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SNEP: SNP-derived Epitope Prediction program for minor H antigens

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Abstract

The single nucleotide polymorphism (SNP)–derived Epitope Prediction program (SNEP) is now available to the public. It predicts minor histocompatibility antigens (miHAgs), which are T-cell epitopes containing polymorphic spots, from proteins listed in the SWISS-PROT database. SNEP recognizes polymorphisms (termed VARIANT or CONFLICT in SWISS-PROT) and predicts potential T-cell epitopes within a chosen distance around the polymorphic residue. The prediction algorithm is based on the SYFPEITHI T-cell epitope prediction program. SNEP is able to search for proteins according to their accession numbers, sequence stretches or gene names, for example. The predictions are available for several human leucocyte antigen class I and class II allelic products, which allow for a rapid and precise evaluation of potential miHAgs within polymorphic antigens.

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References

  • Akatsuka Y, Nishida T, Kondo E, Miyazaki M, Taji H, Iida H, Tsujimura K, Yazaki M, Naoe T, Morishima Y, Kodera Y, Kuzushima K, Takahashi T (2003) Identification of a polymorphic gene, BCL2A1, encoding two novel hematopoietic lineage-specific minor histocompatibility antigens. J Exp Med 197:1489–1500

    Article  PubMed  CAS  Google Scholar 

  • Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh LS (2004) UniProt: the universal protein knowledgebase. Nucleic Acids Res 32:D115–D119

    Article  PubMed  CAS  Google Scholar 

  • Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O'Donovan C, Phan I, Pilbout S, Schneider M (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res 31:365–370

    Article  PubMed  CAS  Google Scholar 

  • Brickner AG, Warren EH, Caldwell JA, Akatsuka Y, Golovina TN, Zarling AL, Shabanowitz J, Eisenlohr LC, Hunt DF, Engelhard VH, Riddell SR (2001) The immunogenicity of a new human minor histocompatibility antigen results from differential antigen processing. J Exp Med 193:195–206

    Article  PubMed  CAS  Google Scholar 

  • Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD, Bairoch A (2003) ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res 31:3784–3788

    Article  PubMed  CAS  Google Scholar 

  • Gilliam AC (2004) Update on graft versus host disease. J Invest Dermatol 123:251–257

    Article  PubMed  CAS  Google Scholar 

  • Goulmy E (2004) Minor histocompatibility antigens: allo target molecules for tumor-specific immunotherapy. Cancer J 10:1–7

    Article  PubMed  CAS  Google Scholar 

  • Kircher B, Wolf M, Stevanovic S, Rammensee HG, Grubeck-Loebenstein B, Gastl G, Nachbaur D (2004) Hematopoietic lineage-restricted minor histocompatibility antigen HA-1 in graft-versus-leukemia activity after donor lymphocyte infusion. J Immunother 27:156–160

    Article  PubMed  CAS  Google Scholar 

  • Kolb HJ, Mittermuller J, Clemm C, Holler E, Ledderose G, Brehm G, Heim M, Wilmanns W (1990) Donor leukocyte transfusions for treatment of recurrent chronic myelogenous leukemia in marrow transplant patients. Blood 76:2462–2465

    PubMed  CAS  Google Scholar 

  • Rammensee H, Bachmann J, Stevanovic S (1997) MHC ligands and peptide motifs. Landes Bioscience, Austin

    Google Scholar 

  • Rammensee H, Bachmann J, Emmerich NP, Bachor OA, Stevanovic S (1999) SYFPEITHI: database for MHC ligands and peptide motifs. Immunogenetics 50:213–219

    Article  PubMed  CAS  Google Scholar 

  • Vogt MH, van den Muijsenberg JW, Goulmy E, Spierings E, Kluck P, Kester MG, van Soest RA, Drijfhout JW, Willemze R, Falkenburg JH (2002) The DBY gene codes for an HLA-DQ5-restricted human male-specific minor histocompatibility antigen involved in graft-versus-host disease. Blood 99:3027–3032

    Article  PubMed  CAS  Google Scholar 

  • Wallny HJ, Rammensee HG (1990) Identification of classical minor histocompatibility antigen as cell-derived peptide. Nature 343:275–278

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgements

SNEP was established with the kind support of Merck KGaA., Darmstadt, Germany. We also acknowledge financial support from the European Union (Integrated Project ALLOSTEM, LSHB-CT-2004-503319) and the Deutsche Forschungsgemeinschaft (SFB 510 and 685). We would also like to thank Boris Töltl for his valuable comments.

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Authors and Affiliations

  1. Abteilung Immunologie, Interfakultäres Institut für Zellbiologie, Universität Tübingen, Auf der Morgenstelle 15, 72076, Tubingen, Germany

    Mathias M. Schuler, Maria-Dorothea Nastke, Hans-Georg Rammensee & Stefan Stevanovic

  2. Division for Simulation of Biological Systems, Wilhelm Schickard Institute for Computer Science/Center for Bioinformatics, Universität Tübingen, Sand 14, 72076, Tübingen, Germany

    Pierre Dönnes & Oliver Kohlbacher

Authors
  1. Mathias M. Schuler
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  2. Pierre Dönnes
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  3. Maria-Dorothea Nastke
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  4. Oliver Kohlbacher
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  5. Hans-Georg Rammensee
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  6. Stefan Stevanovic
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Corresponding author

Correspondence to Stefan Stevanovic.

Additional information

The authors Schuler and Dönnes contributed equally

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Schuler, M.M., Dönnes, P., Nastke, MD. et al. SNEP: SNP-derived Epitope Prediction program for minor H antigens. Immunogenetics 57, 816–820 (2005). https://doi.org/10.1007/s00251-005-0054-5

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  • DOI: https://doi.org/10.1007/s00251-005-0054-5

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