Presentations¶
The shows a probably incomplete following list of presentations (posters, talks, abstracts) from group members. Usually, PDF versions of the slides or posters are linked from the details pages.
Data Resources, Sharing, Discovery in Biomedical Genetics and Cancer Genomics
セミナー at National Cancer Center Hospital Tsukiji Campus
In this seminar you will learn about Progentix, a large open resource in cancer genomics focussing on curation and sharing of somatic copy number variation (CNV) data as well as other resources and research topics of the Theoretical Cytogenetics and Oncogenomics group at the University of Zucrich and teh Swiss Institute of Bioinformatics.
The second part of the presentation will make a case why such resources cannot be sufficient and introduce the approaches shepherded by the Global Alliance for Genomics and Health (GA4GH) Continue reading
Global Alliance for Genomics and Health - Promoting a New Paradigm for Data Discovery in Biomedical Genomics
Seminar at Tohoku University Sendai
The Global Alliance for Genomics and Health (GA4GH) has developed into a major international organization to address the challenges of data discovery in biomedical genomics. The Beacon standard developed by GA4GH with technical support by the European bioinformatics orgabnization ELIXIR and many international stakeholders has become a default for implementing modern concepts of federated data discovery and access. Continue reading
Data Discovery in Biomedical Genomics - Time for a New Paradigm
The XIVth MEDICAL GENETICS TÂRGU MUREȘ
SOCIETATEA ROMÂNĂ DE GENETICĂ MEDICALĂ
In biomedical genetics and genomics the last decades have led to the recognition that the vast amaount and diversity of genomic variations requires large-scale approaches to data analysis for both areas of rare disease genetics as well as cancer genomics. While projects establishing high quality data from large cohorts are highly valuable and necessary to drive the field, the true power of genomics can only be leveraged through access to data from different studies and cohorts beyond geographic or regulatory boundaries.
Since its foundation in 2013 the Global Alliance for Genomics and Health (GA4GH) has emerged as the main international organization to address the challenges of data discovery, access and utilization in genomics and related fields. The Beaconi> standard developed by GA4GH with technical support by the European bioinformatics orgabnization ELIXIR and many international stakeholders has become a default for implementing modern concepts of federated data discovery and access.
This presentation will provide an introduction into data federation in biomedical genomics with emphasis on the use of the Beaconm protocol for genomic data discovery, together with a general introduction into principles and mechanisms of genomics standards development by GA4GH.
Continue readingOpening Cancer Genomics - Deploying the GA4GH Beacon protocol
Zürich Cancer ORD Workshop
The "Moving ORD practices into cancer care" project explores and tests ORD principles in the context of cancer care, through a combination of engagement with relevant communities at the UZH as well as a technical demonstrator of a cutting edge data discovery technology. The cancer community at UZH is being mobilized through a dedicated workshop and topical meetings, to discuss challenges and opportunities of ORD in the oncology domain. A pilot installation of an established ORD approach (Beacon technology by the Global Alliance for Genomics and Health) is being implemented to test the sharing of cancer related -omics and associated data with a focus on the specific data access and security aspects presenting here.
Continue readingGenomic Data Mining and The Case for Open Data Standards
ZHAW ICLS colloquium
The last decades have an enormous amount of data generation in the area of biomedical genomics, driven by a feedback loop of technological developments and increasing recognition of human genomic complexities, in health and disease. While individual projects frequently are tailored towards addressing specific research questions, the approach to many problems especially in rare diseases and cancer genomics requires both curated data collections and the access to data from international repositories and study centers.
Here I will present our oncogenomic data resources and research projects, and how our work on data discovery and exchange standards as part of an international community can improve data accessibility through the support of federated discovery and retrieval protocols.
Continue readingGenomdaten - Chancen und Risiken für Medizin und Gesellschaft
Vortrag an der Seniorenuniversität Winterthur
In der medizinischen Forschung werden Genomdaten für genauere Diagnosen und zur
Auswahl personalisierter Therapien herangezogen. Genomdaten finden aber auch
ausserhalb der Medizin Verwendung – etwa in der genealogischen Forschung oder
in der Forensik. Diesem Potential stehen jedoch auch Risiken gegenüber.
Wenn genomische Daten von Millionen von Menschen erhoben werden, wer soll den Einzelnen und die Gesellschaft vor dem Missbrauch solcher Daten schützen? Der Vortrag beantwortet Fragen im Hinblick auf den Bedarf an solchen Daten in Medizin und Forschung, und die dadurch eventuell entstehenden Risiken.
Warum brauchen wir genomische Daten von Millionen von Individuen? Wie können meine Daten eine Gefahr für mich darstellen? Und wer sollte mich als Individuum vor einem Missbrauch schützen?
Continue readingFederated genomic discoveries: Deploying the GA4GH Beacon protocol
Virtual Seminar
GHGA Lecture Series
With the ever increasing amount of genomic data produced in the context of research studies, population analyses and medical diagnostics the need for access to genomic information beyond administrative or geographic boundaries has become a matter of eminent importance.
Continue reading
Genomic Data Sharing Standard Development with GA4GH and ELIXIR
Opportunities and Pitfalls in Federated Data Discovery
DMLS Lecture Series
University of Zurich Department of Molecular Life Sciences
In this presentation Michael talks about the role of GA4GH (and ELIXIR) in the development
of standards and practices or genomic data exchange, some general principles, how his group got involved into
these efforts - but also some pitfalls ...
Structural Genome Variations in Cancer and the Case for Open Data Standards
Cancer Genomics Seminar at Utrecht
Hubrecht Institute and Princess Maxima Center for Pediatric Oncology
The presentation includes notes about work on improving the representation and
of genomic copy number variations (CNV), GA4GH and its Beacon protocol as well
as challenges towards genomic data privacy.
Beaconize this: Databases for Cancer Genomics and the Development of Open Data Standards
Seminar at the Bioinformatics club of the Centre de Recherche des Cordeliers (CRC)
Université Paris Cité
In this seminar at the Centre de Recherche des Cordeliers in Paris Michael presents the work of the group, with special emphasis on the role of the Progenetix oncogenomics resources and tools in the development, implementation and testing of the Beacon standard of the Global Alliance for Genomics and Health (GA4GH).
Continue readingELIXIR All Hands Dublin
Baudisgroup presentations at the AHM 2023 in Dublin
Rahel, Hangjia & Michael for the group¶
At the ELIXIR All Hands Meeting 2023 in Dublin our group presented several posters about our resources and work in standards development.
Continue readingTheoretical Cytogenetics and Oncogenomics
DMLS Tandem Talks
Michael Baudis¶
In this short presentation Michael provides an overview of the group's work in cancer genomics resources, data analysis and standard development, including the involvement in the Global Alliance for Genomics and Health GA4GH.
- Cancer Genome Profiles
- Oncogenomic Data Resources
- Bioinformatics Methods
- Data Exchange Standards for Genomics and Personalized Health
Genomic Resource Built with GA4GH Standards
EORTC PAMM Firenze
Michael Baudis¶
This brief presentation introduces the Progenetix resource, the Gobal Alliance for Genomics and Health as a developers of standards for data sharing in biomedical genomics as well as the use of Progenetix in GA4GH standards development.
Continue readingBeacon v2 - Onboarding Strategies & Feature Examples
Beacon Sessions at GA4GH Connect
Michael Baudis¶
The Beacon Sessions at GA4GH Connect November 2022 targeted the migration of existing and implementation of new v2 Beacons, with emphasis on the "how to get there easily" rather than on all Beacon v2 features. Continue reading
Genomics Data Federation through Global Alliance for Genomics and Health Standards: Development and Implementation of the GA4GH Beacon Protocol
Seminar Yonsei University Medical School Seoul
Michael Baudis¶
In this Seoul meeting presentation Michael introduces the Global Alliance for Genomics and Healt and its involvement in Genomics standards development, followed by a discussion of the Beacon protocol and the role of the Progenetix resouce in its development. Continue reading
Beacon v2 - Feature-rich Implementation of the Genomic Data Discovery Protocol
GA4GH 2022 Plenary Barcelona
Michael Baudis¶
The “Beacon” protocol - developed with support from ELIXIR, the European bioinformatics infrastructure organization, as a standard of the Global Alliance for Genomics and Health (GA4GH) - represents an emerging standard for an “Internet for Genomics”. While the initial version of the protocol served as a widely adopted test bed for the sharing of genomic variants over federated query systems connecting hundreds of internationally distributed resources, the version 2 of the protocol provides a framework for extended, metadata-rich query and response options in both public and restricted federated access scenarios. Continue reading
Beacon - Ethical & Legal Aspects of a Genomic Data Discovery Protocol
DSI Ethics Project Pitch
Michael Baudis¶
Here Michael provides a very brief presentation about the GA4GH Beacon protocol, especially as a target for projects discussing the ethical implications of genome data discovery & sharing as well as the relevant legal frameworks, with emphasis on the Swiss context. Continue reading
A cancer genomics resource built on GA4GH standards
Rahel Paloots, Michael Baudis¶
CGC St Louis 2022¶
Progenetix is a cancer genomics resource that includes genomic profiling data as well as biomedical annotations and provenance data for cancer studies. The main goal of the Progenetix database is to provide easy, open access for research studies and clinical diagnostics. To facilitate sharing of genomic data, Progenetix complies with and contributes to GA4GH and Beacon data standards. Beacon, developed with the support from ELXIR (the European bioinformatics infrastructure organization), started out as protocol to share genomic variants over federated queries.
Continue readingA cancer genomics reference resource powered by GA4GH standards
Roche Data Science Seminar
Michael Baudis¶
The presentation reports about the Progenetix cancer genomics resource and its role in the GA4GH ecosystem & the Beacon genomics API development process.
Continue readingImplementation of the GA4GH Beacon protocol for discovery and sharing of genomic copy number variation data
ESHG Vienna 2022
Michael Baudis¶
Background & Objectives Genomic copy number variations (CNV) are a major contributor to inter-individual genomic variation, can be causative events in rare diseases, but especially represent the majority of the mutational landscape in the most malignancies. While specific CNV events and some recurring patterns have contributed to the identification of individual cancer drivers and the recognition of cancer subtypes, the complexity of genomic CNV patterns requires large amounts of well-defined genomic profiles for statistically meaningful analyses. At the other end of the spectrum, in the area of rare disease genomics the potential pathogenicity of individual CNV events requires validation against a vast set of disease-related and reference genomic profiles and annotations.
Continue readingProgenetix & BeaconPlus - An open cancer genomics resource on a stack of Beacon code...
ELIXIR All Hands Amsterdam 2022
Michael Baudis¶
Here Michael provides some overview of the multi-year trajectory of the Beacon API development, and how BeaconPlus & Progenetix have been utilized for "implementation driven design".
Continue readinghCNV Implementation Studies Old and New
ELIXIR Human Data Communities
Michael Baudis¶
This presentation provided an overview about the hCNV community, implementation studies and ongoing work, e.g. interaction with the GA4GH VRS standard group and Beacon development.
Continue readingTechnical, legal and ethics aspects of genomic data sharing
Genomes | Privacy | Laws | Society - DSI Ethics Seminar
Michael Baudis¶
The presentation introduces the need for sharing and federated discovery of genome data in the contexts of personalized health and genomic researchand some of teh current developments in international standards and practices in the area. Continue reading
A cancer genomics resource built around and driving GA4GH standards
GRIC sponsored workshop with the Swiss Institute of Bioinformatics
Michael Baudis¶
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.
Continue readingA Standardized Format for Federated Genomic Data Exchange
The GA4GH Beacon Protocol Presented at BC2 Basel 2021
Session "Federating computational analyses with GA4GH standards"
Michael Baudis¶
During the "Federating computational analyses with GA4GH standards" workshop at BC2 2021 Michael presented history and the current status of the Beacon project, as well as its integration with specific data resources and analysis initiatives.
Cancer genomics reference resource and toolkit around GA4GH standards
ESHG 2021
Q. Huang, B. Gao, R. Paloots, P. Carrio-Cordo, Z. Yang, M. Baudis¶
This poster presentation at the European Society of Human Genetics meeting 2021 discusses the integration and development of GA4GH standards by the Progenetix oncogenomics resource.
Progenetix - An open reference resource for copy number vatiation data in cancer
Qingyao Huang¶
hCNV Community and Implementation Studies
Michael Baudis¶
ELIXIR All Hands 2021 Human Data Day¶
At the Human Data Day Michael presents a very brief overview of the ending and upcoming ELIXIR hCNV implementation studies.
Continue readinghCNV data and the Progenetix Beacon
Presentation at ELIXIR All Hands 2021
Michael Baudis¶
ELIXIR All Hands 2021¶
This presentation gives a brief overview of the use of the Progenetix resource to test and implement a genomics reference resource using the emerging Beacon v2 protocol.
Continue readingProgenetix, Beacon and GA4GH at RDA
Research Data Alliance - RDA Virtual Plenary 17
Concepts | Status | History | Outlook¶
Michael Baudis¶
Research Data Alliance - RDA Virtual Plenary 17¶
This seminar gives an overview of current state of the Progenetix Beacon project and the overall connection to the Global Alliance for Genomics and Health (GA4GH).
Continue readingImplementing GA4GH Standards to Drive an Open Oncogenomics Resource
Research Seminar Kinderspital Zürich - Neuroonkologie
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).
Continue readingDiscovering copy number variation across multiple cancer types
Qingyao Huang¶
Abstract
Genomic variations are direct cause of tumor formation and accomplice in its continuous evolution. While point mutations can be pinpointed to a targeted genetic element, copy number variations (CNVs) involve copy number gain or loss of a large DNA segment which often covers hundreds of genetic elements in one event. Continue reading
EACR conference - The Progenetix Oncogenomic Resource
Continue readingGA4GH Connect - Beacon v2 and SchemaBlocks
GA4GH Connect 2020¶
Michael Baudis¶
Beacon v2 Structural Variants [slides]¶
SchemaBlocks {S}[B] [slides]¶
Continue readingGenomic 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.
Continue readingBeacon v2 – Towards flexible use and clinical applications for a reference genomic data protocol
SPHN Webinar¶
Michael Baudis¶
Genomic “Beacons” provide discovery services for genomic data using the Beacon API developed as a key driver project of the Global Alliance for Genomics and Health (GA4GH). The Beacon protocol itself defines an open standard for genomics data discovery and provides a framework for web services responding to queries against genomic data collections, for instance from population based or disease specific genome repositories. Continue reading
Update of Progenetix Oncogenomics Resource
Research Progress Report, DMLS, University of Zurich¶
Qingyao Huang¶
Copy number aberration (CNA) is frequently observed in cancer genomes. Meta-analysis of genomic variations helps to disentangle the multiplex molecular mechanism underlying tumorigenesis as well as identify and characterize molecular subtypes. Over the years, cancer genomic research have resulted in a considerable amount of data segregated by studies. The Progenetix project (www.progenetix.org), initiated in 2001, aims to systematize the published cancer genomic profiles and provide accurate annotation to facilitate integrative analysis. Continue reading
GA4GH Beacon v2 at GA4GH Plenary
GA4GH Beacon v2 - Evolving Reference Standard for Genomic Data Exchange¶
GA4GH 8th Plenary¶
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¶
The Beacon driver project was one of the earliest initiatives of the Global Alliance for Genomics and Health with the Beacon v1.0 API as first approved GA4GH standard. Version 2 of the protocol is slated to provide fundamental changes, towards a Internet of Genomics foundational standard: * requests beyond genomic variants ("filters") * payload responses, secured through open AAI * aligning w/ GA4GH standards (Phenopackets, VRS, DUO...) through SchemaBlocks {S}[B] * Working with international partners on deployment of advanced implementations
Continue readingProgenetix - A cancer genomics reference resource around GA4GH standards
GA4GH 8th Plenary¶
Michael Baudis¶
The Progenetix oncogenomics resource provides sample-specific cancer genome profiling data and biomedical annotations as well as provenance data from cancer studies. Especially through currently 113322 curated genomic copy number number (CNV) profiles from 1600 individual studies representing over 500 cancer types (NCIt), Progenetix empowers aggregate and comparative analyses which vastly exceed individual studies or single diagnostic concepts. Continue reading
Cancer Data - ELIXIR::GA4GH: Advancing genomics resources through standards and ontologies
ECCB2020¶
Michael Baudis¶
Additional Links¶
Continue readingBeacon v2 - Towards Flexible Use and Clinical Applications for a Reference Genomic Data Sharing Protocol
Personalized Health Technologies 2020¶
Michael Baudis¶
Beacons provide discovery services for genomic data using the Beacon API developed under the leadership of ELIXIR, as a key driver project of the Global Alliance for Genomics and Health (GA4GH). The Beacon protocol itself defines an open standard for genomics data discovery. It provides a framework for public web services responding to queries against genomic data collections, for instance from population based or disease specific genome repositories. Sites offering beacons can scale through aggregation in "Beacon Networks", which distribute single genome queries among a potentially large number of international beacons and assemble their responses. Continue reading
ELIXIR All Hands - Beacon Evolution
ELIXIR All Hands 2020 - Beacon Workshop¶
Michael Baudis¶
This presentation covers some of Beacon's origins, features and directions.
Links¶
Continue readingSchemaBlocks and GA4GH TASC
A brief presentation about SchemaBlocks concepts and its possible integration into the new GA4GH TASC effort.
Additional Links¶
Continue readingSWISSNEX SF Lunch Seminar - Data Mining in Genomics
Genomic Research and Personalised Health Strategies¶
Resources | Standards | Protocols | Tools | Discourse¶
These are the slides of a short presentation, given (virtually, since COVID-19) for a SWISSNEX San Francisco lunch meeting.
Additional Links¶
Continue readingBBOP Presentation - Baudisgroup Projects & Interests
Links¶
Continue readingELIXIR Beacon Project - Networking Resources Across and Beyond ELIXIR Human Data Communities
ELIXIR Open Day - Wellcome Trust Genome Campus Hinxton¶
Michael Baudis¶
In this presentation I introduce the Beacon project and provide my opinions about its future trajectory, and especially its role in driving the alignment of ELIXIR and GA4GH projects in related to (human) genome data sharing.
Links¶
Continue readingGA4GH SchemaBlocks for Human Cell Atlas
This is a presentation of the SchemaBlocks initiative and the overall GA4GH context, for the Human Cell Atlas project, given by Michael at one of their teleconferences.
Additional Links¶
Continue readingTalk at St. Gallen Radiation Oncology - Bioinformatics and Data Exchange
3rd St. Gallen Radiation Oncology Informatics Meeting¶
Bioinformatics and data exchange for genomics in an international context¶
Michael Baudis¶
The presentation at the St. Gallen meeting introduced the audience to the group's research and resources, and how this is connected to the different national & international data standards and sharing initiatives.
Continue readingTalk at AMED Tokyo - Cancer Genomics and Standards
Mini-Symposium about CNV and Data Standards at AMED Japan, Tokyo¶
Cancer Genomics and Implementation of Data Driven Standards for Genomic Data Exchange¶
Michael Baudis¶
At this meeting, several Japanese participants presented their research and results, with a focus on Copy Number Variants and other structural genome variations. Continue reading
Minimum Error Calibration and Normalization for Genomic Copy Number Analysis
BC2 2019, Basel¶
Bo Gao¶
Abstract¶
Background:
Copy number variations (CNV) are regional deviations from thenormal autosomal bi-allelic DNA content. While germline CNVs are a majorcontributor to genomic syndromes and inherited diseases, the majority of cancersaccumulate extensive ”somatic” CNV (sCNV or CNA) during the process ofoncogenetic transformation and progression. While specific sCNV have closelybeen associated with tumorigenesis, intriguingly many neoplasias exhibitrecurrent sCNV patterns beyond the involvement of a few cancer driver genes.Currently, CNV profiles of tumor samples are generated using genomicmicro-arrays or high-throughput DNA sequencing. Regardless of the underlyingtechnology, genomic copy number data is derived from the relative assessmentand integration of multiple signals, with the data generation process being proneto contamination from several sources. Estimated copy number values have noabsolute and linear correlation to their corresponding DNA levels, and the extentof deviation differs between sample profiles which poses a great challenge fordata integration and comparison in large scale genome analysis.
Continue reading
Cancer cell lines in focus: somatic copy number & germline variation
BC2 2019, Basel¶
Qingyao Huang¶
Abstract¶
Background:
Human cell lines are convenient model systems in cancer research, for validation of proposed molecular mechanisms as well as to evaluate potential therapeutic approaches, e.g. through high- throughput screening of potential anti-tumour compounds against cancer cell line panels. However, conclusions about biological pathways or pharmacological potential depend on a close molecular relation between the cancer type represented and the cell line model used for analyses.
Continue reading
Structural Genome Variants in Cancer: Research, resources standards
Seminar at the University of Florence
Seminar Universita degli Studi Firenze - Dipartimento di Biologia¶
Structural Genome Variants in Cancer: Research, resources standards¶
Michael Baudis¶
Abstract¶
Genomic copy number variations are major contributors to malignant transformation and progression and constitute - at least in their quantitative extension - the largest contributors to genomic mutation landscapes, in the majority of cancer types. Such mutations occur in the vast majority of tumors as somatic genome alterations (sCNV) during clonal development and expansion and are promoted by a variety of mechanisms leading to extended or focal changes in the number of genomic segments. Continue reading
ELIXIR All Hands - Beacon Introduction
Michael Baudis¶
This presentation was the opener for the ELIXIR Beacon session, and introduces to current developments and especially the interactions between GA4GH :: Discovery and ELIXIR Beacon.
Continue readingHGVS 2019 - Development of Standards for Genomic Data Exchange
Human Genome Variation Society - Gothenburg 2019¶
Implementation Driven Development of Standards for Genomic Data Exchange from Cancer Genome Data Collections¶
Michael Baudis¶
Abstract¶
Cancers are genomic diseases, arising from the clonal propagation of somatic mutation events, with a limited contribution from inherited genomic variants. Genomic copy number variations are major contributors to malignant transformation and progression and constitute - at least in their quantitative extension - the largest contributors to genomic mutation landscapes, in the majority of cancer types. Continue reading
Connecting the silos - Genomic Data Standards, Resources and the Global Alliance for Genomics and Health
R&D Data Intelligence Leaders Forum Basel¶
Michael Baudis¶
Abstract¶
This presentation discusses the need for data sharing in genomics, provides information about the Global Alliance for Genomics and Health (GA4GH), and shows some of our group's contributions, especially regarding Beacon development.
Continue reading2018 09 18 BIO390 Michael Baudis Introduction to Bioinformatics
UZH BIO390 "Introduction to Bioinformatics"¶
Bioinformatics - Introduction¶
Michael Baudis¶
Abstract¶
First lecture in the UZH BIO390 "Introduction to Bioinformatics" series, introducing concepts and scope of bioinformatics as a field - 2018 version.
Continue readingECCB 2018 - Beacon
Abstract: ECCB 2018¶
ELIXIR Beacon - A Driver Project for the Global Alliance for Genomics and Health¶
Michael Baudis for the ELIXIR Beacon Project¶
The Global Alliance for Genomics and Health (GA4GH) develops standards and guidelines to facilitate the international sharing of genomic and health related metadata. The creation of GA4GH work stream products is moved forward through driver projects, which address particular scientific, technical, regulatory or security related aspects of data access and sharing. Continue reading
Qingyao - Institute Progress Report
IMLS Progress Report¶
Towards understanding population effect on cancer¶
Qingyao Huang¶
Abstract¶
With a combination of ~50,000 curated oncogenomic array data from the arrayMap database and ~20,000 profiles from TCGA project depository, we perform a meta- analysis to investigate influence of genetic background on the CNV patterns in cancer. From sequencing data of 26 world-wide populations from 1000 Genomes project, we extract the SNP markers and use them for subsequent sample analysis. Continue reading
The ELIXIR Beacon in 2018: A driver project of GA4GH
ELIXIR All Hands, Berlin¶
Michael Baudis¶
Abstract¶
The core mission of the Global Alliance for Genomics and Health is to "...enable genomic data sharing for the benefit of human health". One of the instruments to enact this mission is the selection and support of driver projects, which address particular scientific, technical, regulatory or security related aspects of federated access to human genomes and related metadata. Continue reading
segment_liftover : a Python tool to convert segments between genome assemblies
Abstract: ELIXIR All Hands 2018
Bo Gao, Qingyao Huang and Michael Baudis¶
The process of assembling a species’ reference genome may be performed in a number of iterations, with subsequent genome assemblies differing in the coordinates of mapped elements. The conversion of genome coordinates between different assemblies is required for many integrative and comparative studies. While currently a number of bioinformatics tools are available to accomplish this task, most of them are tailored towards the conversion of single genome coordinates. When converting the boundary positions of segments spanning larger genome regions, segments may be mapped into smaller sub-segments if the original segment’s continuity is disrupted in the target assembly. Continue reading
ELIXIR Beacon - A Driver Project for the Global Alliance for Genomics and Health
Abstract: ELIXIR All Hands 2018¶
Michael Baudis for the ELIXIR Beacon Project¶
The core mission of the Global Alliance for Genomics and Health is to "...enable genomic data sharing for the benefit of human health". One of the instruments to enact this mission is the selection and support of driver projects, which address particular scientific, technical, regulatory or security related aspects of federated access to human genomes and related metadata.
The "Beacon" project had been initiated at the first GA4GH plenary in 2014, to test the willingness of genome resource providers to allow web-based queries in the most simple format, against aggregated genome variant data. While this particular model had limited practical utility, it established the foundation for automated queries against world-wide data resources, using a unified protocol. A secondary aspect of the Beacon project was the, intentional, challenge of existing notions of data security and privacy protection, including possible re-identification attacks and risk mitigation scenarios.
Now continued through the ELIXIR-Beacon GA4GH driver project, extensions to the Beacon protocol will provide real-world utility for genome resource access under a number of different usage scenarios. With its support for developing the Beacon protocol and distributing it throughout its members, ELIXIR is providing one of the first, widespread implementations of a GA4GH related products. Additionally, the upcoming version of the Beacon protocol is expected to be one of the first official standards which underwent the GA4GH product approval process, facilitating widespread international adoption.
Continue readingBiocuration for cancer genome databases: arrayMap and Progenetix
Abstract: ELIXIR All Hands 2018¶
Paula Carrio Cordo and Michael Baudis¶
Screening for somatic mutations in cancer has become integral to diagnostic and target evaluation for personalized therapeutic approaches. arrayMap is a curated oncogenomic resource, focusing on copy number aberration (CNA) profiles derived from genomic arrays. The information has been processed from data accessed through NCBI’s Gene Expression Omnibus (GEO), EBI’s ArrayExpress, and, importantly, through targeted mining of publication data. Whereas this database is based on raw probe data sets, the parental project, Progenetix, allows for genome variant analysis from additional sources and serves as metadata reference. Continue reading
ELIXIR All Hands 2018 - arrayMap
Abstract: ELIXIR All Hands 2018¶
Update on arrayMap Cancer Genome Resource¶
Qingyao Huang and Michael Baudis¶
arrayMap is a cancer-related genome profile database, curated from public data repositories. The resources’s data processing pipelines handle the homogeneous conversion of available raw data from various genomic array platforms (e.g. cCGH, SNP) and represents pre-computed copy number variation (CNV) profiles, allowing the evaluation of target gene involvement as well as the comparative analysis of whole-genome CNV patterns, e.g. for assessing between-sample CNV heterogeneity and associate sets of similar patterns with metadata qualifiers such as diagnostic classifications. In addition to the representation of cancer-related samples, we also plan to generate copy number profiles from non-cancer samples, in an effort to represent population-related CNV patterns. Continue reading
Genomic profiles of cancer cell lines - A systematic review
Abstract: ELIXIR All Hands 2018¶
Rahel Paloots, Qingyao Huang, Paula Carrio Cordo and Michael Baudis¶
Human cell lines are convenient model systems in cancer research, for validation of proposed molecular mechanisms as well as to evaluate potential therapeutic approaches, e.g. through high-throughput screening of potential antitumor compounds against cancer cell line panels. Thousands of established cell lines are available from commercial or academic providers, covering a wide selection of cancer types. However, conclusions about biological pathways or pharmacological potential depend on a close molecular relation between the cancer type represented and the cell line model used for analyses. Continue reading
2018 02 15 talk DPPH michael
DPPH - Data Protection in Personalized Health 2018, Lausanne¶
Genome Beacons for Data Discovery - Technical advances in a challenging environment¶
Michael Baudis¶
Abstract¶
The core mission of the Global Alliance for Genomics and Health is to "...enable genomic data sharing for the benefit of human health". One of the instruments to enact this mission is the selection and support of driver projects, which address particular scientific, technical, regulatory or security related aspects of federated access to human genomes and related metadata. The "Beacon" project had been initiated at the first GA4GH plenary in 2014, to test the willingness of genome resource providers to allow web-based queries in the most simple format, against aggregated genome variant data. While this particular model had limited practical utility, it established the foundation for automated queries against world-wide data resources, using a unified protocol. A secondary aspect of the Beacon project was the, intentional, challenge of existing notions of data security and privacy protection, including possible re-identification attacks and risk mitigation scenarios. Now continued through the ELIXIR-Beacon GA4GH driver project, extensions to the Beacon protocol will provide real-world utility for genome resource access under a number of different usage scenarios, some of which will be addressed in this presentation.
Continue reading2017 12 07 talk timisoara michael
Special seminar at University of Timisoara Dermatology¶
Cancer Genome (Data) Analysis in Personalised Medicine¶
Michael Baudis¶
Abstract¶
General presentation about challenges and possibilities of cancer genome screening for medical applications.
Continue reading2017 12 01 talk lszgs michael
UZH Cancer Biology course "Research with clinical samples¶
Personalised Medicine - Genome Variation / Data Formats / Resources / Sharing / Privacy¶
Michael Baudis¶
Abstract¶
Personalised Medicine - Genome Variation / Data Formats / Resources / Sharing / Privacy, presented for PhD program in Cancer Biology
Continue readingDeveloping Beacons for Data Discovery
GA4GH 2017 Plenary - Workstream Day
Michael Baudis¶
- presenting concepts on how to advance the Beacon protcol for practical use cases
UZH BIO390 - Introduction to Bioinformatics
Michael Baudis¶
Abstract¶
First lecture in the UZH BIO390 "Introduction to Bioinformatics" series, introducing concepts and scope of bioinformatics as a field.
Continue readingAdvancing the Global Alliance for Genomics and Health data schemas through data-driven implementations
[BC]2 2017 - Basel Computational Biology Conference
###$ Michael Baudis
Abstract¶
The core mission of the Global Alliance for Genomics and Health (GA4GH) is to advance the utility of biomedical data through facilitating of federated analyses, across geographic, regulatory and technical boundaries. A central component is the development of standardised data schemas and application programming interfaces (APIs), for molecular screening data as well as biological and technical metadata. Continue reading
Somatic CNV databases as resources for cancer research && GA4GH schema development
Seminar at SDU Odense
Michael Baudis¶
- Presentation about pProgenetix and the group's research projects
GA4GH Metadata & Beyond
ELIXIR All Hands, Rome
Michael Baudis¶
Presentation about GA4GH metadata standards work
Continue readingPersonalized medicine in cancer
Seminar - Stanford Center for Genomics & Personalized Medicine
Michael Baudis¶
Abstract¶
Some reasoning for the need of genome profiling data in cancer and reference samples, and our own work on structural aberration data in cancer as well as contributions to the projects and standard definitions of the Global Alliance for Genomics and Health
Continue readingImplementing Data Models for the Global Alliance for Genomics and Health
Brupbacher Meeting 2017
Bo Gao¶
Abstract¶
Poster about our implementation studies for testing and developing data schemas and resources for the Global Alliance for Genomics and Health, based on data from our arrayMap resource
Continue readingGenome data access - Application to personalized health and cancer research
R&D Data Intelligence Leaders Forum Basel
Michael Baudis¶
Abstract¶
- Discussing genome data access, with focus ion cancer, GA4GH and own contributions
Cancer Genome (Data) Analysis
Antrittsvorlesung Universität Zürich - Inaugural Lecture at University of Zurich
Michael Baudis¶
Abstract¶
- General lecture introducing the "Why"s of cancer genome analysis and some specific problems, as well as some of our own contributions
Personalized medicine in cancer
LSZGS Cancer Biology course 2016
Michael Baudis¶
Abstract¶
Lecture as part of the LSZGS Cancer Biology PhD program, touching some aspects of cancer genome data analysis (why, amount and cost of genome sequencing, genome variation, privacy & data sharing ...
Continue readingHarvesting Cancer Genome Data
Biocuration 2016, Geneva
Michael Baudis¶
Abstract¶
While the analysis of cancer genomes using high-throughput technologies has generated tens of thousands of oncogenomic profiles, meta-analyses of datasets is greatly inhibited through limited data access, technical fragmentation and a multitude of raw data and annotation formats.
For the arrayMap cancer genome resource, our group collects, re-processes and annotates cancer and associated reference data from genomic array experiments, retrieved from public repositories (e.g. NCBI GEO, EBI ArrayExpress) as well as from publication supplements and through direct requests to the primary producers. Continue reading
Gene-based analysis of focal copy number aberration patterns in cancer genomes
VIB Conference "Applied Bioinformatics in Life Sciences"
Saumya Gupta¶
Poster about the project to evaluate focal copy number variants in cancer, based on data from arraymap.org
Continue readingBCATS 2001 - progenetix.net: storage and visualization of genomic aberration data in human malignancies
First BCATS Meeting - Biocomputing @ Stanford 2001
Michael Baudis¶
Note Down memory lane, for historical reference: The first public presentation of the Progenetix database.
Abstract¶
Over the last decade, techniques for the genome wide scanning for genomic imbalances in malignant neoplasia have been developed, e.g. Comparative Genomic Hybridization (CGH).
Currently, no comprehensive online source for CGH data with a standardized format suitable for data mining procedures has been made available for public access. Such a data repository could be valuable in identifying genetic aberration patterns with linkage to specific disease entities, and provide additional information for validating data from large scale expression array experiments. Continue reading