Skip to main content
. Author manuscript; available in PMC: 2017 Jan 26.
Published in final edited form as: Curr Opin Biotechnol. 2016 Mar 21;42:92–97. doi: 10.1016/j.copbio.2016.03.001

Figure 1.

Figure 1

Identification and validation of immunogenic neoantigens expressed in tumors. Tumor samples and peripheral blood provide tumor infiltrating lymphocytes (TIL) and antigen presenting cells (APC) respectively that are used for validation. Whole exome sequencing of tumor and comparison with autologous healthy tissue (i.e. circulating leukocytes) is utilized for discovery of somatic mutations. A number of mutation callers can be used in conjunction with data annotation tools. After data filtering, algorithms such as such as NetChop, NetMHC and SYFPEITHI are utilized to predict cleavage length and affinity for MHC since less than 1% of somatic mutations bind a particular class of MHC. Finally, candidate antigens (Ag) are loaded onto APC either by pulsing with peptide or electroporation of RNA. TIL are cultured with these APC and monitored for cytokine secretion (IFN-γ, GM-CSF, IL-2) to determine which neoantigens elicit productive T cell responses.