Azizi biorepository: Challenges and opportunities
Absolomon Kihara and Steve Kemp
ILRI seminar on managing biological samp...
Azizi in the ILRI Research Structure
Director General

Institute Management Committee
Dir Corp Services

Dir Human
Resourc...
Funding

Azizi
CRP 3.7

CRP 4.3

Animal Biosciences

Research Projects

ILRI

Support Base (Operational Funds)

Azizi Bior...
A Biorepository
Definition:
A Biorepository is a biological materials repository that
collects, processes, stores and dist...
Operations of a Biorepository
The four main operations of a Biorepository are:
1.

Collection or Accession is the first op...
Functions of Azizi
•

•

•
•
•

Long term storage of samples (Biobanking). Most, but not
all, are held in vapour phase liq...
Adapted from an AVID Scientific Presentation
Why Biobank?
Three overwhelming reasons for biobanking:
Maximise the return on expensive sampling trips –
Use the same sam...
What is a Biobank?
Why Biobank?
Biobanked samples have:
•
Great 'metadata'
•
Visible to potential collaborators (typically...
Sampling Activities
Sampling is a very time-consuming and expensive exercise.
We have an ethical and scientific responsibi...
Sampling Life Cycle
Actual sample collection
Preparation
 Label printing
 Pre-labelling
 Systems preparation

Database ...
Opportunities
- Sampling Hardware
-

Laptops, Netbooks and their accessories
Smart phones and Tablets and their accessorie...
Collection
Azizi:
Samples: Blood, Serum, “Shit”
Animals: Gerenuk, Wildbeest
AVID:
Samples: Blood, Serum, Homogenates, Sing...
ILRI Collection
- ILRI’s Gold
- Trypanosomiasis stabilates
- Tick Materials
- Tissue Cultures

Azizi Biorepository

10th S...
The Team
-

Steve Kemp, Animal Biosciences Leader
Absolomon Kihara, Biorepository Manager
Sammy Kemei
Elizabeth Chesang
Ab...
Platforms
Laboratory Information Management System (LIMS)

LIMS

Azizi Biorepository

10th Sept 2013

Challenges and Oppor...
…/and more…

Azizi Biorepository

10th Sept 2013

Challenges and Opportunities
…/more

Azizi Biorepository

10th Sept 2013

Challenges and Opportunities
Mining the repository

Azizi Biorepository

10th Sept 2013

Challenges and Opportunities
Monitoring Systems
What we monitor:
- Fridges
- Freezers
- Incubators
- Liquid Nitrogen Freezers
- Liquid Nitrogen Plant
-...
Screenshots

Azizi Biorepository

10th Sept 2013

Challenges and Opportunities
Backup

Backups
You may call it too much...we call it paranoia...









Hourly snapshots of the whole system (ex...
Security




Physical server in a secure room
The server is behind ILRI's firewall
Very few people have accounts on the...
Challenges
- Poorly labeled and documented samples
- Wrongly stored samples
- MTAs, Ethical Approvals, Permits, IACUC,
Dat...
•
•
•
•
•
•

Thanks
The Biorepository team
AVID funded by google.org
BT02, now Animal Bioscience Team
CRP 4.3 and 3.7
Alan...
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Azizi biorepository: Challenges and opportunities

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Presentation by Absolomon Kihara and Steve Kemp at an ILRI seminar on managing biological samples held at the ILRI Nairobi campus on 10 September 2013.

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Azizi biorepository: Challenges and opportunities

  1. 1. Azizi biorepository: Challenges and opportunities Absolomon Kihara and Steve Kemp ILRI seminar on managing biological samples International Livestock Research Institute (ILRI) Nairobi campus 10 September 2013
  2. 2. Azizi in the ILRI Research Structure Director General Institute Management Committee Dir Corp Services Dir Human Resources DGs Rep Ethiopia DDG Integrated Sciences Dir CRP L&F Tom Randolph CRP 1.1 Polly. Ericksen CRP 1.2 Alan Duncan CRP 2 Derek Baker CRP 4 Delia Grace CRP 5 An Notenbaert CRP 7 Polly Ericksen Genebank Alexandra CRP Focal Points Jorge Azizi Biorepository Dir Institutional Planning & Partnerships Knowledge Mgmt & Public Awareness DDG Biosciences Capacity Development Integrated Sciences Animal science for sustainability BecA-ILRI Hub Iain Wright Intellectual Property Biosciences Appolinaire Djikeng (Interim Dir.) Business Dev Unit Institutional Support Food safety and zoonoses Vaccine platform Delia Grace Vish Nene (Director) Livestock systems and the environment Regional Reps Feed and forages bioscience John McIntire (Interim) Suzanne Bertrand (Interim) Livelihoods, gender and impact Research Methods Group Research Support Animal bioscience Kathleen Colverson Steve Kemp Policy, trade, value chains Derek Baker BIOSCIENCES FACILITIES AZIZI BIOREPOSITOY 10th Sept 2013 Challenges and Opportunities
  3. 3. Funding Azizi CRP 3.7 CRP 4.3 Animal Biosciences Research Projects ILRI Support Base (Operational Funds) Azizi Biorepository 10th Sept 2013 Challenges and Opportunities
  4. 4. A Biorepository Definition: A Biorepository is a biological materials repository that collects, processes, stores and distributes biospeciments to support future scientific investigation. Biorepositories can contain or manage specimens from animals, including humans, and many other living organisms Purpose: The purpose of a Biorepository is to maintain biological specimens and associated information for future use in research. The Biorepository assures the quality and manages the accessibility and distributions/disposition of the biospecimens in its collection Source: Wikipedia Azizi Biorepository 10th Sept 2013 Challenges and Opportunities
  5. 5. Operations of a Biorepository The four main operations of a Biorepository are: 1. Collection or Accession is the first operation where samples are recorded as having arrived. Today this is typically performed by scanning the sample barcode with a barcode scanning device. Information about the sample is transferred into the laboratory information management system ("LIMS"). Typical data captured would be the origin of the sample and arrival data / time recording in the LIMS. 2. Processing of samples is normally a quality tested process that is performed the same way to each of the samples to minimize variation due to sample handling and prepare the sample for storage. The process is usually one that facilitates long-term storage of a particular sample type - for example DNA samples are processed into a salt buffer (aqueous solution) of proper pH to stabilize the DNA fr storage. 3. Storage and Inventory are where all samples are held prior to being requested via a distribution request. The inventory system is composed of sample holding boxes and the boxes are stored in freezers of various types depending on the sample storage requirements. 4. Distribution is the process of retrieving one or more samples from the Biorepository inventory system. Source: Wikipedia Azizi Biorepository 10th Sept 2013 Challenges and Opportunities
  6. 6. Functions of Azizi • • • • • Long term storage of samples (Biobanking). Most, but not all, are held in vapour phase liquid nitrogen. Coordinating sampling activities by different projects with an aim of standardizing sample and data collection procedures to ensure that the data and samples collected meet the required and acceptable minimum standards. Providing a platform for scientists and researchers to mine the sample and data collection which can be used in their resarch. This in turn means that expesively obtained samples can be used and re-used for additional purposes and that the metadata associated with each sample is continually enriched. To ensure that samples and meta-data meet CGIAR requirements of open access. Azizi Biorepository 10th Sept 2013 Challenges and Opportunities
  7. 7. Adapted from an AVID Scientific Presentation
  8. 8. Why Biobank? Three overwhelming reasons for biobanking: Maximise the return on expensive sampling trips – Use the same sample to ask multiple questions now and in the future.  Maximise the understanding of the biology – different pieces of information about identical samples.  Maximise the value for your study from your sample – the requirements for biobanking force improvements on your sampling methods  Azizi Biorepository 10th Sept 2013 Challenges and Opportunities
  9. 9. What is a Biobank? Why Biobank? Biobanked samples have: • Great 'metadata' • Visible to potential collaborators (typically via a web interface) • Simple tracking (typically barcoding) • Very safe storage (typically in LN) • Access arrangements Azizi Biorepository 10th Sept 2013 Challenges and Opportunities
  10. 10. Sampling Activities Sampling is a very time-consuming and expensive exercise. We have an ethical and scientific responsibility to make the best use of that effort and money. Azizi Biorepository 10th Sept 2013 Challenges and Opportunities
  11. 11. Sampling Life Cycle Actual sample collection Preparation  Label printing  Pre-labelling  Systems preparation Database Update  Backup of temp dbase  Update LIMS(master db) Data Processing  Check data integrity  Logging of samples  Processing GPS Coordinates  …etc Adapted from an AVID Scientific Presentation
  12. 12. Opportunities - Sampling Hardware - Laptops, Netbooks and their accessories Smart phones and Tablets and their accessories Necessary barcode scanners etc - Sampling Systems - Barcode and labeling system, - Actual sample collection systems (tarakibu, ODK, simple sampler) - Aliquoting system (ukasimu) - Sampling Expertise - Maintaining of the vital cold chain - Logistics - Other Systems - Data processing systems Azizi Biorepository 10th Sept 2013 Challenges and Opportunities
  13. 13. Collection Azizi: Samples: Blood, Serum, “Shit” Animals: Gerenuk, Wildbeest AVID: Samples: Blood, Serum, Homogenates, Singletons, Tissues, DNA, RNA Organisms: Human, Sheep, Goats, Cows, Mosquitoes, Ticks, Wildlife(Warthogs, Bats, Baboons, Lizards, Birds, etc) IDEAL: Samples: Blood, Serum, Milk, Isolates, Blood smears, DNA, RNA Organisms: Cow GEF-WA: Samples: Blood, Serum Organisms: Cow, Sheet, Goats BecA ABCF Placements: Samples: Mites singletons, Brood samples, Bee singletons Organisms: Mites, Bees USDA: Samples: Blood, Serum Organisms: Goats Lab 6: Samples: Cell Lines, Blood Azizi Biorepository 10th Sept 2013 Challenges and Opportunities
  14. 14. ILRI Collection - ILRI’s Gold - Trypanosomiasis stabilates - Tick Materials - Tissue Cultures Azizi Biorepository 10th Sept 2013 Challenges and Opportunities
  15. 15. The Team - Steve Kemp, Animal Biosciences Leader Absolomon Kihara, Biorepository Manager Sammy Kemei Elizabeth Chesang Abel Balongo Dickens Odhiambo Raymond Mwangi Jane Ngungu By Extension - The geeks: Jason Rogena, Emmanuel Telewa and Alan Orth - The Sequencing Team: George Michuki, Cecilia Rumberia and Moses Ogugo Azizi Biorepository 10th Sept 2013 Challenges and Opportunities
  16. 16. Platforms Laboratory Information Management System (LIMS) LIMS Azizi Biorepository 10th Sept 2013 Challenges and Opportunities
  17. 17. …/and more… Azizi Biorepository 10th Sept 2013 Challenges and Opportunities
  18. 18. …/more Azizi Biorepository 10th Sept 2013 Challenges and Opportunities
  19. 19. Mining the repository Azizi Biorepository 10th Sept 2013 Challenges and Opportunities
  20. 20. Monitoring Systems What we monitor: - Fridges - Freezers - Incubators - Liquid Nitrogen Freezers - Liquid Nitrogen Plant - The Biorepository - ILRI’s Generator Azizi Biorepository 10th Sept 2013 Challenges and Opportunities
  21. 21. Screenshots Azizi Biorepository 10th Sept 2013 Challenges and Opportunities
  22. 22. Backup Backups You may call it too much...we call it paranoia...        Hourly snapshots of the whole system (external) Daily snapshots of the dbase at 3.15am (internal) Incremental Backups every day (Backuppc) Full Backups every 5 days (Backuppc) Daily dbase snapshots sync'd to the cloud Manual backups when updating the dbase (user or system initiated – internal) Backuppc data saved on a RAID which provides increased storage functions and reliability through redundancy “We've got a good system in place. Guys know their roles, and we've got capable backup. If Mike isn't 100 percent, then Matt will step right in.” Azizi Biorepository 10th Sept 2013 Challenges and Opportunities
  23. 23. Security    Physical server in a secure room The server is behind ILRI's firewall Very few people have accounts on the physical server ALL collaborators have access to ALL the data via tools and systems that we have developed If you want total security, go to prison. There you're fed, clothed, given medical care and so on.... Dwight D. Eisenhower Azizi Biorepository 10th Sept 2013 Challenges and Opportunities
  24. 24. Challenges - Poorly labeled and documented samples - Wrongly stored samples - MTAs, Ethical Approvals, Permits, IACUC, Data Sharing Agreements, etc - Sue Wellburn, Kubata, etc. Azizi Biorepository 10th Sept 2013 Challenges and Opportunities
  25. 25. • • • • • • Thanks The Biorepository team AVID funded by google.org BT02, now Animal Bioscience Team CRP 4.3 and 3.7 Alan Orth Biorepository Users

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