del Movimento, Milano, Italy; 4University of Siena, Siena, Italy; 5University of Padua, Padova, Italy; 6IRCSS - Fondazione Ca` Grande - Ospedale Maggiore, Milano, Italy; 7Istituto Besta, Milano, Italy; 8IRCCS - Casa Sollievo della Sofferenza, San Giovanni Rotondo, FOGGIA, Italy; 9Second University of Naples, Napoli, Italy; 10Istituto Besta, Milano, Italy Background: TGBN is the first national, coordinated resource of biospecimens from patients affected by genetic diseases. Supported by Telethon Foundation, TGBN interconnects well-qualified Italian biobanks with the aim to support both the biomedical community as well as the donors, patients and their families. Methods: TGBN operates in a harmonized environment which ensures the privacy protection of and the donor confidentiality, and the quality throughout the entire process of biobanking that includes collection, storage, distribution and related data recording. TGBN collects various types of biological materials: fetal=adult cell lines and tissues, DNA=RNA, blood=plasma samples from approximately 700 different genetic diseases. Activities and policies are stated in the Charter, which includes ethical guidelines, organization and governance policies, expected benefits and undertaken duties. The governance bodies are represented by the decision-making Network Board and by a consultative Advisory Board composed of legal=ethical experts and a family association representative. Additionally, TGBN can rely on a Coordinator Emeritus and a Telethon Advisor. To achieve its main objectives, TGBN has created a public web-site (www.biobanknetwork.org) and has adopted a common ITinfrastructure, managing all data collection, sample submissions, requests and inventory. Results: Aggregated data are published in the on-line catalogue. The IT-system manages and monitors the complete in=out workflow of samples which is therefore fully handled and shared online by all Partners. Conclusion: Samples will be made available to users for research purposes, provided that an adequate portion of the samples derived from individuals affected by undiagnosed and rare diseases are safeguarded to the patients’ advantage to allow retrospective analysis. HT 05. Tracing the Biorepository Fasciae: The Creation of Metadata Linkages that Reflect the Presence, Use and Application of Biospecimen Repository Inventories in Research J.W. McNally1 1
University of Michigan, Ann Arbor, MI
73 Background: There is growing interest in developing seamless metadata linkages that relate biospecimen inventories with associated external information resources emerging from the use of these specimens. The creation of ‘‘metadata’’, or data about data, is well established among researchers operating repositories. Metadata also includes ‘‘data results’’ emerging from the use of biospecimens in research such as essays or microscopic examination as well as publications and reports. When these various metadata are maintained in unrelated collections this limits their potential value to the research community. Methods: This presentation reviews the state of the archival sciences and the multiple databases that catalog the existence of biospecimen inventories, data records and publications that report analysis of biospecimen data. Examples would include models such as the RAND RD-HUB, NACDA, PubMed and the NIGMS Collection. It will also present on emerging tools that help to organize these independent sources of information into an integrated resource. Results: The potential for integrated systems clearly exists. Examples such as the SWAN biorepository at the University of Michigan show that this process is already being done for individual research projects. New metadata management tools being developed at NACDA show how this process can be extended to multiple collections, housed and maintained at independent sites. Conclusion: The creation of information resources that reflect not only the presence of biospecimens, but their use and contributions to science offers great promise for the future. It requires a multidisciplinary approach but it will ultimately add considerable marginal value collections in biospecimen repositories. HOT TOPICS/RETURN OF RESULTS HT 06. Lack of Information about Clinical Biobanking of Biospecimens Used for Biomarker Discovery in Scientific Publications D. Simeon-Dubach1 1
Foundation biobank-suisse, Bern, Switzerland
Background: Biomarkers are an integrated part of personalized medicine and will play an even more important role in the future. Very promising new biomarkers are discovered every year based on research done with human biospecimens. However little is known about the clinical biobanking activities (e.g. transport, storage, processing) with these biomarkers as quality indicators and how it is described in the scientific literature. Methods: A PubMed search was done with key words ‘‘biomarker discovery, human, English.’’ Open source publication from 2004 and 2009 (excluding reviews and studies not using biospecimens) were analyzed for published information about clinical biobanking of biospecimens used for biomarker discovery. Results: The number of publications (total=open source) on biomarker discovery increased from 266=31 in 2004 to 742 =94 in 2009. In 2004 51.6% and in 2009 56.4% of open source studies did not have any information on clinical biobanking. If available there was mostly information only on storage or processing. Biobanks as source of biospecimens increase from 16.1% to 26.6%. Tissue was used in about 1=3 of studies; blood=serum in 1=4 in 2004 and 1=3 in 2009, respectively. Conclusion: To interpret published results on biomarkers discovery information about clinical biobanking are important (garbage in, garbage out). We found that insufficient amount of information - if at all - was provided. There is a call for action to
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ABSTRACTS
different stakeholders: biobankers should collect the information, researcher should include it in the paper and journal publisher should specifically ask for it. HT 07.
Individual Feed-Back from a Cross Cultural Perspective
E. van Veen1 1
MedLawconsult, The Hague, Zuid-Holland, Netherlands
Background: If individual feed-back of results of research with tissue is the newest hotly debated ELSI issue in biobanking, the question arises which values or interests drive that discussion. Methods: It will be shown that the debate started in the United States. In Europe several biobanks exist, either population based, or hospital integrated banks using residual tissue, where the issue was not raised and the non individual feed-back policy thus far did not give rise to ethical complications or less enrolment. This can be explained by the European health care systems and associated cultural values, like willingness to contribute to the public good. European health care is solidarity based and tightly regulated as to what doctors are allowed to offer as diagnostic tools. That does not include not validated procedures with uncertain implications for clinical management of the patient. Hence guiding principles logically follow that individual donor feedback is only allowed, when it has validated clinical meaning, can meaningful serve the patient’s treatment and would not have been used in the available diagnostic and treatment options of the health care system anyhow. In addition donors generally do not expect priority ranking to access to health care because of their participation in a biobank. Conclusion: The US health care system is very different and so are some social values. The European values will be defended. The US debate should be imported with considerable caution and the United States might even learn something from the more restrictive European approach. REPOSITORIES/ENVIRONMENTAL REPOSITORIES ER 01. NIST’s Environmental Banking Expansion Efforts in the Pacific Islands Region A.J. Moors1, R.S. Pugh1, L.B. Rust1, P.R. Becker1, C.E. Bryan1, S. Vander Pol1 1
National Institute of Standards and Technology, Charleston, SC
Background: The National Institute of Standards and Technology (NIST) has been involved in environmental specimen banking since 1979 through various sponsored programs. Current projects include the National Marine Mammal Tissue Bank (NMMTB), the Seabird Tissue Archival and Monitoring Project (STAMP), and the National Oceanic and Atmospheric Administration’s (NOAA) National Status and Trends (NS&T) Mussel Watch Program. Methods: These existing projects have proven successful in environmental banking producing overwhelming numbers of presentations and publications. Recently, NIST began expanding environmental specimen banking efforts in the Pacific Islands region. Existing banking expansion projects include the NMMTB, the STAMP, and the NS&T Mussel Watch Program. This expansion will increase the number of species available for analysis in NIST’s existing specimen bank. The NS&T program currently has four collection sites in the Hawaiian Islands and expansion
efforts for the banking component may extend throughout the Hawaiian and Pacific islands. Additionally, new banking projects are also being established in the Pacific Islands including sea turtle and coral banking. Protocols for these new projects will be based on the already existing and successful projects, however these new endeavors present challenges when considering storage location, storage type, sample type, and future analysis. Conclusion: In addition to the expansion of the marine animal projects, NIST is looking to establish a branch of the Marine Environmental Specimen Bank (Marine ESB) facility in the Pacific Islands region. Additional details about these projects as well as the new NIST partnerships in the US Pacific Region will be discussed.
ER 02. Monitoring Total Arsenic and Selenium Mass Fractions in Seabird Egg Samples from the Seabird Tissue Archival and Monitoring Project (STAMP) R.S. Pugh1, W.C. Davis1, S.S. Vander Pol1, A.J. Moors1, P.R. Becker1, L. Rust1 1
National Institute of Standards and Technology, Charleston, SC
Background: Environmental specimen banks (ESBs) can be an excellent resource in providing samples for monitoring organic contaminants and trace elements in animals to determine if environmental trends exist. Methods: The Seabird Tissue Archival and Monitoring Project (STAMP) was developed in 1998–1999 to serve as a systematic, long-term (decadal) ESB program that identifies and tracks anthropogenic contaminants in Alaskan seabirds. Seabird eggs are routinely collected from colonies located throughout Alaska and are archived by the National Institute of Standards and Technology (NIST) in the Marine ESB at the Hollings Marine Laboratory, Charleston, SC. Results: Total arsenic (As) and selenium (Se) mass fractions were measured in 78 seabird egg samples representing 3 species of seabirds from 2008. Collection sites focused on colonies located in the Norton Sound region as well as two long-term monitoring sites, St. Lazaria Island in the Gulf of Alaska and St. George Island in the Bering Sea. Egg samples were analyzed using collision cell kinetic energy discrimination inductively coupled plasma mass spectrometry (ICP-MS). Total As mass fractions ranged from 0.015 lg=kg to 0.320 lg=kg while the levels of Se ranged from 0.411 lg=kg to1.02 lg=kg. Total As and Se mass fractions were higher in most of the samples collected from the Norton Sound colonies compared to other colonies. Conclusion: Norton Sound is located in a highly mineralized region of Alaska and is an area of historical gold-mining that continues today and could be a contributing factor to the bioaccumulation of arsenic and selenium in this region. REPOSITORIES/HUMAN SPECIMEN REPOSITORIES HSR 01. Integration of Biobanking Into Multidisciplinary Team Based Cancer Care C. Kennedy1, Y. Chiew1, R. Sharma2, R. Balleine1, A. Stenlake3, G. Wain3, A. Brand3, R. Hogg3, P. Harnett3, A. deFazio1 1 Westmead Institute for Cancer Research, University of Sydney, Westmead, New South Wales, Australia; 2University of Sydney and University of Western Sydney, Westmead, New South Wales, Australia; 3Westmead Hospital, Westmead, New South Wales, Australia
ABSTRACTS Background: Biobanking is now considered a basic tool for oncological research and care and several models have evolved to optimize single-site and multi-site collection of biospecimens. The Gynaecological Oncology Biobank at Westmead functions as part of the Multidisciplinary Care Team (MDT). Multidisciplinary care is an increasingly important component of cancer frameworks, and is recommended in Australian national clinical practice guidelines. The Westmead Gynaecological Oncology MDT meeting involves surgeons, pathologists, oncologists, radiologists, nurses, representatives from social work, psychology, familial cancer, clinical trials and biobank research staff. Methods: Patient cases are presented, pathology results and treatment options discussed and a management plan developed. Gynaecological Oncology researchers have participated in MDT meetings for over 10 years with numerous benefits including increased awareness of biobanking and regular contact with surgeons and pathologists ensuring regular biospecimen collection. MDT meetings also provide the opportunity to collect clinical information and gives researchers insight into the complex diagnoses involved in gynecological oncology. Other information gained includes rationale behind chosen chemotherapy regime, discussion of recurrent cases and identification of patients referred to the familial cancer centre. Conclusion: Involvement of MDTs in research assists in systematic recording of prognostic indicators, and allows coordination of clinical trials and clinical research projects involving collection of biospecimens. Incorporation of research staff into MDTs facilitates participation of clinicians and pathologists in research thereby promoting the benefits of biobanking and expedites translation of results into changes in clinical care. MDT meetings are a conduit for clinicians and research staff to exchange patient information and cooperate for better patient and research outcomes. HSR 02. Development of Tools to Assist Researchers Applying to Australian Breast Cancer Tissue Bank
75 graded to full application status, all on-line. The capacity to upload any required documentation is included in the process. eBAS automatically alerts designated BCTB personnel responsible for processing and tracking applications. Reviews are completed and tracked on-line. 4. To best preserve BCTB resources and assist researchers, nucleic acids are extracted within a central processing facility. This allows for automation, standardization and QC of methodology. Standardization allows for direct comparisons between results on downstream tests. 5. A digital image is obtained on every case and then goes through systematic independent pathology review, prior to marking for TMA construction. Images and TMAs are available to researchers. Conclusion: The BCTB realizes the importance of optimizing services and the measures adopted have received positive feedback from the research community. HSR 03. Growing Biorepository Operations to Meet Today’s Scientific Needs L.A. Ball1 1
BioStorage Technologies, Inc., Indianapolis, IN
Background: The proper storage, tracking and transport of research samples is vital to to pharma and biotech firms who frequently conduct a variety of testing on archived biomaterials. Consequently, temperature-sensitive samples must be maintained in highly specialized and consistent conditions. Therefore, biorepositories – large and small – must develop cost-effective, innovative and streamlined operations that will allow them to meet researchers’ long-term needs for improved sample integrity and chain of custody. Methods: The information presented will emphasize best practices for ensuring the long-term stabilization of samples generated during medical research. The poster will also highlight the demands of adhering to good storage practices. Specific topics that will be covered, include:
J.E. Carpenter1, M. Khushi2, C.L. Clarke3 1
2
Westmead Millennium Institute, Westmead, NSW, Australia; University of Sydney, Westmead, New South Wales, Australia; 3 University of Sydney at Westmead Millennium Institute, Westmead, NSW, Australia Background: The Australian Breast Cancer Tissue Bank (BCTB) recruited the first donor in 2006. The first research application was approved in 2008. Since inception we have explored ways to maximize researcher services and have developed strategies to assist applicants whilst simultaneously increasing operational efficiencies. Methods: Services developed include:
On-line search engine eBAS (electronic Biospecimen Application System) DNA=RNA extraction Pathology review=digital image acquisition Results: 1. The on-line search tool allows researchers to enter specific parameters, e.g. grade, hormone receptor status and specimens required. The search engine talks to our real-time central database returning live information. 2. A novel feature is the ability of the search to return snap-shot images extracted from a representative section of tumor material. 3. eBAS allows researchers to submit an EOI which can subsequently be up-
Comprehensive sample management for the entire sample lifecycle The value of consolidation of global specimen inventories Streamlined relocation of specimen inventories and associated equipment Offsite vs. onsite sample management model Best practices for electronic data capture and flow
Results: To maintain sample integrity for extended periods of time, it requires standardized, secured, and validated processes and procedures. The presenter will examine these challenges, provide practical design guidelines and use real-world case studies that help improve the success of this approach, while looking at sample management from an operational planning perspective. Conclusion: Without careful consideration for comprehensive sample management, including cold chain logistics, compliant storage, information management and audit trails, researchers risk specimen degradation and the loss of valuable clinical information. This misstep could prove costly not only for today’s research initiatives, but for future research needs. HSR 04. Beaumont BioBank a Progressive Biorepository B. Pruetz1, T. Geddes1, D. Larson1, G. Wilson1, J. Akervall1 1
Beaumont Hospital, Royal Oak, MI
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ABSTRACTS
Background: Beaumont BioBank is a successful biorepository model which has addressed and achieved the challenging needs of centralizing, collecting, and annotating biospecimens worthy of the specialized demands of translational research. This has been achieved in a community based academic hospital with investment in staff and equipment to pursue the goals of personalized medicine. Methods: In two and a half years, 1,244 patients have been consented and 34,000 specimens collected, and stored from 28 different clinical investigators. Collections are driven by a clear clinical question and are initiated through a defined process involving an investigator contract and the BioBank staff, the clinical investigator, his=her nursing staff and a scientific committee. Suitable patients are identified in advance, appropriate collection kit(s) assembled and barcoded and consent sought at the most appropriate opportunity. Using direct OR sampling, over 80% of tissue specimens are collected, processed, annotated and placed in the freezer within 30 minutes; average time for plasma and serum samples to be placed in the freezers are 64 and 54 minutes respectively. Conclusion: Informatics is a key component of the BioBank, BIGR was chosen to barcode, track specimen location, document history, clinical outcomes, integrity factors; time of collection and preservation of all biospecimens. Quality control is integrated into daily operations, histological validation, DNA=RNA concentrations and integrity. Specimen audits are performed to confirm each specimen and chain of custody of samples is monitored through material transfer agreements and informatics documentation. Institutional investment in this standardized biobank model will lead to the successes of genomic driven personalized care. HSR 05.
Reducing Cold Ischemia Time for Tissues Banked at NUH-NUS Tissue Repository, Singapore
C. ENG1, R. Singh1, T.P. Thamboo1, W. Cheong1, J.B. So1, S.P. Khor1, H. RAFMAN1, S. Ng1, A. Lee1, F.S. Tee1, L.L. Xu1 1
National University Health System, Singapore, Singapore
Background: A project was undertaken to reduce pre-freezing cold ischemia times for banked cancer tissues. The distance between various hospital departments, manpower constraints, and the hospital staff not being properly educated on the importance of ischemia times for tissue quality contributed to the longer baseline time. Methods: The team comprised of tissue repository staff, surgeons, pathologists, operating theater staff and coordinators from the hospital’s Corporate, Planning and Development office. The pre-project workflow was reviewed and periodically refined, with changes implemented in the timing of typing of the histology form to doing away with the gowning up=down of tissue repository staff in operating theater. Along with, a strict check on the elapsed time between specimen excision in operating theater to freezing down in histopathology lab was ensured, both by the OT and tissue repository staff. Finally, specimen photo taking process was shifted out of the operating theater. Results: At the end of the project in September 2009, the median and mean tissue freezing time had come down to 24 and 28 minutes, respectively, from mean baseline level of 70 minutes. The percent of cases falling within the project goal TAT of 20 min had risen to 37% from the meager baseline level of 4.3%. Conclusion: The ongoing monitoring of the project has ensured a 29% collection within 20 min in the last three months of 2010 with 63% specimens being frozen down within 30 min. This
ensures that high quality tissues are made available for bio medical research across Singapore. HSR 06. The Genomic Medicine Biorepository: Addressing the Challenges of Biobanking for Translational Genomics Research at The Cleveland Clinic N.L. Prescott1, C. Eng1 1
Cleveland Clinic, Cleveland, OH
Background: The Genomic Medicine Institute was established in 2005 during a time when no structural, procedural or humanresource infrastructure existed for translational and clinical research in genetics and genomic medicine. The Genomic Medicine Biorepository was established to support studies for the Genomic Medicine Institute and its local, national and international collaborators. Over the last 5 years, many challenges have given rise to innovative solutions. Methods: The following processes were implemented to address specific challenges: (1) Establishment of a safer method for accessing cryopreserved specimens from the liquid nitrogen freezers using a custom gantry crane system. (2) Redesign of the patient instructions to facilitate the receipt of samples. (3) Incorporation of a laboratory information management system, Labmatrix, for specimen tracking. (4) Implementation of a lymphoblastoid cell line grading system to quantify trends in cell line viability. Results: (1)We can access heavy racks from liquid nitrogen in a safe, ergonomic fashion. This helps reduce the possibility of work related injuries or loss of samples due to accident. (2) Better instructions have reduced patient stress and cut down on the receipt of improperly packaged samples. (3) Labmatrix provides a secure LIMS that can integrate sample and patient medical information. (4) Grading the ficoll separation has provided useful information regarding trends in pre-analytical conditions that may lend to problems during the cell line initiation process. Conclusion: Challenges unique to the process of biobanking, especially in the context of non-existent infrastructure, need to be addressed both at the inception of the facility as well as continuously over the course of time. HSR 07. Tumor Banking in Brazil within the Context of a Pathology Residency Program: The Experience of the A C Camargo Hospital Biobank A.H. Campos1, M.D. Begnami1, C.A. Osorio1, C.A. Pinto1, I.W. Cunha1, F.A. Soares1 1
A C Camargo Hospital, Sao Paulo, Brazil
Background: The A C Camargo Hospital Biobank, established in 1997 to provide human tissues for cancer research, is primarily based in the Department of Anatomical Pathology (DAP), which has a 3-year residency program in surgical pathology, which is the only one in Brazil that includes biobanking activities in the resident curriculum. Methods: We analyzed, from 1998 to 2010, the number of residents enrolled in our residency program, calculating the number of hours each resident performed supervised activities at the frozen section laboratory (FSL), where over 90% of the tissue acquisition takes place, the number of acquisitions over each year and compared the results to quality indicators (tissue representativeness and RNA=DNA quality). Results: There were 39 residents enrolled in the residency program from 1998 to 2010. Each resident spent 672 hours=year
ABSTRACTS at the FSL. Residents who were enrolled in the residency program during the first years of the biobank activities performed an average of 8 tissue collections per resident per week, whereas residents from the last five years of activity performed an average of 13 tissue collections per resident per week. Sample acquisition by residents did not affect quality indicators. Conclusion: Pathologists play a key role in biobanking activities, particularly with respect to quality control issues related to the collection of biospecimens. The involvement of pathology residents in tissue banking activities during their residency program contributes to the formation of professionals familiar with the principles and best practices adopted in biobanking activities. HSR 08. The Next Phase of Biospecimen Management B.J. Chadwick1 1
LookLeft Group, LLC, Flanders, NY
Background: Due to increasing regulatory scrutiny and the harsh reality that many historical biospecimens have proven to be of insufficient quality to bring significant value, systems that manage biological samples must evolve. Methods: While basic location and inventory management functionality is still critical, modern biospecimen management software solutions must be protocol and process driven to enforce best practices for sample collection, annotation and processing. Advanced biospecimen management systems must include functions and features for informed consent management, bioethical and legal controls, and the ability to collect and connect clinical data to biospecimen data. They must be designed as open architecture platforms with flexible data import and export capabilities and enable integration with, and analysis of, public genomics information. They must offer sophisticated ad hoc reporting tools and user defined dashboards. Results: Connecting the phenotype to the genotype is the fuel for translational research and a cornerstone of personalized medicine. To achieve the value proposition of using data derived from biospecimen analysis to impact clinical diagnostics and therapeutics will require biospecimen management software solutions that meet increasing international data and privacy standards. Audit-worthy quality systems must be in place with documented processes and practices that comply with international regulatory requirements. Conclusion: While this will require a commitment to change and the cost of change management, companies that successfully enter the next phase of biospecimen management will be best positioned for the era of personalized medicine. HSR 09. The Challenge of Keeping Your Biobank Current A. Parry-Jones1, M. Mason1, G. Thomas2 1
Wales Cancer Bank, Cardiff, S Wales, United Kingdom (Great Britain); 2Velindre Hospital, Cardiff, S Wales, United Kingdom (Great Britain) Background: Biobank development is an evolutionary process that can only flourish given solid foundations. Initial stages in operational development focus on patient recruitment and sample accrual. The next phase is concerned with ensuring sample integrity and usefulness by consolidating collections and reviewing the use and demand of both samples and data. The number and quality of research projects applying for access to samples becomes an important marker of development and
77 success in biobank growth and one which facilitates the conduct of novel research programs that will ultimately improve the clinical care of patients. Methods: The Wales Cancer Bank recently conducted such a review after consenting 4,000 cancer patients to donate tissue and blood samples for prospective collection. At the time of review, 38,000 aliquots of biosamples were available and 4,500 aliquots had been used, either for extraction or supply to research groups. The profile of tumor and sample types in the collection was compared to the incoming requests for samples to ascertain whether the collection strategy was sound or whether amendments to the methodology were required. An audit of treatment and follow up data was also conducted and a synopsis of available biosamples with associated clinical data was formulated. Conclusion: Biobanks, particularly ones collecting prospectively, must not become complacent once set up and running. Regular scrutiny should form part of the operational program to ensure funding is well utilized and sample use is maximised, to uphold the promise made to donors to use their generous donations to further scientific knowledge and clinical treatment. HSR 10. Global Collaboration for HIV=AIDS Cancer Research: AIDS & Cancer Specimen Resource Biorepositories in East Africa R. Lukande1, L.K. Tumwine1, E.A. Rogena2, J.R. Ndung’u2, L.W. Ayers3 1
Makerere University College of Health Sciences, Kampala, Uganda; University of Nairobi, Nairobi, Kenya; 3The Ohio State University Medical Center, Columbus, OH
2
Background: Biospecimen science and research biorepositories are expanding internationally to provide quality biospecimens for quality research studies. Growth in biorepositories emphasizing biospecimen quality is well underway in the developed world. However, despite the developing world experiencing 70% of the global increase in cancer burden, there is no comparable growth in research contribution. Methods: Affiliates of the Mid-Region AIDS and Cancer Specimen Resource (ACSR=NCI) have been established at Makerere University (MU), Mulago Hospitals (U-ACSR) and the University of Nairobi (UON), Kenyatta National Hospital (K-ACSR) to initiate cancer biorepositories. Memoranda of understanding (MOU) and material transfer agreements (MTA) were developed for the collaboration between MU and UON pathologists and the Mid-Region ACSR (ACSR=NCI) located at The Ohio State University in Columbus, Ohio. IRB approved ACSR protocols are in place at MU and UON and studies using African biospecimens initiated. Results: K-ACSR from 2007–2010 collected 128 AIDS associated malignancies and together with U-ACSR provided 536 source blocks of lymphoma to the Sub-Saharan Africa Lymphoma Consortium (SSALC=ACSR=NCI) with 1388 cores placed in 38 tissue microarray (TMA) blocks through 2010. Nine podium and poster presentations from ACSR tissue studies were presented in 2009 and 2010 at international meetings including AORTIC (Africa), ICMAOI (USA) and APECSA (Africa). Conclusion: Collaborations promote biospecimen science concepts for human tissue archive management to provide research and publication opportunities. African participation in global biospecimen science and quality cancer research uniquely contributes to understanding tumor patterns, interactions among numerous tumorigenic viruses, adverse environments, nutrition and genetics in cancer, particularly HIV=AIDS malignancies.
78 HSR 11.
ABSTRACTS Alignment of a Research Biobank with Pharma Biomarker Validation
J. Swifka1, T. Krahn1, A.A. Schmitz1 1
Company, Wuppertal, Deutschland, Germany
Background: The understanding and treatment of many diseases is severely handicapped by the absence of biomarkers that can be measured in body fluids like blood or urine. To identify and validate biomarkers in pharma research especially in translational medicine excellent clinical material is indispensably needed (e. g. for molecular analyses at mRNA level). To support and empower research, there is a high demand to create utmost ’value’ from scarce samples. Compliance to legal requirements is a must, with additional emphasis on socioethical values. Methods: We analyzed the legal situation in Germany. We then developed a concept for and established a research biobank including both human and animal specimens. Results: The Research Biobank of Bayer Schering Pharma AG leverages the clinical network driven by the research projects by providing human samples and their clinical data for bioanalytics under strict compliance with legal, ethical, biosafety, biotechnology, data privacy and information technology guidelines. Conclusion: We favor a collaborative approach to biobanking where both clinicians and researchers contribute their strengths. By combining our respective experiences and accepting mutual cultural differences during partnering as well as clinical realities during the operations phase in order to minimize risks in clinical sample and data collection we were able to accelerate setting up prospective collections as a reliable, convenient, robust and affordable solution. Experiences gained in the build up of a pharma research biobank can be instrumental in further developing best practices. We will present case studies from our indications which include Oncology, Cardiology, and Gynecology. HSR 12.
Million Veteran Program (MVP): A Tissue and Data Repository of The Office Of Research and Development, US Department of Veterans Affairs (VA) 1
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R. Przygodzki , S. Muralidhar , T. O’Leary , J. Gaziano , J. Concato3, L. D’Avolio2, L.D. Fiore2, D. Humphries2, M.T. Brophy2 1
Department of Veterans Affairs, Washington, DC; 2VA Cooperative Studies Program, Boston, MA; 3VA Cooperative Studies Program, West Haven, CT Background: The objective of the VA Genomic Medicine Program’s MVP is to create a repository to enable genomic investigation and discovery within the VA. This landmark undertaking will enroll as many as 1 million users of the Veterans Healthcare Administration over the next 5–7 years. Subjects will provide informed consent for collection of blood and clinical data, as well as HIPAA authorization for use of these resources by researchers. Methods: Veterans will be invited primarily via mailings to participate at their local hospital or clinic. Phenotype data will be collected via health and lifestyle surveys at entry and longitudinally via health data extracted directly from electronic medical record of the VA. All subjects will contribute a 10 ml EDTA blood sample that will be shipped overnight to the VA Central Biorepository and processed to extract 10–15 lg of DNA and to store two 1 ml aliquots of plasma and one aliquot of buffy coat. Samples will be stored at 808C. Phenotype and biosample data and
analysis results will be stored in Genomic Information System for Integrated Science (GenISIS) databases and will be made available to researchers in a scientific computing environment. Results: The protocol was approved by the VA Central IRB. Recruitment began in January 2011 and will be rolled out to 50 VA sites within a year. Work is continuing to complete laboratory automation and GenISIS development. Conclusion: Collaborative efforts within VA have lead to the launch of MVP, which aims to be one of the largest resources for genomic research. HSR 13. Recovery of MicroRNA from Stored Human Peripheral Blood Samples S. Robinson1 1
University of Colorado, Anschutz Medical Campus, Aurora, CO
Background: Recovery of microRNAs (miRs) from tissue samples of many kinds has become an area of increasing interest and importance in recent years. Methods: We isolated, and then amplified and quantitated, miRs from human peripheral blood samples stored in the University of Colorado Skin Cancer Biorepository to determine if miR recovery was possible and consistent over time in storage. Forty five blood samples from patients with different stages of malignant melanoma were collected in PAX gene RNA tubes and then stored at 808C prior to RNA preparation. The samples examined had been stored from 4 weeks to 3 years. Total RNA was prepared followed by miR isolation, amplification and quantitation using real time PCR. A widely expressed microRNA, miR221, was as a standard for comparison across samples and storage time. miR221 was recovered from all samples with no differences observed with longer storage time. Conclusion: These studies show that miRs can be recovered and quantified from human blood samples stored for up to 3 years. HSR 14. Educating the Public about Tumor Banking: An Outdoor Cancer Exhibition Organized by the A C Camargo Hospital in Sao Paulo, Brazil A.H. Campos1, C. Gonc¸alves1, E.N. Ferreira1, E.H. Olivieri1, M. Maschietto1, D.M. Carraro1 1
A C Camargo Hospital, Sao Paulo, Brazil
Background: In order to demystify cancer and bring cancer research closer to society, Hospital A C Camargo (with the support of the Sao Paulo Research Foundation-FAPESP and the National Council for Scientific and Technological DevelopmentCNPq) held in public parks of Sao Paulo the exhibition "Cancer: Know and Prevent". The importance of tumor banking was addressed in a panel (of a total of twenty-two) containing entertaining and educational concepts on the subject. Methods: The rationale for tumor banking and the Biobank infrastructure and workflow were discussed by the A C Camargo Biobank staff with the hospital press office staff for institutional projects and professionals from the art company Pingado Sociedade Ilustrativa, which created a comic strip with easy-tounderstand text. This comic was mounted on a 1.20 (wide)1.80 (tall) meter panel. Results: Beginning on May 30, the exhibition toured eight public parks in Sao Paulo during the year 2010. An additional park was included in the schedule for early 2011.
ABSTRACTS Conclusion: This exhibition provides an additional means of bringing information to the community about the importance of a tumor bank in cancer research. HSR 15. Protein Extraction and Western Blot Analysis from Formalin Fixed Paraffin Embedded Biobanked Heart Tissue L.A. Matzke1, A.J. Meredith2, D. Singhera3, D.M. McManus4, D.F. Allard4 1
Institute for Heart and Lung Health, Vancouver, BC, Canada; Institute for Heart and Lung Research, Vancouver, BC, Canada; 3 James Hogg Research Centre, Vancouver, BC, Canada; 4Institute for Heart and Lung Health=University of British Columbia, Vancouver, BC, Canada 2
Background: Immunohistochemical (IHC) staining and Western blot (WB) analysis are established analytical techniques providing complementary information on protein quantity, localization and distribution within tissues. Technical challenges have meant that these methods are generally used in isolation. IHC is typically performed on tissues processed with fixatives such as formalin, which denature proteins such that analysis of the same tissues by Western blotting, which generally assays freshly extracted protein, may not be possible. In certain circumstances, such as in forensic pathology, only formalin fixed tissues are routinely retained for evaluation. In this study, we extracted protein from formalin fixed (FF) and corresponding snap frozen (SF) tissues as well as from formalin fixed paraffin embedded (FFPE) tissues from six archived myocardial samples to evaluate their performance in WB analysis. Methods: Myocardial tissue samples from six heart transplant cases were obtained from the James Hogg Research Centre Cardiovascular Biobank at St. Paul’s Hospital. Protein was extracted from matched SF, FF and FFPE heart samples. Extracted proteins were analyzed by WB for expression of both cytoplasmic and membrane proteins. Results: Membrane and cytoplasmic proteins were readily detectable in SF samples. Proteins from FFPE samples were detectable more than 60% of the time and FF samples were not detectable. Conclusion: The results of this study suggest that WB analysis from FFPE human heart tissue can be successful. Optimization of the retrieval of assayable proteins from archived FFPE heart tissues will provide a valuable resource for proteomic analysis, biomarker discovery and validation, and genotype=phenotype studies. HSR 16. Data Coordination for a Multi-Centre Tissue Bank: The Children’s Cancer and Leukaemia Group (CCLG) Tissue Bank G. Mistry1, S. Ablett1, G. Jenner1, H. Middleton1, S. Thornton1, N. Sebire2, K. Brown3 1
Children’s Cancer and Leukaemia Group, Leicester, Leicestershire, United Kingdom (Great Britain); 2Great Ormond Street Hospital for Children NHS Trust, London, United Kingdom (Great Britain); 3 University of Bristol, Bristol, United Kingdom (Great Britain) Background: The CCLG Tissue Bank has been established since 1998. It is a repository of solid tumor specimens and supporting clinical data, designed to facilitate and support childhood cancer research. Frozen, paraffin-embedded tissue and blood samples
79 collected from children (0–16 years old) across multiple sites are locally stored, DNA samples are centrally stored, and all registration and pathological data is centrally managed at the CCLG Coordinating Centre. The datasets collected include patient demographics, pathology reports and clinical follow-up data, as well as monitoring CCLG biological studies through progress reports, sample tracking and publication output. Methods: The logistics of central data collection for tissue stored and dispatched from multiple sites can be challenging. Processes have been developed to ensure this data is captured and processed efficiently. A database is used to log all patient and tissue registration information, clinical outcome data, progress of CCLG biological studies and specimens dispatched. Electronic anonymized pathology reports for all specimens are available to researchers. Annual progress reports and publications arising from biological studies are logged. Results: Supporting pathological data on all 10,112 tissue samples registered to date. Clinical follow-up data has been collected on all registered patients with tissue since 2007. All 80 CCLG biological studies have been supported by clinical data and annual progress documented, including research findings. Conclusion: A comprehensive collection of data on pediatric cancer has been successfully utilized for research, facilitating effective biological and translational research into various childhood cancers. HSR 17. The NHLBI BioLINCC Operational Guidelines: Streamlining the Review of Biospecimen Requests E.L. Wagner1, K.E. Shea2, L.E. Carroll3, L.A. Welniak1, S.S. Berman2, J.T. Adams3, C.A. Giffen3 1
NIH=National Heart, Lung, and Blood Institute, Bethesda, MD; SeraCare Life Sciences, Inc., Gaithersburg, MD; 3Information Management Services, Inc., Silver Spring, MD
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Background: The NIH National Heart, Lung, and Blood Institute (NHLBI) is the custodian of multiple contemporary and historical biospecimen collections. The NHLBI Biologic Specimen and Data Repository Information Coordinating Center (BioLINCC) has linked over 4.2 million biospecimens (26 collections) to their phenotypic data and established a public website where scientific investigators can view available resources and submit requests online. The availability of an online application process resulted in an increase in biospecimen requests and reviewing applications in a timely manner became challenging. A new streamlined review process was developed to address this issue. Methods: A review of publicly available best practices was performed to identify core review elements. The core elements were compared to the type and timing of the information collected during a biospecimen request. A multi-disciplinary team was formed to provide technical reviews early in the request process and a workflow established. Expedited review processes were investigated. Results: The website application form was retooled and a new review tab on the private website was developed for NHLBI, BioLINCC and biorepository staff to document the multidisciplinary review and post recommendations. The recommendations were distributed to the scientific reviewers and expedited reviews were performed for ‘‘low impact’’ requests. Initial results indicate that the expedited reviews can facilitate the process. Conclusion: Implementing best practices to facilitate the search and distribution of biospecimens without introducing unnecessary roadblocks is possible using a multi-disciplinary approach and streamlined workflow.
80 HSR 18.
ABSTRACTS Ambient Temperature Stabilization of Genomic DNA in Saliva Samples
S. Ghirmai1, J. Muller-Cohn1, S. Whitney1, R. Muller1, S. Wilkinson1, L. Shireen1 1
Biomatrica, Inc., San Diego, CA
Background: Saliva provides an alternative to blood as a biological fluid in research and diagnostic applications. The major advantage of saliva over other biological fluids is the fact that it is non-invasive and can be collected without training. Biomatrica has developed a novel reagent that preserves the integrity of genomic DNA in saliva at room and elevated temperatures for up to 6 months. This makes the saliva=preservative mixture ideal for sample storage and shipping as an alternative to freezers or cold-packs. Methods: Samples were collected from 4 donors. Three different DNA extraction methods were employed: Column based, (Qiagen), phenol=chloroform, and precipitation. DNA integrity was analyzed on a 0.8% agarose gel and 10% of eluted DNA was loaded on the gel. DNA yield was determined by fluorescence using the Quant-iTÔ PicoGreen dsDNA Assay Kit (Invitrogen). Results: Biomatrica’s new saliva formulation is based on inhouse developed chemical compounds that are designed to preserve the integrity of DNA in saliva. The new formulation was found to preserve the integrity of DNA in saliva samples when stored at room temperature and elevated temperature for extended periods of time. The formulation was compatible with different DNA isolation methods. The purified DNA did not show intereference with PCR, long range PCR or QPCR. Conclusion: The new reagent for stabilizing DNA in saliva provides excellent stabilization for up to 6 months, with high quality gDNA as well as high recovery. The quality of the extracted DNA was evaluated in downstream applications such as PCR. HSR 19.
Biobanking Management in a Cancer Center
V. Canzonieri1, A. Steffan1, T. Perin1, S. Cervo1, M. Nigris1, B. Canal1, P. De Paoli1 1
CRO (National Cancer Institute), Aviano, Pordenone, Italy
Background: The National Cancer Institute CRO-Biobank represents a long-term source of human biological samples collected at diagnosis and at consecutive therapeutical stages for research purposes. CRO-Biobank is a member of the Italian Network Cancer Biobanks (RIBBO) and participates in the setting up of a European network (BBMRI). Methods: At present the collection comprises serum, plasma, buffy-coat, tissues and DNA of healthy individuals and cancer patients, which are collected and stored in compliance with quality standards and ethical regulations. The traceability is guaranteed by the "Matrix" system based on a software (Easytrack2D Ver 2.0, Twinhelix) for the managing of sample data; particularly it allows to know the physical location of samples thanks to 2D-barcoded tubes. CRO Biobank has developed quality control procedures concerning timing and method to obtain optimal freezing, prevention of hot and cold tissue ischemia and accuracy in the OCT embedding process. Tumor or healthy frozen tissues were also evaluated to establish the percentage of necrotic= fibrotic areas in cryostat histological sections directly obtained from the samples. To warrant the possibility of aliquoting tissue samples, we have also tested the consistency of biomolecular analyses from mul-
tiple cryostat sections of the same tissue block obtained at different times. Conclusion: The major advantages of setting up our Biobank are: first, scientists can readily assess clinical information in conjunction with biological features of samples for research; second, it represents an important tool to provide accurate and high quality linkages with the regional or national cancer registries. HSR 20. Building a New Large-Scale Biobank for Clinical and Epidemiological Research Studies in Sweden A. Brinne1, M. Divers1, C. Rask1, T. Rylander-Rudqvist1, A. Pettersson1, G. Tybring1 1
Karolinska Institutet Biobank, Stockholm, Sweden
Background: A strategic funding on a national biobank infrastructure as a part of BBMRI.se made it possible to further develop KI Biobank and create a new high throughput facility. The development was driven by three major population based studies, two within cancer with a target of 200 000 people, and LifeGene with a target of half a million people in Sweden. Methods and Results: We undertook extensive processmapping to understand how we could increase capacity and where to introduce automation. After a tender process we selected robotic systems for registration and sorting of incoming samples and aliquoting of different sample types into multiple 220 ll fractions and established new processes for DNA extraction. We changed tube format and developed a simple expandable storage strategy. In addition we extended and modified our facility. Big efforts were made to further develop our LIMS system to support the new processes. Conclusion: After installation and testing we were able to launch the new operation on November 1, just 10 months after starting the new development. Our automated processes have given us the big increase in sample processing capacity we needed to start 3 new large studies. We now need to optimize our processes for stability and to further increase capacity, and this will enable us to take on more large studies and improve the efficiency of our smaller studies. Our next steps are to automate sample retrieval and to identify a cost effective strategy for long term storage. HSR 21. Facilitation of Biorepository Functions with PivotÔ by MicrosoftÒ Live LabsÔ A. Kulkarni1, C.R. Handorf1, C. Stanton1, P. Ngutu1 1
UTHSC, Memphis, TN
Background: Pivot is an application intended to simplify viewing and interaction with massive amounts of data in ways that are powerful and informative. Pivot is a data mining system that allows visualization of data that can be sorted, organized, and categorized according to the user’s requirements. Pivot is able to filter through images and information seamlessly because the images are in Deep Zoom format (a component of Seadragon Technology). The Whole Slide Imaging (WSI) system creates a digital replica of the entire content of a glass microscope slide that can be displayed on the computer, emulating traditional viewing of a slide with a conventional microscope. Combining these two technologies makes it possible to create a collection of images and associated information that can be used for sorting biorepository samples.
ABSTRACTS Methods: Digital slide images created by the ScanScope XT scanner (Aperio Technologies, Inc.) are stored in the SVS (ScanScope Virtual Slide) file format. SVS files are TIFF=BigTIFF files. Pivot only accepts JPEG, PNG, and HD photo files. We converted the SVS files to JPEG files using Digital Slide Studio (Aperio) and then entered the JPEG images into a Microsoft Excel based tool that converted the JPEG images to Deep Zoom Image (DZI) files. The DZI files, which enable viewers to zoom in and pan out without loss of significant resolution, were then used to create a Pivot collection. Conclusion: Pivot can be a useful tool for biorepositories since it offers the capability to sort images based on different parameters. HSR 22. Comparison of Pre-Operative and Post-Operative Consenting Protocols at the British Columbia Cancer Agency Tumour Tissue Repository (BCCA-TTR) J.L. Le Blanc1, R.O. Barnes1, S. Dee1, P.H. Watson1 1
BC Cancer Agency, Victoria, British Columbia, Canada
Background: The BCCA-TTR is a cancer biobank that for its first five years of operation has mostly deployed a pre-operative consent protocol. In 2010 the BCCA-TTR began to also deploy a new post-operative consent protocol. Both types of protocols have many benefits to patients and biobanks, however efficiency and outcomes of each protocol may be different. Methods: The rates of consented, declined and decision unknown outcomes were compared between pre and post-operative consent protocols for 3279 cancer patients referred for potential consent. Subsets of breast and colon cancer patient decision rates were also analyzed. Results: There was no significant difference in the global rates for consented (þve) and declined (-ve) using pre or postoperative protocols (97.7% þ ve and 2.3% -ve vs *95.9% þ ve and 4.1% -ve respectively). There was a significant difference in outcomes with respect to decision made (þve or -ve) versus decision unknown between pre and post-operative protocols (1.8% vs 23.4% of all patients approached, chi-square test, p < 0.0001). Consented and declined rates were similar for both protocols for breast cancer patients but a higher decline rate was observed for colon cancer patients (p ¼ 0.007). The proportion of decision made to decision unknown was higher with the post-operative protocol with breast and colon patients (33%, p < 0.0001. Conclusion: These data suggest that pre and post-operative consent protocols are equally acceptable overall to cancer patients. However, pre-operative consent may be more acceptable for some subsets and the rate of ‘decision unknown’ is generally increased with the post-operative consent protocol. HSR 23. Value of Morphological Quality Control of a Cancer Tissue Bank M. Sun1, G. Qin1, Y. Gu1, H. Chen1, Z. Zhang1, X. Zhou1, X. Du1 1 Fudan University Shanghai Cancer Center, Shanghai, Shanghai, China
81 formation for the researchers. When possible for each case, we are collecting an aliquot of tissue exclusively for morphological quality control. Methods: An aliquot of a tissue piece during each case of tumor tissue procurement is collected and snap frozen in liquid nitrogen then transferred to 808C by the end of the day. A frozen section was cut and H&E staining was performed from the aliquots of the tumor tissue. The H&E stained whole section was scanned in whole using the image analyst of Ariol. The tumor percentage of each case is evaluated and the images were stored as a virtual morphological bank. The information including the scanned morphology was provided to researchers along with the research tissue samples. Results: More precise sample information was provided to the researchers. They could tell how much tumor component is contained in the sample they are analyzing. Through the necessary micro- or macrodissection we could provide the research results representing the goal tissue and therefore the research study would be more precise. Conclusion: Morphological information would be helpful for investigators to know more about the samples they are using for scientific study. HSR 24. From Bio Specimen to Biomarker? The Quickest Way for Discovery of Novel Candidate Biomarkers R. Ravid1 1 Royal Dutch Academy of arts and Sciences, Amstelveen, Noord Holland, Netherlands
Background: The search for biomarkers relies completely on the availability of high quality specimens from living donors as well as autopsy material collected and stored by biobanks. The diagnosis of neurological disorders is severely hampered by an absence of reliable biomarkers that can be measured in body fluids such as blood, urine and cerebro-spinal fluid (CSF). Methods: Biomarker discovery copes with extreme data fluctuation due to the huge variability between individuals and the rapid post-mortem changes. We are currently using betaAmyloid and Tau as candidate biomarkers for Alzheimer’s disease (AD) and fronto-temporal lobar degeneration (FTLD). The collected specimens include RNA,DNA and proteins extracted from brain =tissue =body fluids, subsequently correlated to the classical pathological hallmarks of the disorders. Results: So far we have identified and measured biomarkers in blood and CSF. We conduct the correlating tests for total and phosphorylated tau and Ab42 in living donors and in rapid autopsy material and then add the results to MRI imaging results to assist in differential diagnostic procedures. Conclusion: Human biobanks play a major role in the collection of large numbers of high quality specimens for biomarker identification. So far, no single biomarker has been found which discriminates between AD and other dementias. Therefore we are aiming at international collaboration between biobanks and harmonization of SOP’s to enlarge the panel of valid biomarkers which will substantially increase the sensitivity and specificity of the diagnosis. HSR 25. How Do They Do That?
Background: As already well known, pathology is the cornerstone of a tissue bank, where usage of human tissue is an increasing requirement. The morphological information is as critical as the steps of tissue collecting, processing, annotating and preserving. It is of big value to provide morphological in-
T. Mathieson1, A. Storniolo2, S.E. Clare2, C. Rufenbarger1, J. Henry1, E. Way1, H. Zang1, K. Ridley1 1 Komen Tissue Bank, Indianapolis, IN; 2Indiana University School of Medicine, Indianapolis, IN
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ABSTRACTS
Background: Since Oct of 2007 the Susan G. Komen Tissue Bank at the IU Simon Cancer Center in Indianapolis has collected over 1300 normal breast tissue samples with matching blood, plasma, and DNA from women with no signs of breast cancer. There is currently a waiting list of 500 women willing to give tissue from their healthy breasts to be used in breast cancer research. How does the Komen Tissue Bank achieve this? Why are women lining up to donate? What is a collection day like? How are the samples collected and processed to achieve the highest standards of sample integrity possible? We present a brief journey from the inception of the Komen Tissue Bank through IRB, legal, and logistical challenges to the present day summation of what the Bank holds. A sample collection and processing description is included as well as testimonials from the women who have donated their precious healthy breast tissue to the Bank. Methods: A breast tissue collection event utilizes up to 80 volunteers to complete the donation process from consent to biopsy. Samples are immediately processed according to strict SOPs. Results: A typical collection event lasts 7 hours. During this time, samples of breast tissue and matching plasma and serum from 100 donors are collected and processed. Conclusion: The Komen Tissue Bank is the source for normal breast tissue for breast cancer research. When women are asked to personally contribute to breast cancer research, they generously line up to do so. HSR 26.
Creating a Framework for Serial Collection of Residual Clinical Phlebotomy Samples, from Community Consultation to Infrastructure Development
D. Cross1, V. McManus1, J. Eckstrom1, C. McCarty1 1
Marshfield Clinic Research Foundation, Marshfield, WI
Background: Here we describe the development process for the collection of serial samples using residual clinical specimens from participants in a population based biorepository. Methods: We identified three groups essential to the definition and implementation of serial sample collection: the participating community, the scientific community, and the infrastructure development team. Initial steps focused on the participating community, with active community engagement from focus groups, community advisory board discussions, and external ethics advisory board consultations. The scientific community was asked to determine the characteristics of a useful sample; we consulted both internal scientists, and sought external scientific advice. To determine the infrastructure development needs, we identified stakeholders from different departments to plan workflows that transition a sample from clinical collection to biorepository storage. Results: Information from focus groups and advisory committees led to the development of an "opt out" model for incorporation of serial samples; this has resulted in less than 1% of participants requesting removal from the study. Scientist input in serial sample collection helped identify characteristics of a valuable sample including continuous care within the institution, diagnosis of a common condition, age, and overall health of the participant. Stakeholder input identified small changes in workflows that might have the potential to increase sample value, such as fast tracking a sample to a temperature controlled area and tagging potential biorepository samples at the site of initial sample processing. Conclusion: Collecting additional serial samples from an established cohort can be established only with the input of all affected groups.
HSR 27. Best Practices for the Global Distribution of Specialized Biomaterials Generated in Clinical Trials R. Hager1 1
BioStorage Technologies, Indianapolis, IN
Background: The poster will provide attendees with detailed solutions to the intricate processes of global cold chain management of clinical trial samples. Specifically, the poster will highlight various aspects of international transportation and best practices that ensure the on-time and compliant distribution of temperature-sensitive materials. Methods: To mitigate risk of degradation and ensure compliance, biorepositories must have a broad understanding of the complexities involved in global cold chain management. Using real-world applications and industry case studies, the presenter will give insight into the complexities of cold chain management and highlight strategies biorepositories can implement to ensure on time, compliant transportation of temperature-sensitive clinical trial samples and supplies. Results: Pharmaceutical and life science assays often require accurate and constant temperature control to acquire meaningful data. As a result, particular attention must be paid to the effects temperature variances have on the stability of biospecimen samples, and how to overcome these hurdles by addressing them in upstream processes. By adhering to best practices for the shipment and storage of temperature-sensitive materials, companies can reduce risk and increase efficiency throughout the development process. Conclusion: Cold chain logistics is a multifaceted function demanding homogeneous solutions to rising cost concerns, environmental responsibilities, packaging procedures and custom regulations. Without validated, carefully considered planning for the complexities of global cold chain logistics, biorepository operators risk product degradation, and possibly the loss of irreplaceable materials. This pitfall can lead to delayed clinical trials, postponed product launch and ultimately loss of revenue for the trial sponsor. HSR 28. A Flexible Informatics Framework to Guide the Advancement of Personalized Medicine and Improve Patient Outcome in a Community-Based Healthcare System N. Todaro1, R. Mulpuri1, S. Chen2, J. Otridge2, J. Otto1 1
Catholic Health Initiatives, Towson, MD; 2BioFortis, Columbia, MD
Background: In contrast to urban single-site academic hospitals, networks of community-based hospitals enable vast, demographically diverse, biospecimen collection. Catholic Health Initiatives (CHI) is committed to bringing cutting-edge research and treatments to its 73 hospitals in 19 states. Facilitating the advancement and integration of personalized medicine, CHI has established the Center for Translational Research (CTR) comprising of Biorepository, Molecular Diagnostic and Research Laboratories. By engaging CHI physicians and leveraging diagnostic testing infrastructure, CTR has established state-of-the-art Biorepository facilities to enable innovation and advance personalized medicine within their communities. Methods: Using an IRB approved protocol, CTR collects biospecimens from eligible cancer patients and associated clinical and longitudinal follow-up data for up to 10 years. We describe the collaboration with BioFortis in implementing a
ABSTRACTS Labmatrix-based IT framework that guides data collection, management and exploration of patient and molecular data. HIPAA-compliant Labmatrix meets evolving scientific needs and data exchange standards, and is capable of tracking data from donor consent along with their comprehensive clinical profile, bar-coding, sample collection, processing, storage, shipment and disposal, to specimen usage and assay data. Conclusion: With a sophisticated security framework, Labmatrix provides standardized data format and collection, by creating forms or providing interfaces to hospital-based EMR systems (HL7 standards) while maintaining and assuring the quality and chain-of-custody of biospecimens. Through Labmatrix, CTR has a robust compliant infrastructure to standardize procedures across the CHI network - linking patient clinical and outcome data with molecular data enabling the translation of biomarker and health data into useful tests to improve patient outcomes and drive innovation. HSR 29. Introducing the NW Biobank: A Research Repository at Kaiser Permanente Northwest K.S. Smith1, J. Carlston1, M. Hornbrook1, P. Dandamudi1, K. Goddard1 1
Kaiser Permanente Northwest, Portland, OR
Background: The NW Biobank is a multi-modal repository housing legacy research specimens from 37,327 unique subjects and specimens from *3,000 prospectively recruited subjects. The NW Biobank is nested within Kaiser Permanente Northwest (KPNW), an integrated health care system with a large, stable membership (*475,000) and extensive data on members dating back to 1960. Methods: To pilot-test prospective recruitment, we mailed invitations to 2,000 members asking to use their discarded blood samples in a hypertension study. We also asked current members with a history of breast cancer (3,921 cases) and 2,000 matched controls for samples. Results: The response rate for the hypertension study was 34%; 82% of respondents consented to participate. For breast cancer, the response rate was 35%, varying between cases (40%) and controls (19%); 90% of respondents consented to participate. Most of the samples in the NW Biobank are from females (86%) and Caucasians (95%). The gender imbalance reflects the recruitment criteria, and women’s greater willingness to participate in research. We have more than 10 years of medical history for about 50% of subjects. A major factor affecting future use of legacy specimens is limited informed consent. We are now reconsenting subjects to enable broader data sharing. Conclusion: We plan to invite all adult KPNW members to participate in the NW Biobank. The high response rate (>30%) and reliable methods for obtaining blood samples integrated into the health plan infrastructure should lead to successful accrual of specimens for future genomic research. REPOSITORIES/NATIONAL & INTERNATIONAL BIOBANKING NETWORKS NIR 01. Role of National Culture Collection for Pathogens (NCCP) and Pathogen Bank Network in Korea K. Jung1, C. Yoo1, K. Lee1 1
Korea National Institute of Health, KCDC, Chungbuk, Republic of Korea
83 Background: National Culture Collection for Pathogens (NCCP) is the only national pathogenic resource bank in Korea. NCCP is operated by a governmental agency from 1972. The function focuses on collection, preservation, development and distribution of pathogenic microorganisms isolated from patients with infectious diseases including high-risk pathogens. We affiliated the World Federation of Culture Collection (WFCC) under the name NCCP in 2004. Methods: According to the international criteria, the NCCP has managed and collected various standardized pathogens by 2009 ISO 9001 requirements, 345 species for 1,131 strains. Currently, NCCP has established the network among 8 unit banks, 3 of which are specialized banks for pathogens isolated clinically and controlled under KNIH, 2 of which are collaborative banks for special pathogens difficult to be collected or managed as tuberculosis and medical fungi, and 3 of which are regional banks for pathogens isolated from the patient’s clinical specimen by National University Hospital in Korea. NCCP has provided financial support as well as standard operation protocols (SOPs) for management of unit banks and established the network between central and unit banks. Conclusion: An informational network was constructed and is operated by Pathogen Information Management System (PIMS), and all information of pathogenic resources can be accessed through the web-site (http:==nccp.cdc.go.kr). This provides various information including antibiotic resistance, clinical data, biological character, etc, also linked information from the unit bank. NCCP wants to network internationally with similar biobanks about resource information and management systems. NIR 02.
Spanish National Biobank Network [BBMRI-ERIC.es]: A New Dimension in Biobank Collaborative Networking in Spain
M. Morente1, F. Luna-Crespo1 1
CNIO, Madrid, Spain
Background: The Spanish National Biobank Network (SpNBBN) is an initiative of the Spanish National Institute of Heath (ISCIII-Ministry of Science and Innovation), ordered and structured to function as a stable instrument of coordination between its various component institutes. Methods: The main mission focuses on developing a cooperative network of public service, made up of hospital biobanks and other related institutions:
To provide the Scientific Community access to quality sample collections and associated data through a cooperative structure of public service. To integrate existing initiatives related to biobanks and the use of human samples in biomedical research, creating an add value to the whole system To promote the creation of qualitatively varied collections, fitting current needs of researchers and those that can be foreseen for the future. To contribute to ensuring respect for the fundamental rights and freedoms of patients and donors in general, with special reference to the protection of the dignity and identity of the individuals. To promote technological innovation in biobanks. To assist in the development of the pan-European platform BBMRI, and promote the Spanish participation (BBMRIERIC.es).
Conclusion: Initially, the network is composed of 52 hospital biobanks and another 11 institutions with relevant biobanking
84
ABSTRACTS
activity, mainly as regional biobank network promoters, and the Spanish National DNA Bank, integrating a wide range of biobank and collections types including Pathology Department clinical collections, disease oriented collections and population biobanks, all of them in different formats (solid samples, serum and other blood derivatives, brain banks, DNA banks, etc.) NIR 03. AIDS Epidemic Studies Require Access to Multicenter Biorepository Programs for Comparative Data S. Silver1, E.A. Mesri2, A. Chadburn3, E. Cesarman4, B. Ashlock2, L.W. Ayers1, M.S. McGrath1 1
AIDS and Cancer Specimen Resource, Washington, DC; 2University of Miami Miller School of Medicine, Miami, FL; 3Northwestern University-Feinberg School of Medicine, Chicago, IL; 4Joan & Sanford I. Weill Medical College of Cornell University, New York, NY Background: Global HIV=AIDS complications reflect local anti-retroviral (ARV) therapy. While ARVs appear to control HIV replication, cancer continues to cause death and has emerged as the major cause of death within the developed world. AIDS-defining cancers such as Kaposi’s sarcoma (KS) and nonHodgkin’s lymphoma (NHL) are significantly reduced but nonAIDS defining cancers emerge earlier, occur more commonly than in the non-HIV population, and have overtaken the AIDSdefining cancers as major causes of death. The AIDS and Cancer Specimen Resource (ACSR), established by the National Cancer Institute (NCI) in 1994, contains an inventory of over 400,000 biospecimens from its three major regional biospecimen repositories (RBR), east coast, mid-region and west coast and characterizes the U.S. AIDS epidemic. The goal of this study was to determine if the three RBR biospecimens equally represent the AIDS epidemic in the United States. Methods: Large multi-RBR biospecimen collections were evaluated in the course of research performed by the ACSR and collaborative investigators: data on 11 different NHL associated biomarker immunophenotypes from 119 cases on an HIV AIDS diffuse large cell B cell lymphoma (DLBCL) tissue microarray (TMA) and >200 blood specimens from two of the RBRs for KSHV seroprevelance. Results: ACSR RBRs had similar distributions of DLBCL immunophenotypes and the KSHV seroprevalence in the non-KS patients from both the EC and WC collections was identical. Conclusion: This study suggests that the HIV-infected profile within the United States is homogeneous and without regional bias in the diseases. NIR 04. Simultaneous Query of Two Biobank Networks: BBS and CRIP Are Synchronized via Web Services D. Simeon-Dubach1, C. Schro¨der2, O. Gros2, R. Warth3, A. Perren4 1
Methods: Based on a cooperation agreement, BBS and CRIP have synchronized their users’ registration and log-in procedures, and mutually coupled their web-based interactive query tools by web service protocols operated through secure communication channels (HTTPS). Results: The coupling of user’s log-in and web-based interactive query tools allow for a single sign-on with both BBS’s and CRIP’s web sites and simultaneous search of both meta-biobanks without affecting their access rules, contractual framework, privacy regimes, workflow, and corporate design. Putting the principle of data sparing into practice, data is transferred only upon a user’s focused request. Background operation of web services conveniently enhances the users’ query efficiency. Conclusion: Coupling CRIP and BBS provides a model for networking meta-biobanks (‘‘hubs and spokes’’) without impairing their governance, regulatory framework, workflow, and infrastructure. This work was funded by grant 01EZ1021A from the German Federal Ministry for Education and Research (BMBF). NIR 05. CNIO Tumour Bank Unit and Spanish National Tumour Bank Network: 2006-2010 Achievements M. Morente1, L. Cereceda1, A. Maria-Jesu´s1 1
CNIO, Madrid, Spain
Background: The CNIO Tumour Bank Unit provides samples and associated data, as well as ethical and documentation support to CNIO Researchers mainly through the Spanish National Tumour Bank Network. This network was created in September 2000 and currently includes 25 institutions. The biobanks within these institutions are autonomous. The CNIO Tumour Bank maintains collaborations with other biobanks as a part of the Spanish National Biobank Network, and actively participates in research projects in collaboration with different CNIO groups and other external research groups. Main achievements of the 2006–2010 period:
2
Foundation biobank-suisse, Bern, Switzerland; Fraunhofer Institut fu¨r Biomedizinische Technik (IBMT), Potsdam-Golm, Berlin, Germany; 3Stiftung biobank-suisse, Bern, Bern, Switzerland; 4 University of Bern, Bern, Switzerland Background: Both biobank-suisse (BBS; www.biobank-suisse.ch) and the Central Research Infrastructure for molecular pathology (CRIP; www.crip.fraunhofer.de) are biobank networks or meta-biobanks displaying data on biospecimens stored at their partners’ hospitals and serving to acquire research projects for them.
As a Biological Resource Center, we made possible 233 research projects in the 2006–2010 period, most of them for multicenter cooperative groups, corresponding to 505 requests of tissue. The median impact factor of the 96 supported publications in this period was 6,355. We also gave sample and=or documental support to CNIO Molecular Diagnostic Unit (11.829 cases) and familiar cancer activities of the Human Cancer Genetics Program (454 cases), and directly participated in 29 collaborative projects and clinical trials (some of them still ongoing). The CNIO Tumour Bank Unit collaborates in training activities for undergraduate experts in health documentation and develops advisory activities for different emerging biobanks in Europe and Latin America. The Tumour Bank Unit is currently implementing new standards in biobanking according to the new Spanish legal framework for the use of human tissue samples in research. The Central Office of the CNIO TBNetwork was awarded with the ISO-9001:2000 Quality Certification in 2003, renewed in 2007.
NIR 06. Current Status of Biobanking in India U. Bora1, R. Tamuli1 1 Indian Institute Of Technology Guwahati, India, Guwahati, Assam, India
ABSTRACTS Background: India is a natural habitat to several thousand species of microbes, plants and animals that constitute about 8% of global biodiversity including 2.9% of the world’s threatened species. Therefore, India is recognized as one of the 12 megabiodiversity hotspot regions in the world. Among the ten ideas changing the world, listed in Time magazine in March 2009, biobanking is a vital one. Biobanking, an emerging field in India is nationally operated by central government and regionally managed by state governments. The public sector biobanks is comprised of 5 institutions, the National Bureau, gene banks, research institutes, hospitals and universities, which are involved in managing all kinds of biospecimens. Technological advances have made it feasible for India to establish Human DNA Bank in Lucknow as Asia’s first and world’s second Human DNA Bank for Human identification. Another unique type of biobanking found in India is the ‘‘Community Seed Bank’’, run and managed by local communities for themselves. Recently, some community seed banks have also been set up in partnership with government owned various plant breeding research institutes. Conclusion: Though the biobanking sector in India is quite diverse and vast, it lacks organization and coordination for a wider reach and impact. To ameliorate the various problems faced by the biobanking sector in India, currently an initiative has been projected by various institutes, universities and nongovernmental organizations to develop a connection amongst the biobanks for knowledge sharing, sustainable resource management, and a better outlook for future plans to bring forward biobanking in India.
85 1
Korea National Institute of Health, KCDC, Chungbuk, Republic of Korea Background: For the biotechnological research revival and diagnostic development of infectious diseases, we designed the Infectious Disease Biomarker Database (IDBD, http:==biomarker.cdc.go.kr) by web based platform on useful biological contents of biomarkers of pathogens for diagnosis, detection, protection, and characterization of infectious diseases. It supplies information of pathogens and biomarkers, which are the components for modeling and simulation of the infectious diseases and the biological processes. On the other hand, IDBD provides omics to information of biomarkers and the description of pathogens and diseases. It is a community annotation database utilizing collaborative Web 2.0 features and provides a comfortable user interface to enter and improve data on-line. It supports various types of data searches and the application tools to analyze sequence alignment, phylogenetic tree and structural characteristics of the potential and the validated biomarkers. Methods: At present IDBD integrates 1,826 16s rDNA sequence of the pathogens, 710 of biomarkers for the group with 11 diseases, 79 infectious diseases and 80 pathogens including bacterium, viruses, fungi and parasites. Researchers can use this web site as new information entry in the biotechnology field effectively. Conclusion: Contents in IDBD are freely accessible open to the general public. Also, we connect biomarker information with pathogenic resource of National Culture Collection for Pathogens (NCCP, http:==nccp.cdc.go.kr) to distribution service in Korea National Institute of Health (KNIH).
NIR 07. Korea Brassica Genome Resource Bank Y. Lim1 1
Chungnam National University, Daejeon, Republic of Korea
NIR 09.
Integrated Workflow for Digital Pathology in a Biospecimen Repository Environment
S. Abhange1, T. Barr1, A. Hobensack1, N. Ramirez1 Background: The purpose of establishing the Korea Brassica Genome Resource Bank is to maintain various genetic resources of the Brassicacea family including the Brassica rapa ssp. pekinensis (Chinese cabbage). These resources will be distributed on request internationally as well as domestically for research purpose. Moreover, the establishment and distribution of the genetic resources will help in strengthening the on-going research on Brassica genetics and genomics in Korea. 1) Distribution of Genetic Resources: Collection of genetic resources of various Brassica and related species with a wide range of traits, will be helpful in crop improvement. The genetic resource of wild species will play an important role for introducing new agronomically-important traits in the cultivated Brassica crops for improving their productivity, quality, and environment sustainability. Besides, mapping populations will be useful for construction of genetic maps, undertaking marker-assisted selection, and gene cloning. 2) Distribution of DNA Resources 3) Sub-goals of the research are as follows: 1. Development of integrated information systems of genetic resource; 2. Collection of genetic resources; 3. Long-term conservation of genetic resources; 4. Establishment of efficient distribution system; 5. Facilitating related studies; and 6. Supporting education and industrial application. NIR 08. Infectious Disease Biomarker Database (IDBD) K. Jung1, C. Yoo1, K. Lee1
1 The Research Institute at Nationwide Children’s Hospital, Columbus, OH
Background: The increasing demand for more expedient pathology review has led to the expansion of the field of Digital Pathology. The Biomedical Imaging Team (BIT) in the Biopathology Center (BPC), located at The Research Institute at Nationwide Children’s Hospital in Columbus, Ohio, has integrated digital pathology into its biorepository’s operations. The BPC currently serves as the biorepository for the Children’s Oncology Group and the Gynecologic Oncology Group as well as the pediatric division of the Cooperative Human Tissue Network and a Biospecimen Core Resource for The Cancer Genome Atlas (TCGA) project. This integration into banking operations has required the development of specialized applications to support the utilization of this technology. Methods: The BIT utilizes high-capacity scanners to generate high-quality whole slide images and uses its custom-built VIPER (Virtual Imaging for Pathology Education and Research) application to distribute images and QC review forms to reviewing pathologists. The images are uploaded to the Ohio Super Computer Center (OSC) where they are served to users in the United States and Canada. The OSC provides a reliable high performance computing and communications infrastructure and has allocated 50 terabytes of storage capacity to support digital pathology initiatives at the BPC. Results: The integration of digital pathology into BPC’s workflow has decreased pathology review turnaround times and eliminated shipping costs for many projects. Simplified logistical
86 operations have resulted in an overall increase in operational efficiency. Conclusion: This disruptive technology is allowing the BPC to overcome many of the disadvantages of traditional glass slide pathology review. NIR 10. Achievements of the Australian Prostate Cancer BioResource: First 5-Year Round of Funding 2004–2009 J. Clements1, G. Risbridger1, R. Sutherland1, W. Tilley1, D. Horsfall1 1
Australian Prostate Cancer BioResource, Kelvin Grove, Queensland, Australia Background: Funding for the Australian Prostate Cancer BioResource (APCB) network has been renewed by the NHMRC & PCFA for 2010–2014. This funding is to continue the prospective collection of tissue from men with early stage prostate cancer treated by radical surgery for another 5 years to allow 10 year outcome data to start to be accrued. Methods: Tissue is collected from daVinci robot-assisted laproscopic prostatectomy (RALP) as well as retropubic radical prostatectomy (RRP). Results: Over the last 5 years 2,894 participants have been recruited with accrual of 1560 (54%) fresh frozen prostate and 1,871 (65%) blood samples. Although collection and processing times can be different between RALP and RRP, histological examination and RNA extraction performed on representative cohorts showed no difference in tissue histology, RNA integrity or gene expression by quantitative RTPCR for several genes between the 2 procedures, thus allowing a larger pool of tissues for distribution. Over the last 3 years, 1,477 tissues have been distributed nationally leading to 6 publications to date. 336 samples from the Brisbane cohort have been used for genotyping in the PRACTICAL genome-wide association studies. Conclusion: At 5 years, the APCB has a collection of high quality prostate cancer tissues with associated blood samples and clinical and pathological data acquired at diagnosis and surgery. This collection has become an important bioresource for prostate cancer research nationally and internationally. With maturity and accrual of *5,500 men by 2014 with 5–8 year clinical follow up it will become an even more significant research resource. REPOSITORIES/PLANT/SEED REPOSITORIES PSR 01. Plant Biorepository Management in North East India – The Nature’s Biorepository S. Ghosh1, L. Rangan1, R. Tamuli1, N.C. Talukdar2, U. Bora1 1
Indian Institute of Technology Guwahati, India, Guwahati, Assam, India; 2Institute of Bioresources and Sustainable Development, Imphal, Manipur, India Background: North East region (87832’E to 97852’E latitude and 21834’N to 29850’N latitude) of India is a part of the Vavilovian center of origin for several cultivated important crop plants. Climate of the region ranges from Alpine to tropical, 85% of its landmass is mountainous and inhabited by 87 tribes with rich indigenous knowledge of plants. A preliminary survey showed that despite of richness of plant biodiversity, biobanking and biorepository management in the region has been largely in a state of infancy. Methods: The region houses more than 500 orchid species, 10% medicinal plants out of 5,000 angiosperms, 91 species of
ABSTRACTS Zingiberaceae with 22 genera and 151 types of citrus. The ethnic community of the hills maintains a unique set of medicinal plants and indigenous health system. To check the genetic erosion of these rich gene pools, on farm conservation practices have been implemented in the hilly regions. Few germplasm banks of orchids and two research centers for orchids as well as citrus are nascent but vital initiative for the management of biorepository. Conclusion: Several rice research centers maintain a set of more than 50 percent of estimated 10,000 rice landraces of the region and is a spearheading effort towards plant biorepository management. A recent joint initiative between the Indian Institute of Technology Guwahati and Institute of Bioresources and Sustainable Development, Imphal is expected to strengthen plant biobanking with equitable sharing of potential resources and expertise in efficient management of plant bioresources and develop strategy to advance plant biorepositories in the region. REPOSITORY OPERATIONS/BIOSPECIMEN SCIENCE BSS 01.
High-Throughput DNA Extraction and Normalization from Saliva Results in High-Quality DNA for Genotyping and Telomere Analysis
S.Q. Miles1, K.A. Lapham2, S.A. Connell1, C. Aquino1, S. Rowell1, C. Schaefer1 1
Kaiser Permanente Northern California, Oakland, CA; 2University California San Francisco, San Francisco, CA Background: Kaiser Permanente’s Research Program on Genes, Environment, and Health is using saliva as a source of DNA for a NIH-funded project that requires genome-wide genotyping and measurement of telomere lengths on DNA samples from 100,000 individuals; the resulting data will be merged with clinical, survey, and environmental information on the same individuals to create a new research database. DNA was extracted and normalized from more than 120,000 biospecimens in 15 months. To our knowledge, this is one of the largest human DNA extraction projects ever attempted, and the largest to extract DNA from saliva. Methods: Saliva was collected using OrageneÒ kits and was stored at room temperature for 0-3 years prior to extraction. Specimens were weighed and visually inspected prior to DNA extraction with a magnetic bead kit. DNA samples were quantified by PicoGreenÒ and normalized to 30ng=uL for telomere length measurement and 10ng=uL for genotyping assays. Results: 2.5% of saliva biospecimens were excluded from extraction due to particulate matter or low volume. The average DNA yield was 4.86 micrograms per 0.5mL saliva. DNA purity (A(260=280)) ranged from 1.5-1.9. Genotyping results on the first 58,000 samples show a sample success rate of >93%. Preliminary telomere length measurement results show a CV of 24 hours), lowered RIN values. Histology predicted the RIN score for most organs, but not in the pancreas and small intestine. The heart and lung tissue had the highest RIN values (7.1 and 5.8 average, respectively) across the four cases. Conclusion: RIN values in most tissues, except the GI tract, was highly correlated with the clinical medical history and agonal state, and was not influenced by the PMI. Quick refrigeration of the body after death may preserve both post mortem histology and RIN values. BSS 06. Stability of Extracted RNA at Various Storage Temperatures and through Multiple Freeze-Thaw Cycles J. Wu1, L. Kim1, C. Huang1, B. Anekella1 1
SeraCare Life Sciences, Inc., Gaithersburg, MD
Background: RNA degradation during storage makes samples unusable for assays including reverse transcription, in vitro translation, differential display, expression-array and expressionchip analysis. RNA degradation during storage results primarily from base hydrolysis of RNA under low pH conditions or divalent cation catalysis. The effects of different storage temperatures and freeze-thaw regimens on RNA stability during storage are investigated. Methods: Tissue sample RNA was extracted using the Qiagen RNeasy Kit. RNA concentration was adjusted to 300 lg=mL using ultra-pure water. RNA was aliquoted into single-use aliquots and stored at room temperature (RT), 48C, or 208C. Samples were tested after 0, 1, 2, 3, 7, 14, and 28 days of storage. Testing, in duplicate, included concentration, ribosomal RNA ratio (28S:18S), and RIN number. Similarly, a subset of samples were placed at either 808C or 208C and subjected to ten freeze-thaw cycles. Results: RNA stored at RT was stable through 7 days, declining in all three test parameters at 14 and 28 days. No declines in RNA concentration, rRNA ratio, or RIN number were observed for RNA stored at 48C or 208C. RNA cycled between 208C or 808C and RT for 10 freeze-thaw cycles had no concentration or integrity decline. Conclusion: RNA stored in an appropriate buffer is resistant to degradation under sub-optimal conditions encountered during accidental mishandling or shipping delays. Frozen RNA samples can be thawed multiple times without compromising quality. For short-term studies, RNA can be stored at 48C or 208C. RNA at RT showed degradation after 7 days. BSS 07. Genome-Wide Germline Genotypes from Normal Tissue Stored in FFPE Samples L.A. Cannon-Albright1, K.G. Cooper2, A. Georgelas2, P.S. Bernard2 1 University of Utah, Salt Lake City, UT; 2Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
Background: Although large collections of formalin fixed paraffin embedded (FFPE) samples exist, sometimes represent-
ABSTRACTS ing decades of stored samples, they have not typically been considered as a useful resource for studies requiring genomewide genotyping of normal cells. Normal tissue from such samples, however, would be extremely valuable for generation of genotype data for individuals who cannot otherwise provide a DNA sample. Methods: In order to determine the value of using FFPE tissue blocks as a source of normal ‘‘germline’’ DNA for genotyping experiments, we assessed the quality and yield of genome wide (GW) genotyping data generated from archived FFPE tissue aged 18–41 years. Grossly uninvolved regions of tissue from prostate cancer cases were identified and DNA was extracted from corresponding punches in the original FFPE tissue block. GW genotyping was performed using the Illumina 610Q platform. Results: The genotyping call rates for the FFPE samples ranged from 0.873 to 0.989. Additionally, we observed a range of 0.993-0.9998 reproducibility in genotyping calls when we compared results from DNA isolated from whole blood versus normal tissue from FFPE. Conclusion: Our results indicate that DNA extracted from normal tissue in FFPE (even decades old) provides excellent quality GW genotyping data. Overall, this study provides an innovative solution to procuring GW genotyping data for informative individuals not otherwise available for sampling by using stored FFPE blocks. BSS 08.
Software for Generation of Multigene Expression Signature Maps at the Protein Level from Digitized Immunohistochemistry Slides
S. Schmechel1, S. Dankbar1, J. Henriksen1, A. Rizzardi1, N. Rosener1, J. Koopmeiners1, G. Metzger1 1
University of Minnesota, Minneapolis, MN
Background: Biorepositories provide essential specimens for discovery and validation of diagnostic, prognostic and predictive biomarkers. Among validation methods, immunohistochemistry (IHC) is optimal for gene expression profiling (GEP) at the protein level in routine clinical samples. However, analytical methods to perform GEP using standard IHC are lacking. Methods: We developed software that interacts with a wholeslide imaging platform to digitally align slide images to an annotated H&E-stained reference slide, quantify IHC stains in annotated areas, and compute a weighted sum of n-gene expression values. The software provides a tiled display of GEP data (termed a signature map) to reveal heterogeneity within disease areas. For purposes of illustrating software features, we produced a four-gene signature map (representing MKI67, ENO2, CD34 and ACPP gene products) on prostate cancer tissue. Results: Mean aggressiveness signature score (SS) increased with grade from 1.2 for 3 þ 3 tumor areas, indicating nonaggressiveness (negative value due to low expression of aggressiveness genes MKI67, ENO2, and CD34, each with a positively-signed weighting factor, and high expression of nonaggressiveness gene ACPP, with negatively-signed factor), to a mean of 2.1 and 6.9 for 3 þ 4 and 4 þ 3 areas, respectively. Differences in the standard deviation of SS were observed by grade (3 þ 3 SD ¼ 4.71, 3 þ 4 SD ¼ 5.81, 4 þ 3 SD ¼ 4.14), suggesting that the standard deviation, as well as other measures of heterogeneity, may also be useful for predicting aggressiveness. Conclusion: The IHC signature map approach may have broad applicability for validating multigene diagnostic, prognostic and predictive disease classifiers using routine clinical specimens.
ABSTRACTS BSS 09. Effect of High Temperature Thawing on PTEN Enzyme in Human Uterine Tissue T.J. Kokkat1, L.C. Lovecchio1, D. McGarvey1, V. LiVolsi1 1 Cooperative Human Tissue Network (ED), University of Pennsylvania, Philadelphia, PA
Background: Degradation of proteins during the preparation and storage of tissue lysates is an ongoing challenge in proteomic research. During lysate preparation, enzymes and their substrates are brought into closer proximity thereby increasing the chance of enzymatic modification of the substrate (e.g. dephosphorylation by phosphatases). Traditionally, enzymatic activity is decreased through the use of protease and phosphatase inhibitors. However, the introduction of these exogenous inhibitors might interfere with downstream analysis. One demonstrated way to inactivate enzymes without the use of chemical inhibitors is to use heat during thawing. In earlier studies we demonstrated the effectiveness of high temperatures in reducing tyrosine phosphatase activity. In this study, we investigated the inactivation of PTEN enzyme in uterine smooth muscle tissue by comparing high heat thawing with more traditional methods of thawing. Methods: Frozen uterine smooth muscle samples were thawed in the oven (378C), on ice (48C), or at 958C using the heat Stabilizor T1 from Denator AB. Frozen tissues were used as controls. Tissue lysates were prepared without enzyme inhibitors and PTEN Phosphatase activity was assayed using the pNPP Protein Phosphatase Assay kit. Results: Our results indicate that in comparison to frozen controls and tissues thawed at 378C and 48C, specimens thawed using heat stabilization (958C) had a significant reduction in PTEN activity. Conclusion: The use of high temperatures is optimum for thawing tissue by decreasing the amount of enzymatic activity, thereby better preserving the proteome. BSS 10. A Survey of Tissue Specimen Collection Techniques: Impact on Biomarker Data Quality A.C. Allen1, J.A. Sutton1, J.M. Martin1, N.L. Todaro1, R.V. Mulpuri1, J.M. Otto1 1
Catholic Health Initiatives, Towson, MD
Background: Prognostic and diagnostic biomarker development is currently hindered by access to high quality, clinically annotated biospecimens. To address this limiting factor for translational research, we established a state-of-the-art biorepository facility to procure clinically annotated biospecimens from remote network locations, and isolate high quality nucleic acids for long-term storage and molecular analysis. We describe here a long-term project comparing methods of sample collection and storage, including stabilization media, on the quality of RNA for genomics research. Methods: Tissues known for the presence of high and low RNAses (kidney=liver and colon=lung, respectively) were collected as FFPE, fresh, frozen in Liquid Nitrogen (LN2), frozen with stabilization media (RNAlater), and LN2 frozen tissues post-treated with stabilization media (RNAice). Total RNA isolated from all tissues was assessed for quality, and analyzed using expression arrays. Results: At zero time point, no major differences in RNA quantity were observed due to collection and storage treatments.
89 Further analysis of RNA quality with QC arrays revealed intact RNA free of inhibitors of reverse transcription and PCR amplification, genomic and general DNA contamination. Hierarchical clustering of Oncogene and Tumor Suppressor genes revealed three distinct groups; 1) Fresh, LN2 and RNAice, 2) RNAlater and 3) FFPE suggesting that RNA stabilization treatments may influence gene expression patterns. Conclusion: Currently, experiments are underway to assess the RNA quality on global gene expression patterns and establish a baseline, to be compared to the RNA quality and gene expression patterns at 6, 12 and 24 month post-collection. BSS 11. Genomic DNA as a Quality Indicator for Whole Blood Storage J. Wu1, J. Cunanan1, T. Kulatunga1, C. Huang1, B. Anekella1 1
SeraCare Life Sciences, Inc., Gaithersburg, MD
Background: Whole blood is frequently shipped and stored for clinical trials, R&D efforts, and longitudinal studies. Genomic DNA is then extracted for various molecular biology applications including genotyping, sequencing, and PCR amplification. This study compares yield and quality of DNA extracted from whole blood exposed to varying stress conditions. Methods: Whole blood was aliquoted and incubated at 48C for up to two weeks to determine acceptable 48C holding time. Aliquots were also subjected to three freeze-thaw cycles. White blood cells were counted and DNA was extracted using the Qiagen=Gentra Autopure LS. Extracted DNA was quantitated using the Spectramax spectrophotometer to determine yield, and quality assessed by genomic gel electrophoresis and PCR to the b-globin locus. Results: Storage of whole blood at 48C for 7 days had no effect on extracted DNA quality and quantity. Statistically significant declines in DNA yield, *25% less DNA, occurred at 14 days; however, the genomic DNA appeared intact by gel electrophoresis and gave acceptable PCR results. In contrast, freeze-thaw cycles dramatically affected DNA yield and quality. One freezethaw cycle reduced genomic DNA yield by half, two cycles produced extremely low DNA yields with variable A260=280 ratios; the DNA showed visible smearing by gel electrophoresis, with variable PCR results. Conclusion: Whole blood can be safely stored or shipped at 48C for up to 7 days without significant effects on yield or quality of extracted genomic DNA. Freeze-thaws of whole blood significantly affect the extracted DNA quality and quantity. BSS 12. High-Throughput Extraction of Compromised Whole Blood Samples for Genetic Analysis: Implementation of the Chemagic STAR in a Genetics Repository R. Gaglione1, M. DiCola1, A. Lopez2, C. Piccirillo3, A. Bonk3, A. Brooks1 1
Rutgers University, Piscataway, NJ; 2Chemagen USA, Worcester, MA; 3Hamilton Robotics, Reno, NV
Background: Genetic analysis continues to evolve with the utilization of novel technological approaches that require specific sources of genomic DNA. DNA from whole blood is becoming more important in the biomedical research environment with the introduction of epigenetic analyses. To this end, all whole blood sources of DNA, including compromised samples and archived
90 resources, are critical for analysis. In addition, existing large collections (based on retrospective sampling) require a robust high-throughput approach to maximize the yield of DNA from each sample while retaining the highest quality nucleic acid. Methods: The unique challenges of extracting DNA from various volumes of compromised and frozen whole blood samples require extraction chemistries and automated solutions that ensure a high level of success with these precious samples. This presentation describes the protocol development and implementation of the chemagic STAR for frozen whole blood samples. The integration of chemagen’s bead-based chemistry (with modifications for sample source and volume) with the Hamilton STAR creates a robust workflow that maximizes the yield and quality of compromised blood samples, provides a fully integrated ‘‘walk away’’ workflow that catalogues all DNA stocks, and prepares samples for analytical and functional quality control. This platform is tunable from 1ml to 10ml in single extractions providing the flexibility needed for large biorepository projects where samples are processed across many different collections. Conclusion: Both analytical and functional analyses are performed on all DNA samples and are described in this presentation to document the quality and downstream utility of this extraction approach. BSS 13. Proteomic Analyses of Colorectal Tumors by Electrospray Ionization (LC-ESI) and Split Sample Strategy: Effects of Formalin Fixation and Extraction Methods on Peptide Identification G. Hostetter1, M. Syring1, A. Watanabe1, E. Suh1, A. Polpitya1, L. Nagore1, S. Jewell2, J. Trent1, K. Petritis1, C. Selinsky1 1
Translational Genomics Research Institute, Phoenix, AZ; 2Van Andel Institute, Grand Rapids, MI Background: We have extended high performance discoverybased assays to DNA harvests from formalin-fixed paraffinembedded (FFPE) tissue collections. Proteomic surveys of solid tumors present challenges in accurate measures of cross-linked and degraded proteins and peptides. Several studies have shown good spectral correlation with fresh frozen (FF) and FFPE tissue samples but are of limited spectra. Methods: Six colorectal cancer specimens, disparate phenotype by genomic instability, were selected for this multi-tiered comparative study. FFPE scrape macrodissected samples were extracted by Qproteome (Qiagen, Inc) and Liquid Tissue (Expression Pathology, Inc). FF split samples were visualized by 2 ink QC method and histological tumor estimate or obtained by LCM method to include protease inhibitors. FF extractions were performed by Invitrogen kit and by Petritis lab method. A total of 24 protein preparations were analyzed by tandem LC-MS by Orbitrap electrospray ionization (ThermoShandon,Inc). Results: Tumor content was estimated at 30–60% for scrape macrodissected (FFPE) and FF chipped samples. LCM harvests were >95% tumor and 12,000 to 15,000 cells collected. FF & FFPE aliquots showed similar yield, but much sharper bands in FF gels. Slight variance in the peptides was detected in FF and much larger variance in FFPE. Conclusion: Discovery-based proteomics in FF preserved solid tumors is highly informative, but requires detailed sample preparation. FFPE samples with high SDS (Qprotoeme kit) may have limited tryptic digest. Heating of the FFPE sample appears to be critical for efficient protein extraction but could further degrade proteins. Our results indicate limited utility for FFPE samples in whole proteome analyses.
ABSTRACTS BSS 14.
DNA Extraction from Frozen Serum Samples: An Automated Approach for Genetic Analysis Utilizing Qiasymphony Purification and Repli-G Whole Genome Amplification
T. Giesler1, R. Gaglione1, D. D’Ambrosia1, J. Qin2, D. Kobi2, A. Brooks1 1
Rutgers University, Piscataway, NJ; 2Qiagen Inc., Germantown, MD
Background: Tremendous resources are used for the collection of clinical samples in research trials worldwide. Occasionally the analytical criteria for some studies are not well defined based on fiscal and technological uncertainty at the time of project initiation. To this end, there are large numbers of samples stored from various clinical protocols which are currently not considered for mainstream analyses. One example of this is serum and plasma samples which are typically stored for specific analyte interrogation where no other molecular components were collected for additional analyses. Methods: This presentation describes the use of serum (and plasma) derived from whole blood for DNA based genetic and genomic analyses. Given the low quantity and variable quality of this DNA that is mostly cell free, the method of extraction and validation of nucleic acid following processing is of paramount importance. We will describe a fully automated, high throughput, extraction and amplification workflow for these precious clinical isolates. The details of the protocol and QIAsymphony implementation will be discussed specifically in the context of a biorepository setting. Additionally, every nucleic acid sample is subjected to Repli-g amplification in an automated process to maximize the utility of these biological resources for future analyses. Conclusion: The technical issues addressed in these protein rich, cell free fractions include but are not limited to: shearing and nicking of gDNA, clotting of samples during the extraction process, low molecular weight DNA retention, and variable amounts of gDNA yields per sample. REPOSITORY OPERATIONS/CRYOGENICS AND CELL PRESERVATION CCP 01. The Biopreservation Core Resource (BioCoR): A Resource Based on the Science of Biospecimen Preservation A. Hubel1, A. Aksan1, A. Skubitz1 1
University of Minnesota, Minneapolis, MN
The mission of the Biopreservation Core Resource (BioCoR), located at the University of Minnesota, is to advance the science, technology and practice of preservation. BioCoR is not a biorepository=biobank but consists of three distinct resources. The first component consists of a research resource whereby new methods of preserving biospecimens and new technologies to improve biospecimen processing are developed. BioCoR faculty members are actively involved in the development of new methods of preservation, understanding molecular mechanisms of damage, and the development of protocols for specific biospecimens. Secondly, BioCoR has an education resource for educating individuals and institutions on biopreservation. BioCoR offers an annual short course which covers topics such as the scientific basis for preservation, different preservation techniques, facility design, protocol development, as well as quality and regulatory issues in biopreservation. The course is offered on the web in addition to in-class participation. In early 2011, BioCoR faculty provided a
ABSTRACTS webinar entitled, ‘‘Quality in Biopreservation’’ which was endorsed by ISBER and attended by over 120 people. BioCoR’s third component is to act as a service resource for those who need assistance in developing biopreservation protocols for specific biospecimens, evaluating existing protocols, and providing literature summaries of the scientific knowledge related to the preservation of specific biospecimens. This third component of BioCoR is especially important since biobanks typically do not have the resources or expertise to develop new protocols and methods of preservation. In summary, BioCoR fills a niche in the field of biobanking that biobanks alone do not serve. CCP 02. Cryogenic Tracking and Monitoring (bluechiipÔ) For Hematopoietic Progenitor Cell Biostorage: Comparison of Manual and Automated Technologies J. Chaffey1, P. Gambell2, A. Mouminoglu2, M. Miljanic1, H. Prince2, L. Miranda3 Bluechiip Ltd, Scoresby, Victoria, Australia; 2Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia; 3Biobusiness Consulting Inc, Lowell, MA
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Background: Cryopreservation of hematopoietic progenitor cell (HPCs) at 1508C for later use requires HPCs to be stored for several weeks to many years. To ensure quality preservation and interpretation of cellular integrity, HPC material must be appropriately identified, stored, monitored and tracked. Methods: The MEMS tracking device was attached to five medium sized Baxter cryocyte cryopreservation bags containing saline. The aim of the pilot trial was to assess the ability of MEMS technology to consistently measure cryogenic temperature and compare the MEMS tracking capabilities to current manual methods. The on-site trial commenced with identification and initial temperature measurement of the bags. The bags were then transferred to cryogenic storage where they underwent freezethaw cycles. Results: Tags on all bags at both room temperature and 1508C were successfully verified with no failed reads. Conclusion: The MEMS tracking technology demonstrated accurate readings for tracking temperature at 1508C. The MEMS technology appears to offer consistent improvements in decreased tracking labor time over manual methods. Secondly, implementation of the MEMS technology reduced the propensity for damage to biostorage containers and handlers alike. Further investigations with larger sample sizes are warranted to investigate application of the MEMS technology for biobanking cryopreservation, in particular reduction of freeze thaw cycles. CCP 03. Preserving Functionality and Differentiation of Frozen Peripheral Blood Cell Subsets for Repeatable and Large Scale Immunological Studies T. Di Pucchio1, C. Glover1, B. Anekella1
91 vation, processing, and media protocols to isolate and maintain functionality and differentiation in cryopreserved PBMC subsets. Methods: PBMC were collected by leukapheresis; purified cell subsets were isolated using RoboSep Stem Cell Technology. After purification, cells were resuspended in freezing media, frozen in a rate-controlled freezer, and stored in vapor phase liquid nitrogen. Testing included post-thaw cell recovery counts, viability and purity assessments. Fresh and frozen PBMC and lymphocyte cell subsets were tested for proliferation and IFN-g production. Fresh versus cryopreserved monocytes were tested for differentiation into dendritic cells. Results: Frozen PBMC, purified monocytes, and T cell subsets all showed viability greater than 85%. Furthermore, frozen PBMC and purified CD3, CD4, and CD8 T cell subsets maintain a similar ability to proliferate and produce IFN-g in response to specific peptide antigen stimulation when compared to fresh cell subsets. Notably, fresh and frozen purified monocytes were able to differentiate into phenotypic and functional dendritic cells with the capability to stimulate allo-CD3 proliferation. Conclusion: A combination of upstream and downstream handling conditions, standardized cryopreservation protocols and optimized freezing medium allow cryopreservation of PBMC and cell subset populations and preservation of their functionality capabilities. CCP 04. The Integrity Study: Measuring the Impact of Sample Preparation Techniques and Storage Temperatures on the Integrity Of DNA C. Michael1 1
BioStorage Technologies, Indianapolis, IN
Background: To outline the design of a 24-month longitudinal study that analyzes the impact of storage practice methods in regards to the long-term yield integrity of nucleic acids. The poster will compare the use of various aliquoting schema and storage temperatures and highlight the benefits via an end report employing a failure mode and effects analysis. Methods: The study analyzes the various storage methods of nucleic acids when comparing extraction yields on fresh sample, frozen pre-extracted samples, and extracted nucleic acids which require freeze=thaw cycles for processing. Various storage temperatures and aliquoting strategies will be evaluated over a 24month period subsequent to a single patient collection event. Results: The poster will outline study design and discuss the data to be reported. Various methods and procedures to capture and store samples for future research purposes will be discussed and the plan for measuring the impact of preparation method and temperature on nucleic acid sample integrity will be outlined. Conclusion: During drug development, clinical trial samples must be securely managed and properly stored to support prospective or retrospective nucleic acid analysis. The goal of the INTEGRITY study is to determine the best method for preparing samples and the best temperature to store samples for future research.
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CCP 05. Cryopreservation of Cell Lines in the National Institute of Hygiene ‘‘Rafael Rangel’’
Background: Peripheral blood mononuclear cells (PBMC) are used for immunological monitoring in clinical studies, as primary cells in basic research, and as infection models. Handling and preservation methodologies enable longitudinal studies across multiple sites with greater consistency across PBMC lots. In an ongoing effort, we have further extended our cryopreser-
A.C. Oyarzabal1
SeraCare Life Sciences, Inc., Gaithersburg, MD
1
National Institute of Hygiene, Caracas, Dtto. Capital, Venezuela
Background: The Cell Culture Department of the National Institute of Hygiene "Rafael Rangel" is responsible to produce,
92 preserve, manage, and maintain 15 cell lines from different sources such as hamster kidney, mosquito larva, human laryngeal carcinoma, dog kidney, rabbit kidney, green monkey kidney, and others, which are used as biological substrate for viral diagnosis, investigation and research, viral vaccines production, and biological products control. Methods: In response to the needs of providing cell lines, the main objective is to give response of the needs of providing cell lines, the main objective is the preservation of strains without morphological, physiological, and genetic changes. Therefore, the Cell Culture Department maintains and stores cell lines from certified institutions like the American Type Culture Collection (ATCC) and the Center of Disease Control and Prevention (CDC), using freezing medium with 15–20% Fetal Bovine Serum (FBS) and Dimethyl Sulfoxide (DMSO) as cryoprotective agent. The freezing method is with a controlled-rate of freezer that decreases the temperature 18C per minute. The cell lines are amplified to obtain a sufficient cell suspension to prepare the master and working banks to cover the needs of the Department. To ensure that they are free of contaminants, sterility controls are performed to detect bacteria, fungi, and mycoplasma. Conclusion: Conservation of the proper cell lines conservation is important to respond the needs of the users, ensuring appropriate quality certification of the cell lines. CCP 06. Tissue Cryopreservation: Long Term Storage of Tissue Samples in Liquid Nitrogen K. Sabai1, I. Cheong1, S. Lok1, S. Tan1 1
Singapore Health Services Pte Ltd, Singapore, Singapore
Background: Our repository has a collection of frozen gastric cancer with matched normal control tissues dating back to more than a decade ago. Methods: The samples have been snap frozen and stored in liquid nitrogen (vapor phase). In this study, we set out to determine if the quality of nucleic acids in 2 groups of matched gastric samples have altered significantly during long-term storage. Group A (n ¼ 32) consists of normal and tumor tissues harvested in 2010 whilst Group B (n ¼ 24) comprises samples that were harvested between 1997-98. Nucleic acid concentration and purity are assessed spectrophotometrically based on A260=280 ratio and gel electrophoresis is performed to determine integrity of DNA and RNA. Results: There is no significant difference in the yield of RNA (p ¼ 0.1748) or DNA (p ¼ 0.3840) from samples in Groups A and B. Similarly, the average A260=280 ratio for RNA in Groups A & B are comparable at 2.05 þ 0.075 and 2.07 þ 0.06 respectively. For DNA, the average readings are 1.88 þ 0.11 for Group A and 1.81 þ 0.15 for Group B. Based on the presence of distinct 28S and 18S rRNA bands, gel analysis shows intact RNA in 50% of samples in Group A and 37.4% in Group B. DNA integrity is good with all samples showing a band size of over 12kb for both groups. Conclusion: Our preliminary data indicates no significant difference in the yield of nucleic acids with prolonged storage. Likewise, the quality of DNA is not affected, although RNA integrity appears to be poorer in older samples. REPOSITORY OPERATIONS/DISASTER RECOVERY DR 01. Disaster Recovery: An Off-Site Expansion of Biorepository Operations L.C. Monovich1
ABSTRACTS 1
The Research Institute at Nationwide Children’s Hospital, Columbus, OH Background: The Biopathology Center, biorepository for two NCI Cooperative Groups, receives tens of millions of dollars annually from the NIH to conduct scientifically-driven clinicallyrelevant oncology trials at 500 institutions across the United States. These highly successful programs have vastly improved quality of life and survival of cancer patients and collected invaluable research specimens to allow for decades of high quality medical research. The 20 years worth of biospecimens are the tangible product of hundreds of millions of federal dollars spent during this time. Methods: The satellite biorepository was constructed to not only allow for growth at the existing site, but to provide redundant storage of biospecimens. To preserve at least a portion of each biospecimen in our repository, we have built a facility geographically separate from the Research Institute campus. Unless the specimen has insufficient material, duplicate aliquots will be sent to the secondary site as insurance against natural disasters, criminal activity, or other catastrophic events. By storing a piece of each tumor at two sites, the risk of completely losing a specimen is greatly reduced. Results: A build-out of 4,400 square feet of shelled space offsite to accommodate two years of projected growth with the ability to expand into 15,000 additional square feet to accommodate ten years of projected growth. Conclusion: The Biopathology Center has created a redundant, satellite biorepository to allow for storage of biospecimens in separate locations, each with backup power and 24 hour environmental monitoring. This will reduce the risk of catastrophic loss of specimens. REPOSITORY OPERATIONS/‘‘GREEN’’ REPOSITORY SOLUTIONS GRS 01. Dry Storage of Biospecimens for an East Asian Glioma Genome Wide Association Study (GWAS) L. Nordstrom1, G. Hostetter 1, S. Wilkinson2, R. Muller 2, J. Muller-Cohn2, A. Watanabe1, M. Syring1, W. McDonough1, M. Berens1 1
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Translational Genomics Research Institute (TGen), Phoenix, AZ; Biomatrica, San Diego, CA
Background: An international consortium was formed to collect biospecimens in East Asia from 4,000 glioma and 4,000 control participants to identify genetic variants associated with glioma risk. The study will collect biospecimens supportive of post-GWAS experiments to identify how these genetic variants affect tumor biology. A pilot study was initiated at six sites in four Asian countries to demonstrate performance of biospecimen collection, preservation, and shipment to the Translational Genomics Research Institute (TGen) or a collaborating Chinese laboratory. Methods: Blood from 10 glioma cases and 10 controls at each site is stabilized (Biomatrica’s DNA stable blood) then shipped at ambient temperature. Glioma tissue samples are split for flash freeze (-808C) or stored at ambient temperature (Biomatrica’s DNA guard tissue). Biospecimens are shipped to TGen (USA) or the Chinese lab for quality control assays. A cost analysis of shipping and storage costs for frozen versus ambient temperature biospecimen preservation is in process. Results: Quality control of biospecimens will be presented, including quality and yield of DNA extracted from blood and
ABSTRACTS tumor samples and H&E analysis of tumor samples. A savings of US$13,330 was estimated for shipping all samples at ambient temperature, while an additional US$10,000 is projected to be saved in storage costs. Conclusion: It is our expectation that the use of dry storage products for blood and glioma tissue preservation will significantly decrease the cost of biospecimen collection and processing, without a loss of analyte quality. Ambient stabilization of biospecimens for research drastically reduces the risk of failed repository responsibilities. GRS 02. Room Temperature Preservation of RNA Derived from Clinical Samples W. Mojica1 1
93 tected from the atmosphere in airtight, laser sealed stainless steel containers. Apparent degradation rates are measured by determining the average fragment size by gel electrophoresis. Results: Accelerated aging kinetics show some differences among the degradation rates of the samples but there is no apparent correlation between the degradation rates and either the DNA origin or its extraction procedure. Most importantly, a heatsimulated 100 year storage period (simulation conditions being determined from Arrhenius plots) does not lead to any detectable degradation of the samples. Contamination nature, degree, and effects on stability will be further investigated. Conclusion: Regardless their origin and their procedure of extraction, routinely purified DNA samples can be reliably stored at room temperature when efficiently protected from air. Therefore this "green" procedure does not compromise the quality of the stored samples.
University at Buffalo, Buffalo, NY
Background: Preservation of RNA at room temperature (RT) offers several advantages from traditional frozen specimens in terms of cost, space and energy. A commercial product (GenTegra) has recently become available that purports to enable RT stabilization of RNA samples in a dessicated matrix. An assessment of the capabilities of this product with regards to RNA integrity of clinical specimens would be of benefit for all biobanks. Methods: 25 tissue specimens were procured at the time of resection. For every case, the time between receipt and freezing of the tissue specimen was
ABSTRACTS
The International Society of Biological and Environmental Repositories present Abstracts from their Annual Meeting
Impact and Public Benefits of Biorepositories May 15–18, 2011 Arlington, Virginia The abstracts that follow demonstrate the broad range of timely issues addressed in the contributed oral and poster presentations at ISBER’s 12th Annual meeting.
ISBER Abstracts HOT TOPICS/OTHER HOT OPERATIONS TOPICS HT 01.
BreastScreen Victoria (BSV) is part of the national breast cancer screening program in Australia and a key collaborator in lifepool. Using established BSV contact protocols, women are invited to consider joining lifepool. Primary aim: To recruit participants while ensuring no negative impact on screening participation rates. Secondary aim: To determine the recruitment protocol maximizing participation in lifepool. Methods: lifepool, in partnership with the BSV Consumer Advisory Committee and Health Issues Centre, conducted a series of consultation workshops to test participant information and consent forms (PICF) and recruitment protocols. Potential impact on participation in the BSV program and clarity of information were explored with women from urban and regional communities. Amended protocols were tested in pilot recruitment projects. The lifepool project undertakes to inform individual participants about research data of significance to their health, after expert review. The challenge of providing accurate risk disclosure to a healthy population is being addressed with input from a range of legal, insurance and health ethics experts. Results and Conclusion:
Cost Recovery—Researcher Expectations versus Funding Agency Requirements
J. Edgar1, A. Thompson1 1
Victorian Cancer Biobank, Carlton, Victoria, Australia
Background: In 2006 the Victorian Government funded the establishment of the Victorian Cancer Biobank (VCB) Consortium from four pre-existing tissue banks. As a requirement of the funding, the Consortium agreed to implement a cost recovery schedule to subsidize operational costs, by cost recovering approximately 10% of the grant funding in the first 3 years. Methods: A modular format, used by other international biobanks, was adapted to suit our operations and fees. The fees were determined by considering the pre-consortium fees, researcher’s expectations and the operational cost incurred. A two-tier model was proposed, charging a higher rate for the commercial sector to subsidize the cost of collecting and supplying biospecimens to the academic sector. Results: The Consortium Committee approved the proposed cost recovery schedule in 2007. From this time the income from cost recovery has increased steadily. However, as 90% of the cost recovery income is generated from biospecimens provided to the academic sector, cost recovery income for 2010 was only 8% of the funding received. Conclusion: The implementation of a cost recovery schedule did not meet the expectations of all researchers as some previously paid only minimal fees. However, over time, most academic researchers have accepted the need to cost recover. The cost recovery income is nearing the target agreed to in the Business Plan. The VCB is now increasing collaboration with the industry=commercial sector, which should increase the income and exceed the target. This will therefore reduce the dependency on government funding.
No significant impact on screening participation Uptake of invitation varies significantly with timing of invitation Bullet point delivery of key consent elements, backed up by further detail, improves clarity and is more acceptable to participants Consumer input during protocol development is vital to this collaboration
HOT TOPICS/OTHER HOT REPOSITORY TOPICS HT 03. Novartis Translational Research Initiative: Taking Biobanking to Early Pharmaceutical Research D. Mikhailov1
HT 02.
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lifepool: A Collaboration between Women and Researchers
Novartis, Cambridge, MA
Background: Use of high quality, well-annotated human biological material will improve understanding of disease mechanisms, validate biomarkers, and identify novel drug targets. It is also a way to de-risk drug discovery projects by testing early hypotheses in relevant disease context. The Novartis Translational Research Initiative was recently launched to facilitate access to strategically valuable human biosamples, to support early research projects and translational research studies. Methods: Achieving this objective will require a multi-year approach to build capacity and establish processes on specifics of working with human samples. This strategic initiative provides framework and answers to questions such as:
L. Devereux1, I. Campbell1, M.T. Dawson2, S. Fox1, J. Hopper3, A. Kavanagh3, B. Mann4, G. Mitchell1, M. Otlowski5, V. Pridmore6, S. Timbs7, S. Viney6 1
Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Health Issues Centre, Melbourne, Victoria, Australia; 3University of Melbourne, Melbourne, Victoria, Australia; 4The Royal Melbourne Hospital, Melbourne, Victoria, Australia; 5University of Tasmania, Hobart, Tasmania, Australia; 6BreastScreen Victoria, Melbourne, Victoria, Australia; 7Breast Cancer Network Australia, Melbourne, Victoria, Australia 2
Background: lifepool is a large prospective cohort of women on whom health and lifestyle information, mammogram results and health outcome data will be gathered. A subset of participants will provide biospecimens. lifepool will support research into breast cancer and aims to recruit 100,000 women.
-How can research teams propose and implement actionable projects? -How to take advantage of established clinical study processes and apply them for research studies?
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ABSTRACTS -How to build searchable informatics systems for sample tracking and patient annotation and integrate them with existing clinical databases and analytical results? -How to ensure international regulatory compliance and informed consent obligations while maximizing flexibility for research? Conclusion: This presentation outlines some of the operational, informatics and organizational measures the Novartis team has taken to establish best practices for using human bio-specimens in a multinational pharmaceutical research organization. HT 04. TELETHON Network of Genetic Biobanks (TGBN) M. Filocamo1, C. Baldo2, S. Goldwurm3, A. Renieri4, C. Angelini5, M. Moggio6, M. Mora7, G. Merla8, L. POLITANO9, B. Garavaglia10 1
IRCSS - Gaslini - Genova, Genova, Italy; 2S.C.LAB. DI GENETICA, GENOVA, Italy; 3Centro Parkinson e Disturbi del Movimento, Milano, Italy; 4University of Siena, Siena, Italy; 5University of Padua, Padova, Italy; 6IRCSS - Fondazione Ca` Grande - Ospedale Maggiore, Milano, Italy; 7Istituto Besta, Milano, Italy; 8IRCCS - Casa Sollievo della Sofferenza, San Giovanni Rotondo, FOGGIA, Italy; 9Second University of Naples, Napoli, Italy; 10Istituto Besta, Milano, Italy Background: TGBN is the first national, coordinated resource of biospecimens from patients affected by genetic diseases. Supported by Telethon Foundation, TGBN interconnects well-qualified Italian biobanks with the aim to support both the biomedical community as well as the donors, patients and their families. Methods: TGBN operates in a harmonized environment which ensures the privacy protection of and the donor confidentiality, and the quality throughout the entire process of biobanking that includes collection, storage, distribution and related data recording. TGBN collects various types of biological materials: fetal=adult cell lines and tissues, DNA=RNA, blood=plasma samples from approximately 700 different genetic diseases. Activities and policies are stated in the Charter, which includes ethical guidelines, organization and governance policies, expected benefits and undertaken duties. The governance bodies are represented by the decision-making Network Board and by a consultative Advisory Board composed of legal=ethical experts and a family association representative. Additionally, TGBN can rely on a Coordinator Emeritus and a Telethon Advisor. To achieve its main objectives, TGBN has created a public web-site (www.biobanknetwork.org) and has adopted a common ITinfrastructure, managing all data collection, sample submissions, requests and inventory. Results: Aggregated data are published in the on-line catalogue. The IT-system manages and monitors the complete in=out workflow of samples which is therefore fully handled and shared online by all Partners. Conclusion: Samples will be made available to users for research purposes, provided that an adequate portion of the samples derived from individuals affected by undiagnosed and rare diseases are safeguarded to the patients’ advantage to allow retrospective analysis. HT 05. Tracing the Biorepository Fasciae: The Creation of Metadata Linkages that Reflect the Presence, Use and Application of Biospecimen Repository Inventories in Research J.W. McNally1 1
University of Michigan, Ann Arbor, MI
73 Background: There is growing interest in developing seamless metadata linkages that relate biospecimen inventories with associated external information resources emerging from the use of these specimens. The creation of ‘‘metadata’’, or data about data, is well established among researchers operating repositories. Metadata also includes ‘‘data results’’ emerging from the use of biospecimens in research such as essays or microscopic examination as well as publications and reports. When these various metadata are maintained in unrelated collections this limits their potential value to the research community. Methods: This presentation reviews the state of the archival sciences and the multiple databases that catalog the existence of biospecimen inventories, data records and publications that report analysis of biospecimen data. Examples would include models such as the RAND RD-HUB, NACDA, PubMed and the NIGMS Collection. It will also present on emerging tools that help to organize these independent sources of information into an integrated resource. Results: The potential for integrated systems clearly exists. Examples such as the SWAN biorepository at the University of Michigan show that this process is already being done for individual research projects. New metadata management tools being developed at NACDA show how this process can be extended to multiple collections, housed and maintained at independent sites. Conclusion: The creation of information resources that reflect not only the presence of biospecimens, but their use and contributions to science offers great promise for the future. It requires a multidisciplinary approach but it will ultimately add considerable marginal value collections in biospecimen repositories. HOT TOPICS/RETURN OF RESULTS HT 06. Lack of Information about Clinical Biobanking of Biospecimens Used for Biomarker Discovery in Scientific Publications D. Simeon-Dubach1 1
Foundation biobank-suisse, Bern, Switzerland
Background: Biomarkers are an integrated part of personalized medicine and will play an even more important role in the future. Very promising new biomarkers are discovered every year based on research done with human biospecimens. However little is known about the clinical biobanking activities (e.g. transport, storage, processing) with these biomarkers as quality indicators and how it is described in the scientific literature. Methods: A PubMed search was done with key words ‘‘biomarker discovery, human, English.’’ Open source publication from 2004 and 2009 (excluding reviews and studies not using biospecimens) were analyzed for published information about clinical biobanking of biospecimens used for biomarker discovery. Results: The number of publications (total=open source) on biomarker discovery increased from 266=31 in 2004 to 742 =94 in 2009. In 2004 51.6% and in 2009 56.4% of open source studies did not have any information on clinical biobanking. If available there was mostly information only on storage or processing. Biobanks as source of biospecimens increase from 16.1% to 26.6%. Tissue was used in about 1=3 of studies; blood=serum in 1=4 in 2004 and 1=3 in 2009, respectively. Conclusion: To interpret published results on biomarkers discovery information about clinical biobanking are important (garbage in, garbage out). We found that insufficient amount of information - if at all - was provided. There is a call for action to
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ABSTRACTS
different stakeholders: biobankers should collect the information, researcher should include it in the paper and journal publisher should specifically ask for it. HT 07.
Individual Feed-Back from a Cross Cultural Perspective
E. van Veen1 1
MedLawconsult, The Hague, Zuid-Holland, Netherlands
Background: If individual feed-back of results of research with tissue is the newest hotly debated ELSI issue in biobanking, the question arises which values or interests drive that discussion. Methods: It will be shown that the debate started in the United States. In Europe several biobanks exist, either population based, or hospital integrated banks using residual tissue, where the issue was not raised and the non individual feed-back policy thus far did not give rise to ethical complications or less enrolment. This can be explained by the European health care systems and associated cultural values, like willingness to contribute to the public good. European health care is solidarity based and tightly regulated as to what doctors are allowed to offer as diagnostic tools. That does not include not validated procedures with uncertain implications for clinical management of the patient. Hence guiding principles logically follow that individual donor feedback is only allowed, when it has validated clinical meaning, can meaningful serve the patient’s treatment and would not have been used in the available diagnostic and treatment options of the health care system anyhow. In addition donors generally do not expect priority ranking to access to health care because of their participation in a biobank. Conclusion: The US health care system is very different and so are some social values. The European values will be defended. The US debate should be imported with considerable caution and the United States might even learn something from the more restrictive European approach. REPOSITORIES/ENVIRONMENTAL REPOSITORIES ER 01. NIST’s Environmental Banking Expansion Efforts in the Pacific Islands Region A.J. Moors1, R.S. Pugh1, L.B. Rust1, P.R. Becker1, C.E. Bryan1, S. Vander Pol1 1
National Institute of Standards and Technology, Charleston, SC
Background: The National Institute of Standards and Technology (NIST) has been involved in environmental specimen banking since 1979 through various sponsored programs. Current projects include the National Marine Mammal Tissue Bank (NMMTB), the Seabird Tissue Archival and Monitoring Project (STAMP), and the National Oceanic and Atmospheric Administration’s (NOAA) National Status and Trends (NS&T) Mussel Watch Program. Methods: These existing projects have proven successful in environmental banking producing overwhelming numbers of presentations and publications. Recently, NIST began expanding environmental specimen banking efforts in the Pacific Islands region. Existing banking expansion projects include the NMMTB, the STAMP, and the NS&T Mussel Watch Program. This expansion will increase the number of species available for analysis in NIST’s existing specimen bank. The NS&T program currently has four collection sites in the Hawaiian Islands and expansion
efforts for the banking component may extend throughout the Hawaiian and Pacific islands. Additionally, new banking projects are also being established in the Pacific Islands including sea turtle and coral banking. Protocols for these new projects will be based on the already existing and successful projects, however these new endeavors present challenges when considering storage location, storage type, sample type, and future analysis. Conclusion: In addition to the expansion of the marine animal projects, NIST is looking to establish a branch of the Marine Environmental Specimen Bank (Marine ESB) facility in the Pacific Islands region. Additional details about these projects as well as the new NIST partnerships in the US Pacific Region will be discussed.
ER 02. Monitoring Total Arsenic and Selenium Mass Fractions in Seabird Egg Samples from the Seabird Tissue Archival and Monitoring Project (STAMP) R.S. Pugh1, W.C. Davis1, S.S. Vander Pol1, A.J. Moors1, P.R. Becker1, L. Rust1 1
National Institute of Standards and Technology, Charleston, SC
Background: Environmental specimen banks (ESBs) can be an excellent resource in providing samples for monitoring organic contaminants and trace elements in animals to determine if environmental trends exist. Methods: The Seabird Tissue Archival and Monitoring Project (STAMP) was developed in 1998–1999 to serve as a systematic, long-term (decadal) ESB program that identifies and tracks anthropogenic contaminants in Alaskan seabirds. Seabird eggs are routinely collected from colonies located throughout Alaska and are archived by the National Institute of Standards and Technology (NIST) in the Marine ESB at the Hollings Marine Laboratory, Charleston, SC. Results: Total arsenic (As) and selenium (Se) mass fractions were measured in 78 seabird egg samples representing 3 species of seabirds from 2008. Collection sites focused on colonies located in the Norton Sound region as well as two long-term monitoring sites, St. Lazaria Island in the Gulf of Alaska and St. George Island in the Bering Sea. Egg samples were analyzed using collision cell kinetic energy discrimination inductively coupled plasma mass spectrometry (ICP-MS). Total As mass fractions ranged from 0.015 lg=kg to 0.320 lg=kg while the levels of Se ranged from 0.411 lg=kg to1.02 lg=kg. Total As and Se mass fractions were higher in most of the samples collected from the Norton Sound colonies compared to other colonies. Conclusion: Norton Sound is located in a highly mineralized region of Alaska and is an area of historical gold-mining that continues today and could be a contributing factor to the bioaccumulation of arsenic and selenium in this region. REPOSITORIES/HUMAN SPECIMEN REPOSITORIES HSR 01. Integration of Biobanking Into Multidisciplinary Team Based Cancer Care C. Kennedy1, Y. Chiew1, R. Sharma2, R. Balleine1, A. Stenlake3, G. Wain3, A. Brand3, R. Hogg3, P. Harnett3, A. deFazio1 1 Westmead Institute for Cancer Research, University of Sydney, Westmead, New South Wales, Australia; 2University of Sydney and University of Western Sydney, Westmead, New South Wales, Australia; 3Westmead Hospital, Westmead, New South Wales, Australia
ABSTRACTS Background: Biobanking is now considered a basic tool for oncological research and care and several models have evolved to optimize single-site and multi-site collection of biospecimens. The Gynaecological Oncology Biobank at Westmead functions as part of the Multidisciplinary Care Team (MDT). Multidisciplinary care is an increasingly important component of cancer frameworks, and is recommended in Australian national clinical practice guidelines. The Westmead Gynaecological Oncology MDT meeting involves surgeons, pathologists, oncologists, radiologists, nurses, representatives from social work, psychology, familial cancer, clinical trials and biobank research staff. Methods: Patient cases are presented, pathology results and treatment options discussed and a management plan developed. Gynaecological Oncology researchers have participated in MDT meetings for over 10 years with numerous benefits including increased awareness of biobanking and regular contact with surgeons and pathologists ensuring regular biospecimen collection. MDT meetings also provide the opportunity to collect clinical information and gives researchers insight into the complex diagnoses involved in gynecological oncology. Other information gained includes rationale behind chosen chemotherapy regime, discussion of recurrent cases and identification of patients referred to the familial cancer centre. Conclusion: Involvement of MDTs in research assists in systematic recording of prognostic indicators, and allows coordination of clinical trials and clinical research projects involving collection of biospecimens. Incorporation of research staff into MDTs facilitates participation of clinicians and pathologists in research thereby promoting the benefits of biobanking and expedites translation of results into changes in clinical care. MDT meetings are a conduit for clinicians and research staff to exchange patient information and cooperate for better patient and research outcomes. HSR 02. Development of Tools to Assist Researchers Applying to Australian Breast Cancer Tissue Bank
75 graded to full application status, all on-line. The capacity to upload any required documentation is included in the process. eBAS automatically alerts designated BCTB personnel responsible for processing and tracking applications. Reviews are completed and tracked on-line. 4. To best preserve BCTB resources and assist researchers, nucleic acids are extracted within a central processing facility. This allows for automation, standardization and QC of methodology. Standardization allows for direct comparisons between results on downstream tests. 5. A digital image is obtained on every case and then goes through systematic independent pathology review, prior to marking for TMA construction. Images and TMAs are available to researchers. Conclusion: The BCTB realizes the importance of optimizing services and the measures adopted have received positive feedback from the research community. HSR 03. Growing Biorepository Operations to Meet Today’s Scientific Needs L.A. Ball1 1
BioStorage Technologies, Inc., Indianapolis, IN
Background: The proper storage, tracking and transport of research samples is vital to to pharma and biotech firms who frequently conduct a variety of testing on archived biomaterials. Consequently, temperature-sensitive samples must be maintained in highly specialized and consistent conditions. Therefore, biorepositories – large and small – must develop cost-effective, innovative and streamlined operations that will allow them to meet researchers’ long-term needs for improved sample integrity and chain of custody. Methods: The information presented will emphasize best practices for ensuring the long-term stabilization of samples generated during medical research. The poster will also highlight the demands of adhering to good storage practices. Specific topics that will be covered, include:
J.E. Carpenter1, M. Khushi2, C.L. Clarke3 1
2
Westmead Millennium Institute, Westmead, NSW, Australia; University of Sydney, Westmead, New South Wales, Australia; 3 University of Sydney at Westmead Millennium Institute, Westmead, NSW, Australia Background: The Australian Breast Cancer Tissue Bank (BCTB) recruited the first donor in 2006. The first research application was approved in 2008. Since inception we have explored ways to maximize researcher services and have developed strategies to assist applicants whilst simultaneously increasing operational efficiencies. Methods: Services developed include:
On-line search engine eBAS (electronic Biospecimen Application System) DNA=RNA extraction Pathology review=digital image acquisition Results: 1. The on-line search tool allows researchers to enter specific parameters, e.g. grade, hormone receptor status and specimens required. The search engine talks to our real-time central database returning live information. 2. A novel feature is the ability of the search to return snap-shot images extracted from a representative section of tumor material. 3. eBAS allows researchers to submit an EOI which can subsequently be up-
Comprehensive sample management for the entire sample lifecycle The value of consolidation of global specimen inventories Streamlined relocation of specimen inventories and associated equipment Offsite vs. onsite sample management model Best practices for electronic data capture and flow
Results: To maintain sample integrity for extended periods of time, it requires standardized, secured, and validated processes and procedures. The presenter will examine these challenges, provide practical design guidelines and use real-world case studies that help improve the success of this approach, while looking at sample management from an operational planning perspective. Conclusion: Without careful consideration for comprehensive sample management, including cold chain logistics, compliant storage, information management and audit trails, researchers risk specimen degradation and the loss of valuable clinical information. This misstep could prove costly not only for today’s research initiatives, but for future research needs. HSR 04. Beaumont BioBank a Progressive Biorepository B. Pruetz1, T. Geddes1, D. Larson1, G. Wilson1, J. Akervall1 1
Beaumont Hospital, Royal Oak, MI
76
ABSTRACTS
Background: Beaumont BioBank is a successful biorepository model which has addressed and achieved the challenging needs of centralizing, collecting, and annotating biospecimens worthy of the specialized demands of translational research. This has been achieved in a community based academic hospital with investment in staff and equipment to pursue the goals of personalized medicine. Methods: In two and a half years, 1,244 patients have been consented and 34,000 specimens collected, and stored from 28 different clinical investigators. Collections are driven by a clear clinical question and are initiated through a defined process involving an investigator contract and the BioBank staff, the clinical investigator, his=her nursing staff and a scientific committee. Suitable patients are identified in advance, appropriate collection kit(s) assembled and barcoded and consent sought at the most appropriate opportunity. Using direct OR sampling, over 80% of tissue specimens are collected, processed, annotated and placed in the freezer within 30 minutes; average time for plasma and serum samples to be placed in the freezers are 64 and 54 minutes respectively. Conclusion: Informatics is a key component of the BioBank, BIGR was chosen to barcode, track specimen location, document history, clinical outcomes, integrity factors; time of collection and preservation of all biospecimens. Quality control is integrated into daily operations, histological validation, DNA=RNA concentrations and integrity. Specimen audits are performed to confirm each specimen and chain of custody of samples is monitored through material transfer agreements and informatics documentation. Institutional investment in this standardized biobank model will lead to the successes of genomic driven personalized care. HSR 05.
Reducing Cold Ischemia Time for Tissues Banked at NUH-NUS Tissue Repository, Singapore
C. ENG1, R. Singh1, T.P. Thamboo1, W. Cheong1, J.B. So1, S.P. Khor1, H. RAFMAN1, S. Ng1, A. Lee1, F.S. Tee1, L.L. Xu1 1
National University Health System, Singapore, Singapore
Background: A project was undertaken to reduce pre-freezing cold ischemia times for banked cancer tissues. The distance between various hospital departments, manpower constraints, and the hospital staff not being properly educated on the importance of ischemia times for tissue quality contributed to the longer baseline time. Methods: The team comprised of tissue repository staff, surgeons, pathologists, operating theater staff and coordinators from the hospital’s Corporate, Planning and Development office. The pre-project workflow was reviewed and periodically refined, with changes implemented in the timing of typing of the histology form to doing away with the gowning up=down of tissue repository staff in operating theater. Along with, a strict check on the elapsed time between specimen excision in operating theater to freezing down in histopathology lab was ensured, both by the OT and tissue repository staff. Finally, specimen photo taking process was shifted out of the operating theater. Results: At the end of the project in September 2009, the median and mean tissue freezing time had come down to 24 and 28 minutes, respectively, from mean baseline level of 70 minutes. The percent of cases falling within the project goal TAT of 20 min had risen to 37% from the meager baseline level of 4.3%. Conclusion: The ongoing monitoring of the project has ensured a 29% collection within 20 min in the last three months of 2010 with 63% specimens being frozen down within 30 min. This
ensures that high quality tissues are made available for bio medical research across Singapore. HSR 06. The Genomic Medicine Biorepository: Addressing the Challenges of Biobanking for Translational Genomics Research at The Cleveland Clinic N.L. Prescott1, C. Eng1 1
Cleveland Clinic, Cleveland, OH
Background: The Genomic Medicine Institute was established in 2005 during a time when no structural, procedural or humanresource infrastructure existed for translational and clinical research in genetics and genomic medicine. The Genomic Medicine Biorepository was established to support studies for the Genomic Medicine Institute and its local, national and international collaborators. Over the last 5 years, many challenges have given rise to innovative solutions. Methods: The following processes were implemented to address specific challenges: (1) Establishment of a safer method for accessing cryopreserved specimens from the liquid nitrogen freezers using a custom gantry crane system. (2) Redesign of the patient instructions to facilitate the receipt of samples. (3) Incorporation of a laboratory information management system, Labmatrix, for specimen tracking. (4) Implementation of a lymphoblastoid cell line grading system to quantify trends in cell line viability. Results: (1)We can access heavy racks from liquid nitrogen in a safe, ergonomic fashion. This helps reduce the possibility of work related injuries or loss of samples due to accident. (2) Better instructions have reduced patient stress and cut down on the receipt of improperly packaged samples. (3) Labmatrix provides a secure LIMS that can integrate sample and patient medical information. (4) Grading the ficoll separation has provided useful information regarding trends in pre-analytical conditions that may lend to problems during the cell line initiation process. Conclusion: Challenges unique to the process of biobanking, especially in the context of non-existent infrastructure, need to be addressed both at the inception of the facility as well as continuously over the course of time. HSR 07. Tumor Banking in Brazil within the Context of a Pathology Residency Program: The Experience of the A C Camargo Hospital Biobank A.H. Campos1, M.D. Begnami1, C.A. Osorio1, C.A. Pinto1, I.W. Cunha1, F.A. Soares1 1
A C Camargo Hospital, Sao Paulo, Brazil
Background: The A C Camargo Hospital Biobank, established in 1997 to provide human tissues for cancer research, is primarily based in the Department of Anatomical Pathology (DAP), which has a 3-year residency program in surgical pathology, which is the only one in Brazil that includes biobanking activities in the resident curriculum. Methods: We analyzed, from 1998 to 2010, the number of residents enrolled in our residency program, calculating the number of hours each resident performed supervised activities at the frozen section laboratory (FSL), where over 90% of the tissue acquisition takes place, the number of acquisitions over each year and compared the results to quality indicators (tissue representativeness and RNA=DNA quality). Results: There were 39 residents enrolled in the residency program from 1998 to 2010. Each resident spent 672 hours=year
ABSTRACTS at the FSL. Residents who were enrolled in the residency program during the first years of the biobank activities performed an average of 8 tissue collections per resident per week, whereas residents from the last five years of activity performed an average of 13 tissue collections per resident per week. Sample acquisition by residents did not affect quality indicators. Conclusion: Pathologists play a key role in biobanking activities, particularly with respect to quality control issues related to the collection of biospecimens. The involvement of pathology residents in tissue banking activities during their residency program contributes to the formation of professionals familiar with the principles and best practices adopted in biobanking activities. HSR 08. The Next Phase of Biospecimen Management B.J. Chadwick1 1
LookLeft Group, LLC, Flanders, NY
Background: Due to increasing regulatory scrutiny and the harsh reality that many historical biospecimens have proven to be of insufficient quality to bring significant value, systems that manage biological samples must evolve. Methods: While basic location and inventory management functionality is still critical, modern biospecimen management software solutions must be protocol and process driven to enforce best practices for sample collection, annotation and processing. Advanced biospecimen management systems must include functions and features for informed consent management, bioethical and legal controls, and the ability to collect and connect clinical data to biospecimen data. They must be designed as open architecture platforms with flexible data import and export capabilities and enable integration with, and analysis of, public genomics information. They must offer sophisticated ad hoc reporting tools and user defined dashboards. Results: Connecting the phenotype to the genotype is the fuel for translational research and a cornerstone of personalized medicine. To achieve the value proposition of using data derived from biospecimen analysis to impact clinical diagnostics and therapeutics will require biospecimen management software solutions that meet increasing international data and privacy standards. Audit-worthy quality systems must be in place with documented processes and practices that comply with international regulatory requirements. Conclusion: While this will require a commitment to change and the cost of change management, companies that successfully enter the next phase of biospecimen management will be best positioned for the era of personalized medicine. HSR 09. The Challenge of Keeping Your Biobank Current A. Parry-Jones1, M. Mason1, G. Thomas2 1
Wales Cancer Bank, Cardiff, S Wales, United Kingdom (Great Britain); 2Velindre Hospital, Cardiff, S Wales, United Kingdom (Great Britain) Background: Biobank development is an evolutionary process that can only flourish given solid foundations. Initial stages in operational development focus on patient recruitment and sample accrual. The next phase is concerned with ensuring sample integrity and usefulness by consolidating collections and reviewing the use and demand of both samples and data. The number and quality of research projects applying for access to samples becomes an important marker of development and
77 success in biobank growth and one which facilitates the conduct of novel research programs that will ultimately improve the clinical care of patients. Methods: The Wales Cancer Bank recently conducted such a review after consenting 4,000 cancer patients to donate tissue and blood samples for prospective collection. At the time of review, 38,000 aliquots of biosamples were available and 4,500 aliquots had been used, either for extraction or supply to research groups. The profile of tumor and sample types in the collection was compared to the incoming requests for samples to ascertain whether the collection strategy was sound or whether amendments to the methodology were required. An audit of treatment and follow up data was also conducted and a synopsis of available biosamples with associated clinical data was formulated. Conclusion: Biobanks, particularly ones collecting prospectively, must not become complacent once set up and running. Regular scrutiny should form part of the operational program to ensure funding is well utilized and sample use is maximised, to uphold the promise made to donors to use their generous donations to further scientific knowledge and clinical treatment. HSR 10. Global Collaboration for HIV=AIDS Cancer Research: AIDS & Cancer Specimen Resource Biorepositories in East Africa R. Lukande1, L.K. Tumwine1, E.A. Rogena2, J.R. Ndung’u2, L.W. Ayers3 1
Makerere University College of Health Sciences, Kampala, Uganda; University of Nairobi, Nairobi, Kenya; 3The Ohio State University Medical Center, Columbus, OH
2
Background: Biospecimen science and research biorepositories are expanding internationally to provide quality biospecimens for quality research studies. Growth in biorepositories emphasizing biospecimen quality is well underway in the developed world. However, despite the developing world experiencing 70% of the global increase in cancer burden, there is no comparable growth in research contribution. Methods: Affiliates of the Mid-Region AIDS and Cancer Specimen Resource (ACSR=NCI) have been established at Makerere University (MU), Mulago Hospitals (U-ACSR) and the University of Nairobi (UON), Kenyatta National Hospital (K-ACSR) to initiate cancer biorepositories. Memoranda of understanding (MOU) and material transfer agreements (MTA) were developed for the collaboration between MU and UON pathologists and the Mid-Region ACSR (ACSR=NCI) located at The Ohio State University in Columbus, Ohio. IRB approved ACSR protocols are in place at MU and UON and studies using African biospecimens initiated. Results: K-ACSR from 2007–2010 collected 128 AIDS associated malignancies and together with U-ACSR provided 536 source blocks of lymphoma to the Sub-Saharan Africa Lymphoma Consortium (SSALC=ACSR=NCI) with 1388 cores placed in 38 tissue microarray (TMA) blocks through 2010. Nine podium and poster presentations from ACSR tissue studies were presented in 2009 and 2010 at international meetings including AORTIC (Africa), ICMAOI (USA) and APECSA (Africa). Conclusion: Collaborations promote biospecimen science concepts for human tissue archive management to provide research and publication opportunities. African participation in global biospecimen science and quality cancer research uniquely contributes to understanding tumor patterns, interactions among numerous tumorigenic viruses, adverse environments, nutrition and genetics in cancer, particularly HIV=AIDS malignancies.
78 HSR 11.
ABSTRACTS Alignment of a Research Biobank with Pharma Biomarker Validation
J. Swifka1, T. Krahn1, A.A. Schmitz1 1
Company, Wuppertal, Deutschland, Germany
Background: The understanding and treatment of many diseases is severely handicapped by the absence of biomarkers that can be measured in body fluids like blood or urine. To identify and validate biomarkers in pharma research especially in translational medicine excellent clinical material is indispensably needed (e. g. for molecular analyses at mRNA level). To support and empower research, there is a high demand to create utmost ’value’ from scarce samples. Compliance to legal requirements is a must, with additional emphasis on socioethical values. Methods: We analyzed the legal situation in Germany. We then developed a concept for and established a research biobank including both human and animal specimens. Results: The Research Biobank of Bayer Schering Pharma AG leverages the clinical network driven by the research projects by providing human samples and their clinical data for bioanalytics under strict compliance with legal, ethical, biosafety, biotechnology, data privacy and information technology guidelines. Conclusion: We favor a collaborative approach to biobanking where both clinicians and researchers contribute their strengths. By combining our respective experiences and accepting mutual cultural differences during partnering as well as clinical realities during the operations phase in order to minimize risks in clinical sample and data collection we were able to accelerate setting up prospective collections as a reliable, convenient, robust and affordable solution. Experiences gained in the build up of a pharma research biobank can be instrumental in further developing best practices. We will present case studies from our indications which include Oncology, Cardiology, and Gynecology. HSR 12.
Million Veteran Program (MVP): A Tissue and Data Repository of The Office Of Research and Development, US Department of Veterans Affairs (VA) 1
1
1
2
R. Przygodzki , S. Muralidhar , T. O’Leary , J. Gaziano , J. Concato3, L. D’Avolio2, L.D. Fiore2, D. Humphries2, M.T. Brophy2 1
Department of Veterans Affairs, Washington, DC; 2VA Cooperative Studies Program, Boston, MA; 3VA Cooperative Studies Program, West Haven, CT Background: The objective of the VA Genomic Medicine Program’s MVP is to create a repository to enable genomic investigation and discovery within the VA. This landmark undertaking will enroll as many as 1 million users of the Veterans Healthcare Administration over the next 5–7 years. Subjects will provide informed consent for collection of blood and clinical data, as well as HIPAA authorization for use of these resources by researchers. Methods: Veterans will be invited primarily via mailings to participate at their local hospital or clinic. Phenotype data will be collected via health and lifestyle surveys at entry and longitudinally via health data extracted directly from electronic medical record of the VA. All subjects will contribute a 10 ml EDTA blood sample that will be shipped overnight to the VA Central Biorepository and processed to extract 10–15 lg of DNA and to store two 1 ml aliquots of plasma and one aliquot of buffy coat. Samples will be stored at 808C. Phenotype and biosample data and
analysis results will be stored in Genomic Information System for Integrated Science (GenISIS) databases and will be made available to researchers in a scientific computing environment. Results: The protocol was approved by the VA Central IRB. Recruitment began in January 2011 and will be rolled out to 50 VA sites within a year. Work is continuing to complete laboratory automation and GenISIS development. Conclusion: Collaborative efforts within VA have lead to the launch of MVP, which aims to be one of the largest resources for genomic research. HSR 13. Recovery of MicroRNA from Stored Human Peripheral Blood Samples S. Robinson1 1
University of Colorado, Anschutz Medical Campus, Aurora, CO
Background: Recovery of microRNAs (miRs) from tissue samples of many kinds has become an area of increasing interest and importance in recent years. Methods: We isolated, and then amplified and quantitated, miRs from human peripheral blood samples stored in the University of Colorado Skin Cancer Biorepository to determine if miR recovery was possible and consistent over time in storage. Forty five blood samples from patients with different stages of malignant melanoma were collected in PAX gene RNA tubes and then stored at 808C prior to RNA preparation. The samples examined had been stored from 4 weeks to 3 years. Total RNA was prepared followed by miR isolation, amplification and quantitation using real time PCR. A widely expressed microRNA, miR221, was as a standard for comparison across samples and storage time. miR221 was recovered from all samples with no differences observed with longer storage time. Conclusion: These studies show that miRs can be recovered and quantified from human blood samples stored for up to 3 years. HSR 14. Educating the Public about Tumor Banking: An Outdoor Cancer Exhibition Organized by the A C Camargo Hospital in Sao Paulo, Brazil A.H. Campos1, C. Gonc¸alves1, E.N. Ferreira1, E.H. Olivieri1, M. Maschietto1, D.M. Carraro1 1
A C Camargo Hospital, Sao Paulo, Brazil
Background: In order to demystify cancer and bring cancer research closer to society, Hospital A C Camargo (with the support of the Sao Paulo Research Foundation-FAPESP and the National Council for Scientific and Technological DevelopmentCNPq) held in public parks of Sao Paulo the exhibition "Cancer: Know and Prevent". The importance of tumor banking was addressed in a panel (of a total of twenty-two) containing entertaining and educational concepts on the subject. Methods: The rationale for tumor banking and the Biobank infrastructure and workflow were discussed by the A C Camargo Biobank staff with the hospital press office staff for institutional projects and professionals from the art company Pingado Sociedade Ilustrativa, which created a comic strip with easy-tounderstand text. This comic was mounted on a 1.20 (wide)1.80 (tall) meter panel. Results: Beginning on May 30, the exhibition toured eight public parks in Sao Paulo during the year 2010. An additional park was included in the schedule for early 2011.
ABSTRACTS Conclusion: This exhibition provides an additional means of bringing information to the community about the importance of a tumor bank in cancer research. HSR 15. Protein Extraction and Western Blot Analysis from Formalin Fixed Paraffin Embedded Biobanked Heart Tissue L.A. Matzke1, A.J. Meredith2, D. Singhera3, D.M. McManus4, D.F. Allard4 1
Institute for Heart and Lung Health, Vancouver, BC, Canada; Institute for Heart and Lung Research, Vancouver, BC, Canada; 3 James Hogg Research Centre, Vancouver, BC, Canada; 4Institute for Heart and Lung Health=University of British Columbia, Vancouver, BC, Canada 2
Background: Immunohistochemical (IHC) staining and Western blot (WB) analysis are established analytical techniques providing complementary information on protein quantity, localization and distribution within tissues. Technical challenges have meant that these methods are generally used in isolation. IHC is typically performed on tissues processed with fixatives such as formalin, which denature proteins such that analysis of the same tissues by Western blotting, which generally assays freshly extracted protein, may not be possible. In certain circumstances, such as in forensic pathology, only formalin fixed tissues are routinely retained for evaluation. In this study, we extracted protein from formalin fixed (FF) and corresponding snap frozen (SF) tissues as well as from formalin fixed paraffin embedded (FFPE) tissues from six archived myocardial samples to evaluate their performance in WB analysis. Methods: Myocardial tissue samples from six heart transplant cases were obtained from the James Hogg Research Centre Cardiovascular Biobank at St. Paul’s Hospital. Protein was extracted from matched SF, FF and FFPE heart samples. Extracted proteins were analyzed by WB for expression of both cytoplasmic and membrane proteins. Results: Membrane and cytoplasmic proteins were readily detectable in SF samples. Proteins from FFPE samples were detectable more than 60% of the time and FF samples were not detectable. Conclusion: The results of this study suggest that WB analysis from FFPE human heart tissue can be successful. Optimization of the retrieval of assayable proteins from archived FFPE heart tissues will provide a valuable resource for proteomic analysis, biomarker discovery and validation, and genotype=phenotype studies. HSR 16. Data Coordination for a Multi-Centre Tissue Bank: The Children’s Cancer and Leukaemia Group (CCLG) Tissue Bank G. Mistry1, S. Ablett1, G. Jenner1, H. Middleton1, S. Thornton1, N. Sebire2, K. Brown3 1
Children’s Cancer and Leukaemia Group, Leicester, Leicestershire, United Kingdom (Great Britain); 2Great Ormond Street Hospital for Children NHS Trust, London, United Kingdom (Great Britain); 3 University of Bristol, Bristol, United Kingdom (Great Britain) Background: The CCLG Tissue Bank has been established since 1998. It is a repository of solid tumor specimens and supporting clinical data, designed to facilitate and support childhood cancer research. Frozen, paraffin-embedded tissue and blood samples
79 collected from children (0–16 years old) across multiple sites are locally stored, DNA samples are centrally stored, and all registration and pathological data is centrally managed at the CCLG Coordinating Centre. The datasets collected include patient demographics, pathology reports and clinical follow-up data, as well as monitoring CCLG biological studies through progress reports, sample tracking and publication output. Methods: The logistics of central data collection for tissue stored and dispatched from multiple sites can be challenging. Processes have been developed to ensure this data is captured and processed efficiently. A database is used to log all patient and tissue registration information, clinical outcome data, progress of CCLG biological studies and specimens dispatched. Electronic anonymized pathology reports for all specimens are available to researchers. Annual progress reports and publications arising from biological studies are logged. Results: Supporting pathological data on all 10,112 tissue samples registered to date. Clinical follow-up data has been collected on all registered patients with tissue since 2007. All 80 CCLG biological studies have been supported by clinical data and annual progress documented, including research findings. Conclusion: A comprehensive collection of data on pediatric cancer has been successfully utilized for research, facilitating effective biological and translational research into various childhood cancers. HSR 17. The NHLBI BioLINCC Operational Guidelines: Streamlining the Review of Biospecimen Requests E.L. Wagner1, K.E. Shea2, L.E. Carroll3, L.A. Welniak1, S.S. Berman2, J.T. Adams3, C.A. Giffen3 1
NIH=National Heart, Lung, and Blood Institute, Bethesda, MD; SeraCare Life Sciences, Inc., Gaithersburg, MD; 3Information Management Services, Inc., Silver Spring, MD
2
Background: The NIH National Heart, Lung, and Blood Institute (NHLBI) is the custodian of multiple contemporary and historical biospecimen collections. The NHLBI Biologic Specimen and Data Repository Information Coordinating Center (BioLINCC) has linked over 4.2 million biospecimens (26 collections) to their phenotypic data and established a public website where scientific investigators can view available resources and submit requests online. The availability of an online application process resulted in an increase in biospecimen requests and reviewing applications in a timely manner became challenging. A new streamlined review process was developed to address this issue. Methods: A review of publicly available best practices was performed to identify core review elements. The core elements were compared to the type and timing of the information collected during a biospecimen request. A multi-disciplinary team was formed to provide technical reviews early in the request process and a workflow established. Expedited review processes were investigated. Results: The website application form was retooled and a new review tab on the private website was developed for NHLBI, BioLINCC and biorepository staff to document the multidisciplinary review and post recommendations. The recommendations were distributed to the scientific reviewers and expedited reviews were performed for ‘‘low impact’’ requests. Initial results indicate that the expedited reviews can facilitate the process. Conclusion: Implementing best practices to facilitate the search and distribution of biospecimens without introducing unnecessary roadblocks is possible using a multi-disciplinary approach and streamlined workflow.
80 HSR 18.
ABSTRACTS Ambient Temperature Stabilization of Genomic DNA in Saliva Samples
S. Ghirmai1, J. Muller-Cohn1, S. Whitney1, R. Muller1, S. Wilkinson1, L. Shireen1 1
Biomatrica, Inc., San Diego, CA
Background: Saliva provides an alternative to blood as a biological fluid in research and diagnostic applications. The major advantage of saliva over other biological fluids is the fact that it is non-invasive and can be collected without training. Biomatrica has developed a novel reagent that preserves the integrity of genomic DNA in saliva at room and elevated temperatures for up to 6 months. This makes the saliva=preservative mixture ideal for sample storage and shipping as an alternative to freezers or cold-packs. Methods: Samples were collected from 4 donors. Three different DNA extraction methods were employed: Column based, (Qiagen), phenol=chloroform, and precipitation. DNA integrity was analyzed on a 0.8% agarose gel and 10% of eluted DNA was loaded on the gel. DNA yield was determined by fluorescence using the Quant-iTÔ PicoGreen dsDNA Assay Kit (Invitrogen). Results: Biomatrica’s new saliva formulation is based on inhouse developed chemical compounds that are designed to preserve the integrity of DNA in saliva. The new formulation was found to preserve the integrity of DNA in saliva samples when stored at room temperature and elevated temperature for extended periods of time. The formulation was compatible with different DNA isolation methods. The purified DNA did not show intereference with PCR, long range PCR or QPCR. Conclusion: The new reagent for stabilizing DNA in saliva provides excellent stabilization for up to 6 months, with high quality gDNA as well as high recovery. The quality of the extracted DNA was evaluated in downstream applications such as PCR. HSR 19.
Biobanking Management in a Cancer Center
V. Canzonieri1, A. Steffan1, T. Perin1, S. Cervo1, M. Nigris1, B. Canal1, P. De Paoli1 1
CRO (National Cancer Institute), Aviano, Pordenone, Italy
Background: The National Cancer Institute CRO-Biobank represents a long-term source of human biological samples collected at diagnosis and at consecutive therapeutical stages for research purposes. CRO-Biobank is a member of the Italian Network Cancer Biobanks (RIBBO) and participates in the setting up of a European network (BBMRI). Methods: At present the collection comprises serum, plasma, buffy-coat, tissues and DNA of healthy individuals and cancer patients, which are collected and stored in compliance with quality standards and ethical regulations. The traceability is guaranteed by the "Matrix" system based on a software (Easytrack2D Ver 2.0, Twinhelix) for the managing of sample data; particularly it allows to know the physical location of samples thanks to 2D-barcoded tubes. CRO Biobank has developed quality control procedures concerning timing and method to obtain optimal freezing, prevention of hot and cold tissue ischemia and accuracy in the OCT embedding process. Tumor or healthy frozen tissues were also evaluated to establish the percentage of necrotic= fibrotic areas in cryostat histological sections directly obtained from the samples. To warrant the possibility of aliquoting tissue samples, we have also tested the consistency of biomolecular analyses from mul-
tiple cryostat sections of the same tissue block obtained at different times. Conclusion: The major advantages of setting up our Biobank are: first, scientists can readily assess clinical information in conjunction with biological features of samples for research; second, it represents an important tool to provide accurate and high quality linkages with the regional or national cancer registries. HSR 20. Building a New Large-Scale Biobank for Clinical and Epidemiological Research Studies in Sweden A. Brinne1, M. Divers1, C. Rask1, T. Rylander-Rudqvist1, A. Pettersson1, G. Tybring1 1
Karolinska Institutet Biobank, Stockholm, Sweden
Background: A strategic funding on a national biobank infrastructure as a part of BBMRI.se made it possible to further develop KI Biobank and create a new high throughput facility. The development was driven by three major population based studies, two within cancer with a target of 200 000 people, and LifeGene with a target of half a million people in Sweden. Methods and Results: We undertook extensive processmapping to understand how we could increase capacity and where to introduce automation. After a tender process we selected robotic systems for registration and sorting of incoming samples and aliquoting of different sample types into multiple 220 ll fractions and established new processes for DNA extraction. We changed tube format and developed a simple expandable storage strategy. In addition we extended and modified our facility. Big efforts were made to further develop our LIMS system to support the new processes. Conclusion: After installation and testing we were able to launch the new operation on November 1, just 10 months after starting the new development. Our automated processes have given us the big increase in sample processing capacity we needed to start 3 new large studies. We now need to optimize our processes for stability and to further increase capacity, and this will enable us to take on more large studies and improve the efficiency of our smaller studies. Our next steps are to automate sample retrieval and to identify a cost effective strategy for long term storage. HSR 21. Facilitation of Biorepository Functions with PivotÔ by MicrosoftÒ Live LabsÔ A. Kulkarni1, C.R. Handorf1, C. Stanton1, P. Ngutu1 1
UTHSC, Memphis, TN
Background: Pivot is an application intended to simplify viewing and interaction with massive amounts of data in ways that are powerful and informative. Pivot is a data mining system that allows visualization of data that can be sorted, organized, and categorized according to the user’s requirements. Pivot is able to filter through images and information seamlessly because the images are in Deep Zoom format (a component of Seadragon Technology). The Whole Slide Imaging (WSI) system creates a digital replica of the entire content of a glass microscope slide that can be displayed on the computer, emulating traditional viewing of a slide with a conventional microscope. Combining these two technologies makes it possible to create a collection of images and associated information that can be used for sorting biorepository samples.
ABSTRACTS Methods: Digital slide images created by the ScanScope XT scanner (Aperio Technologies, Inc.) are stored in the SVS (ScanScope Virtual Slide) file format. SVS files are TIFF=BigTIFF files. Pivot only accepts JPEG, PNG, and HD photo files. We converted the SVS files to JPEG files using Digital Slide Studio (Aperio) and then entered the JPEG images into a Microsoft Excel based tool that converted the JPEG images to Deep Zoom Image (DZI) files. The DZI files, which enable viewers to zoom in and pan out without loss of significant resolution, were then used to create a Pivot collection. Conclusion: Pivot can be a useful tool for biorepositories since it offers the capability to sort images based on different parameters. HSR 22. Comparison of Pre-Operative and Post-Operative Consenting Protocols at the British Columbia Cancer Agency Tumour Tissue Repository (BCCA-TTR) J.L. Le Blanc1, R.O. Barnes1, S. Dee1, P.H. Watson1 1
BC Cancer Agency, Victoria, British Columbia, Canada
Background: The BCCA-TTR is a cancer biobank that for its first five years of operation has mostly deployed a pre-operative consent protocol. In 2010 the BCCA-TTR began to also deploy a new post-operative consent protocol. Both types of protocols have many benefits to patients and biobanks, however efficiency and outcomes of each protocol may be different. Methods: The rates of consented, declined and decision unknown outcomes were compared between pre and post-operative consent protocols for 3279 cancer patients referred for potential consent. Subsets of breast and colon cancer patient decision rates were also analyzed. Results: There was no significant difference in the global rates for consented (þve) and declined (-ve) using pre or postoperative protocols (97.7% þ ve and 2.3% -ve vs *95.9% þ ve and 4.1% -ve respectively). There was a significant difference in outcomes with respect to decision made (þve or -ve) versus decision unknown between pre and post-operative protocols (1.8% vs 23.4% of all patients approached, chi-square test, p < 0.0001). Consented and declined rates were similar for both protocols for breast cancer patients but a higher decline rate was observed for colon cancer patients (p ¼ 0.007). The proportion of decision made to decision unknown was higher with the post-operative protocol with breast and colon patients (33%, p < 0.0001. Conclusion: These data suggest that pre and post-operative consent protocols are equally acceptable overall to cancer patients. However, pre-operative consent may be more acceptable for some subsets and the rate of ‘decision unknown’ is generally increased with the post-operative consent protocol. HSR 23. Value of Morphological Quality Control of a Cancer Tissue Bank M. Sun1, G. Qin1, Y. Gu1, H. Chen1, Z. Zhang1, X. Zhou1, X. Du1 1 Fudan University Shanghai Cancer Center, Shanghai, Shanghai, China
81 formation for the researchers. When possible for each case, we are collecting an aliquot of tissue exclusively for morphological quality control. Methods: An aliquot of a tissue piece during each case of tumor tissue procurement is collected and snap frozen in liquid nitrogen then transferred to 808C by the end of the day. A frozen section was cut and H&E staining was performed from the aliquots of the tumor tissue. The H&E stained whole section was scanned in whole using the image analyst of Ariol. The tumor percentage of each case is evaluated and the images were stored as a virtual morphological bank. The information including the scanned morphology was provided to researchers along with the research tissue samples. Results: More precise sample information was provided to the researchers. They could tell how much tumor component is contained in the sample they are analyzing. Through the necessary micro- or macrodissection we could provide the research results representing the goal tissue and therefore the research study would be more precise. Conclusion: Morphological information would be helpful for investigators to know more about the samples they are using for scientific study. HSR 24. From Bio Specimen to Biomarker? The Quickest Way for Discovery of Novel Candidate Biomarkers R. Ravid1 1 Royal Dutch Academy of arts and Sciences, Amstelveen, Noord Holland, Netherlands
Background: The search for biomarkers relies completely on the availability of high quality specimens from living donors as well as autopsy material collected and stored by biobanks. The diagnosis of neurological disorders is severely hampered by an absence of reliable biomarkers that can be measured in body fluids such as blood, urine and cerebro-spinal fluid (CSF). Methods: Biomarker discovery copes with extreme data fluctuation due to the huge variability between individuals and the rapid post-mortem changes. We are currently using betaAmyloid and Tau as candidate biomarkers for Alzheimer’s disease (AD) and fronto-temporal lobar degeneration (FTLD). The collected specimens include RNA,DNA and proteins extracted from brain =tissue =body fluids, subsequently correlated to the classical pathological hallmarks of the disorders. Results: So far we have identified and measured biomarkers in blood and CSF. We conduct the correlating tests for total and phosphorylated tau and Ab42 in living donors and in rapid autopsy material and then add the results to MRI imaging results to assist in differential diagnostic procedures. Conclusion: Human biobanks play a major role in the collection of large numbers of high quality specimens for biomarker identification. So far, no single biomarker has been found which discriminates between AD and other dementias. Therefore we are aiming at international collaboration between biobanks and harmonization of SOP’s to enlarge the panel of valid biomarkers which will substantially increase the sensitivity and specificity of the diagnosis. HSR 25. How Do They Do That?
Background: As already well known, pathology is the cornerstone of a tissue bank, where usage of human tissue is an increasing requirement. The morphological information is as critical as the steps of tissue collecting, processing, annotating and preserving. It is of big value to provide morphological in-
T. Mathieson1, A. Storniolo2, S.E. Clare2, C. Rufenbarger1, J. Henry1, E. Way1, H. Zang1, K. Ridley1 1 Komen Tissue Bank, Indianapolis, IN; 2Indiana University School of Medicine, Indianapolis, IN
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ABSTRACTS
Background: Since Oct of 2007 the Susan G. Komen Tissue Bank at the IU Simon Cancer Center in Indianapolis has collected over 1300 normal breast tissue samples with matching blood, plasma, and DNA from women with no signs of breast cancer. There is currently a waiting list of 500 women willing to give tissue from their healthy breasts to be used in breast cancer research. How does the Komen Tissue Bank achieve this? Why are women lining up to donate? What is a collection day like? How are the samples collected and processed to achieve the highest standards of sample integrity possible? We present a brief journey from the inception of the Komen Tissue Bank through IRB, legal, and logistical challenges to the present day summation of what the Bank holds. A sample collection and processing description is included as well as testimonials from the women who have donated their precious healthy breast tissue to the Bank. Methods: A breast tissue collection event utilizes up to 80 volunteers to complete the donation process from consent to biopsy. Samples are immediately processed according to strict SOPs. Results: A typical collection event lasts 7 hours. During this time, samples of breast tissue and matching plasma and serum from 100 donors are collected and processed. Conclusion: The Komen Tissue Bank is the source for normal breast tissue for breast cancer research. When women are asked to personally contribute to breast cancer research, they generously line up to do so. HSR 26.
Creating a Framework for Serial Collection of Residual Clinical Phlebotomy Samples, from Community Consultation to Infrastructure Development
D. Cross1, V. McManus1, J. Eckstrom1, C. McCarty1 1
Marshfield Clinic Research Foundation, Marshfield, WI
Background: Here we describe the development process for the collection of serial samples using residual clinical specimens from participants in a population based biorepository. Methods: We identified three groups essential to the definition and implementation of serial sample collection: the participating community, the scientific community, and the infrastructure development team. Initial steps focused on the participating community, with active community engagement from focus groups, community advisory board discussions, and external ethics advisory board consultations. The scientific community was asked to determine the characteristics of a useful sample; we consulted both internal scientists, and sought external scientific advice. To determine the infrastructure development needs, we identified stakeholders from different departments to plan workflows that transition a sample from clinical collection to biorepository storage. Results: Information from focus groups and advisory committees led to the development of an "opt out" model for incorporation of serial samples; this has resulted in less than 1% of participants requesting removal from the study. Scientist input in serial sample collection helped identify characteristics of a valuable sample including continuous care within the institution, diagnosis of a common condition, age, and overall health of the participant. Stakeholder input identified small changes in workflows that might have the potential to increase sample value, such as fast tracking a sample to a temperature controlled area and tagging potential biorepository samples at the site of initial sample processing. Conclusion: Collecting additional serial samples from an established cohort can be established only with the input of all affected groups.
HSR 27. Best Practices for the Global Distribution of Specialized Biomaterials Generated in Clinical Trials R. Hager1 1
BioStorage Technologies, Indianapolis, IN
Background: The poster will provide attendees with detailed solutions to the intricate processes of global cold chain management of clinical trial samples. Specifically, the poster will highlight various aspects of international transportation and best practices that ensure the on-time and compliant distribution of temperature-sensitive materials. Methods: To mitigate risk of degradation and ensure compliance, biorepositories must have a broad understanding of the complexities involved in global cold chain management. Using real-world applications and industry case studies, the presenter will give insight into the complexities of cold chain management and highlight strategies biorepositories can implement to ensure on time, compliant transportation of temperature-sensitive clinical trial samples and supplies. Results: Pharmaceutical and life science assays often require accurate and constant temperature control to acquire meaningful data. As a result, particular attention must be paid to the effects temperature variances have on the stability of biospecimen samples, and how to overcome these hurdles by addressing them in upstream processes. By adhering to best practices for the shipment and storage of temperature-sensitive materials, companies can reduce risk and increase efficiency throughout the development process. Conclusion: Cold chain logistics is a multifaceted function demanding homogeneous solutions to rising cost concerns, environmental responsibilities, packaging procedures and custom regulations. Without validated, carefully considered planning for the complexities of global cold chain logistics, biorepository operators risk product degradation, and possibly the loss of irreplaceable materials. This pitfall can lead to delayed clinical trials, postponed product launch and ultimately loss of revenue for the trial sponsor. HSR 28. A Flexible Informatics Framework to Guide the Advancement of Personalized Medicine and Improve Patient Outcome in a Community-Based Healthcare System N. Todaro1, R. Mulpuri1, S. Chen2, J. Otridge2, J. Otto1 1
Catholic Health Initiatives, Towson, MD; 2BioFortis, Columbia, MD
Background: In contrast to urban single-site academic hospitals, networks of community-based hospitals enable vast, demographically diverse, biospecimen collection. Catholic Health Initiatives (CHI) is committed to bringing cutting-edge research and treatments to its 73 hospitals in 19 states. Facilitating the advancement and integration of personalized medicine, CHI has established the Center for Translational Research (CTR) comprising of Biorepository, Molecular Diagnostic and Research Laboratories. By engaging CHI physicians and leveraging diagnostic testing infrastructure, CTR has established state-of-the-art Biorepository facilities to enable innovation and advance personalized medicine within their communities. Methods: Using an IRB approved protocol, CTR collects biospecimens from eligible cancer patients and associated clinical and longitudinal follow-up data for up to 10 years. We describe the collaboration with BioFortis in implementing a
ABSTRACTS Labmatrix-based IT framework that guides data collection, management and exploration of patient and molecular data. HIPAA-compliant Labmatrix meets evolving scientific needs and data exchange standards, and is capable of tracking data from donor consent along with their comprehensive clinical profile, bar-coding, sample collection, processing, storage, shipment and disposal, to specimen usage and assay data. Conclusion: With a sophisticated security framework, Labmatrix provides standardized data format and collection, by creating forms or providing interfaces to hospital-based EMR systems (HL7 standards) while maintaining and assuring the quality and chain-of-custody of biospecimens. Through Labmatrix, CTR has a robust compliant infrastructure to standardize procedures across the CHI network - linking patient clinical and outcome data with molecular data enabling the translation of biomarker and health data into useful tests to improve patient outcomes and drive innovation. HSR 29. Introducing the NW Biobank: A Research Repository at Kaiser Permanente Northwest K.S. Smith1, J. Carlston1, M. Hornbrook1, P. Dandamudi1, K. Goddard1 1
Kaiser Permanente Northwest, Portland, OR
Background: The NW Biobank is a multi-modal repository housing legacy research specimens from 37,327 unique subjects and specimens from *3,000 prospectively recruited subjects. The NW Biobank is nested within Kaiser Permanente Northwest (KPNW), an integrated health care system with a large, stable membership (*475,000) and extensive data on members dating back to 1960. Methods: To pilot-test prospective recruitment, we mailed invitations to 2,000 members asking to use their discarded blood samples in a hypertension study. We also asked current members with a history of breast cancer (3,921 cases) and 2,000 matched controls for samples. Results: The response rate for the hypertension study was 34%; 82% of respondents consented to participate. For breast cancer, the response rate was 35%, varying between cases (40%) and controls (19%); 90% of respondents consented to participate. Most of the samples in the NW Biobank are from females (86%) and Caucasians (95%). The gender imbalance reflects the recruitment criteria, and women’s greater willingness to participate in research. We have more than 10 years of medical history for about 50% of subjects. A major factor affecting future use of legacy specimens is limited informed consent. We are now reconsenting subjects to enable broader data sharing. Conclusion: We plan to invite all adult KPNW members to participate in the NW Biobank. The high response rate (>30%) and reliable methods for obtaining blood samples integrated into the health plan infrastructure should lead to successful accrual of specimens for future genomic research. REPOSITORIES/NATIONAL & INTERNATIONAL BIOBANKING NETWORKS NIR 01. Role of National Culture Collection for Pathogens (NCCP) and Pathogen Bank Network in Korea K. Jung1, C. Yoo1, K. Lee1 1
Korea National Institute of Health, KCDC, Chungbuk, Republic of Korea
83 Background: National Culture Collection for Pathogens (NCCP) is the only national pathogenic resource bank in Korea. NCCP is operated by a governmental agency from 1972. The function focuses on collection, preservation, development and distribution of pathogenic microorganisms isolated from patients with infectious diseases including high-risk pathogens. We affiliated the World Federation of Culture Collection (WFCC) under the name NCCP in 2004. Methods: According to the international criteria, the NCCP has managed and collected various standardized pathogens by 2009 ISO 9001 requirements, 345 species for 1,131 strains. Currently, NCCP has established the network among 8 unit banks, 3 of which are specialized banks for pathogens isolated clinically and controlled under KNIH, 2 of which are collaborative banks for special pathogens difficult to be collected or managed as tuberculosis and medical fungi, and 3 of which are regional banks for pathogens isolated from the patient’s clinical specimen by National University Hospital in Korea. NCCP has provided financial support as well as standard operation protocols (SOPs) for management of unit banks and established the network between central and unit banks. Conclusion: An informational network was constructed and is operated by Pathogen Information Management System (PIMS), and all information of pathogenic resources can be accessed through the web-site (http:==nccp.cdc.go.kr). This provides various information including antibiotic resistance, clinical data, biological character, etc, also linked information from the unit bank. NCCP wants to network internationally with similar biobanks about resource information and management systems. NIR 02.
Spanish National Biobank Network [BBMRI-ERIC.es]: A New Dimension in Biobank Collaborative Networking in Spain
M. Morente1, F. Luna-Crespo1 1
CNIO, Madrid, Spain
Background: The Spanish National Biobank Network (SpNBBN) is an initiative of the Spanish National Institute of Heath (ISCIII-Ministry of Science and Innovation), ordered and structured to function as a stable instrument of coordination between its various component institutes. Methods: The main mission focuses on developing a cooperative network of public service, made up of hospital biobanks and other related institutions:
To provide the Scientific Community access to quality sample collections and associated data through a cooperative structure of public service. To integrate existing initiatives related to biobanks and the use of human samples in biomedical research, creating an add value to the whole system To promote the creation of qualitatively varied collections, fitting current needs of researchers and those that can be foreseen for the future. To contribute to ensuring respect for the fundamental rights and freedoms of patients and donors in general, with special reference to the protection of the dignity and identity of the individuals. To promote technological innovation in biobanks. To assist in the development of the pan-European platform BBMRI, and promote the Spanish participation (BBMRIERIC.es).
Conclusion: Initially, the network is composed of 52 hospital biobanks and another 11 institutions with relevant biobanking
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ABSTRACTS
activity, mainly as regional biobank network promoters, and the Spanish National DNA Bank, integrating a wide range of biobank and collections types including Pathology Department clinical collections, disease oriented collections and population biobanks, all of them in different formats (solid samples, serum and other blood derivatives, brain banks, DNA banks, etc.) NIR 03. AIDS Epidemic Studies Require Access to Multicenter Biorepository Programs for Comparative Data S. Silver1, E.A. Mesri2, A. Chadburn3, E. Cesarman4, B. Ashlock2, L.W. Ayers1, M.S. McGrath1 1
AIDS and Cancer Specimen Resource, Washington, DC; 2University of Miami Miller School of Medicine, Miami, FL; 3Northwestern University-Feinberg School of Medicine, Chicago, IL; 4Joan & Sanford I. Weill Medical College of Cornell University, New York, NY Background: Global HIV=AIDS complications reflect local anti-retroviral (ARV) therapy. While ARVs appear to control HIV replication, cancer continues to cause death and has emerged as the major cause of death within the developed world. AIDS-defining cancers such as Kaposi’s sarcoma (KS) and nonHodgkin’s lymphoma (NHL) are significantly reduced but nonAIDS defining cancers emerge earlier, occur more commonly than in the non-HIV population, and have overtaken the AIDSdefining cancers as major causes of death. The AIDS and Cancer Specimen Resource (ACSR), established by the National Cancer Institute (NCI) in 1994, contains an inventory of over 400,000 biospecimens from its three major regional biospecimen repositories (RBR), east coast, mid-region and west coast and characterizes the U.S. AIDS epidemic. The goal of this study was to determine if the three RBR biospecimens equally represent the AIDS epidemic in the United States. Methods: Large multi-RBR biospecimen collections were evaluated in the course of research performed by the ACSR and collaborative investigators: data on 11 different NHL associated biomarker immunophenotypes from 119 cases on an HIV AIDS diffuse large cell B cell lymphoma (DLBCL) tissue microarray (TMA) and >200 blood specimens from two of the RBRs for KSHV seroprevelance. Results: ACSR RBRs had similar distributions of DLBCL immunophenotypes and the KSHV seroprevalence in the non-KS patients from both the EC and WC collections was identical. Conclusion: This study suggests that the HIV-infected profile within the United States is homogeneous and without regional bias in the diseases. NIR 04. Simultaneous Query of Two Biobank Networks: BBS and CRIP Are Synchronized via Web Services D. Simeon-Dubach1, C. Schro¨der2, O. Gros2, R. Warth3, A. Perren4 1
Methods: Based on a cooperation agreement, BBS and CRIP have synchronized their users’ registration and log-in procedures, and mutually coupled their web-based interactive query tools by web service protocols operated through secure communication channels (HTTPS). Results: The coupling of user’s log-in and web-based interactive query tools allow for a single sign-on with both BBS’s and CRIP’s web sites and simultaneous search of both meta-biobanks without affecting their access rules, contractual framework, privacy regimes, workflow, and corporate design. Putting the principle of data sparing into practice, data is transferred only upon a user’s focused request. Background operation of web services conveniently enhances the users’ query efficiency. Conclusion: Coupling CRIP and BBS provides a model for networking meta-biobanks (‘‘hubs and spokes’’) without impairing their governance, regulatory framework, workflow, and infrastructure. This work was funded by grant 01EZ1021A from the German Federal Ministry for Education and Research (BMBF). NIR 05. CNIO Tumour Bank Unit and Spanish National Tumour Bank Network: 2006-2010 Achievements M. Morente1, L. Cereceda1, A. Maria-Jesu´s1 1
CNIO, Madrid, Spain
Background: The CNIO Tumour Bank Unit provides samples and associated data, as well as ethical and documentation support to CNIO Researchers mainly through the Spanish National Tumour Bank Network. This network was created in September 2000 and currently includes 25 institutions. The biobanks within these institutions are autonomous. The CNIO Tumour Bank maintains collaborations with other biobanks as a part of the Spanish National Biobank Network, and actively participates in research projects in collaboration with different CNIO groups and other external research groups. Main achievements of the 2006–2010 period:
2
Foundation biobank-suisse, Bern, Switzerland; Fraunhofer Institut fu¨r Biomedizinische Technik (IBMT), Potsdam-Golm, Berlin, Germany; 3Stiftung biobank-suisse, Bern, Bern, Switzerland; 4 University of Bern, Bern, Switzerland Background: Both biobank-suisse (BBS; www.biobank-suisse.ch) and the Central Research Infrastructure for molecular pathology (CRIP; www.crip.fraunhofer.de) are biobank networks or meta-biobanks displaying data on biospecimens stored at their partners’ hospitals and serving to acquire research projects for them.
As a Biological Resource Center, we made possible 233 research projects in the 2006–2010 period, most of them for multicenter cooperative groups, corresponding to 505 requests of tissue. The median impact factor of the 96 supported publications in this period was 6,355. We also gave sample and=or documental support to CNIO Molecular Diagnostic Unit (11.829 cases) and familiar cancer activities of the Human Cancer Genetics Program (454 cases), and directly participated in 29 collaborative projects and clinical trials (some of them still ongoing). The CNIO Tumour Bank Unit collaborates in training activities for undergraduate experts in health documentation and develops advisory activities for different emerging biobanks in Europe and Latin America. The Tumour Bank Unit is currently implementing new standards in biobanking according to the new Spanish legal framework for the use of human tissue samples in research. The Central Office of the CNIO TBNetwork was awarded with the ISO-9001:2000 Quality Certification in 2003, renewed in 2007.
NIR 06. Current Status of Biobanking in India U. Bora1, R. Tamuli1 1 Indian Institute Of Technology Guwahati, India, Guwahati, Assam, India
ABSTRACTS Background: India is a natural habitat to several thousand species of microbes, plants and animals that constitute about 8% of global biodiversity including 2.9% of the world’s threatened species. Therefore, India is recognized as one of the 12 megabiodiversity hotspot regions in the world. Among the ten ideas changing the world, listed in Time magazine in March 2009, biobanking is a vital one. Biobanking, an emerging field in India is nationally operated by central government and regionally managed by state governments. The public sector biobanks is comprised of 5 institutions, the National Bureau, gene banks, research institutes, hospitals and universities, which are involved in managing all kinds of biospecimens. Technological advances have made it feasible for India to establish Human DNA Bank in Lucknow as Asia’s first and world’s second Human DNA Bank for Human identification. Another unique type of biobanking found in India is the ‘‘Community Seed Bank’’, run and managed by local communities for themselves. Recently, some community seed banks have also been set up in partnership with government owned various plant breeding research institutes. Conclusion: Though the biobanking sector in India is quite diverse and vast, it lacks organization and coordination for a wider reach and impact. To ameliorate the various problems faced by the biobanking sector in India, currently an initiative has been projected by various institutes, universities and nongovernmental organizations to develop a connection amongst the biobanks for knowledge sharing, sustainable resource management, and a better outlook for future plans to bring forward biobanking in India.
85 1
Korea National Institute of Health, KCDC, Chungbuk, Republic of Korea Background: For the biotechnological research revival and diagnostic development of infectious diseases, we designed the Infectious Disease Biomarker Database (IDBD, http:==biomarker.cdc.go.kr) by web based platform on useful biological contents of biomarkers of pathogens for diagnosis, detection, protection, and characterization of infectious diseases. It supplies information of pathogens and biomarkers, which are the components for modeling and simulation of the infectious diseases and the biological processes. On the other hand, IDBD provides omics to information of biomarkers and the description of pathogens and diseases. It is a community annotation database utilizing collaborative Web 2.0 features and provides a comfortable user interface to enter and improve data on-line. It supports various types of data searches and the application tools to analyze sequence alignment, phylogenetic tree and structural characteristics of the potential and the validated biomarkers. Methods: At present IDBD integrates 1,826 16s rDNA sequence of the pathogens, 710 of biomarkers for the group with 11 diseases, 79 infectious diseases and 80 pathogens including bacterium, viruses, fungi and parasites. Researchers can use this web site as new information entry in the biotechnology field effectively. Conclusion: Contents in IDBD are freely accessible open to the general public. Also, we connect biomarker information with pathogenic resource of National Culture Collection for Pathogens (NCCP, http:==nccp.cdc.go.kr) to distribution service in Korea National Institute of Health (KNIH).
NIR 07. Korea Brassica Genome Resource Bank Y. Lim1 1
Chungnam National University, Daejeon, Republic of Korea
NIR 09.
Integrated Workflow for Digital Pathology in a Biospecimen Repository Environment
S. Abhange1, T. Barr1, A. Hobensack1, N. Ramirez1 Background: The purpose of establishing the Korea Brassica Genome Resource Bank is to maintain various genetic resources of the Brassicacea family including the Brassica rapa ssp. pekinensis (Chinese cabbage). These resources will be distributed on request internationally as well as domestically for research purpose. Moreover, the establishment and distribution of the genetic resources will help in strengthening the on-going research on Brassica genetics and genomics in Korea. 1) Distribution of Genetic Resources: Collection of genetic resources of various Brassica and related species with a wide range of traits, will be helpful in crop improvement. The genetic resource of wild species will play an important role for introducing new agronomically-important traits in the cultivated Brassica crops for improving their productivity, quality, and environment sustainability. Besides, mapping populations will be useful for construction of genetic maps, undertaking marker-assisted selection, and gene cloning. 2) Distribution of DNA Resources 3) Sub-goals of the research are as follows: 1. Development of integrated information systems of genetic resource; 2. Collection of genetic resources; 3. Long-term conservation of genetic resources; 4. Establishment of efficient distribution system; 5. Facilitating related studies; and 6. Supporting education and industrial application. NIR 08. Infectious Disease Biomarker Database (IDBD) K. Jung1, C. Yoo1, K. Lee1
1 The Research Institute at Nationwide Children’s Hospital, Columbus, OH
Background: The increasing demand for more expedient pathology review has led to the expansion of the field of Digital Pathology. The Biomedical Imaging Team (BIT) in the Biopathology Center (BPC), located at The Research Institute at Nationwide Children’s Hospital in Columbus, Ohio, has integrated digital pathology into its biorepository’s operations. The BPC currently serves as the biorepository for the Children’s Oncology Group and the Gynecologic Oncology Group as well as the pediatric division of the Cooperative Human Tissue Network and a Biospecimen Core Resource for The Cancer Genome Atlas (TCGA) project. This integration into banking operations has required the development of specialized applications to support the utilization of this technology. Methods: The BIT utilizes high-capacity scanners to generate high-quality whole slide images and uses its custom-built VIPER (Virtual Imaging for Pathology Education and Research) application to distribute images and QC review forms to reviewing pathologists. The images are uploaded to the Ohio Super Computer Center (OSC) where they are served to users in the United States and Canada. The OSC provides a reliable high performance computing and communications infrastructure and has allocated 50 terabytes of storage capacity to support digital pathology initiatives at the BPC. Results: The integration of digital pathology into BPC’s workflow has decreased pathology review turnaround times and eliminated shipping costs for many projects. Simplified logistical
86 operations have resulted in an overall increase in operational efficiency. Conclusion: This disruptive technology is allowing the BPC to overcome many of the disadvantages of traditional glass slide pathology review. NIR 10. Achievements of the Australian Prostate Cancer BioResource: First 5-Year Round of Funding 2004–2009 J. Clements1, G. Risbridger1, R. Sutherland1, W. Tilley1, D. Horsfall1 1
Australian Prostate Cancer BioResource, Kelvin Grove, Queensland, Australia Background: Funding for the Australian Prostate Cancer BioResource (APCB) network has been renewed by the NHMRC & PCFA for 2010–2014. This funding is to continue the prospective collection of tissue from men with early stage prostate cancer treated by radical surgery for another 5 years to allow 10 year outcome data to start to be accrued. Methods: Tissue is collected from daVinci robot-assisted laproscopic prostatectomy (RALP) as well as retropubic radical prostatectomy (RRP). Results: Over the last 5 years 2,894 participants have been recruited with accrual of 1560 (54%) fresh frozen prostate and 1,871 (65%) blood samples. Although collection and processing times can be different between RALP and RRP, histological examination and RNA extraction performed on representative cohorts showed no difference in tissue histology, RNA integrity or gene expression by quantitative RTPCR for several genes between the 2 procedures, thus allowing a larger pool of tissues for distribution. Over the last 3 years, 1,477 tissues have been distributed nationally leading to 6 publications to date. 336 samples from the Brisbane cohort have been used for genotyping in the PRACTICAL genome-wide association studies. Conclusion: At 5 years, the APCB has a collection of high quality prostate cancer tissues with associated blood samples and clinical and pathological data acquired at diagnosis and surgery. This collection has become an important bioresource for prostate cancer research nationally and internationally. With maturity and accrual of *5,500 men by 2014 with 5–8 year clinical follow up it will become an even more significant research resource. REPOSITORIES/PLANT/SEED REPOSITORIES PSR 01. Plant Biorepository Management in North East India – The Nature’s Biorepository S. Ghosh1, L. Rangan1, R. Tamuli1, N.C. Talukdar2, U. Bora1 1
Indian Institute of Technology Guwahati, India, Guwahati, Assam, India; 2Institute of Bioresources and Sustainable Development, Imphal, Manipur, India Background: North East region (87832’E to 97852’E latitude and 21834’N to 29850’N latitude) of India is a part of the Vavilovian center of origin for several cultivated important crop plants. Climate of the region ranges from Alpine to tropical, 85% of its landmass is mountainous and inhabited by 87 tribes with rich indigenous knowledge of plants. A preliminary survey showed that despite of richness of plant biodiversity, biobanking and biorepository management in the region has been largely in a state of infancy. Methods: The region houses more than 500 orchid species, 10% medicinal plants out of 5,000 angiosperms, 91 species of
ABSTRACTS Zingiberaceae with 22 genera and 151 types of citrus. The ethnic community of the hills maintains a unique set of medicinal plants and indigenous health system. To check the genetic erosion of these rich gene pools, on farm conservation practices have been implemented in the hilly regions. Few germplasm banks of orchids and two research centers for orchids as well as citrus are nascent but vital initiative for the management of biorepository. Conclusion: Several rice research centers maintain a set of more than 50 percent of estimated 10,000 rice landraces of the region and is a spearheading effort towards plant biorepository management. A recent joint initiative between the Indian Institute of Technology Guwahati and Institute of Bioresources and Sustainable Development, Imphal is expected to strengthen plant biobanking with equitable sharing of potential resources and expertise in efficient management of plant bioresources and develop strategy to advance plant biorepositories in the region. REPOSITORY OPERATIONS/BIOSPECIMEN SCIENCE BSS 01.
High-Throughput DNA Extraction and Normalization from Saliva Results in High-Quality DNA for Genotyping and Telomere Analysis
S.Q. Miles1, K.A. Lapham2, S.A. Connell1, C. Aquino1, S. Rowell1, C. Schaefer1 1
Kaiser Permanente Northern California, Oakland, CA; 2University California San Francisco, San Francisco, CA Background: Kaiser Permanente’s Research Program on Genes, Environment, and Health is using saliva as a source of DNA for a NIH-funded project that requires genome-wide genotyping and measurement of telomere lengths on DNA samples from 100,000 individuals; the resulting data will be merged with clinical, survey, and environmental information on the same individuals to create a new research database. DNA was extracted and normalized from more than 120,000 biospecimens in 15 months. To our knowledge, this is one of the largest human DNA extraction projects ever attempted, and the largest to extract DNA from saliva. Methods: Saliva was collected using OrageneÒ kits and was stored at room temperature for 0-3 years prior to extraction. Specimens were weighed and visually inspected prior to DNA extraction with a magnetic bead kit. DNA samples were quantified by PicoGreenÒ and normalized to 30ng=uL for telomere length measurement and 10ng=uL for genotyping assays. Results: 2.5% of saliva biospecimens were excluded from extraction due to particulate matter or low volume. The average DNA yield was 4.86 micrograms per 0.5mL saliva. DNA purity (A(260=280)) ranged from 1.5-1.9. Genotyping results on the first 58,000 samples show a sample success rate of >93%. Preliminary telomere length measurement results show a CV of 24 hours), lowered RIN values. Histology predicted the RIN score for most organs, but not in the pancreas and small intestine. The heart and lung tissue had the highest RIN values (7.1 and 5.8 average, respectively) across the four cases. Conclusion: RIN values in most tissues, except the GI tract, was highly correlated with the clinical medical history and agonal state, and was not influenced by the PMI. Quick refrigeration of the body after death may preserve both post mortem histology and RIN values. BSS 06. Stability of Extracted RNA at Various Storage Temperatures and through Multiple Freeze-Thaw Cycles J. Wu1, L. Kim1, C. Huang1, B. Anekella1 1
SeraCare Life Sciences, Inc., Gaithersburg, MD
Background: RNA degradation during storage makes samples unusable for assays including reverse transcription, in vitro translation, differential display, expression-array and expressionchip analysis. RNA degradation during storage results primarily from base hydrolysis of RNA under low pH conditions or divalent cation catalysis. The effects of different storage temperatures and freeze-thaw regimens on RNA stability during storage are investigated. Methods: Tissue sample RNA was extracted using the Qiagen RNeasy Kit. RNA concentration was adjusted to 300 lg=mL using ultra-pure water. RNA was aliquoted into single-use aliquots and stored at room temperature (RT), 48C, or 208C. Samples were tested after 0, 1, 2, 3, 7, 14, and 28 days of storage. Testing, in duplicate, included concentration, ribosomal RNA ratio (28S:18S), and RIN number. Similarly, a subset of samples were placed at either 808C or 208C and subjected to ten freeze-thaw cycles. Results: RNA stored at RT was stable through 7 days, declining in all three test parameters at 14 and 28 days. No declines in RNA concentration, rRNA ratio, or RIN number were observed for RNA stored at 48C or 208C. RNA cycled between 208C or 808C and RT for 10 freeze-thaw cycles had no concentration or integrity decline. Conclusion: RNA stored in an appropriate buffer is resistant to degradation under sub-optimal conditions encountered during accidental mishandling or shipping delays. Frozen RNA samples can be thawed multiple times without compromising quality. For short-term studies, RNA can be stored at 48C or 208C. RNA at RT showed degradation after 7 days. BSS 07. Genome-Wide Germline Genotypes from Normal Tissue Stored in FFPE Samples L.A. Cannon-Albright1, K.G. Cooper2, A. Georgelas2, P.S. Bernard2 1 University of Utah, Salt Lake City, UT; 2Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
Background: Although large collections of formalin fixed paraffin embedded (FFPE) samples exist, sometimes represent-
ABSTRACTS ing decades of stored samples, they have not typically been considered as a useful resource for studies requiring genomewide genotyping of normal cells. Normal tissue from such samples, however, would be extremely valuable for generation of genotype data for individuals who cannot otherwise provide a DNA sample. Methods: In order to determine the value of using FFPE tissue blocks as a source of normal ‘‘germline’’ DNA for genotyping experiments, we assessed the quality and yield of genome wide (GW) genotyping data generated from archived FFPE tissue aged 18–41 years. Grossly uninvolved regions of tissue from prostate cancer cases were identified and DNA was extracted from corresponding punches in the original FFPE tissue block. GW genotyping was performed using the Illumina 610Q platform. Results: The genotyping call rates for the FFPE samples ranged from 0.873 to 0.989. Additionally, we observed a range of 0.993-0.9998 reproducibility in genotyping calls when we compared results from DNA isolated from whole blood versus normal tissue from FFPE. Conclusion: Our results indicate that DNA extracted from normal tissue in FFPE (even decades old) provides excellent quality GW genotyping data. Overall, this study provides an innovative solution to procuring GW genotyping data for informative individuals not otherwise available for sampling by using stored FFPE blocks. BSS 08.
Software for Generation of Multigene Expression Signature Maps at the Protein Level from Digitized Immunohistochemistry Slides
S. Schmechel1, S. Dankbar1, J. Henriksen1, A. Rizzardi1, N. Rosener1, J. Koopmeiners1, G. Metzger1 1
University of Minnesota, Minneapolis, MN
Background: Biorepositories provide essential specimens for discovery and validation of diagnostic, prognostic and predictive biomarkers. Among validation methods, immunohistochemistry (IHC) is optimal for gene expression profiling (GEP) at the protein level in routine clinical samples. However, analytical methods to perform GEP using standard IHC are lacking. Methods: We developed software that interacts with a wholeslide imaging platform to digitally align slide images to an annotated H&E-stained reference slide, quantify IHC stains in annotated areas, and compute a weighted sum of n-gene expression values. The software provides a tiled display of GEP data (termed a signature map) to reveal heterogeneity within disease areas. For purposes of illustrating software features, we produced a four-gene signature map (representing MKI67, ENO2, CD34 and ACPP gene products) on prostate cancer tissue. Results: Mean aggressiveness signature score (SS) increased with grade from 1.2 for 3 þ 3 tumor areas, indicating nonaggressiveness (negative value due to low expression of aggressiveness genes MKI67, ENO2, and CD34, each with a positively-signed weighting factor, and high expression of nonaggressiveness gene ACPP, with negatively-signed factor), to a mean of 2.1 and 6.9 for 3 þ 4 and 4 þ 3 areas, respectively. Differences in the standard deviation of SS were observed by grade (3 þ 3 SD ¼ 4.71, 3 þ 4 SD ¼ 5.81, 4 þ 3 SD ¼ 4.14), suggesting that the standard deviation, as well as other measures of heterogeneity, may also be useful for predicting aggressiveness. Conclusion: The IHC signature map approach may have broad applicability for validating multigene diagnostic, prognostic and predictive disease classifiers using routine clinical specimens.
ABSTRACTS BSS 09. Effect of High Temperature Thawing on PTEN Enzyme in Human Uterine Tissue T.J. Kokkat1, L.C. Lovecchio1, D. McGarvey1, V. LiVolsi1 1 Cooperative Human Tissue Network (ED), University of Pennsylvania, Philadelphia, PA
Background: Degradation of proteins during the preparation and storage of tissue lysates is an ongoing challenge in proteomic research. During lysate preparation, enzymes and their substrates are brought into closer proximity thereby increasing the chance of enzymatic modification of the substrate (e.g. dephosphorylation by phosphatases). Traditionally, enzymatic activity is decreased through the use of protease and phosphatase inhibitors. However, the introduction of these exogenous inhibitors might interfere with downstream analysis. One demonstrated way to inactivate enzymes without the use of chemical inhibitors is to use heat during thawing. In earlier studies we demonstrated the effectiveness of high temperatures in reducing tyrosine phosphatase activity. In this study, we investigated the inactivation of PTEN enzyme in uterine smooth muscle tissue by comparing high heat thawing with more traditional methods of thawing. Methods: Frozen uterine smooth muscle samples were thawed in the oven (378C), on ice (48C), or at 958C using the heat Stabilizor T1 from Denator AB. Frozen tissues were used as controls. Tissue lysates were prepared without enzyme inhibitors and PTEN Phosphatase activity was assayed using the pNPP Protein Phosphatase Assay kit. Results: Our results indicate that in comparison to frozen controls and tissues thawed at 378C and 48C, specimens thawed using heat stabilization (958C) had a significant reduction in PTEN activity. Conclusion: The use of high temperatures is optimum for thawing tissue by decreasing the amount of enzymatic activity, thereby better preserving the proteome. BSS 10. A Survey of Tissue Specimen Collection Techniques: Impact on Biomarker Data Quality A.C. Allen1, J.A. Sutton1, J.M. Martin1, N.L. Todaro1, R.V. Mulpuri1, J.M. Otto1 1
Catholic Health Initiatives, Towson, MD
Background: Prognostic and diagnostic biomarker development is currently hindered by access to high quality, clinically annotated biospecimens. To address this limiting factor for translational research, we established a state-of-the-art biorepository facility to procure clinically annotated biospecimens from remote network locations, and isolate high quality nucleic acids for long-term storage and molecular analysis. We describe here a long-term project comparing methods of sample collection and storage, including stabilization media, on the quality of RNA for genomics research. Methods: Tissues known for the presence of high and low RNAses (kidney=liver and colon=lung, respectively) were collected as FFPE, fresh, frozen in Liquid Nitrogen (LN2), frozen with stabilization media (RNAlater), and LN2 frozen tissues post-treated with stabilization media (RNAice). Total RNA isolated from all tissues was assessed for quality, and analyzed using expression arrays. Results: At zero time point, no major differences in RNA quantity were observed due to collection and storage treatments.
89 Further analysis of RNA quality with QC arrays revealed intact RNA free of inhibitors of reverse transcription and PCR amplification, genomic and general DNA contamination. Hierarchical clustering of Oncogene and Tumor Suppressor genes revealed three distinct groups; 1) Fresh, LN2 and RNAice, 2) RNAlater and 3) FFPE suggesting that RNA stabilization treatments may influence gene expression patterns. Conclusion: Currently, experiments are underway to assess the RNA quality on global gene expression patterns and establish a baseline, to be compared to the RNA quality and gene expression patterns at 6, 12 and 24 month post-collection. BSS 11. Genomic DNA as a Quality Indicator for Whole Blood Storage J. Wu1, J. Cunanan1, T. Kulatunga1, C. Huang1, B. Anekella1 1
SeraCare Life Sciences, Inc., Gaithersburg, MD
Background: Whole blood is frequently shipped and stored for clinical trials, R&D efforts, and longitudinal studies. Genomic DNA is then extracted for various molecular biology applications including genotyping, sequencing, and PCR amplification. This study compares yield and quality of DNA extracted from whole blood exposed to varying stress conditions. Methods: Whole blood was aliquoted and incubated at 48C for up to two weeks to determine acceptable 48C holding time. Aliquots were also subjected to three freeze-thaw cycles. White blood cells were counted and DNA was extracted using the Qiagen=Gentra Autopure LS. Extracted DNA was quantitated using the Spectramax spectrophotometer to determine yield, and quality assessed by genomic gel electrophoresis and PCR to the b-globin locus. Results: Storage of whole blood at 48C for 7 days had no effect on extracted DNA quality and quantity. Statistically significant declines in DNA yield, *25% less DNA, occurred at 14 days; however, the genomic DNA appeared intact by gel electrophoresis and gave acceptable PCR results. In contrast, freeze-thaw cycles dramatically affected DNA yield and quality. One freezethaw cycle reduced genomic DNA yield by half, two cycles produced extremely low DNA yields with variable A260=280 ratios; the DNA showed visible smearing by gel electrophoresis, with variable PCR results. Conclusion: Whole blood can be safely stored or shipped at 48C for up to 7 days without significant effects on yield or quality of extracted genomic DNA. Freeze-thaws of whole blood significantly affect the extracted DNA quality and quantity. BSS 12. High-Throughput Extraction of Compromised Whole Blood Samples for Genetic Analysis: Implementation of the Chemagic STAR in a Genetics Repository R. Gaglione1, M. DiCola1, A. Lopez2, C. Piccirillo3, A. Bonk3, A. Brooks1 1
Rutgers University, Piscataway, NJ; 2Chemagen USA, Worcester, MA; 3Hamilton Robotics, Reno, NV
Background: Genetic analysis continues to evolve with the utilization of novel technological approaches that require specific sources of genomic DNA. DNA from whole blood is becoming more important in the biomedical research environment with the introduction of epigenetic analyses. To this end, all whole blood sources of DNA, including compromised samples and archived
90 resources, are critical for analysis. In addition, existing large collections (based on retrospective sampling) require a robust high-throughput approach to maximize the yield of DNA from each sample while retaining the highest quality nucleic acid. Methods: The unique challenges of extracting DNA from various volumes of compromised and frozen whole blood samples require extraction chemistries and automated solutions that ensure a high level of success with these precious samples. This presentation describes the protocol development and implementation of the chemagic STAR for frozen whole blood samples. The integration of chemagen’s bead-based chemistry (with modifications for sample source and volume) with the Hamilton STAR creates a robust workflow that maximizes the yield and quality of compromised blood samples, provides a fully integrated ‘‘walk away’’ workflow that catalogues all DNA stocks, and prepares samples for analytical and functional quality control. This platform is tunable from 1ml to 10ml in single extractions providing the flexibility needed for large biorepository projects where samples are processed across many different collections. Conclusion: Both analytical and functional analyses are performed on all DNA samples and are described in this presentation to document the quality and downstream utility of this extraction approach. BSS 13. Proteomic Analyses of Colorectal Tumors by Electrospray Ionization (LC-ESI) and Split Sample Strategy: Effects of Formalin Fixation and Extraction Methods on Peptide Identification G. Hostetter1, M. Syring1, A. Watanabe1, E. Suh1, A. Polpitya1, L. Nagore1, S. Jewell2, J. Trent1, K. Petritis1, C. Selinsky1 1
Translational Genomics Research Institute, Phoenix, AZ; 2Van Andel Institute, Grand Rapids, MI Background: We have extended high performance discoverybased assays to DNA harvests from formalin-fixed paraffinembedded (FFPE) tissue collections. Proteomic surveys of solid tumors present challenges in accurate measures of cross-linked and degraded proteins and peptides. Several studies have shown good spectral correlation with fresh frozen (FF) and FFPE tissue samples but are of limited spectra. Methods: Six colorectal cancer specimens, disparate phenotype by genomic instability, were selected for this multi-tiered comparative study. FFPE scrape macrodissected samples were extracted by Qproteome (Qiagen, Inc) and Liquid Tissue (Expression Pathology, Inc). FF split samples were visualized by 2 ink QC method and histological tumor estimate or obtained by LCM method to include protease inhibitors. FF extractions were performed by Invitrogen kit and by Petritis lab method. A total of 24 protein preparations were analyzed by tandem LC-MS by Orbitrap electrospray ionization (ThermoShandon,Inc). Results: Tumor content was estimated at 30–60% for scrape macrodissected (FFPE) and FF chipped samples. LCM harvests were >95% tumor and 12,000 to 15,000 cells collected. FF & FFPE aliquots showed similar yield, but much sharper bands in FF gels. Slight variance in the peptides was detected in FF and much larger variance in FFPE. Conclusion: Discovery-based proteomics in FF preserved solid tumors is highly informative, but requires detailed sample preparation. FFPE samples with high SDS (Qprotoeme kit) may have limited tryptic digest. Heating of the FFPE sample appears to be critical for efficient protein extraction but could further degrade proteins. Our results indicate limited utility for FFPE samples in whole proteome analyses.
ABSTRACTS BSS 14.
DNA Extraction from Frozen Serum Samples: An Automated Approach for Genetic Analysis Utilizing Qiasymphony Purification and Repli-G Whole Genome Amplification
T. Giesler1, R. Gaglione1, D. D’Ambrosia1, J. Qin2, D. Kobi2, A. Brooks1 1
Rutgers University, Piscataway, NJ; 2Qiagen Inc., Germantown, MD
Background: Tremendous resources are used for the collection of clinical samples in research trials worldwide. Occasionally the analytical criteria for some studies are not well defined based on fiscal and technological uncertainty at the time of project initiation. To this end, there are large numbers of samples stored from various clinical protocols which are currently not considered for mainstream analyses. One example of this is serum and plasma samples which are typically stored for specific analyte interrogation where no other molecular components were collected for additional analyses. Methods: This presentation describes the use of serum (and plasma) derived from whole blood for DNA based genetic and genomic analyses. Given the low quantity and variable quality of this DNA that is mostly cell free, the method of extraction and validation of nucleic acid following processing is of paramount importance. We will describe a fully automated, high throughput, extraction and amplification workflow for these precious clinical isolates. The details of the protocol and QIAsymphony implementation will be discussed specifically in the context of a biorepository setting. Additionally, every nucleic acid sample is subjected to Repli-g amplification in an automated process to maximize the utility of these biological resources for future analyses. Conclusion: The technical issues addressed in these protein rich, cell free fractions include but are not limited to: shearing and nicking of gDNA, clotting of samples during the extraction process, low molecular weight DNA retention, and variable amounts of gDNA yields per sample. REPOSITORY OPERATIONS/CRYOGENICS AND CELL PRESERVATION CCP 01. The Biopreservation Core Resource (BioCoR): A Resource Based on the Science of Biospecimen Preservation A. Hubel1, A. Aksan1, A. Skubitz1 1
University of Minnesota, Minneapolis, MN
The mission of the Biopreservation Core Resource (BioCoR), located at the University of Minnesota, is to advance the science, technology and practice of preservation. BioCoR is not a biorepository=biobank but consists of three distinct resources. The first component consists of a research resource whereby new methods of preserving biospecimens and new technologies to improve biospecimen processing are developed. BioCoR faculty members are actively involved in the development of new methods of preservation, understanding molecular mechanisms of damage, and the development of protocols for specific biospecimens. Secondly, BioCoR has an education resource for educating individuals and institutions on biopreservation. BioCoR offers an annual short course which covers topics such as the scientific basis for preservation, different preservation techniques, facility design, protocol development, as well as quality and regulatory issues in biopreservation. The course is offered on the web in addition to in-class participation. In early 2011, BioCoR faculty provided a
ABSTRACTS webinar entitled, ‘‘Quality in Biopreservation’’ which was endorsed by ISBER and attended by over 120 people. BioCoR’s third component is to act as a service resource for those who need assistance in developing biopreservation protocols for specific biospecimens, evaluating existing protocols, and providing literature summaries of the scientific knowledge related to the preservation of specific biospecimens. This third component of BioCoR is especially important since biobanks typically do not have the resources or expertise to develop new protocols and methods of preservation. In summary, BioCoR fills a niche in the field of biobanking that biobanks alone do not serve. CCP 02. Cryogenic Tracking and Monitoring (bluechiipÔ) For Hematopoietic Progenitor Cell Biostorage: Comparison of Manual and Automated Technologies J. Chaffey1, P. Gambell2, A. Mouminoglu2, M. Miljanic1, H. Prince2, L. Miranda3 Bluechiip Ltd, Scoresby, Victoria, Australia; 2Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia; 3Biobusiness Consulting Inc, Lowell, MA
1
Background: Cryopreservation of hematopoietic progenitor cell (HPCs) at 1508C for later use requires HPCs to be stored for several weeks to many years. To ensure quality preservation and interpretation of cellular integrity, HPC material must be appropriately identified, stored, monitored and tracked. Methods: The MEMS tracking device was attached to five medium sized Baxter cryocyte cryopreservation bags containing saline. The aim of the pilot trial was to assess the ability of MEMS technology to consistently measure cryogenic temperature and compare the MEMS tracking capabilities to current manual methods. The on-site trial commenced with identification and initial temperature measurement of the bags. The bags were then transferred to cryogenic storage where they underwent freezethaw cycles. Results: Tags on all bags at both room temperature and 1508C were successfully verified with no failed reads. Conclusion: The MEMS tracking technology demonstrated accurate readings for tracking temperature at 1508C. The MEMS technology appears to offer consistent improvements in decreased tracking labor time over manual methods. Secondly, implementation of the MEMS technology reduced the propensity for damage to biostorage containers and handlers alike. Further investigations with larger sample sizes are warranted to investigate application of the MEMS technology for biobanking cryopreservation, in particular reduction of freeze thaw cycles. CCP 03. Preserving Functionality and Differentiation of Frozen Peripheral Blood Cell Subsets for Repeatable and Large Scale Immunological Studies T. Di Pucchio1, C. Glover1, B. Anekella1
91 vation, processing, and media protocols to isolate and maintain functionality and differentiation in cryopreserved PBMC subsets. Methods: PBMC were collected by leukapheresis; purified cell subsets were isolated using RoboSep Stem Cell Technology. After purification, cells were resuspended in freezing media, frozen in a rate-controlled freezer, and stored in vapor phase liquid nitrogen. Testing included post-thaw cell recovery counts, viability and purity assessments. Fresh and frozen PBMC and lymphocyte cell subsets were tested for proliferation and IFN-g production. Fresh versus cryopreserved monocytes were tested for differentiation into dendritic cells. Results: Frozen PBMC, purified monocytes, and T cell subsets all showed viability greater than 85%. Furthermore, frozen PBMC and purified CD3, CD4, and CD8 T cell subsets maintain a similar ability to proliferate and produce IFN-g in response to specific peptide antigen stimulation when compared to fresh cell subsets. Notably, fresh and frozen purified monocytes were able to differentiate into phenotypic and functional dendritic cells with the capability to stimulate allo-CD3 proliferation. Conclusion: A combination of upstream and downstream handling conditions, standardized cryopreservation protocols and optimized freezing medium allow cryopreservation of PBMC and cell subset populations and preservation of their functionality capabilities. CCP 04. The Integrity Study: Measuring the Impact of Sample Preparation Techniques and Storage Temperatures on the Integrity Of DNA C. Michael1 1
BioStorage Technologies, Indianapolis, IN
Background: To outline the design of a 24-month longitudinal study that analyzes the impact of storage practice methods in regards to the long-term yield integrity of nucleic acids. The poster will compare the use of various aliquoting schema and storage temperatures and highlight the benefits via an end report employing a failure mode and effects analysis. Methods: The study analyzes the various storage methods of nucleic acids when comparing extraction yields on fresh sample, frozen pre-extracted samples, and extracted nucleic acids which require freeze=thaw cycles for processing. Various storage temperatures and aliquoting strategies will be evaluated over a 24month period subsequent to a single patient collection event. Results: The poster will outline study design and discuss the data to be reported. Various methods and procedures to capture and store samples for future research purposes will be discussed and the plan for measuring the impact of preparation method and temperature on nucleic acid sample integrity will be outlined. Conclusion: During drug development, clinical trial samples must be securely managed and properly stored to support prospective or retrospective nucleic acid analysis. The goal of the INTEGRITY study is to determine the best method for preparing samples and the best temperature to store samples for future research.
1
CCP 05. Cryopreservation of Cell Lines in the National Institute of Hygiene ‘‘Rafael Rangel’’
Background: Peripheral blood mononuclear cells (PBMC) are used for immunological monitoring in clinical studies, as primary cells in basic research, and as infection models. Handling and preservation methodologies enable longitudinal studies across multiple sites with greater consistency across PBMC lots. In an ongoing effort, we have further extended our cryopreser-
A.C. Oyarzabal1
SeraCare Life Sciences, Inc., Gaithersburg, MD
1
National Institute of Hygiene, Caracas, Dtto. Capital, Venezuela
Background: The Cell Culture Department of the National Institute of Hygiene "Rafael Rangel" is responsible to produce,
92 preserve, manage, and maintain 15 cell lines from different sources such as hamster kidney, mosquito larva, human laryngeal carcinoma, dog kidney, rabbit kidney, green monkey kidney, and others, which are used as biological substrate for viral diagnosis, investigation and research, viral vaccines production, and biological products control. Methods: In response to the needs of providing cell lines, the main objective is to give response of the needs of providing cell lines, the main objective is the preservation of strains without morphological, physiological, and genetic changes. Therefore, the Cell Culture Department maintains and stores cell lines from certified institutions like the American Type Culture Collection (ATCC) and the Center of Disease Control and Prevention (CDC), using freezing medium with 15–20% Fetal Bovine Serum (FBS) and Dimethyl Sulfoxide (DMSO) as cryoprotective agent. The freezing method is with a controlled-rate of freezer that decreases the temperature 18C per minute. The cell lines are amplified to obtain a sufficient cell suspension to prepare the master and working banks to cover the needs of the Department. To ensure that they are free of contaminants, sterility controls are performed to detect bacteria, fungi, and mycoplasma. Conclusion: Conservation of the proper cell lines conservation is important to respond the needs of the users, ensuring appropriate quality certification of the cell lines. CCP 06. Tissue Cryopreservation: Long Term Storage of Tissue Samples in Liquid Nitrogen K. Sabai1, I. Cheong1, S. Lok1, S. Tan1 1
Singapore Health Services Pte Ltd, Singapore, Singapore
Background: Our repository has a collection of frozen gastric cancer with matched normal control tissues dating back to more than a decade ago. Methods: The samples have been snap frozen and stored in liquid nitrogen (vapor phase). In this study, we set out to determine if the quality of nucleic acids in 2 groups of matched gastric samples have altered significantly during long-term storage. Group A (n ¼ 32) consists of normal and tumor tissues harvested in 2010 whilst Group B (n ¼ 24) comprises samples that were harvested between 1997-98. Nucleic acid concentration and purity are assessed spectrophotometrically based on A260=280 ratio and gel electrophoresis is performed to determine integrity of DNA and RNA. Results: There is no significant difference in the yield of RNA (p ¼ 0.1748) or DNA (p ¼ 0.3840) from samples in Groups A and B. Similarly, the average A260=280 ratio for RNA in Groups A & B are comparable at 2.05 þ 0.075 and 2.07 þ 0.06 respectively. For DNA, the average readings are 1.88 þ 0.11 for Group A and 1.81 þ 0.15 for Group B. Based on the presence of distinct 28S and 18S rRNA bands, gel analysis shows intact RNA in 50% of samples in Group A and 37.4% in Group B. DNA integrity is good with all samples showing a band size of over 12kb for both groups. Conclusion: Our preliminary data indicates no significant difference in the yield of nucleic acids with prolonged storage. Likewise, the quality of DNA is not affected, although RNA integrity appears to be poorer in older samples. REPOSITORY OPERATIONS/DISASTER RECOVERY DR 01. Disaster Recovery: An Off-Site Expansion of Biorepository Operations L.C. Monovich1
ABSTRACTS 1
The Research Institute at Nationwide Children’s Hospital, Columbus, OH Background: The Biopathology Center, biorepository for two NCI Cooperative Groups, receives tens of millions of dollars annually from the NIH to conduct scientifically-driven clinicallyrelevant oncology trials at 500 institutions across the United States. These highly successful programs have vastly improved quality of life and survival of cancer patients and collected invaluable research specimens to allow for decades of high quality medical research. The 20 years worth of biospecimens are the tangible product of hundreds of millions of federal dollars spent during this time. Methods: The satellite biorepository was constructed to not only allow for growth at the existing site, but to provide redundant storage of biospecimens. To preserve at least a portion of each biospecimen in our repository, we have built a facility geographically separate from the Research Institute campus. Unless the specimen has insufficient material, duplicate aliquots will be sent to the secondary site as insurance against natural disasters, criminal activity, or other catastrophic events. By storing a piece of each tumor at two sites, the risk of completely losing a specimen is greatly reduced. Results: A build-out of 4,400 square feet of shelled space offsite to accommodate two years of projected growth with the ability to expand into 15,000 additional square feet to accommodate ten years of projected growth. Conclusion: The Biopathology Center has created a redundant, satellite biorepository to allow for storage of biospecimens in separate locations, each with backup power and 24 hour environmental monitoring. This will reduce the risk of catastrophic loss of specimens. REPOSITORY OPERATIONS/‘‘GREEN’’ REPOSITORY SOLUTIONS GRS 01. Dry Storage of Biospecimens for an East Asian Glioma Genome Wide Association Study (GWAS) L. Nordstrom1, G. Hostetter 1, S. Wilkinson2, R. Muller 2, J. Muller-Cohn2, A. Watanabe1, M. Syring1, W. McDonough1, M. Berens1 1
2
Translational Genomics Research Institute (TGen), Phoenix, AZ; Biomatrica, San Diego, CA
Background: An international consortium was formed to collect biospecimens in East Asia from 4,000 glioma and 4,000 control participants to identify genetic variants associated with glioma risk. The study will collect biospecimens supportive of post-GWAS experiments to identify how these genetic variants affect tumor biology. A pilot study was initiated at six sites in four Asian countries to demonstrate performance of biospecimen collection, preservation, and shipment to the Translational Genomics Research Institute (TGen) or a collaborating Chinese laboratory. Methods: Blood from 10 glioma cases and 10 controls at each site is stabilized (Biomatrica’s DNA stable blood) then shipped at ambient temperature. Glioma tissue samples are split for flash freeze (-808C) or stored at ambient temperature (Biomatrica’s DNA guard tissue). Biospecimens are shipped to TGen (USA) or the Chinese lab for quality control assays. A cost analysis of shipping and storage costs for frozen versus ambient temperature biospecimen preservation is in process. Results: Quality control of biospecimens will be presented, including quality and yield of DNA extracted from blood and
ABSTRACTS tumor samples and H&E analysis of tumor samples. A savings of US$13,330 was estimated for shipping all samples at ambient temperature, while an additional US$10,000 is projected to be saved in storage costs. Conclusion: It is our expectation that the use of dry storage products for blood and glioma tissue preservation will significantly decrease the cost of biospecimen collection and processing, without a loss of analyte quality. Ambient stabilization of biospecimens for research drastically reduces the risk of failed repository responsibilities. GRS 02. Room Temperature Preservation of RNA Derived from Clinical Samples W. Mojica1 1
93 tected from the atmosphere in airtight, laser sealed stainless steel containers. Apparent degradation rates are measured by determining the average fragment size by gel electrophoresis. Results: Accelerated aging kinetics show some differences among the degradation rates of the samples but there is no apparent correlation between the degradation rates and either the DNA origin or its extraction procedure. Most importantly, a heatsimulated 100 year storage period (simulation conditions being determined from Arrhenius plots) does not lead to any detectable degradation of the samples. Contamination nature, degree, and effects on stability will be further investigated. Conclusion: Regardless their origin and their procedure of extraction, routinely purified DNA samples can be reliably stored at room temperature when efficiently protected from air. Therefore this "green" procedure does not compromise the quality of the stored samples.
University at Buffalo, Buffalo, NY
Background: Preservation of RNA at room temperature (RT) offers several advantages from traditional frozen specimens in terms of cost, space and energy. A commercial product (GenTegra) has recently become available that purports to enable RT stabilization of RNA samples in a dessicated matrix. An assessment of the capabilities of this product with regards to RNA integrity of clinical specimens would be of benefit for all biobanks. Methods: 25 tissue specimens were procured at the time of resection. For every case, the time between receipt and freezing of the tissue specimen was
