Biobanking at the Natural History Museum London. ESBB Marseille

Biobanking at the Natural History
Museum London.
ESBB Marseille Nov2011
Jackie MackenzieMackenzie-Dodds.
The Natural History Museum is the UK's national museum of
natural history, and a world centre of scientific excellence in
t
taxonomy
and
d biodiversity.
bi di
it
The Museum has 70 million specimens in it’s
reference collections. There are over 300 scientific
staff (curators and researchers) actively involved in
collections-based research. The reference
collections are housed in 5 science departments:
Botany, Entomology, Mineralogy, Palaeontology, Zoology
The Museum holds material from the collections of Hans Sloane, Captain Cook,
Charles Darwin, David Livingstone, Ernest Shackleton and many other key
explorers/naturalists.
explorers/naturalists
Top left: DC1 at the Natural History Museum, the new
home of the Department of Zoology. Opened in October
2002, the DC1 was designed to allow members of the
public to have controlled access to Museum staff,
laboratories and collections areas.
The DC1 houses 22 million zoological specimens
preserved in 70-80% alcohol.
Top right: One of the seven floors of specimen collections.
Bottom right: The Tank Room on the ground floor of DC1,
home to larger zoology specimens such as dolphins,
sharks, sturgeon, crocodiles and giant squid.
DC2
Cocoon
Botany and Entomology
Top: Mammal
collection South
collection,
London storage facility
Left: Osteology
collection, South
Kensington
Right: Mammal study
skins, NW Tower,
South Kensington
Types
yp of material
• Dry (skins, bones, pinned, plants)
• Wet (EtOH, IMS, Formalin)
• Slides
• SEM stubs
• Frozen tissues/DNA
• Models
• Literature and field note books
Collections at the NHM:
Objectives:
j
– To maintain the NHM collections as a relevant and comprehensive
research infrastructure of world importance.
– To develop the infrastructure such that the range of the collections is
enhanced and maintained for future generations.
– To continue to provide national and international access to the specimens
and knowledge contained within the collections.
– To maintain and develop the scientific scholarship and expertise of the
NHM staff who research and manage the collections.
How does the material come in?
An average of 25,000 new specimens are received
each year:
y
• Focussed collection by NHM researchers
• Opportunistic collecting (with Collections
Impact Statements in advance)
• Donation by scientists who regularly work on
NHM collections
Co scat o s by HM Customs
Custo s & Excise
c se ((formal
o a
• Confiscations
links required, forensics).
• Donations or bequests from the public
Molecular Collections from Field
• Dry Shipper:
New priority areas
• British Biodiversity (cf former British Colony specimens)
g and Biodiversityy Crisis (ID
( endangered
g areas/taxa
/ to
• Global Climate Change
develop programmes). FArk/Customs.
• Environmental Time Series (before and after pollutants, pesticides, Hg etc).
• High quality ‘genome ready’ tissue collections for NGS and genomics.
Molecular Collections: Preliminary Audit 2008
• Legacy collections: 0.5 – 0.75 Million in
2011
• Predicted growth (fieldwork and
molecular studies): 0.5 – 1.5 Million
samples by 2015
• FTA: 24K specimens (SCORE 23.5K,
Aidan Emery)
TAXON
SAMPLE #
GENUS #
SPECIES #
Birds
~20K
>280
>440
Higher Plants
~22K
tbc
tbc
Lower Plants
~15K
tbc
tbc
Fish
~10K
>100 - 1000
>1000 - 5000
Protists
~4K
tbc
tbc
Insects
>20K
>44
>91
Mammals
~1K
tbc
tbc
Parasitic Worms
~11K
tbc
tbc
Molluscs
>2K
>76
>370
E hi d
Echinoderms
>0.5KK
tbc
b
tbc
b
Bryozoa
~11K
>30
>42
Molecular Collections: Current Storage
Storage in a variety of media:
• +4°C: tissues in alcohol
• -20°C Freezers :Tissues (some in alcohol), DNA
• -80
80°CC Freezers: Tissues (some in alcohol),
alcohol) DNA
DNA, RNA
• -196°C Liquid Nitrogen (LN2), small collection
• Ambient Temperature Storage
• with silica (Leaves)
• Whatman FTA Cards
Biorepository: Main Aims:
• Centralised storage facility for molecular collections destined for or created by
molecular research
• In parallel with “traditional collections’’
• Collection
ll
resource to support bbothh current andd ffuture researchh
• Enhancement of sample value
• Designed to minimise risks to these collections and staff and ensure maximum
future access internally and externally
The Central Facility
• On NHM South Kensington site
g methods LN2,, +4,, -20,, -80,, ambient
• Mixture of storage
• Phased development towards LN2 and ambient
• Integration withh NHM Facilities:
l
Seq Fac, aDNA, Moll Labs.
b
• Laboratory Information Management System (LIMS)
• KE EMu, FreezerPro, Eltek, QA/QC, sample tracking
Management
g
Researchers
Locall Storage
L
S
-current
research
Field Collection
External
E
t
l
Users
Archival Samples
Loans/Gifts
Manager- Policy and Procedures
Central Storage
Facility
Facilit
Molecular Collections Facility
y
Facility Layout
Biorepository Capacity
• 14 x -80 upright freezers (20 - 40K ea 560K)
• 3 x -80 large chest freezers (large specimens/back up)
20 freezers (10 -20K
20K ea 400K)
• 24 x -20
• 3 x LN2 Tanks (60K/240K ea 720K)
• Ambient Storage:
– 2 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:
p y approx
pp 2 million samples
p
Technical:
• Ambient Storage Technologies (SCORE: Schisto on FTA cards: Dr Aidan Emery)
• DNA Extraction Optimisation: SYNTHESYS JRAs
• DNA Damage: evaluation and repair (GE/Whatman-NHM FTA project Dr Aidan
Emery)
• Epigenetics and transcriptomics
• Next/Third Generation Sequencing
– Illumina: MiSeq, Ion Torrent, Oxford Nanopore
• Automation and Robotics
• LIMS (KE EMu, FreezerPro)
NHM MCF LIMS
Accession/de-accession
Documentation
Loans
Shipments
Conservation
Valuation
Metadata
Darrellll Siebert
b
Basic lab information
Location/plates
Tracking/barcodes
Volume
Freeze/thaw cycles
Access for different user group
RURO
Aidan Emery
Future Proofing: trajectory
• Audit: Identify Strengths/Gaps
• Collection enhancement; targeted, environmental monitoring
• Business models: cost recovery, incentives
• Policy: IPR, ABS, CBD (Chris Lyal, John Jackson), loans
• Phase review: transfer, expansion
• Networking: Distributed Collections:
– ESBB, SYNTHESYS, CPB (CETAF), ECBOL, Global: ISBER, iBOL, GBIF,
S b k FArk,
Snowbank,
FA k GGI.
GGI
Questions?