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

hCNV Community and Implementation Studies

Michael Baudis

hCNV data and the Progenetix Beacon

Michael Baudis

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

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.

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

Update of Progenetix Oncogenomics Resource

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

Beacon v2 - Towards Flexible Use and Clinical Applications for a Reference Genomic Data Sharing Protocol

ELIXIR All Hands - Beacon Evolution

ELIXIR All Hands 2020 - Beacon Workshop

Michael Baudis

SchemaBlocks and GA4GH TASC

SWISSNEX SF Lunch Seminar - Data Mining in Genomics

Genomic Research and Personalised Health Strategies

Resources | Standards | Protocols | Tools | Discourse

BBOP Presentation - Baudisgroup Projects & Interests

GA4GH SchemaBlocks for Human Cell Atlas

3rd St. Gallen Radiation Oncology Informatics Meeting

Bioinformatics and data exchange for genomics in an international context

Michael Baudis

BC2 2019, Basel

Minimum Error Calibration and Normalization for Genomic Copy Number Analysis

Bo Gao

BC2 2019, Basel

Minimum Error Calibration and Normalization for Genomic Copy Number Analysis

Bo Gao

Seminar Universita degli Studi Firenze - Dipartimento di Biologia

Structural Genome Variants in Cancer: Research, resources standards

Michael Baudis

ELIXIR All Hands - Lisbon 2019

Introduction to Beacon

Michael Baudis

Human Genome Variation Society - Gothenburg 2019

Implementation Driven Development of Standards for Genomic Data Exchange from Cancer Genome Data Collections

Michael Baudis

R&D Data Intelligence Leaders Forum Basel

Connecting the silos - Genomic Data Standards, Resources and the Global Alliance for Genomics and Health

Michael Baudis

UZH BIO390 “Introduction to Bioinformatics”

Bioinformatics - Introduction

Michael Baudis

IMLS Progress Report

Towards understanding population effect on cancer

Qingyao Huang

Special seminar at University of Timisoara Dermatology

Cancer Genome (Data) Analysis in Personalised Medicine

Michael Baudis

UZH Cancer Biology course “Research with clinical samples

Personalised Medicine - Genome Variation / Data Formats / Resources / Sharing / Privacy

Michael Baudis

GA4GH 2017 Plenary / Workstream Day

Developing Beacons for Data Discovery

Michael Baudis

UZH BIO390 “Introduction to Bioinformatics”

Bioinformatics - Introduction

Michael Baudis

ELIXIR All Hands, Rome

GA4GH Metadata & Beyond

Michael Baudis

Seminar - Stanford Center for Genomics & Personalized Medicine

Personalized medicine in cancer

Michael Baudis

R&D Data Intelligence Leaders Forum Basel

Genome data access - Application to personalized health and cancer research

Michael Baudis

Antrittsvorlesung Universität Zürich - Inaugural Lecture at University of Zurich

Cancer Genome (Data) Analysis

Michael Baudis

LSZGS Cancer Biology course 2016

Personalized medicine in cancer

Michael Baudis

Biocuration 2016, Geneva

Harvesting Cancer Genome Data

Michael Baudis

VIB Conference “Applied Bioinformatics in Life Sciences”

Gene-based analysis of focal copy number aberration patterns in cancer genomes

Saumya Gupta

First BCATS Meeting - Biocomputing @ Stanford 2001

progenetix.net: storage and visualization of genomic aberration data in human malignancies

Michael Baudis