Biological sample Collection, Processing and Banking for Academic Centers

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Biological sample Collection, Processing and
Banking for Academic Centers
Biorepository Workshop, Milan, Italy,
October 22, 2002

• Nina Holland
• School of Public Health, University of
  California, Berkeley, CA
• ninah_at_uclink4.berkeley.edu

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Superfund Center
Biomarkers of Carcinogenesis Project 1
New Methods
Samples
Data
Chemical Exposures And Leukemia Risk Project 2
Arsenic Biomarker Epidemiology Project 3
Core B Biomarker Lab
Samples
Samples
Data
Data Management System
Information of Relevance to Childrens Health
Samples
Samples
Core D Outreach Childrens Environmental Health
Network
Core C
Computer and Statistical Support
Determinants for Chromosomally Defective Human
Sperm Project 4
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A Community-University Partnership
Childrens Hospital Oakland
Research Institute
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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

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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

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Biorepository at UC Berkeley

• Whole blood
• Buccal cells
• Urine and urothelial cells
• Blood (plasma, serum, viable
• lymphocytes, COMET stabilized, 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

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CHAMACOSSamples Collected
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Biorepository includes

• Inventory of already accumulated samples
• In progress , samples in the process of
  collection
• Provisions for samples from future projects

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Sample Sources for Biorepository

• Projects 3-7
• 2. Study subjects per project 15-500
• upcoming several
  1000s
• 3. Number of aliquots per individual 12-70

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Whole blood processing for Superfund project
http//ehs.sph.berkeley.edu/superfund/
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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)

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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 yield DNA yield Resting Go
lymphocytes 2 - 3 pg/cell 6 - 8 pg/cell Dividing
lymphocytes 4 - 9 pg/cell 7 - 9 pg/cell (in
culture)
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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

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Components of Database Management System
Labels
Software
Hardware
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Choices and Decisions
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Sample Master File (original samples entry)
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Sample Master File (final aliquots generated)
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Process Templates
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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.
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Our Lab Team
More information on the Web Site http//ehs.sph.b
erkeley.edu/holland