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

NHM Molecular Collections Facility 2011/12

Disaster Plan:

Backup generator.

Temperature monitoring and

alarms.

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

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

Molecular Collections from Field

Dry Shipper

‘Cold Chain’ challenge:

‘Jungle to Biobank’:

Couriers/IATA regs etc.

Cryo-tube Format: 2D Barcode

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).

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

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

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

Collections Management System: Axiell ‘EMu7’

https://emu.kesoftware.com/about-emu/overview

Biobank Inventory System: FreezerPro

https://ruro.com/

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)

EMu Specimen RecordsEMu Modules

Parent Record

Determination Child Record: Preparation

Prep Record Link

Collection

Event/Site

Records

Link

Specimen Record Type

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

FreezerPro Records

Rapid sample retrieval: happy customers!

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).

MCf CASE STUDIES

• UK INSECT POLLINATORS INITIATIVE ARCHIVE, 50K specimens

• CRYOARKS: UK ZOO/VET/ENDANGERED ANIMALS, 250K samples

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)

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

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.

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

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

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

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

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.

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

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!

THANKS and Questions?