Dr Venkata Satagopam (VS) is bioinformatics scientist at the LCSB (Luxembourg Centre for Systems Biomedicine) of the University of Luxembourg, where people with broad and multidisciplinary backgrounds focus on understanding the mechanisms of diseases. Dr Satagopam is a senior researcher within the Bioinformatics Core group led by Prof. Reinhard Schneider, which enables other researchers from different backgrounds to efficiently manage, analyse and interpret their data. In the context of the COVID-19 pandemic, he is leading the data collection and integration within the CON-VINCE study. In this short interview, he illustrates his expertise and involvement in ongoing COVID-19 projects.
Could you tell us more about your background and expertise?
Venkata Satagopam: I have a background in pharmaceutical sciences and information technology and I did a PhD in Bioinformatics. In the past 20 years I have been working in different areas of bio medical informatics domains – comparative genomics, omics data analysis, clinical and translational medicine data collection, curation, integration and analysis, text-mining etc. Our group has a central role in the LCSB, as it enables the researchers to efficiently manage, analyse and interpret their data. We ensure that data can efficiently flow within and between different groups of researchers such as experimental, computational and medical oriented groups. We work in close collaboration with computer scientists and biologists covering a broad spectrum of disciplines on how to best develop, deploy and store (clinical) data as well as how to perform data analysis in a cost- and time-efficient automated way. To this end, our research in the Bioinformatics Core group evolves around better accessibility and interpretation of the ever increasing but often heterogenous data.
How is your expertise relevant in the current COVID context?
VS: At the LCSB I am involved in several projects like the National Centre for Excellence in Research on Parkinson’s Disease ( or NCER-PD). NCER-PD is a clinical and translational research project involving many actors, from fundamental researchers to clinicians from different institutions such as LCSB, Luxembourg Institute of Health (LIH), IBBL, University of Luxembourg, CHL and LNS. This project aims at deciphering the causes of Parkinson’s disease and to study how the disease develops. The role of the Biocore group is to collect the data sent by the clinical research teams, integrate it in a structured database and analyse it. I am also technical coordinator for ELIXIR-LU, the Luxembourgish node of ELIXIR-LU, the European infrastructure for life science information, which focuses on long-term sustainability of tools and data for Translational Medicine. Translational Medicine data integrates clinical information with molecular and cellular data for a better understanding of diseases. The experience built through NCER-PD and ELIXIR-LU helped in providing the infrastructure needed to collect, structure, clean and share the data coming from COVID-19 projects. Moreover, our expertise in building tools for clinical and translational research were key for some COVID-19 projects like ELIXIR (COvid-19 National survey for assessing VIral spread by Non-affected CarriErs), which is the national representative cohort aiming to evaluate the dynamics of the spread of the COVID-19 disease within the Luxembourgish population.CON-VINCE
What is your specific role in ongoing COVID projects?
VS: I am part of the national COVID-19 Task Force and I am leading the data collection, cleaning, integration and sharing of the CON-VINCE study. As mentioned before, the study is a national project aiming to evaluate the dynamics of the spread of the COVID-19 disease within the Luxembourgish population. By screening a statistically representative panel of volunteers for the presence of the SARS-CoV-2 virus, the study will identify asymptomatic and mildly symptomatic individuals and follow them up for a year.
Ultimately, the study aims to generate accurate data on the prevalence and transmission of the disease, assisting policy-makers in taking evidence-based decisions over the course of the coming weeks. The collection and integration of data is thus fundamental. We collaborate with several other research institutions like the Luxembourg Institute of Health (LIH), the Integrated Biobank of Luxembourg (IBBL) and the Laboratoire Nationale de la Santé (LNS), as well as private partners including TNS-Ilres and the private laboratories (BioNext, Ketterthill and Laboratoires Réunis), who all contribute samples and related clinical and analytical data and send it to us. We then structure it, clean it, loaded in our secure database and then share it to the partners of the study for analysis. Ensuring data protection was a high priority for us in this study, therefore the help of DPO’s such as Laurent Prévotat from LIH, Sandrine Munoz, and data steward Pinar Alper, and legal processes foreseen by Linda Eberman and Clemens from LCSB were absolutely key.
I was also involved in the design and development of the Research Luxembourg Platform for the submission of COVID-19 related projects, in close collaboration with the Fonds National de la Recherche (FNR) and also leading text-mining of available COVID-19 literature.
How did you live this experience with so many new collaborators?
I was amazed to see how fast CON-VINCE was deployed. Such a study usually takes 6 months to 1 year to get all approvals and to set up the legal framework, but here, we were ready to start within a few days only! And this has been possible only thanks to the fantastic people we had the chance to work with!
What is nice about it, is that everything worked beautifully even with people we’ve actually never met “physically”. We quickly developed a virtual network (based on slack, WebEx and Whatsapp mostly). Apart from LCSB Biocore colleagues Soumyabrata Ghosh, Piotr Gawron, Carlos Vega Moreno, Sascha Herzinger, Maharshi Vyas, Kirsten Rump, Xinhui Wang, Wei Gu, Christophe Trefois and other R3& IT infrastructure team, I can mention for instance Katy Beaumont, Estelle Sandt and Alexander Hundt from the IBBL, Laurent Prévotat, Manon Gantenbein, Michael Vaillant, Jonathan Turner, Chantal Snoeck, Markus Ollert from the LIH, Tamir Abdelrahman from LNS, entire clinical team, TNS Ilres, study managers Clarissa Gomes, Joëlle Fritz, and Rejko Krüger with whom I mostly worked remotely and who did an outstanding job in this study! Together, even remotely, we managed to create a real strong and dedicated team! It was not only about science, but much more, an incredible human experience!
Everybody worked so hard, with a sense of urgency and went the extra mile to make this unprecedented study happen and succeed. I would like to mention several hands who played important role in the needy hours: Marek Ostaszewski, Patrick May, Valentin Groues, Yohan Jarosz, Jacek Lebioda, Laurent Heirendt, Marcio Luis Acencio, Kavita Rege, Noua Toukourou, Sarah Peter, Daniele Welter, David Hoksza, Thijs Van Beek and Muhammad Shoaib from the LCSB.
We knew deadlines were extremely tight and everybody spared no effort to deliver in due time, even if it meant working until midnight or during the weekend. But no one ever complained! It was an intense but fantastic experience.
Picture: ©University of Luxembourg