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The Immuno Polymorphism Database

  • James Robinson
  • Steven G. E. MarshEmail author
Chapter
Part of the Immunomics Reviews: book series (IMMUN, volume 3)

Abstract

The Immuno Polymorphism Database (IPD) (http://www.ebi.ac.uk/ipd/) is a set of specialist databases developed for the study of polymorphic genes of the immune system. The Database includes both information on allelic sequences of various genes and a cell bank of immunologically characterised melanoma cell lines. The sequence databases are developed in collaboration with specialist groups and nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. These databases include: IPD-KIR, which contains the allelic sequences of Killer-cell Immunoglobulin-like Receptors; IPD-MHC, a database of sequences of the major histocompatibility complex of different species; and IPD-HPA, alloantigens expressed only on platelet. The IPD-ESTAB section of the project provides access to the European Searchable Tumour Cell-Line Database (ESTDAB), a cell bank of immunologically characterised melanoma cell lines.

Keywords

Major Histocompatibility Complex Single Nucleotide Polymorphism Cell Bank Nomenclature Committee European Molecular Biology Laboratory 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgements

We would like to thank Peter Parham, Libby Guethlein, Christian Garcia and Chrissy Roberts for their work on IPD-KIR; our IPD-MHC collaborators Shirley Ellis, Lorna Kennedy, Ronald Bontrop, Natasja de Groot, Lutz Walter, Douglas Smith, Keith Ballingall, Mike Stear and René Stet; Nick Watkins and Paul Metcalfe for IPD-HPA and Graham Pawelec for ESTDAB. Our thanks also go to Matthew Waller and Sylvie Fail for their work on the tools and processing of submissions for the various databases and finally Peter Stoehr at the EBI for assisting in the continued collaboration between our group and the EBI.

References

  1. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL (2008) GenBank. Nucleic Acids Res 36:D25–D30CrossRefPubMedGoogle Scholar
  2. Bimber B, O’Connor DH (2008) KIRigami: the case for studying NK cell receptors in SIV+ macaques. Immunol Res 40:235–243CrossRefPubMedGoogle Scholar
  3. Cochrane G, Akhtar R, Aldebert P, Althorpe N, Baldwin A, Bates K, Bhattacharyya S, Bonfield J, Bower L, Browne P, Castro M, Cox T, Demiralp F, Eberhardt R, Faruque N, Hoad G, Jang M, Kulikova T, Labarga A, Leinonen R, Leonard S, Lin Q, Lopez R, Lorenc D, McWilliam H, Mukherjee G, Nardone F, Plaister S, Robinson S, Sobhany S, Vaughan R, Wu D, Zhu W, Apweiler R, Hubbard T, Birney E (2008) Priorities for nucleotide trace sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database. Nucleic Acids Res 36:D5–D12CrossRefPubMedGoogle Scholar
  4. Ellis SA, Bontrop RE, Antczak DF, Ballingall K, Davies CJ, Kaufman J, Kennedy LJ, Robinson J, Smith DM, Stear MJ, Stet RJ, Waller MJ, Walter L, Marsh SGE (2006) ISAG/IUIS-VIC Comparative MHC Nomenclature Committee report, 2005. Immunogenetics 57:953–958CrossRefPubMedGoogle Scholar
  5. Garcia CA, Robinson J, Guethlein LA, Parham P, Madrigal JA, Marsh SGE (2003) Human KIR sequences 2003. Immunogenetics 55:227–239CrossRefPubMedGoogle Scholar
  6. Gumperz JE, Barber LD, Valiante NM, Percival L, Phillips JH, Lanier LL, Parham P (1997) Conserved and variable residues within the Bw4 motif of HLA-B make separable contributions to recognition by the NKB1 killer cell-inhibitory receptor. J Immunol 158:5237–5241PubMedGoogle Scholar
  7. Harte N, Silventoinen V, Quevillon E, Robinson S, Kallio K, Fustero X, Patel P, Jokinen P, Lopez R (2004) Public web-based services from the European Bioinformatics Institute. Nucleic Acids Res 32:W3–W9CrossRefPubMedGoogle Scholar
  8. Kennedy LJ, Altet L, Angles JM, Barnes A, Carter SD, Francino O, Gerlach JA, Happ GM, Ollier WE, Polvi A, Thomson W, Wagner JL (1999) Nomenclature for factors of the dog major histocompatibility system (DLA), 1998. First report of the ISAG DLA Nomenclature Committee. International Society for Animals Genetics. Tissue Antigens 54:312–321CrossRefPubMedGoogle Scholar
  9. Khakoo SI, Thio CL, Martin MP, Brooks CR, Gao X, Astemborski J, Cheng J, Goedert JJ, Vlahov D, Hilgartner M, Cox S, Little AM, Alexander GJ, Cramp ME, O’Brien SJ, Rosenberg WM, Thomas DL, Carrington M (2004) HLA and NK cell inhibitory receptor genes in resolving hepatitis C virus infection. Science 305:872–874CrossRefPubMedGoogle Scholar
  10. Klein J, Bontrop RE, Dawkins RL, Erlich HA, Gyllensten UB, Heise ER, Jones PP, Parham P, Wakeland EK, Watkins DI (1990) Nomenclature for the major histocompatibility complexes of different species: a proposal. Immunogenetics 31:217–219PubMedGoogle Scholar
  11. Marsh SGE, Parham P, Dupont B, Geraghty DE, Trowsdale J, Middleton D, Vilches C, Carrington M, Witt C, Guethlein LA, Shilling H, Garcia CA, Hsu KC, Wain H (2003) Killer-cell immunoglobulin-like receptor (KIR) nomenclature report, 2002. Immunogenetics 55:220–226CrossRefPubMedGoogle Scholar
  12. Metcalfe P, Watkins NA, Ouwehand WH, Kaplan C, Newman P, Kekomaki R, De Haas M, Aster R, Shibata Y, Smith J, Kiefel V, Santoso S (2003) Nomenclature of human platelet antigens. Vox Sang 85:240–245CrossRefPubMedGoogle Scholar
  13. Parham P (1999) Virtual reality in the MHC. Immunol Rev 167:5–15CrossRefPubMedGoogle Scholar
  14. Pawelec G, Marsh SG (2006) ESTDAB: a collection of immunologically characterised melanoma cell lines and searchable databank. Cancer Immunol Immunother 55(6):623–627CrossRefPubMedGoogle Scholar
  15. Robinson J, Marsh SGE (2006) Immunoinformatics: predicting immunogenicity in silico. In: Flower D (ed) The IMGT/HLA Database. Humana, Totowa, pp 43–60Google Scholar
  16. Robinson J, Marsh SGE (2008) In: Davies MN, Ranganathan S, Flower DR (eds) Bioinformatics for immunomics, Springer, pp 33–45Google Scholar
  17. Robinson J, Waller MJ, Parham P, de Groot N, Bontrop R, Kennedy LJ, Stoehr P, Marsh SGE (2003) IMGT/HLA and IMGT/MHC: sequence databases for the study of the major histocompatibility complex. Nucleic Acids Res 31:311–314CrossRefPubMedGoogle Scholar
  18. Ruggeri L, Capanni M, Casucci M, Volpi I, Tosti A, Perruccio K, Urbani E, Negrin RS, Martelli MF, Velardi A (1999) Role of natural killer cell alloreactivity in HLA-mismatched hematopoietic stem cell transplantation. Blood 94:333–339PubMedGoogle Scholar
  19. Ruiz M, Giudicelli V, Ginestoux C, Stoehr P, Robinson J, Bodmer J, Marsh SGE, Bontrop R, Lemaitre M, Lefranc G, Chaume D, Lefranc MP (2000) IMGT the international ImMunoGeneTics database. Nucleic Acids Res 28:219–221CrossRefPubMedGoogle Scholar
  20. Stear MJ, Pokorny TS, Fryda-Bradley S, Lie O, Bull RW (1990) Genetic analysis of the antigens defined at the third international BoLA workshop. J Immunogenet 17:21–28CrossRefPubMedGoogle Scholar
  21. Sugawara H, Ogasawara O, Okubo K, Gojobori T, Tateno Y (2008) DDBJ with new system and face. Nucleic Acids Res 36:D22–D24CrossRefPubMedGoogle Scholar
  22. Tateno Y (2008) [International collaboration among DDBJ EMBL Bank and GenBank]. Tanpakushitsu Kakusan Koso 53:182–189PubMedGoogle Scholar
  23. von dem Borne AE, Decary F (1990a) ICSH/ISBT Working Party on platelet serology. Nomenclature of platelet-specific antigens. Vox Sang 58:176CrossRefPubMedGoogle Scholar
  24. von dem Borne AE, Decary F (1990b) Nomenclature of platelet-specific antigens. Hum Immunol 29:1–2CrossRefPubMedGoogle Scholar
  25. Yun G, Tolar J, Yerich AK, Marsh SGE, Robinson J, Noreen H, Blazar BR, Miller JS (2007) A novel method for KIR-ligand typing by pyrosequencing to predict NK cell alloreactivity. Clin Immunol 123:272–280CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2009

Authors and Affiliations

  1. 1.The Anthony Nolan Research Institute, Royal Free HospitalHampsteadUK
  2. 2.UCL Cancer Institute, Royal Free CampusHampsteadUK

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