Virtual Poster Session: Poster Directory

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2Accelerating Research in Genomic Oncology: Updates from the next phase of the International Cancer Genome Consortium

Amber Johns1, Rita Lawlor2, Jan Korbel3, Keunchil Park4, Christina Yung5, Lincoln Stein5, Andrew Biankin6

1International Cancer Genome Consortium, Australia; 2University of Verona, Italy; 3European Molecular Biology Laboratory, Germay; 4Samsung Medical Center, South Korea; 5Ontario Institute for Cancer Research, Canada; 6University of Glasgow, United Kingdom

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4Are They Incidental, Secondary or Additional Findings? A Survey of Opinions and Practices Across Australian Genetic Testing Laboratories

Emma Tudini1,2, Matilda Haas2,3, Tessa Mattiske2,3 and Amanda B. Spurdle1, on behalf of Australian Genomics

1QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia; 2Australian Genomics Health Alliance, Australia; 3Murdoch Children’s Research Institute, Parkville, Victoria, Australia.

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6ClinGen Linked Data Hub: a scalable infrastructure to support variant pathogenicity assessment by modeling and linking diverse types of evidence about variants using the GA4GH Variant Annotation standards

Sai Lakshmi Subramanian1, Andrew R. Jackson1, Neethu Shah1, Kevin Riehle1, Deborah. I. Ritter1,2, Christine Preston3, Matt W. Wright3, Matthew Brush4, Larry Babb5, Carlos D. Bustamante3, Sharon E. Plon1,2, Aleksandar Milosavljevic1, on behalf of the Clinical Genome Resource

1Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX; 2Department of Pediatrics, Baylor College of Medicine, Houston, TX; 3Department of Pathology, Stanford University School of Medicine, Stanford, CA; 4Oregon Health and Science University, Portland, OR; 5Broad Institute, Cambridge, MA.

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42EJP RD: Building a Virtual Platform for Rare Disease Research

Sergi Beltran1, Tanguy Onakoy2, Daria Julwoska2, Franz Schaefer3, Ana Rath2, Anthony Brookes4 on behalf of the EJP-RD Consortium

1Centro Nacional de Análisis Genómico, CNAG-CRG, Barcelona Spain. (Additional: BIST, UPF, UB)
2INSERM, Paris, France
3University of Heidelberg, Heidelberg, Germany
4University of Leicester, Leicester, United Kingdom

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14EpiShare: an open platform to securely share epigenomic data

David Bujold1,2, Ksenia Zaytseva1,2, Palmira Granados Moreno2,3, Hanshi Liu2,3, Sebastian Ballesteros Ramirez1,2, Romain Grégoire1,2, David Lougheed1,2, Katie Saulnier2,3, Yann Joly2,3, Guillaume Bourque1,2

1Canadian Center for Computational Genomics, McGill University, Montreal, Quebec, Canada
2Department of Human Genetics, McGill University, Montreal, Quebec, Canada
3Centre of Genomics and Policy, Faculty of Medicine, McGill University, Canada

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41Federating Co-occurrence Analysis to Interpret Genetic Variants While Preserving Privacy

James Casaletto, Melissa Cline, Amanda Spurdle, Michael Parsons, Bingjian Feng, Yusuke Iwasaki, Yukhide Momozawa

University of California Santa Cruz, QIMR Berghofer, University of Utah, Biobank Japan at Riken

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15GA4GH DURI Work Stream in GEM Japan 2020; localizing the Data Use Ontology and Machine-Readable Consent in the local research community.

Chisato Yamasaki1,9*, Satoshi Nagaie2,9, Minae Kawashima3,9, Chihiro Hata4,9, Shuichi Kawashima5,9, Yuichi Kodama4,9, Mizuki Morita6,9, Natsuko Yamamoto1,9, Akio Nagano 7,9, Keiko Katsui8,9, Takako Takai8,9, Soichi Ogishima2,9

1Osaka Univ., 2ToMMo3NBDC, 4DDBJ; 5DBCLS; 6Okayama Univ.; 7PENQE inc.; 8AMED; 9DURI Work Stream in GEM Japan.

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43Genomics England: World’s largest whole genome database

Augusto Rendon, Mark Caulfield, Anna Need, Tom Fowler, Tim Hubbard, Richard Scott, Ellen Thomas, Nirupa Murugaesu, Graham Binns, Antonio Rueda, Javier López, Christine Patch

Genomics England, London, UK

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39Health Genomics within the Swiss Personalized Health Network (SPHN) initiative

Jan Armida1, Sabine Österle1,  Shubham Kapoor1, Katrin Männik2, Marc Friedli2, and Katrin Crameri1 on behalf of the SPHN Consortia

1Swiss Institute of Bioinformatics.
2Health2030 Genome Center.

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40Human Heredity and Health in Africa (H3Africa): Alignment with GA4GH Standards

Mamana Mbiyavanga1, Nicola Mulder1, Mogomotsi Matshaba2, on behalf of the H3Africa Consortium

1University of Cape Town, Cape Town, South Africa.
2Botswana Baylor Clinical Centre of Excellence, Gaborone, Botswana .

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23National Health Research for a Federal Canada - CanDIG in 2020

Jonathan Dursi1, David Bujold2, Jimmy Li3, Shaikh Farhan Rashid1, Amanjeev Sethi1, Dashaylan Naidoo3, Felipe Coral-Sasso3, Zhibin Lu3, Kat Pavlova1, Samarth Patel1, Brennan Brouillette2, P-O Quirion2, Krista Pace1, Carl Virtanen1, Trevor Pugh1,4, Pierre-Étienne Jacques5, Yann Joly2, Steven Jones3, Guillaume Bourque2, Michael Brudno1

1University Health Network; 2McGill University; 3Canada's Michael Smith Genome Sciences Centre; 4 Ontario Institute for Cancer Research; 5Université de Sherbrooke.

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38NHLBI's Trans-Omics for Precision Medicine (TOPMed) Program

Mollie A. Minear, PhD1; Meagan Grant, PhD1,2; Marie-Luise Brennan, MD, PhD1,3; Hwaida Hannoush, MD1,3; James Luo, PhD1; Julie L. Mikulla, MSc, RN1; Pankaj Qasba, PhD1; Jonathan R. Kaltman, MD1; Alastair Thomson1; Sarah C. Nelson, PhD4; Kenneth M. Rice, PhD4; Gonçalo R. Abecasis, PhD5; Thomas W. Blackwell, PhD5; Albert V. Smith, PhD5; and Weiniu Gan, PhD1 on behalf of the TOPMed Consortium6

1 National Heart, Lung, and Blood Institute (NHLBI), Bethesda, MD;
2 AAAS Science & Technology Policy Fellow, Washington, DC;
3 American College of Medical Genetics and Genomics, Bethesda, MD;
4 University of Washington, Seattle, WA;
5 University of Michigan, Ann Arbor, MI;
6 A full list of TOPMed Consortium members can be found at: https://www.nhlbiwgs.org/topmed-banner-authorship

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30Risk assessment of a local clinical MME implementation as a route to regulatory approval

Sharmini Alagaratnam1, Tor Solli-Nowlan2, Tony Håndstad2.

1Precision Medicine programme, Group Technology and Research, DNV GL, 1363 Høvik, Norway; 2Department of Medical Genetics, Oslo University Hospital, 0424 Oslo, Norway.

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34The ELIXIR Cloud: The ELIXIR Cloud & AAI Community

Alexander Kanitz1 and Jonathan Tedds2

1Swiss Institute of Bioinformatics;
2ELIXIR Europe.

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36Variant Atlas: A Scalable Cohort Analysis and Query Platform

Dmitry Degrave1, Andre Hermanto1, Shyamsundar Ravishankar1, Joe Copty1, Shane Husson1, Marie-Jo Brion2, Warren Kaplan1

1Kinghorn Centre for Clinical Genomics (KCCG), Garvan Institute of Medical Research, Sydney; 2QIMR Berghofer Medical Research Institute and Australian Genomics Health Alliance.

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16GA4GH Standards (DRS, Passports) underlying the Data Ecosystems supported by Gen3

Jiaqi Liu, Garrett Rupp, Michael Lukowski, Fantix King, Robert Grossman

University of Chicago, Center for Translational Data Science.

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19GraphQL back end Beacon API

Yeo Kee Hern Nathan1,2, SG10K_Health Consortium, Tan Boon Ooi Patrick1, Prabhakar Shyam1 , Bertin Nicolas1 and Hebrard Maxime1

1Genome Research Informatics and Data Science Platform, Genome Institute of Singapore, A*STAR, Singapore; 2 School of Computing, National University of Singapore, Singapore

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24Nextflow Tower: Bringing GA4GH WES to Nextflow

Kevin Sayers1, Evan Floden1, Paolo Di Tommaso1

1Seqera Labs, Barcelona, Spain

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27Progenetix - A cancer genomics reference resource around GA4GH standards

Qingyao Huang, Paula Carrio-Cordo, Rahel Paloots, Bo Gao and Michael Baudis

Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Switzerland

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11Automating access to controlled dataset with DUO, the Data Use Ontology

Mélanie Courtot1 and Jonathan Lawson2 on Behalf of the GA4GH DURI Workstream

1EMBL-EBI; 2Broad Institute of MIT and Harvard; To view the full list of contributors, please visit: bit.ly/duocontributors

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8Crypt4GH 1.0: An encrypted file format supporting direct & transparent access

Alexander Senf1, Robert Davies2, Frédéric Haziza3.

1European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK.
2Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK.
3Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain.

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10Data Security Infrastructure Policy (DSIP)

Francesco Marino1, Joao Sa Sousa1, Juan Troncoso-pastoriza1, Dixie Baker2, David Bernik3, Jean-pierre Hubaux1

1École Polytechnique Fédérale de Lausanne, Switzerland.
2Martin, Blanck & Associates, VA, USA
3Broad Institute of MIT and Harvard, MA, USA.

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5GA4GH Beacon v2 - Evolving Reference Standard for Genomic Data Exchange

Gary Saunders, Jordi Rambla de Argila, Anthony Brookes, Juha Törnroos and Michael Baudis 

For the ELIXIR Beacon project, GA4GH Discovery work stream and the international network of Beacon API developers 

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7GA4GH CRAM File Format

James Bonfield1, Chris Norman2, Vadmin Zalunin3/sup>.

1Wellcome Sanger Institute; 2Broad Institute; 3European Bioinformatics Institute.3 National Center for Biotechnology Information.

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20Htsget: Standardized retrieval of HTS alignments and variants over the web

Mike Lin, Jerome Kelleher1, John Marshall2, Antonio Rueda Martin3, Bob Dolin4, Oliver Hofmann5, Jaime M Tovar Corona6, David Liu7, Jeremy Adams7

1Big Data Institute, University of Oxford, Oxford, UK. 2Glasgow Precision Oncology Laboratory, University of Glasgow, Scotland. 3Genomics England, London, UK. 4Elimu Informatics, Richmond, CA, US. 5University of Melbourne Center for Cancer Research, Melbourne, AU. 6Wellcome Sanger Institute, Hinxton, UK. 7Global Alliance for Genomics and Health, Ontario Institute for Cancer Research, Toronto, ON, CA.

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22Machine Readable Consent Guidance

Adrian Thorogood1, Tiffany Boughtwood2, Jonathan Lawson3, Melanie Courtot4, DURI and REWS Work Stream Members

1ELIXIR-LU, University of Luxembourg.
2Australian Genomics Health Alliance, Melbourne, Australia
3Broad Institute of MIT and Harvard, MA, USA.
4European Bioinformatics Institute, Hinxton, England.

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21Modeling Therapeutic Response Statements using the GA4GH GKS Variation Annotation Modeling Framework

Yiqing Zhao, PhD1, Matthew Brush, PhD2, Robert R. Freimuth, PhD1

1Division of Digital Health Sciences, Department of Health Sciences Research, Mayo Clinic; 2Oregon Clinical and Translational Research Institute, Oregon Health and Sciences University.

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26Phenopackets: A schema for patient phenotype data capture and exchange

Julius O.B. Jacobsen & Peter N. Robinson on behalf of the GA4GH Clinical & Phenotypic Data Capture Work Stream

Queen Mary University of London & The Jackson Laboratory

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28Refget: standardised access to reference sequences

Andrew D. Yates1, Jeremy Adams2, Robert Davies3, Oliver Hofmann4, Thomas Keane1, Rasko Leinonen1, Michael I Love5

1European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridgeshire, UK.
2Global Alliance for Genomics and Health, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.
3Wellcome Sanger
Institute, Hinxton, Cambridgeshire, CB10 1SA, UK.
4University of Melbourne Centre for Cancer Research, Melbourne, VIC.
5Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27516, USA

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29Regulatory and Ethics Work Stream: Summary of 2019-2020 Outputs

Edward Dove1, Yann Joly2, Kristina Kekesi-Lafrance2, Michael Beauvais2 on behalf of the GA4GH Regulatory and Ethics Work Stream

1School of Law, University of Edinburgh; 2Centre of Genomics and Policy, McGill University.

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31RNAget: An API for retrieving processed RNA-derived measurements

GA4GH RNA Working Group* Presented By Sean Upchurch1, Emilio Palumbo2, Jeremy Adams3, David Bujold4

1California Institute of Technology, Pasadena, CA, US.
2Centre de Regulacio Genomica, Barcelona, Spain.
3Global Alliance for Genomics and Health, Ontario Institute for Cancer Research, Toronto, ON, CA.
McGill University, Montreal, Quebec, CA.
*https://tinyurl.com/GA4GH-RNA-seq

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32Service Info and Service Registry: Towards a federated Internet of Genomics

GA4GH Discovery Networks Group* Led By Jeremy Adams1,2, Miro Cupak3, Andy Yates4, Jordi Rambla5, Milan Panik3, Juha Törnroos6.

1Global Alliance for Genomics and Health, Toronto, CA. 2Ontario Institute for Cancer Research, Toronto, CA. 3DNAstack, Toronto, CA.4European Bioinformatics Institute, Hinxton, UK. 5Centre for Genomic Regulation, Barcelona, Spain. 6CSC - IT Center for Science, Espoo, Finland.

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25Transporting identity and access between environments with Passports

Craig Voisin1, Mikael Linden2, Stephanie Li3, Sarion Bowers4 on behalf of the DURI Workstream

1Google, 2ELIXIR, 3GA4GH, 4Sanger Institute

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37VR Specification: An extensible schema for all classes of variation

Reece Hart1,2, Alex Wagner3, Lawrence Babb1, Robert Freimuth4, and the VR team

1Broad Institute; 2Invitae, Inc.; 3Washington University; 4Mayo Clinic

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1A bioinformatics platform for clinical genomics in Argentina

Patricio Yankilevich

Genomap Bioinformatics

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3An introduction to the Global Parkinson's Genetics Program (GP2)

Hampton L. Leonard1,2, Cornelis Blauwendraat1, Mary Makarious1, Dan Vitale1,2, Yeajin Song1,2, Mike A. Nalls1,2, and Andrew B. Singleton1 on behalf of the Global Parkinson’s Genetics Program (GP2)

1 National Institutes on Aging (NIA), Bethesda, MD, USA; 2 Data Tecnica International, Glen Echo, MD, USA.

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12DyCons: Enabling Dynamic Consent on Distributed Computing Infrastructures

Kat Pavlova1, Jonathan Dursi1, Guillaume Bourque2, Michael Brudno1

1Univeristy Health Network; 2Department of Human Genetics, McGill University.

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13ELIXIR::GA4GH Strategic Partnership Capability Maturity Model

Gary Saunders1, Melissa Konopko2

1ELIXIR, Wellcome Genome Campus, Hinxton CB10 1SD, UK; 2Global Alliance for Genomics and Health, Wellcome Genome Campus, Hinxton CB10 1SA, UK.

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17GA4GH Technical Team: Current Accomplishments and Future Plans

Jeremy Adams1,2, David Liu1,2, Anders Leung1,2, Louis Bergelson3

1Global Alliance for Genomics and Health, Toronto, CA. 2Ontario Institute for Cancer Research, Toronto, CA. 3Broad Institute, Cambridge, MA, US.

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18Genome Adventures Comic Books as a Model for Effective Community Engagement in the Collaborative African Genomics Network (CAfGEN) in Botswana Schools

Thato Regonamanye, Abraham Mamela, Tapiwa Kangwa, Albert Lekgaba, Keofentse Mathuba, Edward Pettitt, Gabriel Anabwani, Mogomotsi Matshaba

1Collaborative African Genomics Network (CAfGEN) Botswana Baylor Clinical Centre of Excellence, Gaborone, Botswana; 2Baylor College of Medicine, Houston, USA.

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33SQLite: Grand Unified Genomics File Format?

Michael F. Lin, PhD

@DNAmlin; dna@mlin.net

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9Supporting Rare Disease Clinical Genomics: The future of genotype phenotype data standards & sharing for analysis to improve medical outcomes

Nicolas Bryant MBA, Robert Denison MEng, Alistair Johnson, Nick Lench PhD, Christine Waters PhD MBA

Congenica

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35The Matched Annotation from the NCBI and EMBL-EBI (MANE) project: a genome-wide transcript set for standardising clinical reporting and for browser display

J. Morales1, J. Loveland1, S Pujar2, A. Astashyn2, R. Bennett1, A.E. Berry, C. Davidson1, O. Ermolaeva2, C. Farrell2, R. Fatima, L. Gil1, T. Goldfarb, J.M. Gonzalez1, J. Jackson, V. Joardar2, M. Kay1, V. Kodali2, K. Mcgarvey2, A. Mcmahon1, M. Murphy, L. Riddick, G. Threadgold1, C. Wallin, D. Webb, A. Frankish1, F. Cunningham1, T. Murphy2

1European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK CB10 1SD; 2National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, U.S.A. 20894.

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