Presentation to clinicians on what they need to think about to do a large-scale Open Science project where they want to share clinical, genomic and imaging data.

2. Open Science:
An essential component to any
International Collaborative Network
BF Francis Ouellette
Executive Director, Neuro Bioinformatics Core Facility
TOSI Open Science Of
fi
cer, The Neuro, McGill University
ORCID ID: https://orcid.org/0000-0003-4676-675X @bffo on

3. Slides available on SlideShare: https://bit.ly/3Mo0CLd

5. Outline
Open Science
International Collaborations
ICGC
GA4GH
How to make clinical data, international collaborations and
Open Science work together.

6. Open Science
“Open science is the movement to make scienti
fi
c
research (including publications, data, physical samples,
and software) and its dissemination accessible to all levels
of an inquiring society, amateur or professional.”
Michael Woel
fl
e, Piero Olliaro & Matthew H. Todd
Open science is a research accelerator
Nature Chemistry 3, pages 745–748 (2011) https://go.nature.com/3ziZCoq

8. Open Data
Clinical patient data
Genomic data
Imaging data
Flow Cytometry Data
Other data
Metadata
Data Management Plans (DMP)

9. Data Access: patient samples?
GA4GH Passport standard for digital identity and
access permissions.
Voisin C, Linden M, Dyke SOM, Bowers SR, Alper P, Barkley MP, Bernick D, Chao
J, Courtot M, Jeanson F, Konopko MA, Kuba M, Lawson J, Leinonen J, Li S, Ota
Wang V, Philippakis AA, Reinold K, Rushton GA, Spalding JD, Törnroos J,
Tulchinsky I, Guidry Auvil JM, Nyrönen TH.
Cell Genom. 2021 Nov 10;1(2):None.
doi: 10.1016/j.xgen.2021.100030.
PMID: 34820660

10. Prepublication data sharing
Prepublication data sharing.
Toronto International Data Release Workshop Authors, Birney E, Hudson TJ, Green ED, Gunter C, Eddy S, Rogers J, Harris JR, Ehrlich SD, Apweiler R, Austin CP, Berglund L, Bobrow M, Bountra C, Brookes AJ, Cambon-Thomsen A,
Carter NP, Chisholm RL, Contreras JL, Cooke RM, Crosby WL, Dewar K, Durbin R, Dyke SO, Ecker JR, El Emam K, Feuk L, Gabriel SB, Gallacher J, Gelbart WM, Granell A, Guarner F, Hubbard T, Jackson SA, Jennings JL, Joly Y, Jones
SM, Kaye J, Kennedy KL, Knoppers BM, Kyrpides NC, Lowrance WW, Luo J, MacKay JJ, Martín-Rivera L, McCombie WR, McPherson JD, Miller L, Miller W, Moerman D, Mooser V, Morton CC, Ostell JM, Ouellette BF, Parkhill J, Raina PS,
Rawlings C, Scherer SE, Scherer SW, Scho
fi
eld PN, Sensen CW, Stodden VC, Sussman MR, Tanaka T, Thornton J, Tsunoda T, Valle D, Vuorio EI, Walker NM, Wallace S, Weinstock G, Whitman WB, Worley KC, Wu C, Wu J, Yu J.
Nature. 2009 Sep 10;461(7261):168-70. doi: 10.1038/461168a.
PMID: 19741685

11. … arguments can be made for the release of data for studies
involving human subjects, as doing so can augment the
opportunities for new discoveries that could ultimately bene
fi
t
individuals, communities, and society at large.
Sharing Data about
human subjects

17. ICGC community
Setting ambitious goals
Writing things down:
Inaugural paper
Data Access Policy (what is Open, and what is Controlled Access)
Data submission and data release rules
Organizing working groups
Monthly call, organized centrally, recorded, minute taking etc.

19. Things to do before you start your
Open Science project?
Data sharing rules
Who can be part of the gang? (Inclusion & Exclusion criteria)
How Controlled Access (Registered Access) will be addressed, monitored and managed.
How will Open Data access be monitored and managed.
Where data will be hosted (multiple sites, different sites for different data types?)
Web Development group(s) to develop multiple web sites:
Description of the governance structure
Data submission portal
Data access request portal
Data retrieval portal
Published Protocols for sample selection, manipulation, storage, access, and distribution and governance
Other publications, direct and derived.

20. Lots of Tools, Documentation, and experience, leverage it!
Set guidelines and rules of engagement before your start.
Bring together the expertise you need in each team:
Clinician
Genomics
Bioinformatics
Imaging
Write it all down in a foundational publication: tell the world what you are up to!
Measure as you progress, meet often, make your data Open before you publish.

21. Other things to worry about (1 of 2)
Set a timeline with clear objectives
Consider Preregistration of your study design
https://plos.org/open-science/preregistration/

22. Other things to worry about (2 of 2)
$$$ to do the project
Curation and maintenance of the bio banking (long term)
Curation and maintenance of the data (long term)
$$$ to keeps things going after the project is done.
(Institutional support, or other awards)

23. Global Alliance for
Genomics and Health
(GA4GH)
ga4gh.org
GA4GH is a policy-framing and technical standards-setting
organization, seeking to enable responsible genomic data
sharing within a human rights framework.

24. GA4GH has many resources
Genomic Data Toolkit (23 documents)
VCF v4 / BCF v2 File Formats
Machine Readable Consent Guidance
Regulatory & Ethics Toolkit (14 documents)
Consent Clauses for Large Scale Initiatives
Data Security Toolkit (3 documents)
Authentication & Authorization Infrastructure v1

25. https://pubmed.ncbi.nlm.nih.gov/35072136/

27. … major challenges to achieving the broad goal of responsible
sharing of genomic and related health data.
1. Inconsistency and lack of version control in data-generating pipelines
2. Lack of dataset interoperability due to disparate data models and terminologie
3. Inadequate infrastructure for ingesting and storing data
4. Difficulty or lack of resources for enabling access to data
5. Insufficient consent for data sharing and lack of resources to support the
consent process

28. … major challenges to achieving the broad goal of responsible
sharing of genomic and related health data.
6. Data privacy and security issues, as well as real and perceived
regulatory issues
7. Challenges to ensuring patients understand how their data are used
and have sufficient autonomy around data sharing participation
8. Differences in priorities, experiences, and trust levels concerning
data sharing between different population groups and stakeholders
9. Lack of incentives in the clinical care system for prioritizing data
sharing and research
10. Lack of data-sharing mandates

29. On line resources
My slides: https://bit.ly/3Mo0CLd
ICGC: https://dcc.icgc.org/
ICGC ARGO: https://www.icgc-argo.org/
GA4GH: https://www.ga4gh.org/
PCAWG papers: https://www.nature.com/collections/afdejfafdb/ (28 papers)
Cell Genomics GA4GH special issue: (10 papers)
https://www.cell.com/cell-genomics/issue?pii=S2666-979X(21)X0003-1

30. Last message to students and young PDFs and all
investigators:

31. Last message to students and young PDFs and all
investigators:
Be open so people can
see how great you are!

32. Merci!