1

Revisions to the GA4GH Consent Policy

Kristina Kekesi-Lafrance ( Center of Genomics and Policy, McGill University)

Adrian Thorogood (Centre of Genomics and Policy, McGill University), Susan Wallace (University of Leicester), Edward Dove (University of Edinburgh), Bartha Maria Knoppers (Centre of Genomics and Policy, McGill University)

2

Data Security Infrastructure Policy

Jean-Pierre Hubaux (École Polytechnique Fédérale de Lausanne)

3

Implementing GA4GH Data Use & Researcher ID Standards for Improved Data Access & Sharing

Jonathan Lawson ( Broad Institute)

Jonathan Lawson (Broad Institute)

4

GA4GH Cloud Work Stream Testbed: Testing APIs for compliance and interoperability

Brian O'Connor (UCSC)

James Eddy (Sage Bionetworks), Denis Yuen (OICR), David Glazer (Verily), Brian O'Connor (UCSC)

5

GA4GH Cloud Worksteam: TRS - Approval of a standard for workflow sharing

Denis Yuen (OICR)

Denis Yuen (OICR), Susheel Varma (Elixir), James Eddy (Sage), David Glazer (Verily), Brian O'Connor(UCSC)

6

Refget: access to reference sequences

Andrew Yates (EMBL-EBI)

Jeremy Adams: Global Alliance for Genomics and Health Headquarters, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
Robert Davies: Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
Oliver Hofmann: University of Melbourne Centre for Cancer Research, Melbourne, VIC
Thomas Keane & Rasko Leinonen: European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridgeshire, UK
Mike Love: Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27516, USA
 

7

htsget

Jeremy Adams (GA4GH)

8

RNAget

9

Crypt4GH 1.0: An encrypted file format supporting direct & transparent access

Alexander Senf (EMBL-EBI)

10

CRAM

11

Schemablocks

12

Phenopackets: A schema for patient phenotype data capture and exchange

Jules Jacobsen ( Queen Mary University of London)

Jules Jacobsen - Queen Mary University of London, Peter Robinson - The Jackson Laboratory

13

VR Specification: An extensible schema for all classes of variation

Reece Hart (ClinGen)

Reece Hart (Broad Institute) , Alex Wagner (Washington University School of Medicine) , Lawrence Babb (Broad Institute) , Robert Freimuth (Mayo Clinic), and the VR team

14

The Variant Interpretation for Cancer Consortium: A GA4GH Driver Project

Alex Wagner ( Washington University School of Medicine)

Obi Griffith (WU SoM), Malachi Griffith (WU SoM), Debyani Chakravarty (MSKCC), and the VICC

15

Beacon v2.0: Towards a modular Beacon protocol empowering clinical use

Jordi Rambla (CRG)

Sabela de la Torre. Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
Frederic Haziza. Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
Marta Ferri. Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
Michael Baudis. Institute of Molecular Life Sciences (IMLS) and Swiss Institute of Bioinformatics (SIB), University of Zurich
Joaquin Dopazo, Clinical Bioinformatics Area, Fundacion Progreso y Salud, Hospital Virgen del Rocio, Sevilla, Spain
Niclas Jareborg. National Bioinformatics Infrastructure Sweden / ELIXIR-SE
Gary Saunders, ELIXIR Hub, Wellcome Genome Campus, Cambridge, CB10 1SD, UK.
Dylan Spalding, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Juha Tornroos, CSC - IT Center for Science Ltd
Jordi Rambla. Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
Arcadi Navarro. Universitat Pompeu Fabra and Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
 

16

Local EGA: A portable toolkit to securely deposit and share human sensitive data

Jordi Rambla (CRG)

Jordi Rambla. Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
Frederic Haziza. Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
Oscar Martinez. Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
Thomas Keane. European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Niclas Jareborg. National Bioinformatics Infrastructure Sweden / ELIXIR-SE
Gary Saunders. ELIXIR Hub, Wellcome Genome Campus, Cambridge, CB10 1SD, UK.
Arcadi Navarro. Universitat Pompeu Fabra and Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
Dylan Spalding. European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Juha Tornroos, CSC - IT Center for Science Ltd
The Tryggve project
 

17

ELIXIR Service Network specification: improving discoverability, access and data sharing by connecting services

Frederic Haziza (CRG)

Frederic Haziza. Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
Sabela de la Torre. Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
Marta Ferri. Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
Dmitry Repchevsky, INB/ELIXIR-ES Computational Node. Life Sciences Department, Barcelona Supercomputing Center (BSC). Barcelona, 08034, Spain.
José M. Fernández, INB/ELIXIR-ES Coordination Node. Life Sciences Department, Barcelona Supercomputing Center (BSC). Barcelona, 08034, Spain.
Vicky Sundesha, INB/ELIXIR-ES Coordination Node. Life Sciences Department, Barcelona Supercomputing Center (BSC). Barcelona, 08034, Spain.
Teemu Kataja, CSC - IT Center for Science Ltd
Niclas Jareborg, National Bioinformatics Infrastructure Sweden / ELIXIR-SE
Gary Saunders ELIXIR Hub, Wellcome Genome Campus, Cambridge, CB10 1SD, UK.
Salvador Capella-Gutierrez, INB/ELIXIR-ES Coordination Node. Life Sciences Department, Barcelona Supercomputing Center (BSC). Barcelona, 08034, Spain.
Dylan Spalding. European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Juha Tornroos, CSC - IT Center for Science Ltd
Jordi Rambla. Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
Arcadi Navarro. Universitat Pompeu Fabra and Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
 

18

ELIXIR Cloud & AAI: Standardised and Interoperable Cloud Services for Human Data Communities.

Shubham Kapoor (ELIXIR-FI), Susheel Varma (EMBL-EBI), Tommi Nyrönen (ELIXIR-FI), Steven Newhouse (EMBL-EBI) Ludek Matyska (ELIXIR-CZ), Jonathan Tedds (ELIXIR-Hub), ELIXIR Tools Platform, ELIXIR Compute Platform, ELIXIR Communities

19

EGA & GA4GH

20

Design and Implementation of Shariant: a platform to share clinically curated variants across Australia

Amanda B Spurdle (Australian Genomics Health Alliance)

Emma Tudini, David Lawrence, James Andrews, Sarah King-Smith, Amanda B Spurdle (Australian Genomics Health Alliance)

21

Deep Phenotyping for Improved Diagnostics and Analysis

Monica Munoz-Torres (Monarch Initiative)

Melissa Haendel, Oregon State University, Oregon Health and Science University
Monica Munoz-Torres, Oregon State University
Peter Robinson, Jackson Laboratory for Genomic Medicine
Jules Jacobsen, Queen Mary University of London, Genomics England
Matthew Brush, Oregon Health and Science University
and The Members of the Monarch Initiative.

22

Interoperability demonstration via the DRS API between the Cancer Genomics Cloud and Cavatica

Michele Mattioni (Seven Bridges)

Michele Mattioni, Manisha Ray, Jack DiGiovanna, Brandi Davis-Dusenbery -
Seven Bridges

23

Matchmaker Exchange

24 

Developing a data resource for pediatric genomics research: The Gabriella Miller Kids First Pediatric Research Program (Kids First)

Valerie Cotton (NICHD, Gabriella Miller Kids First)

Authors:
D. Winchester 1; V. Cotton 2; The Gabriella Miller Kids First Pediatric Research Program Working Group

Affiliations:
1) Office of the Director, Office of Strategic Coordination - The Common Fund, National Institutes Health, Rockville MD; 2) Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health Rockville,MD

25

Gabriella Miller Kids First Data Resource Center: Collaborative platforms for accelerating cross-disease pediatric research across development and cancer

Allison P. Heath ( Children's Hospital of Philadelphia)

Allison P. Heath PhD1, Christina Yung PhD2, Yuankun Zhu BS1, Michele Mattioni PhD3 ,Zachary L. Flamig PhD4 ,Yajing Tang MS4 ,Bailey Farrow MS1,Jena Lilly MS1,Yiran Guo PhD1 ,Pichai Raman PhD1,5,Phillip B. Storm MD1,9, Luca Graglia, MS13, Samuel L. Volchenboum MD PhD8, 13, Javad Nazarian PhD6, Nicole Vasilevsky PhD11, Jack DiGiovanna PhD3, Melissa Haendel PhD11,12, Robert L. Grossman PhD4, Brandi Davis-Dusenbery PhD3, Deanne M. Taylor PhD5,7, Vincent Ferretti PhD10, Adam Resnick PhD1,5,9

1Center for Data-Driven Discovery (D3b) Children’s Hospital of Philadelphia, Philadelphia, PA, USA;
2Ontario Institute of Cancer Research, Toronto, Ontario, Canada;
3Seven Bridges Genomics, Cambridge, MA, USA;
4Center for Translational Data Science, The University of Chicago, Chicago, Illinois, USA;
5Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA;;
6Children's National Medical Center, Washington, DC, USA;
7Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA;
8Department of Pediatrics, Biological Sciences Division, The University of Chicago, Chicago, Illinois, USA; 9Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA;
10CHU Sainte-Justine Research Center, Montreal, Quebec, Canada;
11Translational and Integrative Sciences Lab, Oregon Health & Science University, Portland, OR, USA;;
12Oregon State University, Corvallis, Oregon, USA;
13Center for Research Informatics, The University of Chicago, Chicago, Illinois, USA;
 

26

User need-driven redesign of clinical NGS reports

Sharmini Alagaratnam (DNV GL)

Sharmini Alagaratnam(1), Oleg Agafonov(1), Kaja Kjolås(2) and Sigrun Vik(2)

1. Precision Medicine programme, Group Technology and Research, DNV GL, Høvik, Norway
2. EGGS Design, Oslo, Norway
 

27

Development of needs-driven informed consent guidelines for clinical genome sequencing at a Norwegian hospital

Bobbie N. Ray-Sannerud (DNV GL)

Sharmini Alagraratnam1, Guro Pedresen,1Oda Bakken,2 and Yngve Sejersted3
1Precision Medicine program, Group Technology and Research, DNV GL AS, Høvik, Norway
2 Oslo University Hospital, Legal Department
3 Oslo University Hospital, Department of Medical Genetics
 

28

DNV GL’s Variant Exchange and BigMed paving the way for sharing of variant classification data – a European case

Guro Meldre Pedersen (DNV GL)

Guro Meldre Pedersen, Thina Ytterhorn & Stephen McAdam

All: DNV GL AS, Høvik, Norway

29

Open standards for semantic interoperability of clinical and genomic data: a proof-of-concept bridging openEHR, Phenopacket and FHIR.

Francesca Frexia ( CRS4/EJP-RD)

Cecilia Mascia (CRS4/EJP-RD), Luca Lianas (CRS4), Giovanni Delussu (CRS4), Paolo Uva (CRS4), Gianluigi Zanetti (CRS4/EJP-RD), Heather Leslie (openEHR Foundation), Ian McNicoll (openEHR Foundation), Silje Ljosland Bakke (openEHR Foundation), Diego Boscá (VeraTech), Gideon Giacomelli (EUCANCan & HiGHmed)

30

The National Human Genome Research Institute (NHGRI) Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL)

Nataliya Kucher (National Human Genome Research Institute)

Joanna Chau, Heidi Sofia, Elena Ghanaim, Ken Wiley, Valentina Di Francesco; Affiliation: National Human Genome Research Institute, NIH, Bethesda, MD, 20892

31

Assuring Data Quality with Variant Benchmarking tools from GIAB and GA4GH

Nathan D Olson ( National Institute of Standards and Technology)

Nathan D. Olson, Jennifer McDaniel, Justin Wagner, Justin Zook
National Institute of Standards and Technology

32

GA4GH Standards & Arvados Open Source Software

Tom Morris ( Veritas Genetics)

Peter Amstutz, Tom Morris - both of Veritas Genetics

33

NeIC Tryggve - cross-border services for human data utilising GA4GH outcomes

Juha Törnroos (ELIXIR-FI)

Juha Törnroos (ELIXIR-FI), Niclas Jareborg (ELIXIR-SE), Abdulrahman Azab, (ELIXIR-NO), Ali Syed (ELIXIR-DK), Jonas Hagberg (ELIXIR-SE), Henric Zazzi (ELIXIR-SE), Antti Pursula (ELIXIR-FI)

34

Illumina’s secure, enterprise grade, and GA4GH compliant data platform

Pratik Soares (Illumina)

Pratik Soares, Charles Aylward, Claudia Dennler, Angel Pizarro, Jessica Gordon

35

Bioinformatics at the National Danish Genome Center

Ole Lund ( Danish National Genome Center)

Ole Lund, Wibrow Arindrarto, Philip Alstrup Andersen, Cathrine Jespersgaard, Birgitte Nielson, Isabelle de Piedade, Brian Stridsen, Ali Syed, Mark Thomas Østerlund, Peter Løngreen. Danish National Genome Center (NGC), Ørestads Boulevard 5, DK-2300 Copenhagen S, Denmark.