title: Prediction of HLA-A2-restricted CTL epitope specific to HCC by SYFPEITHI combined with polynomial method.
abstract: OBJECTIVE
  To predict the HLA-A2-restricted CTL epitopes of tumor antigens associated with hepatocellular carcinoma (HCC).
  
  
  METHODS
  MAGE-1, MAGE-3, MAGE-8, P53 and AFP were selected as objective antigens in this study for the close association with HCC. The HLA-A*0201 restricted CTL epitopes of objective tumor antigens were predicted by SYFPEITHI prediction method combined with the polynomial quantitative motifs method. The threshold of polynomial scores was set to -24.
  
  
  RESULTS
  The SYFPEITHI prediction values of all possible nonamers of a given protein sequence were added together and the ten high-scoring peptides of each protein were chosen for further analysis in primary prediction. Thirty-five candidates of CTL epitopes (nonamers) derived from the primary prediction results were selected by analyzing with the polynomial method and compared with reported CTL epitopes.
  
  
  CONCLUSIONS
  The combination of SYFPEITHI prediction method and polynomial method can improve the prediction efficiency and accuracy. These nonamers may be useful in the design of therapeutic peptide vaccine for HCC and as immunotherapeutic strategies against HCC after identified by immunology experiment.
authors.affiliation: Department of Pathology, Fourth Military Medical University, Xi'an 710032, Shaanxi Province, China.
authors.forename: Hai-Long
authors.initials: HL
authors.lastname: Dong
authors.forename: Yan-Fang
authors.initials: YF
authors.lastname: Sui
mesh_terms: D000595:Amino Acid Sequence; D006528:Carcinoma, Hepatocellular / Q000276:immunology*; D030562:Databases, Protein; D000939:Epitopes / Q000737:chemistry / Q000276:immunology; D015789:HLA-A2 Antigen / Q000276:immunology*; D006801:Humans; D008113:Liver Neoplasms / Q000276:immunology*; D008285:Major Histocompatibility Complex; D013602:T-Lymphocytes, Cytotoxic / Q000276:immunology*
chemical_list: D000939:Epitopes; D015789:HLA-A2 Antigen