Bioinformatics tools for investigating the tumor-immune cell interface

Tumor-infiltrating immune cells profoundly influence tumor progression and response to therapy. Specific cells of the immune system have the unique capability to recognize and kill malignant cells displaying tumor-specific antigens (called neoantigens). However, tumors are infiltrated with different types of immune cells that can have either pro- or anti-tumorigenic roles.

Thanks to next-generation sequencing (NGS) technologies we have now access to high-throughput data from tumors and associated tumor-infiltrating cells. This workshop will give you an overview of the bioinformatics approaches that can be used to mine NGS data to extract features describing the tumour-immune cell interface, with a particular focus on:

  • Prediction of patient-specific tumor neoantigens that can elicit anticancer immune responses;

  • Quantification of different immune cell subtypes from bulk tumors.


(2 hours)

Francesca Finotello