Interview: Optimisation and validation of a nanopore-based sequencing method for potential molecular testing of CNS tumours

Mashiat Mimosa is a research-based MSc. student at University of Toronto’s Department of Laboratory Medicine and Pathobiology where her work focusses on cancer research, neuro-oncology, and genomics. We caught up with her to discuss what inspires her, the challenges she faces in her work, and how the use of nanopore sequencing is benefitting her research.

To learn more about Mashiat's research, you can also watch her recent talk, where she discussed the challenges posed by current NGS technologies for the identification of mutations for glioma and presented her work on the development and optimization of a nanopore-based SNV detection assay.

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What are your current research interests?

My current research interests are to identify the key challenges in brain cancer diagnostics and to look for potential solutions to these using nanopore sequencing.

What first ignited your interest in cancer genomics?

I lost some close family members to cancer which inspired me to contribute to cancer research in any capacity so that I can improve the quality of cancer patients’ lives. Moreover, my interest in genomics stemmed from my 4th year genomics thesis course at undergraduate level. So when I was ready to start graduate school, the combination of cancer research and genomics seemed like the best option.

How is nanopore sequencing changing your field of work?  How has it benefitted your work?

Nanopore sequencing is becoming more common in our field of work because now many small and new labs like us are able to perform sequencing at the lab bench without a large capital cost and within a shorter timeframe. It allows me to test different hypotheses and detect different types of tumour markers in brain cancer without relying on outsourcing our samples.

What impact could the ability to accurately detect SNV’s have for cancer research?

Detecting SNVs in cancer research could aid pathologists in diagnosing and predicting prognosis of patients in a shorter timeframe, and possibly in developing a personalised treatment plan for them. This will also reduce the stress that patients experience while waiting for a diagnosis, since this has the potential to give patients an answer in a few days instead of several weeks.

What have been the main challenges in your work and how have you approached them?

The main challenges in my work with nanopore sequencing have been the bioinformatics steps. As someone from a life sciences background with limited computer programming experience, I often find it difficult to understand and use the different programs and software required for data analysis. We are currently relying on a collaborator to help us with the bioinformatics processes for data analysis.

What’s next for your research?

My next goal is to continue to develop and optimise new potential diagnostic assays for brain cancer and other cancers using nanopore sequencing tools.

To learn more about other applications of nanopore sequencing in cancer research, click here.