biobanking at nhm london's cryofacility: case studies: uk ... · quantity/quality/vol sample...
TRANSCRIPT
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The Fourth Thailand Biodiversity BioBank Conference and Workshop: “2018 International Forum
on Community BioBank: Thailand Initiatives” Centra Government Complex Hotel Chaeng
Watthana, Bangkok, Thailand, September 12 –15, 2018
Biobanking at NHM London's Cryofacility:
Case Studies:
• UK Insect Pollinators Initiative Archive.
• CryoArks Project: UK Zoo/Vet/Endangered
Animals
Jackie Mackenzie-Dodds,
Molecular Collections Manager,
Natural History Museum, London UK
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NHM Molecular Collections Facility 2011/12
Disaster Plan:
Backup generator.
Temperature monitoring and
alarms.
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Alarm & Temp Monitoring System
Freezer temperatures
LN2 Tank Temperatures and Pressures
LN2 Bulk Tank Pressure and Volume
Oxygen sensors
Emergency Call Out
Cascade:
1. Biobank Manager
and Security
(Emergency
Services)
2. Biobank Staff
3. Departmental
Staff
4. Head of
Department
5. Science Director
6. Institution
Director
Audio-visual alarms on site
Temperature Alarm Control Box
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Biorepository Capacity
• 14 x -80 upright freezers (20 - 40K ea 560K)
• 3 x -80 large chest freezers (large specimens/back up)
• 24 x -20 freezers (10 -20K ea 400K)
• 3 x LN2 Tanks (60K/240K ea 720K)
• Ambient Storage:
– 4 x large humidity controlled cabinets (cap tbc)
– 1 x large ambient collections cabinet (FTA/Silica: 250K samples)
– 1 x GenVault Personal Archive (GenTegra 990 x 96/284 plates: 95 – 380K)
• Total capacity: approx 2 million samples
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Molecular Collections from Field
Dry Shipper
‘Cold Chain’ challenge:
‘Jungle to Biobank’:
Couriers/IATA regs etc.
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Cryo-tube Format: 2D Barcode
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Molecular Specimens and Samples
• deep-frozen specimens or tissues in liquid nitrogen (-196°C)
• frozen tissues in freezers (-80°C)
• alcohol-preserved specimens specifically collected for molecular work or tissues (-20, +4, +16°C)
• silica-dried material (RT)
• lyophilised/freeze-dried material (RT)
• samples on proprietary ambient storage systems e.g Whatman FTA cards (RT)
• Viable/functional cell lines cultured from fresh tissues (cryo banks).
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Molecular Products
• extracted genomic/mitochondrial/chloroplast DNA in water or buffers (-20°C)
• extracted RNA (-80 °C)
• genomic / expression libraries in culture (-80°C, LN2)
• proteins
• Mixed Environmental Genomic DNA / RNA / protein and amino acid survey samples
• historical contaminant sample series
• lipid and metabolite sample series.
• returned material from all destructive sampling loans (including some rare PCR products and sequencing reactions)
• unforeseen future analyses and cellular components
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NHM MOLECULAR PIPELINE NETWORK
Stakeholders
RESEARCH
Internal/External
MOLECULAR
COLLECTIONS
FACILITY
BIOBANK PRE-PCR
DNA/RNA X’Ns
SEQUENCING FACILITY:
SANGER + NGS
FIELD
New
LAB
Archive
ANCIENT
DNA X’N LAB
LIMS +
DATABASES
CURATION:
Traditional
Collections
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Data and Sample Workflow Overview
EMu
Specimen
Record
EMu Preparation
RecordFreezerPro
Records
Collections Event
Record
Provenance
Permits, PIC/MAT/MTA,
Parties, Expedition
Acquisition
NHM
Data Portal
Collections Site
Record
EMu Preparation
RecordEMu Preparation
RecordEMu Preparation
Records
Location, GPS
Date, Time, Temp,
Altitude, Depth
Aquatic/Terrestrial
Habitat, Geology
Taxonomy
Type status,
Voucher location
Age, Sex, parasites
References
Valuation
Deaccession
Sample type: Tissue, DNA
Preparation Process
Previous sample history
NHM Specimen barcode
Location in biobank
EMu Taxonomy
Sample type
Tube/Plate Format
Sample Vial Barcode
Quantity/Quality/Vol
Location in biobank
Sample history/temp
Freeze/Thaw cycles
Loans Research
Labs
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Collections Management System: Axiell ‘EMu7’
https://emu.kesoftware.com/about-emu/overview
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Biobank Inventory System: FreezerPro
https://ruro.com/
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NHM MCF proto-LIMS
Accession/de-accession
Documentation
Loans
Shipments
Conservation
Valuation
Metadata
Voucher specimen
Images
Molecular lab information:
Location in 96/384 plates
Tracking/barcodes
Volume change (destructive
sampling)
Freeze/thaw cycles
Sample temp history
HTP equipment links (robot,
QC/QA)
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EMu Specimen RecordsEMu Modules
Parent Record
Determination Child Record: Preparation
Prep Record Link
Collection
Event/Site
Records
Link
Specimen Record Type
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EMu Preparation Records
Preparation Catalogue
Prep/Analyses FreezerPro Link
Preparation Record Type
Specimen
Record
parent link
Prep record
selected from a
number FreezerPro link
Location in biobank
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FreezerPro Records
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Rapid sample retrieval: happy customers!
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Technical Considerations / Future-proofing:
STAKEHOLDERS, FUTURE USERS (int/ext), Themes/Initiatives
• Ambient Storage Technologies (SCAN: Schisto on FTA cards)
• DNA Extraction Optimisation: SYNTHESYS
• Cryobiology (viable/functional samples, taxon specific CRF protocols).
• Epigenetics and ‘omics
• Next/Third Generation Sequencing
– Illumina: MiSeq, NextSeq
– Oxford Nanopore: MinIon
• Automation and Robotics for HTP processing
• QC/QA, QMS, ISO, standards, compatibility, harmonisation, definitions.
• LIMS (Laboratory Information Management Systems).
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MCf CASE STUDIES
• UK INSECT POLLINATORS INITIATIVE ARCHIVE, 50K specimens
• CRYOARKS: UK ZOO/VET/ENDANGERED ANIMALS, 250K samples
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Building a specimen archive of UK
Pollinators: a model for linking collections and research
Graham Stone, Damien Hicks (University of Edinburgh),
Jacqueline Mackenzie-Dodds , Alfried Vogler (NHM, London),
Adam Vanbergen (Centre for Ecology and Hydrology, Edinburgh)
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Miracles can happen
• Storage in Natural History Museum’s Molecular
Collections Facility (£40k pa).
• IPI funders agreed if legal transfer documentation in
place.
• Drafting and completion of documentation took a year,
over 500 emails….
Graham
Stone
Jackie Mackenzie-Dodds
Kaylin Martin
AlfriedVogler
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The Plan
• Store all specimens individually at -80°C (some -20).
• Maintain specimen integrity (parasites, pollen loads..).
• Compile a combined project metadata resource.
• Make specimens and metadata publically available (NHM
portal, GBIF, GGBN).
• Announce by publication (including project designs).
• Access by application to NHM, allowing destructive use.
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EDINBURGH University Workflow (2 x full time techs 1yr):
• IPI project metadata resources assembled (9 x data sets).
• 43,593 specimens (891 taxa) transferred from pins to tubes (~6% of NHM
entomology specimens).
• Labels (orig) + NHM Barcode, 2D barcoded cryovials (s/m/l: 0.5/2/4ml), Box
(96/48/24 place) barcode.
• Flat Bed Bulk Scan 2D barcodes imported into NHM Template Spread Sheet
with Metadata
• Batches to NHM: Ship Specimens by DHL and send Data electronically.
Damien Hicks Dr. Tom GodfreyNatalia de la Torre
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NHM Workflow (1 x full time Data Techs 6 months + JMD):
• MoU/MTA/Title Transfer/Ownership/Technical Schedules for 9 projects (6 institutions): NHM Registrar
• IPI Data Tech : accession specimens and data with LS data managers and JMD/MCf.
• Bulk Data import to KE EMu:
• Acquisition Records, Registration, Provenance MoU/MTA/Technical Schedule, embargoes
• Metadata, Site, Collection Events
• Taxonomy: link to existing clean records in EMu.
• Specimen and Preparation Records.
• Specimens into MCf (with JMD):
• Link EMu Prep Records to MCf’s FreezerPro.
• Cross check and develop workflows to link specimens to data and final freezer locations in MCf.
• Data and Samples discoverable and accessible to Researchers worldwide via NHM Portals.
• Data copies sent to NHM: Collection Usage Reports to BBSRC IPI Archive Steering Committee.
KE EMu
FPro
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Discoverability & Accessibility: Data Portals
UK IPI Archive data searchable on Biodiversity Data Portals:
NHM http://data.nhm.ac.uk/ 891 taxa GBIF https://www.gbif.org/search?
GGBNhttp://data.ggbn.org/ggbn_portal/search/browseNew: 5 families, 68 Genera
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UK IPI Archive Specimens: Use since 2016• Published study on pollen beetle population genetics and
phylogenetics.
• Genome sequencing of the Ringlet Butterfly Aphantopus
hyperantus, Red Mason Bee Osmia rufia, Orange Tailed Mining
Bee Andrena haemorrhoa (Sanger Institute’s 25 Genomes
project).
• Genomic analyses of honeybees.
• Pollen load barcoding research.
• Pollinator biodiversity response to drought.
Charlesjsharp (Wikipedia) Brassicogethes aeneus
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CRYOARKS
• Major new UK coordinated biobanking initiative for endangered and non-model animal species, £1.2M financed by UK’s Biological Resources Fund BBSRC-BBR (1/7/2018 –30/6/2021). Zoo/Aquaria/ Museum/Vet/Wildlife/Livestock/Endangered Animals.
• Cardiff, Edinburgh and Nottingham Universities, NHM, National Museums Scotland and Edinburgh Zoo (EAZA)
• Coordinated infrastructure, databasing (Specify), sampling initiative.
• Collating ~250K samples and data from UK universities, zoos, museums and institutes – and beyond. Launched July 2018.
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CRYOARKSBiobank for the European Zoo communityBiobanking Hubs:▪ Antwerp Zoo, ▪ Copenhagen Zoo▪ Royal Zoological Society of Scotland
(RZSS)
Zoos
Museums▪ Existing collections of different
animal species, and often at the population level
▪ Facilities to store tissue and DNA samples
▪ Research capacity
© Hayley Campbell / BuzzFeed © NHM
Universities▪ Biosciences departments –
conservation projects▪ Existing tissue and DNA samples▪ Capacity to conduct research on
cryopreservation techniques
Molecular Ecology and Evolution Lab – Cardiff University
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CRYOARKS
STRATEGY SUMMARY:• Audit, inventory, Survey User Needs, Prioritise (e.g. taxonomic uniqueness:
use GGI/GGBN Novelty Score).• Aggregate Data (create std templates) using Specify software (open source,
web browser based: http://www.sustain.specifysoftware.org/ ).• Link to Museum/Zoo/Aquaria databases: EMu, Species 360, ZIMS.• Link to Biodiversity Data Portals (NHM, GBIF, GGBN). Go Live• Aggregate samples and specimens: ship, reformat, store frozen (-80/LN2).• Gap Analysis and New Field Sampling Initiative.• Standard Collecting Protocols/SOPS/QA/QC for field collection and
processing (Zoo/Wildlife Vets).• NB Legal/Ethical considerations: Nagoya/CITES/ownership/Data
Protection/FOI etc.• Outreach/Brand/Sustainability..
• Watch this space!
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THANKS and Questions?