Unraveling the genetic predisposition to cancer with whole-genome and RNA sequencing
Johanna Schleutker is a Professor of Medical Genetics at the University of Turku, and a Head Geneticist working in the field of diagnostics at the Department of Genomics, Turku University Hospital. For a couple of decades, she has been studying hereditary prostate cancer. Genomic studies with various types of sequencing data, and connections to the Genevia team have led to a fruitful collaboration.
– I focus on genetic cancer predisposition and especially on aggressive prostate cancer. Another topic that I study is early onset aggressive, hereditary breast cancer. So naturally, we have done a lot of genomic studies and produced a lot of sequencing data, she elaborates.
Her first project with Genevia took place around 2016, and since then, there have been two more projects. The most recent work focused on inherited prostate cancer in families which lacked previously known predisposing genetic variants.
– We performed whole-genome sequencing (WGS) on the index patients from more than 70 families. We got the results from Genevia last summer, and that’s only when the work really got started on our end, so it’s still an ongoing project. In addition to the WGS data, our projects have included RNA sequencing, both basic and extra deep, and also whole-exome sequencing (WES) data, professor Schleutker explains.
Splicing analysis based on DNA- and RNA-seq data. Splicing from exon 3 to exon 5 (=exon skipping) and splicing from exon 3 to cryptic intronic splice sites is upregulated (red) in variant carriers, whereas normal splicing from exon 3 to exon 4, and from exon 4 to exon 5 is downregulated (blue).
Clear project structure and reliable timelines
Professor Schleutker continues by describing their experiences working with Genevia.
– As is known, bioinformatics is often the bottleneck in research: a group focusing on wet-lab experiments doesn’t usually have its own bioinformatician, and finding one is very difficult, as everyone seems to be overworked. So, an external service provider for the most part has been a good solution for us so far, she says.
– We have the privilege of getting to work with Tommi Rantapero who had worked with my group already years ago, and is familiar with what we do. It’s so easy communicating with him about what we should do next, and there’s no need to explain too much what exactly we want from the analyses.
Professor Schleutker and her group have been very pleased with the quality of Genevia's data analysis work and have found the results useful. In addition to getting to interpret and discuss the results together with the bioinformatician, she thinks that detailed documentation is extremely important.
– Sometimes it can take a lot of fine-tuning and explaining to find the right details to focus on, and I wonder whether we could have still added something to the analysis. But the communication has been working well in these situations. Even though we haven’t really faced any problems in the projects we’ve had with Genevia, I understand that it can be a great challenge to find bioinformaticians who understand both the biology and the data analysis side, she says.
– Obviously, financing the use of this kind of service can be a challenge to many researchers. However, what I find that one of the biggest advantages is the clear structure and timeline of the projects. In academia, these kinds of projects tend to drag on. When using a service provider you can rely on the timeline they give, and trust that they use best-practice pipelines. I also enjoy the planning part together with the bioinformatician. I would recommend Genevia, and, in fact, have already mentioned them to some colleagues struggling with bioinformatics.