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Table 1 Glossary of relevant abbreviations used

From: Multi-omics discovery of exome-derived neoantigens in hepatocellular carcinoma

Var Somatic variant (single nucleotide variant [SNV], insertion/deletion [InDel], frameshift variant)
Varns Non-synonymous somatic variant (i.e., somatic mutation)
Varexp Expressed non-synonymous somatic variant
PNE Predicted mutated neoepitope
PNEexp Predicted mutated neoepitope with evidence on transcript level
PNEprot Predicted mutated neoepitope with evidence on proteome level
NElig Mutated neoantigen with evidence on HLA ligandome level (HLA class I)
WTlig Wild-type peptide corresponding to PNE with evidence on HLA ligandome level (HLA class I)
neoantigen/neoepitope Mutated HLA-presented peptide (potentially) recognizable by (T cells of) the immune system
TMB Tumor mutational burden (non-synonymous somatic variants per megabase)