SiPep: a system for the prediction of tissue‐specific minor histocompatibility antigens
Identifieur interne : 002D90 ( Main/Exploration ); précédent : 002D89; suivant : 002D91SiPep: a system for the prediction of tissue‐specific minor histocompatibility antigens
Auteurs : M. Halling-Brown [Royaume-Uni] ; R. Quartey-Papafio [Royaume-Uni] ; P. J. Travers [Royaume-Uni] ; D. S. Moss [Royaume-Uni]Source :
- International Journal of Immunogenetics [ 1744-3121 ] ; 2006-08.
English descriptors
- Teeft :
- Adoptive immunotherapy, Aggregated protein, Algorithm, Allele, Amino acids, Anking regions, Antigenic peptides, Authors journal compilation, Binding predictions, Binding score, Binding scores, Birkbeck college, Blackwell publishing, Candidate peptides, Cdna, Cdna encoding, Cdna expression, Cell surface, Cleavage, Database, Dbsnp, Different methods, Epitope, Example protein entry, Experimental medicine, Expression data, Gene name, Genes encoding mhags, Histocompatibility, Histocompatibility antigen, Histocompatibility antigens, Immunogenetics, Immunological reviews, Initial data sources, International journal, Major histocompatibility, Malet street, Mass spectrometry, Mhags, Minor histocompatibility antigen, Minor histocompatibility antigens, Mutation, Ncbi, Ncbi dbsnp, Nucleic, Nucleic acids research, Open reading frame, Peptide, Peptide binding, Peptide binding entries, Peptide generation, Peptide nlvpmvatv, Polymorphism, Possible mhags, Previous step, Proteasomal, Proteasomal cleavage, Proteasomal cleavage prediction, Protein antigens, Protein expression data, Protein sequence, Refolding, Refolding assay, Refolding score, Search facilities, Sipep, Sipep algorithm, Snp, Snpbinder, Snpbinder database, Syfpeithi algorithm, Tissue expression, User, User interface.
Abstract
Approximately 50 years ago it was found that inbred strains of mice were able to reject tumours and skin grafts from major histocompatibility complex (MHC) identical donors. They proposed that additional transplantation antigens must exist outside the MHC. These were described as minor histocompatibility antigens (mHAgs). Since then, related studies in humans have identified 16 human mHAgs. The aim of this work is to increase the number of known mHAgs by prediction of candidate minor histocompatibility loci by identifying coding single nucleotide polymorphisms (SNPs) where the amino acid variation lies within an MHC‐binding peptide and alters the ability of that peptide to bind. We have developed an algorithm called SiPep which uses peptide sequences derived from the flanking regions of known non‐synonymous SNPs, various MHC‐binding and proteolytic cleavage evaluation methods and protein expression data to predict mHAgs. We have processed 45094 SNPs using the SiPep algorithm and have stored the results in a database called SNPBinder. The facilities to process submitted proteins through the SiPep algorithm as well as the SNPBinder database are available to the public. A set of peptides that are predicted as possible mHAgs by the SiPep algorithm have been tested using refolding assays and gel filtration and the results are presented in this paper. The SiPep tools and SNPBinder database are available free of charge via the internet. An HTML interface providing search facilities can be found at the following address: http://www.sipep.org/.
Url:
DOI: 10.1111/j.1744-313X.2006.00615.x
Affiliations:
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Halling-Brown</name><affiliation wicri:level="4"><country>Royaume-Uni</country><wicri:regionArea> Institute of Structural Molecular Biology, School of Crystallography, Birkbeck College, University of London, Malet Street, London, WC1E 7HX</wicri:regionArea><orgName type="university">Université de Londres</orgName><placeName><settlement type="city">Londres</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Londres</region></placeName></affiliation></author><author><name sortKey="Quartey Apafio, R" sort="Quartey Apafio, R" uniqKey="Quartey Apafio R" first="R." last="Quartey-Papafio">R. Quartey-Papafio</name><affiliation wicri:level="1"><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Anthony Nolan Research Institute, Royal Free and University College Medical School, Royal Free Campus, Fleet Road, Hampstead, London NW3 2QG</wicri:regionArea><wicri:noRegion>London NW3 2QG</wicri:noRegion></affiliation></author><author><name sortKey="Travers, P J" sort="Travers, P J" uniqKey="Travers P" first="P. J." last="Travers">P. J. Travers</name><affiliation wicri:level="1"><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Anthony Nolan Research Institute, Royal Free and University College Medical School, Royal Free Campus, Fleet Road, Hampstead, London NW3 2QG</wicri:regionArea><wicri:noRegion>London NW3 2QG</wicri:noRegion></affiliation></author><author><name sortKey="Moss, D S" sort="Moss, D S" uniqKey="Moss D" first="D. S." last="Moss">D. S. Moss</name><affiliation wicri:level="4"><country>Royaume-Uni</country><wicri:regionArea> Institute of Structural Molecular Biology, School of Crystallography, Birkbeck College, University of London, Malet Street, London, WC1E 7HX</wicri:regionArea><orgName type="university">Université de Londres</orgName><placeName><settlement type="city">Londres</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Londres</region></placeName></affiliation></author></analytic><monogr></monogr><series><title level="j" type="main">International Journal of Immunogenetics</title><title level="j" type="alt">INTERNATIONAL JOURNAL OF IMMUNOGENETICS</title><idno type="ISSN">1744-3121</idno><idno type="eISSN">1744-313X</idno><imprint><biblScope unit="vol">33</biblScope><biblScope unit="issue">4</biblScope><biblScope unit="page" from="289">289</biblScope><biblScope unit="page" to="295">295</biblScope><biblScope unit="page-count">7</biblScope><publisher>Blackwell Publishing Ltd</publisher><pubPlace>Oxford, UK</pubPlace><date type="published" when="2006-08">2006-08</date></imprint><idno type="ISSN">1744-3121</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">1744-3121</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="Teeft" xml:lang="en"><term>Adoptive immunotherapy</term><term>Aggregated protein</term><term>Algorithm</term><term>Allele</term><term>Amino acids</term><term>Anking regions</term><term>Antigenic peptides</term><term>Authors journal compilation</term><term>Binding predictions</term><term>Binding score</term><term>Binding scores</term><term>Birkbeck college</term><term>Blackwell publishing</term><term>Candidate peptides</term><term>Cdna</term><term>Cdna encoding</term><term>Cdna expression</term><term>Cell surface</term><term>Cleavage</term><term>Database</term><term>Dbsnp</term><term>Different methods</term><term>Epitope</term><term>Example protein entry</term><term>Experimental medicine</term><term>Expression data</term><term>Gene name</term><term>Genes encoding mhags</term><term>Histocompatibility</term><term>Histocompatibility antigen</term><term>Histocompatibility antigens</term><term>Immunogenetics</term><term>Immunological reviews</term><term>Initial data sources</term><term>International journal</term><term>Major histocompatibility</term><term>Malet street</term><term>Mass spectrometry</term><term>Mhags</term><term>Minor histocompatibility antigen</term><term>Minor histocompatibility antigens</term><term>Mutation</term><term>Ncbi</term><term>Ncbi dbsnp</term><term>Nucleic</term><term>Nucleic acids research</term><term>Open reading frame</term><term>Peptide</term><term>Peptide binding</term><term>Peptide binding entries</term><term>Peptide generation</term><term>Peptide nlvpmvatv</term><term>Polymorphism</term><term>Possible mhags</term><term>Previous step</term><term>Proteasomal</term><term>Proteasomal cleavage</term><term>Proteasomal cleavage prediction</term><term>Protein antigens</term><term>Protein expression data</term><term>Protein sequence</term><term>Refolding</term><term>Refolding assay</term><term>Refolding score</term><term>Search facilities</term><term>Sipep</term><term>Sipep algorithm</term><term>Snp</term><term>Snpbinder</term><term>Snpbinder database</term><term>Syfpeithi algorithm</term><term>Tissue expression</term><term>User</term><term>User interface</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Approximately 50 years ago it was found that inbred strains of mice were able to reject tumours and skin grafts from major histocompatibility complex (MHC) identical donors. They proposed that additional transplantation antigens must exist outside the MHC. These were described as minor histocompatibility antigens (mHAgs). Since then, related studies in humans have identified 16 human mHAgs. The aim of this work is to increase the number of known mHAgs by prediction of candidate minor histocompatibility loci by identifying coding single nucleotide polymorphisms (SNPs) where the amino acid variation lies within an MHC‐binding peptide and alters the ability of that peptide to bind. We have developed an algorithm called SiPep which uses peptide sequences derived from the flanking regions of known non‐synonymous SNPs, various MHC‐binding and proteolytic cleavage evaluation methods and protein expression data to predict mHAgs. We have processed 45094 SNPs using the SiPep algorithm and have stored the results in a database called SNPBinder. The facilities to process submitted proteins through the SiPep algorithm as well as the SNPBinder database are available to the public. A set of peptides that are predicted as possible mHAgs by the SiPep algorithm have been tested using refolding assays and gel filtration and the results are presented in this paper. The SiPep tools and SNPBinder database are available free of charge via the internet. An HTML interface providing search facilities can be found at the following address: http://www.sipep.org/.</div></front></TEI><affiliations><list><country><li>Royaume-Uni</li></country><region><li>Angleterre</li><li>Grand Londres</li></region><settlement><li>Londres</li></settlement><orgName><li>Université de Londres</li></orgName></list><tree><country name="Royaume-Uni"><region name="Angleterre"><name sortKey="Halling Rown, M" sort="Halling Rown, M" uniqKey="Halling Rown M" first="M." last="Halling-Brown">M. Halling-Brown</name></region><name sortKey="Moss, D S" sort="Moss, D S" uniqKey="Moss D" first="D. S." last="Moss">D. S. Moss</name><name sortKey="Quartey Apafio, R" sort="Quartey Apafio, R" uniqKey="Quartey Apafio R" first="R." last="Quartey-Papafio">R. Quartey-Papafio</name><name sortKey="Travers, P J" sort="Travers, P J" uniqKey="Travers P" first="P. J." last="Travers">P. J. Travers</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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