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Biological sample Collection, Processing and Banking for Academic Centers

“ Biorepository” Workshop, Milan, Italy, October 22, 2002. Biological sample Collection, Processing and Banking for Academic Centers. Nina Holland School of Public Health, University of California, Berkeley, CA ninah@uclink4.berkeley.edu. Superfund Center. Biomarkers of Carcinogenesis

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Biological sample Collection, Processing and Banking for Academic Centers

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  1. “Biorepository” Workshop, Milan, Italy, October 22, 2002 Biological sample Collection, Processing and Banking for Academic Centers Nina Holland School of Public Health, University of California, Berkeley, CA ninah@uclink4.berkeley.edu

  2. Superfund Center Biomarkers of Carcinogenesis Project 1 New Methods Samples Data Arsenic Biomarker Epidemiology Project 3 Chemical Exposures And Leukemia Risk Project 2 Core B Biomarker Lab Samples Samples Data Data Management System Information of Relevance to Children’s Health Samples Samples Core D Outreach: Children’s Environmental Health Network Core C Computer and Statistical Support Determinants for Chromosomally Defective Human Sperm Project 4

  3. A Community-University Partnership Children’s Hospital Oakland Research Institute

  4. Goals of the database system: • Centralize information • Optimize the use of storage space • Minimize errors and inconsistencies • Facilitate sample tracking (bar-coding) • Be compatible with other databases • Allow flexibility and expansion

  5. Benefits of Biorepository • Maximize the utility of the specimens as new tests are developed. • Provide a specimen bank for future intra-Center collaboration. • Provide a specimen bank for development of new methods. • Source of numerous student projects. • Better chances for extramural funding

  6. Biorepository at UC Berkeley: • Whole blood • Buccal cells • Urine and urothelial cells • Blood (plasma, serum, viable • lymphocytes, COMETstabilized, folate stablized, • granulocytes etc.) • Cryopreserved lymphocytes • Isolated RNA and DNA • Plasma • Red blood cells • Blood smears • Breast milk • These samples come from selected populations including pregnant women, children, lab volunteers, children with disease • Dust samples

  7. Present Status CHAMACOSSamples Collected

  8. Biorepository includes: • Inventory of already accumulated samples • In progress , samples in the process of collection • Provisions for samples from future projects

  9. Sample Sources for Biorepository • Projects: 3-7 • 2. Study subjects per project: 15-500 • upcoming several 1000’s • 3. Number of aliquots per individual: 12-70

  10. Whole blood processing for Superfund project CA Tubes x1 4oC 9 ml media 1 ml WB CA Harvest Protocol CA Slides x10 -20oC Whole Blood Cultures 1ml x2 Plasma -80oC 2 ml 1 ml Green Top (Heparin) 1 ml CA MN Harvest Protocol 1.8ml x2 Lymph Cryo 1 ml MN Slides x10 -20oC MN 0.5 ml x2 WB -80oC 9 ml media 1 ml WB 1.8ml x2 Gran Cryo 200 ul 200 ul 9 ml 1ml x2 RBC -80oC ~400 ul Comet Assay 100ul, x2, -80oC 100ul x2 Fol -80oC Blood Smears x6 -20oC Remaining WB Ficoll Isolation 1340rpm, 30min Red Top 0.5 ml x2 Serum -80oC UCB Lab Centrifuge 1200rpm 10min CHO UCSF 0.5 ml x2 Clot -80oC 3 ml http://ehs.sph.berkeley.edu/superfund/

  11. How to Improve Sample Collection and Processing • Stabilizing buffers for retrieval of components • Maximum use of valuable samples • Viability of cells for cryopreservation • Tissue culture • Storing of multiple aliquots • Safe handling procedures (collection, transportation and processing)

  12. Microarray Technology and Mutational Bioassays Require Large Amounts of DNA or RNA • 10 ml blood contains 1-2 x 107 lymphocytes • 10 ml blood contains 200-600 µg leukocyte DNA RNA yieldDNA yield Resting Go lymphocytes 2 - 3 pg/cell 6 - 8 pg/cell Dividing lymphocytes 4 - 9 pg/cell 7 - 9 pg/cell (in culture)

  13. Requirements • Space: • Centralized short-term processing and storage 600ft2, • Long-term storage in the different location, 400ft2 • Freezers(in the next 2-3 years): up to 40 • Nitrogen tanks: up to 20 • Bench space and Flow hoods • Security monitoring provisions • Database terminals

  14. Components of Database Management System: Labels Hardware Software

  15. Label type(cryo, size, orientation, quality) Barcode type(1D, 2D, density) Printer (200dpi, 300dpi…) Software Database Scanner (Attached/portable) Choices and Decisions…

  16. Sample Master File (original samples entry)

  17. Sample Master File (final aliquots generated)

  18. Process Templates

  19. Future directions • Expansion of the Superfund and CHAMACOS Biorepositories to include needs of other researchers at the School of Public Health • Upgrade of the database system to a higher capacity

  20. Acknowledgements This project is supported by NIEHS grant P42 ES04705. Maria Bastaki, PhD, UC Berkeley Kelly Birch, Childrens’ Hospital Oakland Research Institute. Eileen Berger, Input Automation, Inc. Our student team: Paurene Duramad, Rominder Nomi, Jin Bae, Marsha Kadze, Connie Chen, Christine Tran, Kristina Vander Wall, Sean Swearingen.

  21. Our Lab Team More information on the Web Site: http://ehs.sph.berkeley.edu/holland

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