MiHA-Match: Computational detection of tissue-specific minor histocompatibility antigens

Journal of Immunological Methods

Volumn 386, Issue 1-2, 2012, Pages 94-100

  Feldhahn, Magdalena ^a   Dönnes, Pierre ^a,b   Schubert, Benjamin ^a   Schilbach, Karin ^c   Rammensee, Hans Georg ^a   Kohlbacher, Oliver ^a  

^a UNIVERSITY OF TÜBINGEN   (Germany)

^b UNIVERSITY OF SKÖVDE   (Sweden)

^c UNIVERSITY HOSPITAL TÜBINGEN   (Germany)

Author keywords

Immunoinformatics; Minor histocompatibility antigens; Transplantation

Indexed keywords

MINOR HISTOCOMPATIBILITY ANTIGEN;

ANTIGEN DETECTION; ARTICLE; CANCER THERAPY; DIAGNOSTIC TEST; GENETIC VARIABILITY; HLA SYSTEM; HUMAN; INTERMETHOD COMPARISON; MATHEMATICAL ANALYSIS; PRIORITY JOURNAL; PROTEIN BINDING; SINGLE NUCLEOTIDE POLYMORPHISM; TISSUE SPECIFICITY;

COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; GRAFT VS LEUKEMIA EFFECT; HIGH-THROUGHPUT SCREENING ASSAYS; HISTOCOMPATIBILITY; HUMANS; INDIVIDUALIZED MEDICINE; LEUKEMIA; MINOR HISTOCOMPATIBILITY ANTIGENS; ORGAN SPECIFICITY; POLYMORPHISM, GENETIC; PROTEIN BINDING; STEM CELL TRANSPLANTATION;

EID: 84867445887     PISSN: 00221759     EISSN: 18727905     Source Type: Journal    
DOI: 10.1016/j.jim.2012.09.004     Document Type: Article

References (17)

1. Appelbaum F.R. The current status of hematopoietic cell transplantation. Annu. Rev. Med. 2003, 54:491.
2. Bleakley M., Riddell S.R. Molecules and mechanisms of the graft-versus-leukaemia effect. Nat. Rev. Cancer 2004, 4:371.
3. Donnes P., Kohlbacher O. Integrated modeling of the major events in the MHC class I antigen processing pathway. Protein Sci. 2005, 14:2132.
4. Feldhahn M., Donnes P., Thiel P., Kohlbacher O. FRED-a framework for T-cell epitope detection. Bioinformatics 2009, 25:2758.
5. Feng X., Hui K.M., Younes H.M., Brickner A.G. Targeting minor histocompatibility antigens in graft versus tumor or graft versus leukemia responses. Trends Immunol. 2008, 29:624.
6. Ferrara J.L., Levine J.E., Reddy P., Holler E. Graft-versus-host disease. Lancet 2009, 373:1550.
7. Gonzalez-Galarza F.F., Christmas S., Middleton D., Jones A.R. Allele frequency net: a database and online repository for immune gene frequencies in worldwide populations. Nucleic Acids Res. 2011, 39:D913.
8. Goulmy E. Minor histocompatibility antigens: from transplantation problems to therapy of cancer. Hum. Immunol. 2006, 67:433.
9. Hombrink P., Hadrup S.R., Bakker A., Kester M.G., Falkenburg J.H., von dem Borne P.A., Schumacher T.N., Heemskerk M.H. High-throughput identification of potential minor histocompatibility antigens by MHC tetramer-based screening: feasibility and limitations. PLoS One 2011, 6:e22523.
10. Nielsen M., Lundegaard C., Blicher T., Lamberth K., Harndahl M., Justesen S., Roder G., Peters B., Sette A., Lund O., Buus S. NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence. PLoS One 2007, 2:e796.
11. Pruitt K.D., Tatusova T., Klimke W., Maglott D.R. NCBI Reference Sequences: current status, policy and new initiatives. Nucleic Acids Res. 2009, 37:D32.
12. Sayers E.W., Barrett T., Benson D.A., Bolton E., Bryant S.H., Canese K., Chetvernin V., Church D.M., DiCuccio M., Federhen S., Feolo M., Fingerman I.M., Geer L.Y., Helmberg W., Kapustin Y., Landsman D., Lipman D.J., Lu Z., Madden T.L., Madej T., Maglott D.R., Marchler-Bauer A., Miller V., Mizrachi I., Ostell J., Panchenko A., Phan L., Pruitt K.D., Schuler G.D., Sequeira E., Sherry S.T., Shumway M., Sirotkin K., Slotta D., Souvorov A., Starchenko G., Tatusova T.A., Wagner L., Wang Y., Wilbur W.J., Yaschenko E., Ye J. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2011, 39:D38.
13. Sherry S.T., Ward M.H., Kholodov M., Baker J., Phan L., Smigielski E.M., Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001, 29:308.
14. Shlomchik W.D. Graft-versus-host disease. Nature reviews. Immunology 2007, 7:340.
15. Toussaint N.C., Feldhahn M., Ziehm M., Stevanovic S., Kohlbacher O. T-cell epitope prediction based on self-tolerance. Proc. ICIW 2011.
16. Tung C.W., Ziehm M., Kamper A., Kohlbacher O., Ho S.Y. POPISK: T-cell reactivity prediction using support vector machines and string kernels. BMC Bioinformatics 2011, 12:446.
17. van Bergen C.A., Rutten C.E., van Der Meijden E.D., van Luxemburg-Heijs S.A., Lurvink E.G., Houwing-Duistermaat J.J., Kester M.G., Mulder A., Willemze R., Falkenburg J.H., Griffioen M. High-throughput characterization of 0 new minor histocompatibility antigens by whole genome association scanning. Cancer Res. 2010, 70:9073-9083.