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Table 1 The binding scores of individual peptides for the patient’s HLA class I and II haplotypes and CD1d

From: Immune monitoring and TCR sequencing of CD4 T cells in a long term responsive patient with metastasized pancreatic ductal carcinoma treated with individualized, neoepitope-derived multipeptide vaccines: a case report

Peptide Protien origin Peptide sequence MHC class I Net MHC [32, 33] Syfpeithi [34] CD1d Castano [55] MHC class II Net MHC II pan3.1 [35]
1 RIM1 WEAKPSRIL B*18 WB +(17) CD1d DRB1*1101 NB
    B*44 WB   CD1d DRB1*1301 NB
   (WEAKPSRI) B*44 SB +(21)   
2 KIF4B GIAARVKNWL A*02 NB +(22) CD1d + DRB1*1101 WB
         DRB1*1301 WB
3 KIF4B KEGIAARVKNW B*44 WB −(14) CD1d + DRB1*1101 NB
         DRB1*1301 NB
   (EGIAARVKNW) B*44 SB −(14) CD1d +   
4 RIM1 EAKPSRILM A*02 NB −(6) CD1d DRB1*1101 NB
         DRB1*1301 NB
  1. The binding scores of individual peptides for the patient’s HLA haplotypes were determined via NetMHC [32, 33], SYFPEITHI [34], CD1d-binding algorithm according to “Castano” (1-4-7 rule) [55] and NetMHCIIpan version 3.1 [35]
  2. Then likelihood for presentation is given as “+” and “−” respectively; SYFPEITHI half max scores regarding MHC class I presentation are given in brackets. Mutations in the peptides are indicated by underline
  3. WB weak binder, SB strong binder, NB no binding predicted