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GA4GH Community Spotlight: Michael Baudis


This GA4GH Community Post is the tenth in our series featuring individuals from across our organization. This month we are turning the spotlight on Michael Baudis! Baudis is a Professor of Bioinformatics at the Institute of Molecular Life Sciences, University of Zurich, and a group leader at the Swiss Institute of Bioinformatics. Michael studied Medicine at Heidelberg University, from which he graduated in 1998 and received his German medical license after internships at Heidelberg University Hospital. He received his doctorate from the Medical Faculty of the Ruprecht-Karls Universität Heidelberg in 1999. Since its founding in 2014, Michael has been a member of the Global Alliance for Genomics and Health (GA4GH), currently serving in the steering committee and as co-lead of the Discovery Work Stream. Baudis also co-chairs the ELIXIR Beacon project, which develops APIs to query genomic data collections in a privacy-protecting manner. 

How did you get involved with GA4GH?

For more than a decade, my group at the University of Zürich and the Swiss Institute of Bioinformatics (SIB) has participated in the use and sharing of genomic and associated data from cancer profiling studies. We are both “data parasites” – for our own research – as well as resource providers, which share the curated data through our “Progenetix” project. While constantly updating our data collection – which currently contains more than 130,000 cancer-associated genome profiles – we became increasingly aware of the barriers to a truly comprehensive representation of cancer genomics data. Therefore, when in 2013, the Swiss Institute of Bioinformatics became one of the first organizations to join GA4GH; I immediately saw an opportunity to participate in this endeavour.

What current projects are you working on/what is your research focused on?

My research has somehow always revolved around cancer genomics, specifically the analysis of structural genome aberrations with a focus on copy number variations. Here, my group tries to understand the recurring mutation patterns observed across all different types of malignancies and to find connections between such patterns and diagnostic, clinical and other annotations – even involving geographic provenance or population background. Chiefly due to the work in a variety of GA4GH related projects, I now spend a considerable amount of time working on the development and implementation of data standards and protocols such as the Beacon API.

How does interoperability/data sharing help your work and its importance?

At this point, we don’t see too many benefits for the core data we’re using in our own studies – genomic profiling data and associated annotations still come in various formats and frequently have to be processed or converted with custom bioinformatics pipelines. However, two areas where we start to make use of GA4GH community output are the rapid improvement of annotated genomic variations as well as the emerging standards and tools we use to share our own data with cancer genomics communities.

The biggest impact on our research comes from the direct participation in GA4GH projects and constant interaction with experts from many different domains. The learning curve has been steep but led to deep changes in some of the ways we address projects and highly increased our interactions with international research communities, away from custom formats and workflows and towards a more active exchange of data and knowledge.

What scientific discovery throughout history is most fascinating to you? 

That is a tricky one. Working in life sciences, I’m ought to say “Darwin’s theory of evolution by natural selection” – however, this is a way to understand the living world, based on meticulous studies and reasoning. So, maybe general relativity – especially since Albert Einstein graduated from the University of Zurich…

What is your favourite thing about the GA4GH Community and why?

What I love most is the combination of voluntary contributions by its members combined with very flat hierarchies and softly but expertly guided GA4GH’s administrative staff. Well known, world-class researchers closely interact with junior scientists, students, tech company CEOs and employees as well as data curators, from very different areas; I’m not aware of another place in life sciences where something like this happens – ELIXIR in some aspects comes close but then also has quite a bit of overlap & collaboration with GA4GH.

What is your favourite GA4GH event, and why?

This is a bit hard to say these days – but I would pick GA4GH Connect, since this is more of a “working event”, compared to the plenary. 

Why is diverse global representation critical to advancing progress in the field?

Our research addresses the relation between mutational patterns in cancers with disease types, clinical and environmental parameters as well as inherited genetic variations. Our assessment of e.g. the geographic provenance of available studies and of the cancer genomic publication landscape, in general, has shown us extreme biases, e.g. with a current near-total absence of such studies from the African continent or Central Asia. Here, we may miss out on specific cancer biologies – influenced by specific lifestyles, environmental exposures or genetically modified disease risk – which otherwise could help us in detecting “new” biologies and potentially improve outcomes for the affected patients.

What advice would you give to individuals seeking to get more involved with GA4GH?

I think the biggest impact and satisfaction of being a part of the GA4GH community comes from working on something which informs and influences an area you love as a researcher, and where advances directly impact your own work. These improvements – of standards, protocols, data or research methods – may not necessarily have an impact on the outcomes of your ongoing research projects; but your contributions as an expert will be most productive when informed by work you’re deeply involved in. Also: Don’t be shy to propose, discuss, contribute – GA4GH groups are very open & welcoming! 

How do you think genomic data standards will shape the world in 20 years?

With improved genomic data standards and exchange protocols – and based on the expectation that genomic analyses become “commodity” procedures – many new biomedical and consumer-oriented applications will see the light of day. For the next decade, I expect some groundbreaking shifts in the diagnosis of rare diseases and oncology, a move towards diagnoses and therapies becoming much more tailored to molecular observations than to summary diagnoses.

However, such advances are threatened through the broad use of “black box” diagnostics by point-of-care providers, and on a broader level by potential abuse of genomic tools and data for non-medical usage scenarios – think about the misconstrued genomic determinism and pervasive personal identification in “Gattaca”-like scenarios. The creation of genomic standards provides the groundwork for more powerful genomics research; the benefits depend a lot on a continuous dialogue with scientists, medical service providers, politicians and the society at large.