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.

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. 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. 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. 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. 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. Functions of Azizi
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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. Adapted from an AVID Scientific Presentation

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. What is a Biobank?
Why Biobank?
Biobanked samples have:
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Great 'metadata'
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Visible to potential collaborators (typically via a web
interface)
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Simple tracking (typically barcoding)
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Very safe storage (typically in LN)
•
Access arrangements
Azizi Biorepository
10th Sept 2013
Challenges and Opportunities

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. 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. Opportunities
- Sampling Hardware
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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. 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. ILRI Collection
- ILRI’s Gold
- Trypanosomiasis stabilates
- Tick Materials
- Tissue Cultures
Azizi Biorepository
10th Sept 2013
Challenges and Opportunities

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. Platforms
Laboratory Information Management System (LIMS)
LIMS
Azizi Biorepository
10th Sept 2013
Challenges and Opportunities

17. …/and more…
Azizi Biorepository
10th Sept 2013
Challenges and Opportunities

18. …/more
Azizi Biorepository
10th Sept 2013
Challenges and Opportunities

19. Mining the repository
Azizi Biorepository
10th Sept 2013
Challenges and Opportunities

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. Screenshots
Azizi Biorepository
10th Sept 2013
Challenges and Opportunities

22. Backup
Backups
You may call it too much...we call it paranoia...
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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. Security
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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. 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

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Thanks
The Biorepository team
AVID funded by google.org
BT02, now Animal Bioscience Team
CRP 4.3 and 3.7
Alan Orth
Biorepository Users