Management of experimental biosamples
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Transcript of Management of experimental biosamples
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www.australianphenomics.org.au
Management of experimental biosamples
CSIRO-GA-ANDS IGSN Symposium
ANU, 2 November 2016
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Biomedical “Google Mapping”
www.australianphenomics.org.au
https://www.nap.edu/catalog/13284/toward-precision-medicine-building-a-knowledge-network-for-biomedical-research (2011)
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Model ApplicationTarget & Small Molecule
Screening
Chemical Biology
Preclinical testingCharacterisation
DNA SequencingPathology
Model GenerationGene EditingMutagenesis
DrugDevelopment
MolecularMechanism
GenomicDNA
HumanDATA
PhenomicClinical
IT Data Storage, Analysis (Bioinformatics), Annotation, Integration, Sharing
Human Model OrganismBiobanking
Discovery Health Genomic-Phenomic Pipeline Innovation
www.australianphenomics.org.au
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Basic components of experimental phenomics
www.australianphenomics.org.au
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APN service matrix
CreationDisease Model
Animal ProductionGene Knockout
Models•• Melbourne
Gene Editing by CRISPR
•• Canberra•• Melbourne•• Adelaide
Complex Trait Models
•• Canberra
CharacterisationGenotypingPhenotyping
DNA Sequencing•• Canberra
High-throughput Quantitative Protein Phenotyping (RNAi)
•• Melbourne•• Perth
Pathology•• Melbourne
CurationCryopreservation
Biobanking
The Australian Phenome Bank•• Canberra•• Melbourne•• Perth
Data Management
•• Storage•• Analysis•• Annotation•• Aggregation•• Access
www.australianphenomics.org.au
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Mouse colony management system
Dataset 1
Dataset 2
Dataset 3
Dataset 4
Mouse 1
Tissue 1
Tissue 2
Tissue 3
LN2 -80ºCBank 1
Bank 2
Sample storage database system
www.australianphenomics.org.au
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Australian Phenome BankAccess to phenotypic data and strains in an integrated
database and archiving & distribution system
http://pb.apf.edu.au/phenbank/
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http://pb.apf.edu.au/phenbank/
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http://pb.apf.edu.au/phenbank/
APB strain information – Descriptors
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APB strain information – Publications & ownership
http://pb.apf.edu.au/phenbank/
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Sample storage database system
Parameters:• Barcode• Sample name or strain name• Sample type• Location (where the sample is stored)• Species• Team access level• Comments• Audit history• Custom attributes as defined by the user
www.australianphenomics.org.au
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http://databases.apf.edu.au/mutations/
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Sample information & linkage to other datasets
http://databases.apf.edu.au/mutations/
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Discoverability – mutant library
http://databases.apf.edu.au/mutations/
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Biobank sample management issues
• No standardised sample identification method
• No standardised sample information set
• No formally recognised standard sample preparation protocol
• Not dynamically linked to publications
www.australianphenomics.org.au
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“Google Mouse” virtual histology
Ø Mouse and experimental animal histopathologyØ H&E plus special stains, immunohistochemistry of targeted organs or tissuesØ Expert histopathological evaluation of client slides and on-line reportingØ Digital slide scanning to produce publication quality images
The Google Earth of data visualisation
www.australianphenomics.org.au
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Challenge of human sample management
https://cpi.org.au/ http://ncig.anu.edu.au/
Balancing privacy, sensitivity and discoverability