michael.dobbie@anu.edu.au

www.australianphenomics.org.au

Management of experimental biosamples

CSIRO-GA-ANDS IGSN Symposium

ANU, 2 November 2016

Biomedical “Google Mapping”

www.australianphenomics.org.au

https://www.nap.edu/catalog/13284/toward-precision-medicine-building-a-knowledge-network-for-biomedical-research (2011)

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

Basic components of experimental phenomics

www.australianphenomics.org.au

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

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

Australian Phenome BankAccess to phenotypic data and strains in an integrated

database and archiving & distribution system

http://pb.apf.edu.au/phenbank/

http://pb.apf.edu.au/phenbank/

http://pb.apf.edu.au/phenbank/

APB strain information – Descriptors

APB strain information – Publications & ownership

http://pb.apf.edu.au/phenbank/

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

http://databases.apf.edu.au/mutations/

Sample information & linkage to other datasets

http://databases.apf.edu.au/mutations/

Discoverability – mutant library

http://databases.apf.edu.au/mutations/

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

“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

Challenge of human sample management

https://cpi.org.au/ http://ncig.anu.edu.au/

Balancing privacy, sensitivity and discoverability