University of Cambridge > > Cambridge Mathematics Placements Seminars > Deconvolution of immune cells in tumour tissue using gene expression data

Deconvolution of immune cells in tumour tissue using gene expression data

Add to your list(s) Download to your calendar using vCal

If you have a question about this talk, please contact Dr Vivien Gruar.

The tumour microenvironment is a mixture of heterogeneous cell types including cancer, immune, and stromal cells. Recent studies have shown that the interaction between tumour and non-tumour cells influences the fate of the tumour. For example, we have previously shown significant variability in tumour-immune microenvironments among different tumours within the same patient leading to differing outcomes (Jiménez-Sánchez, et al. Cell 2017). However, the immune cell type characterisation of tumours using bulk gene expression data is still challenging. Thus we propose the following well-defined project: Can we reliably estimate the relative proportion of different immune cells present in a tumour using gene expression data? Multiple groups have tried to address this question, however the current state-of-the-art methods present at least one of the following issues: a) inaccuracy, b) cell bias, c) not comprehensive enough. We have already derived consensus gene signatures that outperform previous methods when benchmarked using a small set of tumour tissue samples. However, we want to make a more thoroughly benchmark and refine the consensus signatures/method (optional). Therefore, the specific aims in sequential order for the project are: 1) Compile benchmark data used by the other methods, 2) benchmark our consensus method against each of the other methods using their own test data, 3) (optional) refine/improve consensus method and signatures, 4) (optional) search and compile independent test data fro additional benchmarking. If aims 1 and 2 are completed and there is time, then aims 3 and 4 could be explored, however completing aims 1 and 2 would be enough to submit for publication.

This talk is part of the Cambridge Mathematics Placements Seminars series.

Tell a friend about this talk:

This talk is included in these lists:

Note that ex-directory lists are not shown.


© 2006-2024, University of Cambridge. Contact Us | Help and Documentation | Privacy and Publicity