We designed the Christmas Light Plot (CLP) for easy visualization of identified neoantigens (below). The CLP incorporates pre-defined criteria for neoantigen prioritization, including MHC binding affinities, expression level, HLA class types, and the mutant clonal status.
- X-axis: Variant allele fraction (VAF) in WES, which can be used to infer clonal status
- Y-axis: The predicted binding affinity of the mutant peptide
Each dot represents a neoantigen with the following characteristics displayed:
- Size: The gene expression level by RNASeq; shape – HLA binding classes (I, II, or both)
- Vertical bar: The difference between mutant and wildtype binding affinities
- Color: Stratified based on the mutant versus wildtype binding and mutant expression level
Gene symbols are displayed for neoantigens selected for screening.
Selected papers
Yang Y, Jain RK, Glenn ST, Xu B, Singh PK, Wei L, Hu Q, Long M, Hutson N, Wang J, Battaglia S, George S. Complete response to anti-PD-L1 antibody in a metastatic bladder cancer associated with novel MSH4 mutation and microsatellite instability. J Immunother Cancer. 2020 Mar;8(1):e000128. doi: 10.1136/jitc-2019-000128. PMID: 32221012; PMCID: PMC7206971.
Liu S, Matsuzaki J, Wei L, Tsuji T, Battaglia S, Hu Q, Cortes E, Wong L, Yan L, Long M, Miliotto A, Bateman NW, Lele SB, Chodon T, Koya RC, Yao S, Zhu Q, Conrads TP, Wang J, Maxwell GL, Lugade AA, Odunsi K. Efficient identification of neoantigen-specific T-cell responses in advanced human ovarian cancer. J Immunother Cancer. 2019 Jun 20;7(1):156. doi: 10.1186/s40425-019-0629-6. PMID: 31221207; PMCID: PMC6587259.