The GA4GH Phenopacket schema: A computable representation of clinical data for precision medicine

Jacobsen JOB, Baudis M, Baynam GS, Beckmann JS, Beltran S, Callahan TJ, Chute CG, Courtot M, Danis D, Elemento O, Freimuth RR, Gargano MA, Groza T, Hamosh A, Harris NL, Kaliyaperumal R, Khalifa A, Krawitz PM, Koehler S, Laraway BJ, Lehvaeslaiho H, Lloyd KC, Matalonga L, McMurry JA, Metke-Jimenez A, Mungall CJ, Munoz-Torres MC, Ogishima S, Papakonstantinou A, Piscia D, Pontikos N, Queralt-Rosinach N, Roos M, Schofield PN, Siapos A, Smedley D, Smith LD, Steinhaus R, Sundaramurthi JC, Swietlik EM, Thun S, Vasilevsky NA, Wagner AH, Warner JL, Weiland C, Haendel MA, Robinson PN.

medRxiv, 2021.11.27.21266944. doi:10.1101/2021.11.27.21266944

GA4GH: International policies and standards for data sharing across genomic research and healthcare

Heidi L. Rehm, Angela J.H. Page, Lindsay Smith, Jeremy B. Adams, Gil Alterovitz, Lawrence J. Babb, Maxmillian P. Barkley, Michael Baudis, Michael J.S. Beauvais, Tim Beck, Jacques S. Beckmann, Sergi Beltran, David Bernick, Alexander Bernier, James K. Bonfield, Tiffany F. Boughtwood, Guillaume Bourque, Sarion R. Bowers, Anthony J. Brookes, Michael Brudno, Matthew H. Brush, David Bujold, Tony Burdett, Orion J. Buske, Moran N. Cabili,

International federation of genomic medicine databases using GA4GH standards

Adrian Thorogood, Heidi L. Rehm, Peter Goodhand, Angela J.H. Page, Yann Joly, Michael Baudis, Jordi Rambla, Arcadi Navarro, Tommi H. Nyronen, Mikael Linden, Edward S. Dove, Marc Fiume, Michael Brudno, Melissa S. Cline, Ewan Birney

Thorogood, Adrian et al. Cell Genomics, Volume 1, Issue 2, 100032

Note

The GA4GH Variation Representation Specification (VRS): a Computational Framework for the Precise Representation and Federated Identification of Molecular Variation.

Alex H. Wagner, Lawrence Babb, Gil Alterovitz, Michael Baudis, Matthew Brush, Daniel L. Cameron, Melissa Cline, Malachi Griffith, Obi L. Griffith, Sarah E. Hunt, David Kreda, Jennifer M. Lee, Stephanie Li, Javier Lopez, Eric Moyer, Tristan Nelson, Ronak Y. Patel, Kevin Riehle, Peter N. Robinson, Shawn Rynearson, Helen Schuilenburg, Kirill Tsukanov, Brian Walsh, Melissa Konopko, Heidi L. Rehm, Andrew D. Yates, Robert R. Freimuth, Reece K. Hart

Wagner, Alex H. et al. Cell Genomics, Volume 1, Issue 2, 100027

bioRxiv. version 20212021.01.15.426843. (2021-01-15)

Note

Progenetix & GA4GH Beacon

A cancer genomics resource built around and driving GA4GH standards

Michael Baudis

GRIC sponsored workshop with the Swiss Institute of Bioinformatics

The Progenetix oncogenomics resource provides sample-specific cancer genome profiling data and biomedical annotations as well as provenance data for cancer studies. With more than 100k genomic copy number number (CNV) profiles from over 700 cancer types, Progenetix empowers comparative analyses beyond individual studies and diagnostic concepts.

The GA4GH Beacon Protocol at BC2

A Standardized Format for Federated Genomic Data Exchange

Michael Baudis

A cancer genomics reference resource and implementation toolkit around GA4GH standards

Q. Huang, B. Gao, R. Paloots, P. Carrio-Cordo, Z. Yang, M. Baudis

Progenetix - An open reference resource for copy number vatiation data in cancer

Qingyao Huang

Cancer Genomics Consortium Annual Meeting 2021 Aug 1-4

The Progenetix oncogenomic resource in 2021

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

Database (Oxford). 2021 Jul 17;2021:baab043.

• doi: 10.1093/database/baab043.
• PMID: 34272855
• PMCID: PMC8285936.
• bioRxiv. doi: https://doi.org/10.1101/2021.02.15.428237

This article provides an overview of recent changes and additions to the Progenetix database and the services provided through the resource.

hCNV Community and Implementation Studies

Michael Baudis

hCNV data and the Progenetix Beacon

Michael Baudis

Signatures of Discriminative Copy Number Aberrations in 31 Cancer Subtypes

Bo Gao and Michael Baudis (2021)

Published at Frontiers in Genetics, 2021-05-13

Abstract

Copy number aberrations (CNA) are one of the most important classes of genomic mutations relatedto oncogenetic effects. In the past three decades, a vast amount of CNA data has been generated bymolecular-cytogenetic and genome sequencing based methods. While this data has been instrumentalin the identification of cancer-related genes and promoted research into the relation between CNA andhisto-pathologically defined cancer types, the heterogeneity of source data and derived CNV profilespose great challenges for data integration and comparative analysis. Furthermore, a majority of exist-ing studies have been focused on the association of CNA to pre-selected ”driver” genes with limitedapplication to rare drivers and other genomic elements.

ELIXIR Beacon Project

Concepts | Status | History | Outlook

Michael Baudis

A Reference Resource for Copy Number Variations in Cancer

Implementing GA4GH Standards to Drive an Open Oncogenomics Resource

Michael Baudis

Seminar Neurooncology Childrens Hospital Zürich

This seminar gives an overview of the history & current state of the Progenetix resource, it’s role in Beacon API development and the overall connection to the Global Alliance for Genomics and Health (GA4GH).

ZH Sem Bioinfo - Qingyao Huang

Discovering copy number variation across multiple cancer types

• Thursday, 2021-03-25
• 12:15 om ZOOM Call

EACR conference - The Progenetix Oncogenomic Resource

The Progenetix Oncogenomic Resource

GA4GH Connect - Beacon v2 and SchemaBlocks

Copy number variant heterogeneity among cancer types reflects inconsistent concordance with diagnostic classifications

Paula Carrio Cordo and Michael Baudis

Ontology Term Contributions

Genomic data and Privacy

Michael Baudis

ETHZ Lecture

The understanding of the impact of individual inherited and somatic genome variants on phenotypes and diseases requires a thorough understanding of the occurrence of such variants amongst populations in general and carriers of the phenotypes and diseases in particular. This information can only be provided through the inclusion of data from a multitude of genome resources in variant evaluation efforts, including such from outside (international) jurisdictions. However, opening such resources carries the inherent risk of breaching privacy, particularly through re-identification of individuals or their relatives and potentially through the exposure of individual genome-related personal information including phenotypic and “performance” prediction and relative disease risk.

DNA Copy Number Changes in Diffuse Large B Cell Lymphomas (Review)

Luciano Cascione, Luca Aresu, Michael Baudis and Francesco Bertoni

Beacon v2 – Towards flexible use and clinical applications for a reference genomic data protocol

Update of Progenetix Oncogenomics Resource

Welcome to Ziying

The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research

Salgado D, Armean IM, Baudis M et al.

F1000Research 2020, 9 (ELIXIR):1229

Progenetix - A cancer genomics reference resource around GA4GH standards

GA4GH Beacon v2 - Evolving Reference Standard for Genomic Data Exchange

Cancer Data - ELIXIR::GA4GH: Advancing genomics resources through standards and ontologies

The Ubiquitin Ligase TRIP12 Limits PARP1 Trapping and Constrains PARP Inhibitor Efficiency

Marco Gatti, Ralph Imhof, Qingyao Huang, Michael Baudis, Matthias Altmeyer

ELIXIR All Hands - Beacon Evolution

ELIXIR All Hands 2020 - Beacon Workshop

Michael Baudis

Oncology Informatics: Status Quo and Outlook.

Paul Martin Putora, Michael Baudis, Beth M. Beadle, Issam El Naqa, Frank A. Giordano and Nils H. Nicolay

Minimum Error Calibration and Normalization for Genomic Copy Number Analysis.

Bo Gao and Michael Baudis (2020)

Swissnex SF: Laura & Michael Baudis - Life & Family

Geographic assessment of cancer genome profiling studies.

Paula Carrio Cordo, Elise Acheson, Qingyao Huang and Michael Baudis (2020)

Enabling population assignment from cancer genomes with SNP2pop.

Huang Q and Baudis M. (2020)

Michael @ BBOP

Geographic assessment of cancer genome profiling studies.

Paula Carrio Cordo, Elise Acheson, Qingyao Huang and Michael Baudis (2020)

Leveraging European infrastructures to access 1 million human genomes by 2022

Gary Saunders, Michael Baudis, Regina Becker, Sergi Beltran, Christophe Béroud, Ewan Birney, Cath Brooksbank, Søren Brunak, Marc Van den Bulcke, Rachel Drysdale, Salvador Capella-Gutierrez, Paul Flicek, Francesco Florindi, Peter Goodhand, Ivo Gut, Jaap Heringa, Petr Holub, Jef Hooyberghs, Nick Juty, Thomas M. Keane, Jan O. Korbel, Ilkka Lappalainen, Brane Leskosek, Gert Matthijs, Michaela Th. Mayrhofer, Andres Metspalu, Steven Newhouse, Tommi Nyrönen, Angela Page, Bengt Persson, Aarno Palotie, Helen Parkinson, Jordi Rambla, David Salgado, Erik Steinfelder, Morris A. Swertz, Susheel Varma, Niklas Blomberg, and Serena Scollen

Nature Reviews Genetics volume 20, pages693–701 (2019)

Minimum Error Calibration and Normalization for Genomic Copy Number Analysis.

Bo Gao and Michael Baudis (2019)

Federated discovery and sharing of genomic data using Beacons

Miroslav Cupak , Stephen Keenan , Jordi Rambla , Sabela de la Torre , Stephanie Dyke , Anthony Brookes , Knox Carey , David Lloyd , Peter Goodhand , Maximilian Haeussler , Michael Baudis , Heinz Stockinger , Lena Dolman , Ilkka Lappalainen , Juha Törnroos , Mikael Linden , John Spalding , Saif Ur-Rehman , Angela Page , Paul Flicek , Susheel Varma , Gary Saunders , Serena Scollen , Stephen Sherry , David Haussler , Beacon Project Team

Nat Biotechnol (2019), accepted 2019-01-23

DNA copy number imbalances in primary cutaneous lymphomas (PCL)

Gug G, Huang Q, Chiticariu E, Solovan C and Baudis M (2019)

JEADV, 2019-01-19. https://doi.org/10.1111/jdv.15442

Enabling population assignment from cancer genomes with SNP2pop.

Huang Q and Baudis M. (2019)

bioRxiv, 2019-01-14. https://doi.org/10.1101/368647 (first version 2018-07-14)

DNA copy number imbalances in primary cutaneous lymphomas (PCL)

Gug G, Huang Q, Chiticariu E, Solovan C and Baudis M (2018)

bioRxiv, 2018-09-14. doi:10.1101/417766

Registered access: authorizing data access

Dyke SOM, Linden M, Lappalainen I, De Argila JR, Carey K, Lloyd D, Spalding JD, Cabili MN, Kerry G, Foreman J, Cutts T, Shabani M, Rodriguez LL, Haeussler M, Walsh B, Jiang X, Wang S, Perrett D, Boughtwood T, Matern A, Brookes AJ, Cupak M, Fiume M, Pandya R, Tulchinsky I, Scollen S, Törnroos J, Das S, Evans AC, Malin BA, Beck S, Brenner SE, Nyrönen T, Blomberg N, Firth HV, Hurles M, Philippakis AA, Rätsch G, Brudno M, Boycott KM, Rehm HL, Baudis M, Sherry ST, Kato K, Knoppers BM, Baker D, and Flicek P

European Journal of Human Genetics (2018)

Mountains and Chasms - Surveying the Oncogenomic Publication Landscape

Carrio Cordo P and Baudis M. (2018)

Preprints 2018, 2018070618 (doi: 10.20944/preprints201807.0618.v1).

Oncology (2018; online Oct 26)

Population assignment from cancer genome profiling data.

Huang Q and Baudis M. (2018)

bioRxiv, 2018-07-14. doi:10.1101/368647

Website changes - info.progenetix.org now locally hosted …

To unify the general website handling processes, I’ve implemented some changes:

Public site removed from Github

Launch of new baudisgroup resource site

arrayMap manuscript accepted at PLoS ONE