Global Initiatives in Genomics and HealthPeter Goodhand
CEO • GA4GH

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Outline1

Why do we need standards?

2GA4GH

3

Global Collaborations

4Japanese Example

5

Getting Involved

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Since data is
distributed globally,
we need interoperable
standards to answer
research questions

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Standards are essential
Interoperability is key to data sharing and enabling the necessary ecosystem

Findable, Accessible,
Interoperable, andReusable Datasets

Interoperable
tools

Interoperable
computeInteroperable
data access methods

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What makes a good standard?

Clear and speciﬁcspeciﬁcation

Meets the needs ofeveryone in thesystem

Easy to adopt

Works as part of abroader ecosystem

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For standards to help...

...they need to be deployed.

To be deployed...

...they need to built withadoption in mind.

To be adopted...

...we need to check what
people need (everywhere).

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How dowe advancegenomics
globally?

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The 1000 Genomes Project ecosystem

Common consent acrossall 26 populations and5 continents

Common resources:
Cell lines, arrays, exomes
and genomic sequences

File formats (SAM andVCF) and data sharing
methods

Software: samtools,FreeBayes, GATK,VCFtools, tabix, etc.

Interoperable
Together, able to address research questions and lay foundation for future projects

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➔ To fully realize the beneﬁtsof genomics in health, it isnecessary to work globally➔ Collaboration is the only
way to build standards andachieve global data sharing

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GA4GH is a
global forum

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ga4gh.org

THE GA4GH MISSION...
The Global Alliance for Genomics and Health aims toaccelerate progress in genomic science and humanhealth by developing standards and framing policy for
responsible genomic and health-related data sharing.

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The GA4GH Ecosystem

90+
Countries
450+
Active3000+
Participants
Subscribers
650+
Organizational
Organizational
Members

20+ TechnicalStandards
40+
Implementations& Deployments

8 WorkStreams

Enabling the Global
Learning Health System

9 Regulatory
Policies &Frameworks

4000+
90+
Subscribers
Countries
24 Driver
Projects

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GA4GH aims to...
Enable international data sharing

GA4GH achieves this by...
Convening stakeholders
Catalyzing sharing of data

Promote sharing across thetranslational continuum

Creating harmonized approaches
Acting as a clearinghouse

Encourage technology-enabledfederated approaches

Promote interoperability

Fostering innovation
Commiting to responsible datasharing

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Use cases: what are we trying to do?
We have many sources of real world scientiﬁc and health use cases

Cancer Community...and many more
Driver Projects
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Australian Genomics: Data Management Work Flow and Capabilities
PanelApp Australia
Curated gene-diseaseassociations and virtual
gene panels

ClinicalFlagships

Clinical Consultation(32 clinical sites)

Acute Care

‘Shariant’ Platform

Contribute tointernational
databases

Classiﬁed variants
and curation evidence sharedacross laboratories

9 Sequencing or
Research
Laboratories(4 uploading)

Data Quality Assessment

Data Access Agreements
Data Governance Policies
Data Access Committee

Quality reports on BAM + VCF
data produced by
qProﬁler & NGScheck software

Data Access and Approvals System

Classiﬁed Variants
Reported &UnreportedApprovals issued automatically (low-sensitivity) or
via data access review (high-sensitivity)

Genomic Data
Repository

Curation Evidence

Phase 1 genomic data store

MitoGenomic Data
VCFBAMFASTQ

EpilepsyBrain Malf

Metadata
laboratory,sequencer, library
preparation etc

Leukodys
KidgenHiddenCardiac

Access toindividual-level
data

UploadGenomic Data+AssociatedMetadata
Phase 2 comprehensive
genomic data catalogue

Gen-Phen Platform‘Variant Atlas’

Biospecimen

Genotypes
Accredited
Pathology Reports

Minimal Clinical
Datasets

Access tosummary-level
data

Genotypes and Phenotypes available
for interactive summary-level queries
and visualisations

Gen Immun
Int Disab

CTRL Consent
PortalInt Lung
Neuromusc

ICCon

australiangenomics.org.au

Standardised Clinical Phenotypes
AustralianGenomics
Study Database

Flagship
Clinical Phenotypes
Patient phenotype
data

Patient phenotype data coded in
SNOMED / HPO terms andrepresented in FHIR format

Phenotypes
Phenotype Tools and Resources
Phenotype Analytics
Phenotype Queries

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Current GHIF Members

Foundation
members:

International HundredK+Cohorts Consortium (IHCC)

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Collaborations
Human Pangenome
Project (HPP)

Common Infrastructure for National
Cohorts in Europe, Canada, and Africa
Beyond One Million
Genomes ProjectInternational 100K Cohort Consortium

Science Council

DataVisiting
Human Genome Organisation

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Global Collaborations
Human PangenomeProject (HPP)Science Council

International 100K Cohort Consortium

DataVisiting
Human Genome Organisation

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Alignment with Other Standards Organizations
ResearchClinical ResearchClinical CareTC215/SC1
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Recent implementation updates

Watch these implementer talks from 9th Plenary: bit.ly/9thplenary-videos
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Example
Melissa Cline & Japanga4gh.org

CIHR COVID-19 Interoperability Initiative

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BRCA Variation and Cancer Risk

BRCA variation can also lead to ovarian, prostate, and pancreatic cancers
Slide credits: Melissa Cline, UCSC

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Allele FrequenciesProof of Concept with BioBank Japan•

Rationale: Disease-causingcancer variants are rare bydeﬁnition•

If a variant is frequent in somecontinental population, it can beclassiﬁed as benign with nofurther evidence

Slide credits: Melissa Cline, UCSC

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Federated analysis of BioBank Japan Data
● RIKEN holds a large cohort of cancer

patients and controls from BioBank Japan,
which they cannot share directly.
● We shared a Docker container with themto analyze their patient cohort for variant
co-occurrences and allele frequencies

Yukihide Momozawa, RIKEN● The container generated variant-level

data, which we are now using together
with the ENIGMA Consortium to interpret
BRCA variants!
Slide credits: Melissa Cline, UCSC

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ga4gh.org

Acknowledgements
GA4GH Host Institutions

GA4GH Core Funders

GA4GH Supporting Funders

GA4GH Staﬀ and Contributors
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Contact us

Join a Work Stream!
Contact secretariat@ga4gh.org

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