Identify deleterious mutations in antigen presentation pathways

[iskandr]

e.g. B2M, TAP, &c.

Identifying loss in MHC might require running a custom program which first does genotyping of the germline MHC and then calls somatic variants against those specific alleles.

[iskandr]

The set of genes from immunophenogram is a good start:

The right side looks like an immune deconvolution so look at gene names on the left. Need a distinct way to figure out mutations in MHC.

[iskandr]

• TAP1
• TAP2
• B2M
• IDO1
• ICOS
• CD27
• PDCDL1LG2
• CD274
• HAVCR2
• TIGIT
• LAG3
• CTLA4
• PDCD1

And maybe non-canonical HLA:

• HLA-E
• HLA-F

[iskandr]

The list above isn't exhaustive btw. Drawn from a larger list: http://icbi.at/TCIA/SupplementaryTables.pdf

[iskandr]

Full list of immunophenoscore features:

Mutation load Somatic mutation Neoantigen Somatic mutation Neoantigen frequency Somatic mutation B2M MHC-classical, class-I TAP1 MHC-classical, class-I TAP2 MHC-classical, class-I TAPBP MHC-classical, class-I HLA-A MHC-classical, class-I HLA-B MHC-classical, class-I HLA-C MHC-classical, class-I HLA-DPA1 MHC-classical, class-II HLA-DPB1 MHC-classical, class-II HLA-DQA1 MHC-classical, class-II HLA-DQA2 MHC-classical, class-II HLA-DQB1 MHC-classical, class-II HLA-DRA MHC-classical, class-II HLA-DRB1 MHC-classical, class-II HLA-E MHC-non-class, class-I HLA-F MHC-non-class, class-I HLA-G MHC-non-class, class-I HLA-DMA MHC-non-class, class-II HLA-DMB MHC-non-class, class-II HLA-DOA MHC-non-class, class-II HLA-DOB MHC-non-class, class-II CTLA4 Immunoinhibitor PDCD1 Immunoinhibitor LAG3 Immunoinhibitor BTLA Immunoinhibitor CD160 Immunoinhibitor IDO1 Immunoinhibitor IL10 Immunoinhibitor IL10RB Immunoinhibitor TGFB1 Immunoinhibitor TGFBR1 Immunoinhibitor VTCN1 Immunoinhibitor CD244 Immunoinhibitor LGALS9 Immunoinhibitor HAVCR2 Immunoinhibitor ADORA2A Immunoinhibitor TIGIT Immunoinhibitor CSF1R Immunoinhibitor KIR2DL1 Immunoinhib KDR Immunoinhibitor CD96 Immunoinhibitor PVRL2 Immunoinhibitor MICA Immunostimulator MICB Immunostimulator CD27 Immunostimulator CD274 Immunostimulator CD28 Immunostimulator CD40 Immunostimulator CD40LG Immunostimulator CD70 Immunostimulator CD80 Immunostimulator CD86 Immunostimulator ICOS Immunostimulator ICOSLG Immunostimulator IL6 Immunostimulator IL6R Immunostimulator PDCD1LG2 Immunostimulator TMEM173 Immunostimulator TNFRSF13B Immunostimulator TNFRSF13C Immunostimulator TNFRSF14 Immunostimulator TNFRSF17 Immunostimulator TNFRSF18 Immunostimulator TNFRSF4 Immunostimulator TNFRSF9 Immunostimulator TNFSF13 Immunostimulator TNFSF13B Immunostimulator TNFSF18 Immunostimulator TNFSF4 Immunostimulator TNFSF9 Immunostimulator TNFSF15 Immunostimulator TNFRSF25 Immunostimulator HHLA2 Immunostimulator TMIGD2 Immunostimulator C10orf54 Immunostimulator BTNL2 Immunostimulator CD276 Immunostimulator CD48 Immunostimulator TNFSF14 Immunostimulator TNFRSF8 Immunostimulator CD70 Immunostimulator PVR Immunostimulator LTA Immunostimulator MICA Immunostimulator MICB Immunostimulator IL2RA Immunostimulator ENTPD1 Immunostimulator NT5E Immunostimulator CXCR4 Immunostimulator CXCL12 Immunostimulator KLRK1 Immunostimulator NKG2A Immunostimulator RAET1E Immunostimulator ULBP1 Immunostimulator Activated B cell Adaptive immunity Activated CD4 T cell Adaptive immunity Activated CD8 T cell Adaptive immunity Central memory CD4 T cell Adaptive immunity Central memory CD8 T cell Adaptive immunity Effector memeory CD4 T cell Adaptive immunity Effector memeory CD8 T cell Adaptive immunity Gamma delta T cell Adaptive immunity Immature B cell Adaptive immunity Memory B cell Adaptive immunity Regulatory T cell Adaptive immunity T follicular helper cell Adaptive immunity Type 1 T helper cell Adaptive immunity Type 17 T helper cell Adaptive immunity Type 2 T helper cell Adaptive immunity Activated dendritic cell Innate immunity CD56bright natural killer cell Innate immunity CD56dim natural killer cell Innate immunity Eosinophil Innate immunity Immature dendritic cell Innate immunity Macrophage Innate immunity Mast cell Innate immunity Monocyte Innate immunity Myeloid-derived suppressor cell Innate immunity Natural killer cell Innate immunity Natural killer T cell Innate immunity Neutrophil Innate immunity Plasmacytoid dendritic cell Innate immunity