Submit your questions during the Q&A at

Sli.do or the Slido app using event code #GA4GHConnect

You may need to minimize your Zoom window in order to view both the meeting and Slido on your screen.

ga4gh.org

Virtual Connect: Housekeeping �Ashley Hobb

ga4gh.org

Virtual Participation Guidelines

• Use the video function during all breakout sessions
• Ensure a good wifi connection, as well as audio and visual outputs
• Use the Raise Hand function to speak during the plenary sessions
• Mute yourself when you aren't speaking
• Do not multitask (or at least try really hard not to...)
• Be prepared to introduce yourself; you may be called on!
• Send all operational questions to operations@ga4gh.org or #questions-4-secretariat as soon as they arise

ga4gh.org

GA4GH Connect Virtual Meeting Agenda

Part 1: 12:00 - 15:00 UTC

Part 3: 12:00 - 15:00 UTC

Part 2: 20:00 - 00:00 UTC

Part 4: 20:00 - 21:45 UTC

SC: 21:45 - 10:45 UTC

12:00

13:00

14:00

15:00

16:00

17:00

18:00

19:00

20:00

21:00

22:00

23:00

00:00

ga4gh.org

GA4GH Connect Virtual Meeting Agenda

2

8

14

Plenary Sessions

Roadmap Sessions

(one for each work stream)

Cross Work Stream Breakouts

ga4gh.org

Navigating the Agenda

bit.ly/2020connecta

ga4gh.org

ga4gh.org

ga4gh.org

ga4gh.org

GA4GH is on

Use the GA4GH Connect Slack channels to to chat with your colleagues and carry on discussions between sessions:

• #connect-networking: to connect with new and old faces, share updates, and learn more about the community
• #connect-wins: to discuss standards development work and advance the GA4GH Strategic Roadmap
• #questions-4-secretariat: Have a question or challenge? Secretariat is here to help!

​

Links in Welcome Email

ga4gh.org

Virtual Coffee Breaks

Connect with colleagues or continue a conversation on Zoom.

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ga4gh.org

Welcome

�Ewan Birney

ga4gh.org

Plenary Session Agenda

ga4gh.org

WELCOME

ga4gh.org

Thank You

Thank you for participating while:

• Taking on new responsibilities relating to COVID-19
• Working on the front line in clinical settings
• Adjusting to new work environments

​

GA4GH has an amazing community and this is an opportunity for us to support each other.

This is not business as usual!

ga4gh.org

GA4GH & COVID-19

Share your feedback and work:

• Slack #connect-wins
• Email operations@ga4gh.org

Role for GA4GH:

• Encourage data sharing
• Highlight positive work in our community

ga4gh.org

Goals of Virtual Connect

• Advance the 2020 Strategic Roadmap
• Facilitate collaboration across Work Streams
• Advance standards development for release at 8th Plenary

ga4gh.org

Expectations for Conduct

GA4GH expects all attendees to help us create an inclusive environment.

• Be Respectful
• Be transparent about potential conflicts of interest

The following will not be tolerated

• Discrimination
• Harassment
• Sexual harassment
• Disrespectful behaviours
• Violence

ga4gh.org

Practice Session

1. Navigate to sli.do in your web browser or open the app
2. Enter “GA4GHConnect” as the meeting code
3. Tell us: What’s one good tip to successfully work from home?
• Up and down vote your favorite answers
4. Answer the poll: Are you wearing slippers? Yes/No

ga4gh.org

2020 Roadmap Updates

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GA4GH Work Stream Leads

ga4gh.org

Cloud

• Cloud Work Stream Goals for 2020
• Demonstrate utility of Cloud Work Stream APIs in federated analyses
• Provide a “deployment toolkit” for projects new to our APIs
• Make it easy to find available services and implementations of our APIs
• Cloud Work Stream Efforts
• Build the Cloud API implementation registry
• Refine our APIs and make new releases (WES, TRS, DRS, and likely TES)
• White paper in 2020
• Support cross-work stream efforts
• Cross Work Stream Efforts
• Federated Analysis Systems Pilot (FASP)
• Contribute our API and systems
• Demo federated analysis
• Incorporate feedback into our APIs

21

ga4gh.org

Data Use & Researcher Identities

• DUO Data Use Ontology
• Expanded Documentation
• Extend to work with outside resources: Call for FHIR expert!
• GA4GH Passports “from v1.0 to v1.1”
• Additional user role values
• Expanded guidance and documentation
• Working with FASP for integration and interoperability with Cloud and Discovery
• Leadership change
• Computable Consent Forms (lead by REWS)
• Based on DUO
• Interoperability with DURI products
• DUO-Passport Connector (NEW, relatively)
• Both products will be updated to allow for integration and increased automation of the DAC process

​

22

ga4gh.org

Discovery

• Discovery Work Stream Efforts
• Service Info / Service Registry
• Contemplating an “Object Registry” for registering and searching GA4GH data types (e.g. files via DRS, variants using VR, etc.)
• Search
• Demonstrated support for federation across instances with different underlying data models
• Beacon v2
• “Genomics API” for multiple scenarios, with focus on “clinical” use cases
• Recent example: Support for Variant Interpretation Sharing Network
• Cross Work Stream Efforts
• SchemaBlocks
• Expanding content (DUO, Beacon, Checksum…); soon HCA, Search - contribute!
• In-workstream integrator function for Search and Beacon
• Federated Analysis & Search Pilot (FASP)
• Working implementation of integration between Discovery, DURI, and Cloud standards. Demo here

23

ga4gh.org

Genomic Knowledge Standards

Variation Representation Specification

• Supporting collections of variations (sets) to represent more complex variation, e.g. haplotypes
• Expanding the ways to locate variation when the original record is imprecise, e.g. specifies a cytoband
• Describing large scale variation events: insertion, deletion, copy number events, fusion events

​

Variation Annotation

• Limited alpha release of initial framework for variation annotation
• Generalised core information model
• Specialised information models for a subset of annotation types
• e.g. molecular consequence, variant pathogenicity
• Expansion of the alpha framework to a v1 release of the specification
• Refined core information model
• Revised set of annotation-specific models
• JSON schema and implementation examples for each model

​

Proposed Roadmap Additions - in development

• Supporting novel HLA alleles in collaboration with GEM-Japan
• Sequence annotation support as a cross workstream project with Large Scale Genomics
• Implementation of VRS within Phenopackets

24

ga4gh.org

Clinical & Phenotypic Data Capture

Pedigree Standard

• Standardizing the way systems represent family structure, allowing information to be more easily shared between healthcare systems and help tools use this information to improve genome analysis and diagnosis
• Currently collecting use cases and identifying gaps to develop a minimal dataset for collection

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Phenopackets

• Focus on community adoption and implementation- currently discussing with journals the use of Phenopackets in article submissions
• Minor update to include addition cancer elements
• Integration with GKS Variant Representation (VRS)
• xSDO work
• Phenopackets has been proposed as work item (“Phenopackets: A Format for Phenotypic Data Exchange”) in ISO/TC 215/SC1 - Genomics Informatics
• FHIR Implementation Guide (IG)

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Future Roadmap Additions

• Representing Treatment Course
• Cohort Representation

25

ga4gh.org

Large Scale Genomics

File Formats

• Initial SV improvements tagged for VCF 4.4
• Decision on VCF 5 or alternative based on UK Biobank dataset testing
• CRAM v4 approval documentation started
• Other: Compression gains, large chromosome support and improved long read support

Htsget

• Support for two-dimensional slices (genome range + samples), more complex queries

RNAget

• Server implementations with CanDIG, IHEC, ENCODE DCC, EMBL-EBI

Refget

• Support for sequence collections, reverse lookups

Crypt4GH

• Benchmarking, initial paper, integration with other GA4GH standards

Future Roadmap Additions

• Focus on implementations and adoption of standards & APIs

26

ga4gh.org

Data Security

• AAI -
• In conjunction with DURI Passports, AAI continues to evolve and is being adopted by US NIH’s RAS project. Feedback from that has brought a few changes.
• DSIP -
• Milestone of “self-assessment” checklist for people to use.
• This will enable projects to quantify their risk without large security expertise.
• Status - A few weeks behind: We aimed for deliverables for this meeting but was derailed by COVID-related responsibilities.
• Detecting behavior -
• Milestone of Brainstorming
• This is in the early stages as it’s a complex “moonshot” of an idea. 2020 goal is brainstorming and getting a plan in place. We have interested people.
• Status - Ongoing
• Federated Cohort Exploration and Analysis
• Status: testbed deployed within with SPHN driver project
• Setting up international consortium for COVID around MedCo technology (https://medco.epfl.ch)
• Cloud Security and Privacy
• Status - Actively working with Cloud Workstream and FASP (Federated Analysis Systems Project)
• BlockChains for Query Recording

27

ga4gh.org

Regulatory & Ethics

• GA4GH’s work on Harmonisation of Consent
• Large Scale Population Studies
• 2020 update of 2015 genomic research data sharing consent clauses
• WGS testing in routine medical care and variations on the return of results to relatives
• Standard Genomic Data Licenses and Agreements
• Standard licenses for open genetic knowledgebases
• Standard data access agreements for controlled access genomic databases
• GDPR and Data Sharing Forum
• Monthly briefs on European data protection law and its impact on data sharing
• Machine readable consent guidance
• Example consent clauses for data sharing aligned with the Data Use Ontology
• Participant Values Survey (Your DNA Your Say)
• Global online survey on public attitudes towards genomic data sharing w/ innovative films.
• Participant Engagement Best Practices
• Best practices for large scale sequencing projects to engage with their local publics
• Return of Results - Survey of Stakeholder Perspectives

​

28

ga4gh.org

Gap Analysis Summary

​

Heidi Rehm & Andrew Morris

ga4gh.org

Aims of the Gap Analysis

• Identify gaps that may not be identified through the Work Stream Roadmap process
• Identify new opportunities for GA4GH
• Areas that have not been on our radar
• Improve internal and external interoperability & collaboration
• Improve uptake and usage

ga4gh.org

Goals for this Session

• Clarify results of the gap analysis
• Identify red flags or potential for harm
• Identify gaps in the gap analysis
• Identify high level solutions to tackle multiple gaps simultaneously
• Identify priorities and solutions for Work Stream & Driver Projects
• Identify priorities and solutions for GA4GH operations

ga4gh.org

Process

14 Calls

Driver Project Champions

& Work Stream Leads

59 Survey Responses

All Active Contributors

ga4gh.org

Summary of Survey Respondents

ga4gh.org

Summary of Survey Respondents

ga4gh.org

Survey: Roadmap Deliverables of Most Interest

Variation Representation

Data Use Ontology

Variant Annotation

Beacon API

AAI

VCF/BCF

REWS Policy Framework

WES

Phenopackets

Researcher Identity & Access Claims

DRS

TRS

SAM/BAM/CRAM

refget API

Cloud Testbed

Return of Results Policy

Search API

TES

Discovery networks

htsget API

Breach Response

Pedigree

Case discovery

RNAget API

Service registry

Participant values

Browser extensible data

Proteomics Tool

ga4gh.org

Survey: Alignment Gaps

What further alignment is needed between data sharing initiatives to maximize data sharing? (40 responses)

9

Internal coordination on technical

and policy alignment

6

Harmonization with other SDOs

4

Integration with EHR systems

Top 3 Responses:

ga4gh.org

Survey: Alignment Gaps

What groups or programs are missing from the community of active GA4GH contributors? (35 responses)

5

Industry

4

HL7

6

Healthcare, Clinicians, Patients

Top 5 Responses:

ga4gh.org

Survey: Strengths

Overall, what is GA4GH doing well? (53 responses)

16

Convening Stakeholders

6

Driver Project Model

6

Valuable Deliverables

Top 3 Responses:

ga4gh.org

Survey: Weaknesses

Overall, what is GA4GH NOT doing well? (45 responses)

7

Broad community / stakeholder engagement

6

Getting new projects / organizations on board

6

Uptake / implementation of standards

Top 4 Responses:

6

Communication / collaboration between Work Streams

!

ga4gh.org

Gap Analysis Themes

1. Standards Development
2. Suite of Standards
3. Implementation & Adoption
4. Documentation, Maintenance, & Versioning
5. Cross-Work Stream Alignment
6. Engagement
7. Metrics
8. Open Standards
9. External Standards
10. Federation

ga4gh.org

(1) Standards Development

Find the right pace; need adequate input while keeping pace with industry

Improve landscape analysis to avoid duplication of efforts

Expand data types

ga4gh.org

Standards Development (Cont’d)

Collaborate with healthcare, EHRs & HL7

Develop smaller, easy to implement components

​

Increase number of developers

​

ga4gh.org

(2) Suite of Standards

Improve interoperability between standards

Utilize testbeds to identify friction areas

Highlight end-to-end implementation demonstrations

ga4gh.org

(3) Implementation & Adoption

Increase facilitation, training & support

Create tooling & testbeds to support implementation

Facilitate community discussions on best practices, challenges, etc.

ga4gh.org

(4) Documentation, Maintenance, & Versioning

Add capacity to adapt to new technologies

Ensure implementations are dependable and documented

ga4gh.org

Documentation, Maintenance, & Versioning (Continued)

Harmonize terminologies & data models across organization

Create consistent definitions of maturity and versioning

ga4gh.org

(5) Cross-Work Stream Alignment

Improve bilateral integration internally

Establish technical alignment across Work Streams

​

Improve cross Work Stream communication

ga4gh.org

(6) Engagement

Improve onboarding for new contributors

Reduce time zone & language barriers

Reduce resource barriers to participation

ga4gh.org

(7) Metrics

Create mechanism to track implementation metrics

Create clear KPIs for success

(Key Performance Indicators)

ga4gh.org

(8) Open Standards

Be clear on what GA4GH means by open standards

Ensure we don’t overlook valuable standards that aren’t open

ga4gh.org

(9) External Standards

Create mechanism to endorse external standards

Work more closely with external SDOs

(Standards Development Organizations)

ga4gh.org

(10) Federation

Clarify what federation is and the different types

Consider different approaches & where each is best

ga4gh.org

What We’re Doing

• Collaborate with healthcare, EHRs & HL7
• Participation from/in HL7 & ISO
• pursuing trilateral agreement
• Increase number of developers / add capacity to adapt to new technologies
• Assigned expert model
• Pursuing funding in house technical team
• Establish technical alignment across Work Streams / Improve interoperability between standards / Improve bilateral integration internally
• Technical Alignment Sub Committee
• Improve cross Work Stream communication
• Emphasizing X-WS collaboration in meetings and using newsletters for better communication

ga4gh.org

What We’re Doing (Cont’d)

• Highlight end-to-end implementation demonstrations
• Federated Analysis Systems Project
• Create mechanism to track implementation metrics
• Developing an Implementation Tracker
• Clarify what federation is and when/where it is in/appropriate
• Paper on Federation
• Facilitate community discussions on best practices, challenges, etc.
• Genomics and Health Implementation Forum

ga4gh.org

Clarification &

Questions

ga4gh.org

Poll - Help Us Prioritize the Top 6 Gaps

1. Establish GA4GH position on federation
2. Create mechanism to endorse external standards
3. Establish GA4GH position on open standards and ensure we don’t overlook valuable non-open standards
4. Create metrics and key performance indicators with mechanisms to track results
5. Improve onboarding for new contributors
6. Reduce barriers to participation
7. Establish robust framework to support cross-WS alignment
8. Add developer capacity
9. Ensure implementations are dependable and documented
10. Harmonize terminologies, data models, definitions of maturity, and versioning across the organization
11. Increase facilitation, training & support for implementations

• Create tooling & testbeds to support implementation
• Facilitate community discussions on best practices, challenges, etc.
• Improve interoperability and alignment between standards
• Utilize testbeds to identify friction areas
• Highlight end-to-end implementation demonstrations
• Find the right pace; need adequate input while keeping pace with industry
• Improve landscape analysis to avoid duplication of efforts
• Expand data types
• Develop smaller, easy to implement components
• Collaborate with healthcare, EHRs & HL7
• Add capacity to adapt to new technologies

​

Submit your vote at Slido.com with event code #GA4GHConnect

ga4gh.org

Feedback

Are there other priorities we should include in the top 6?

Make your case now.

ga4gh.org

Feedback

How can GA4GH Secretariat & Leadership address the priority gaps?

ga4gh.org

Feedback

How can Work Streams and Driver Projects address the priority gaps?

ga4gh.org

Next Steps

1

Work Streams to continue to refine individual Strategic Roadmaps with Gap Analysis feedback in mind

2

Andrew and Heidi to make recommendations for overarching strategic focus based on feedback throughout the meeting

3

Steering Committee to vote on key areas for strategic focus & contribute suggestion for solutions

4

GA4GH Secretariat to work with Exec and Steering Committee to develop solutions to address areas of focus

5

Finalize, release & activate (Sep)

ga4gh.org