hERV and retroelement neoantigens

[dlaehnemann]

Neoantigens generated by tumor-specific expression of retroelements (LINEs, SINEs, hERV, etc.). They require a differential expression analysis between tumour and normal samples, to ensure that the element is not expressed in the normal cells.

Available tools:

• hervQuant

Alternative idea:

• Create reference sequence database of such elements and do kallisto + sleuth differential expression analysis, then turn tumour-only elements into potential peptides.