Integrating scRNA-Seq and CUT&Tag data to investigate genomic instability in aging models
Dr. Robert Hänsel-Hertsch leads the Laboratory for Genome Biology at the University of Cologne’s Center for Molecular Medicine Cologne. His group focuses on structural alterations in the epigenome in the context of aging and disease development. In late 2023, Dr. Hänsel-Hertsch reached out to Genevia Technologies for bioinformatics support. Almost a year later, we sat down with him in a video call to hear his thoughts on the collaboration.
Towards big stories with Genevia Technologies
Dr. Hänsel-Hertsch explains that he has a background in structural biology and began working with nucleic acids during his PhD in Frankfurt. He became interested in a specific type of secondary DNA structure called guanine quadruplexes and spent six years in Cambridge as a postdoc. During that time, his focus shifted to genomics, aiming to better understand the biological significance and genome-wide occurrence of these structures. In 2019, he moved to Cologne to establish his own research group.
– In my earlier work, I investigated whether these structures were related to genomic instability and cancer. Now, we want to know if they appear during aging, predisposing the genome to cancer, he elaborates.
Dr. Hänsel-Hertsch’s group is relatively young. For the first three and a half years, they had their own bioinformatician working on multiple projects. However, when she transitioned to another career path, the need for bioinformatics support became urgent. Dr. Hänsel-Hertsch searched online for commercial bioinformatics providers and came across Genevia Technologies. Genevia’s website and experience in epigenetic research convinced him to reach out.
The project where Genevia provided bioinformatics support focused on epigenome mapping methods. Genevia’s Scientific Project Managers Dr. Eva Domènech-Moreno and Dr. Joana Viana analyzed and integrated CUT&Tag and single-cell RNA-sequencing data to uncover new insights into the connection between epigenetics and genomic instability in aging models. Dr. Hänsel-Hertsch shares that the results, along with a new method developed during the project, will be central to a manuscript his team is preparing.
– This is the biggest yet unpublished story in my lab so far, and Genevia helped us immensely. Joana and Eva are great academic thinkers. They did more than I would have expected even from a hired bioinformatician in my group. For instance, Eva came up with some really creative ideas—it’s the kind of creativity I’d expect only from someone at a very high-level lab. That was just fantastic, Dr. Hänsel-Hertsch praises, adding:
– What was key for me was how easy it was to communicate with them, in which my own bioinformatics background also helped. I could really see them develop what we wanted rather than just handing over the data and waiting for them to do the magic.
Reflecting on outsourcing bioinformatics
Dr. Hänsel-Hertsch notes that finding a good bioinformatician is challenging in any field, and especially in his. The hiring process demands significant time and money, and in a young group, it can be difficult to attract strong candidates. Even when someone is hired, getting them up to speed takes time. Moreover, academic bioinformaticians naturally want to drive their own careers, which can lead to conflicts of interest over questions such as authorship. This prompted Dr. Hänsel-Hertsch to consider alternatives.
– It never occurred to me that I would use an external bioinformatics provider. In the end, it was a very practical decision. I have a self-taught background in bioinformatics myself, so I know what I want from the analyses, but as the group leader, I simply don’t have the capacity to focus on developing code and performing the analyses myself. I thought working with a company would be quicker and more efficient—without the need for the hiring process, he explains.
Dr. Hänsel-Hertsch admits he was initially hesitant about certain aspects of the service, such as communication, especially when he was assigned two bioinformaticians instead of one. However, his concerns quickly dissipated. The division of work and communication between Genevia’s team and his group was well-structured and clear. He also acknowledges that data security and uncertainty about outcomes are common concerns for many researchers considering external bioinformatics services. What reassured him was Genevia’s long-standing experience as a 13-year-old company—not a startup that might disappear after receiving his data.
After nine months of using Genevia’s services, Dr. Hänsel-Hertsch is more than satisfied with his decision to outsource bioinformatics. He emphasizes that one of the best aspects of the FTE-based service is its flexibility: when the workload increased, they could simply ramp up the amount of allocated time. Now that he’s built a trusting relationship with Genevia, he hopes to continue working with their bioinformaticians and find ways to incorporate the service into future grant applications as well.
– Of course, at first it was a risk to invest money without knowing how things would turn out, but now that I have the experience, I can absolutely recommend Genevia. You essentially gain the support of an army of bioinformaticians: if the people you are working with don’t know something, they have many colleagues to exchange ideas with. This actually happened in our project, too. It’s a whole different level of professionalism; a service, but on an academic level, he concludes.
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