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SUMMARY:Deconvolution of immune cells in tumour tissue using gene expressi
 on data - Alejandro Jiménez-Sánchez\, Cancer Research UK Cambridge Insti
 tute
DTSTART:20180130T130000Z
DTEND:20180130T140000Z
UID:TALK100729@talks.cam.ac.uk
CONTACT:Dr Vivien Gruar
DESCRIPTION: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 wi
 thin the same patient leading to differing outcomes (Jiménez-Sánchez\, e
 t al. Cell 2017). However\, the immune cell type characterisation of tumou
 rs using bulk gene expression data is still challenging. Thus we propose t
 he following well-defined project: Can we reliably estimate the relative p
 roportion of different immune cells present in a tumour using gene express
 ion data? Multiple groups have tried to address this question\, however th
 e current state-of-the-art methods present at least one of the following i
 ssues: a) inaccuracy\, b) cell bias\, c) not comprehensive enough. We have
  already derived consensus gene signatures that outperform previous method
 s when benchmarked using a small set of tumour tissue samples. However\, w
 e want to make a more thoroughly benchmark and refine the consensus signat
 ures/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 s
 ignatures\, 4) (optional) search and compile independent test data fro add
 itional benchmarking. If aims 1 and 2 are completed and there is time\, th
 en aims 3 and 4 could be explored\, however completing aims 1 and 2 would 
 be enough to submit for publication.\n
LOCATION:MR3 Centre for Mathematical Sciences
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