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Table 1 Summary of predicted epitope candidates through pVAC-Seq pipeline

From: pVAC-Seq: A genome-guided in silico approach to identifying tumor neoantigens

  MEL21 MEL38 MEL218 MEL69
  LN Skin Skin Axilla Breast AbWall LN Skin / Limb Skin / Scalp
(2011) (2012) (2013) (2012) (2013) (2013) (2005) (2013) (2013)
Total SNVs 702 838 1099 359 402 385 695 256 282
Missense SNVs 443 515 598 219 247 238 437 141 162
21-mer FASTA entries (WT & MT) 856 1,004 1,002 424 482 462 850 272 314
Raw NETMHC output (9-mers) 11,152*2 (HLA-A02:01, HLA-A01:01) 13,072*2 (HLA-A02:01, HLA-A01:01) 13,044*2 (HLA-A02:01, HLA-A01:01) 5,512*3 (HLA-A02:01, HLA-A31:01, HLA-B07:02) 6,270*3 (HLA-A02:01, HLA-A31:01, HLA-B07:02) 6,010 *3 (HLA-A02:01, HLA-A31:01, HLA-B07:02) 11,050*3 (HLA-A02:01, HLA-A03:01, HLA-B44:02 3,542*2 (HLA-A02:01, HLA-A11:01) 4,088*2 (HLA-A02:01, HLA-A11:01)
Parsed NetMHC output (compared WT with MT) 3,796*2 (HLA-A02:01, HLA-A01:01) 4,465*2 (HLA-A02:01, HLA-A01:01) 4,458*2 (HLA-A02:01, HLA-A01:01) 1,871*3 (HLA-A02:01, HLA-A31:01, HLA-B07:02) 2,131*3 (HLA-A02:01, HLA-A31:01, HLA-B07:02) 2,042*3 (HLA-A02:01, HLA-A31:01, HLA-B07:02) 3,770*3 (HLA-A02:01, HLA-A03:01, HLA-B44:02 1,217*2 (HLA-A02:01, HLA-A11:01) 1,395*2 (HLA-A02:01, HLA-A11:01)
Filter 1: Binding based 110 121 144 103 112 111 161 50 65
HLA-A02:01 candidates only 79 96 111 52 48 46 93 25 34
Filter 2: Manually reviewed HLA-A02:01 candidates (Exome plus RNA-Seq) 11 11 12 14 16 16 24 6 12
Filter 3: Experimentally tested 16 14 18 12
Filter 4: Vaccine tested 7 7 7 10
Immunogenicity 3 3 3 4
  1. The table illustrates the number of raw candidates predicted by NetMHC, and the parsing and filtering strategies applied thereafter to the final list of neoantigen candidates. These candidates were then communicated to our vaccine design collaborators who evaluated this list by patient-specific immunological assays (Filters 3 & 4) [20]