The IPD and IMGT/HLA database: allele variant databases

The Immuno Polymorphism Database (IPD) was developed to provide a centralized system for the study of polymorphism in genes of the immune system. Through the IPD project we have established a central platform for the curation and publication of locus-specific databases involved either directly or related to the function of the Major Histocompatibility Complex in a number of different species. We have collaborated with specialist groups or nomenclature committees that curate the individual sections before they are submitted to IPD for online publication. IPD consists of five core databases, with the IMGT/HLA Database as the primary database. Through the work of the various nomenclature committees, the HLA Informatics Group and in collaboration with the European Bioinformatics Institute we are able to provide public access to this data through the website http://www.ebi.ac.uk/ipd/. The IPD project continues to develop with new tools being added to address scientific developments, such as Next Generation Sequencing, and to address user feedback and requests. Regular updates to the website ensure that new and confirmatory sequences are dispersed to the immunogenetics community, and the wider research and clinical communities.

[1]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[2]  Sue Povey,et al.  Gene map of the extended human MHC , 2004, Nature Reviews Genetics.

[3]  S G E Marsh,et al.  Killer-cell immunoglobulin-like receptor (KIR) nomenclature report, 2002 , 2003, Immunogenetics.

[4]  G. Pawelec,et al.  ESTDAB: a collection of immunologically characterised melanoma cell lines and searchable databank , 2006, Cancer Immunology, Immunotherapy.

[5]  Rodrigo Lopez,et al.  Web services at the European Bioinformatics Institute-2009 , 2009, Nucleic Acids Res..

[6]  J. Robinson,et al.  A single nomenclature and associated database for alleles at the major histocompatibility complex class II DRB1 locus of sheep. , 2011, Tissue antigens.

[7]  M. Torres,et al.  Nomenclature for factors of the HLA system. , 2011, Bulletin of the World Health Organization.

[8]  D. Lipman,et al.  Improved tools for biological sequence comparison. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[9]  James Robinson,et al.  The IMGT/HLA database , 2008, Nucleic Acids Res..

[10]  Albert E.G. von dem Borne,et al.  Nomenclature of platelet‐specific antigens , 1990, Human immunology.

[11]  Johan T den Dunnen,et al.  Describing structural changes by extending HGVS sequence variation nomenclature , 2011, Human mutation.

[12]  W. Bodmer,et al.  Nomenclature for factors of the HLA system, 2010 , 2010, Tissue antigens.

[13]  J K Lunney,et al.  Nomenclature for factors of the swine leukocyte antigen class II system, 2005. , 2005, Tissue antigens.

[14]  S. Antonarakis,et al.  Corrigendum: Mutation nomenclature extensions and suggestions to describe complex mutations: A discussion , 2002, Human mutation.

[15]  David H. O’Connor,et al.  Nomenclature report on the major histocompatibility complex genes and alleles of Great Ape, Old and New World monkey species , 2012, Immunogenetics.

[16]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[17]  P. Parham,et al.  16th IHIW : Review of HLA typing by NGS , 2013, International journal of immunogenetics.

[18]  Peter Parham,et al.  Virtual reality in the MHC , 1999, Immunological reviews.

[19]  T. Yoshiki,et al.  Polymorphism of the class II gene of rat major histocompatibility complex, RT1: partial sequence comparison of the first domain of the RT1.Bβ 1 alleles , 2004, Immunogenetics.

[20]  Peter Parham,et al.  Killer-cell immunoglobulin-like receptor (KIR) nomenclature report, 2002. , 2003, Immunogenetics.

[21]  Harriet Noreen,et al.  High-resolution donor-recipient HLA matching contributes to the success of unrelated donor marrow transplantation. , 2007, Blood.

[22]  Lorna J. Kennedy,et al.  ISAG/IUIS-VIC Comparative MHC Nomenclature Committee report, 2005 , 2006, Immunogenetics.

[23]  P. Parham,et al.  Human KIR sequences 2003 , 2003, Immunogenetics.

[24]  Elizabeth M. Smigielski,et al.  dbSNP: the NCBI database of genetic variation , 2001, Nucleic Acids Res..

[25]  S Mackinnon,et al.  Diverging effects of HLA–DPB1 matching status on outcome following unrelated donor transplantation depending on disease stage and the degree of matching for other HLA alleles , 2010, Leukemia.

[26]  J A Gerlach,et al.  Nomenclature for factors of the dog major histocompatibility system (DLA), 2000: Second report of the ISAG DLA Nomenclature Committee. , 1999, Tissue antigens.

[27]  James Robinson,et al.  IMGT/HLA and IMGT/MHC: sequence databases for the study of the major histocompatibility complex , 2003, Nucleic Acids Res..

[28]  A. Radford,et al.  The use of reference strand‐mediated conformational analysis for the study of cheetah (Acinonyx jubatus) feline leucocyte antigen class II DRB polymorphisms , 2004, Molecular ecology.

[29]  H A Erlich,et al.  High throughput HLA genotyping using 454 sequencing and the Fluidigm Access Array™ System for simplified amplicon library preparation. , 2013, Tissue antigens.

[30]  Tim R. Mosmann,et al.  Nomenclature for chicken MHC (B) antigens defined by monoclonal antibodies , 2004, Immunogenetics.

[31]  Judith A. Blake,et al.  The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse , 2011, Nucleic Acids Res..

[32]  Rodrigo Lopez,et al.  A new bioinformatics analysis tools framework at EMBL–EBI , 2010, Nucleic Acids Res..

[33]  Peter Parham,et al.  Nomenclature for the major histocompatibility complexes of different species: a proposal , 2004, Immunogenetics.

[34]  L. Andersson,et al.  CHARACTERIZATION OF BOVINE MHC CLASS II POLYMORPHISM USING THREE TYPING METHODS: SEROLOGY, RFLP AND IEF , 1992, European journal of immunogenetics : official journal of the British Society for Histocompatibility and Immunogenetics.

[35]  S G E Marsh,et al.  Genotype List String: a grammar for describing HLA and KIR genotyping results in a text string , 2013, Tissue antigens.

[36]  Rodrigo Lopez,et al.  Fast and efficient searching of biological data resources - using EB-eye , 2010, Briefings Bioinform..

[37]  K. Ballingall.  Progress of the comparative MHC Committee and a summary of the Comparative MHC Workshops held at the 32nd ISAG, Edinburgh and the 9th IVIS, Tokyo, 2010. , 2012, Veterinary Immunology and Immunopathology.

[38]  J A Gerlach,et al.  Nomenclature for factors of the dog major histocompatibility system (DLA), 1998: first report of the ISAG DLA Nomenclature Committee. , 2000, Animal genetics.

[39]  R. Wilson,et al.  Modernizing Reference Genome Assemblies , 2011, PLoS biology.

[40]  D. L. Ewert,et al.  Nomenclature for chicken major histocompatibility (B) complex , 2004, Immunogenetics.

[41]  J. Bodmer,et al.  IMGT/HLA Database - a sequence database for the human major histocompatibility complex , 2000, Nucleic Acids Res..

[42]  J Smith,et al.  Nomenclature of human platelet antigens , 2003, Vox sanguinis.

[43]  S. Turner,et al.  Real-time DNA sequencing from single polymerase molecules. , 2010, Methods in enzymology.

[44]  Jan Naessens,et al.  2.1 Nomenclature , 1993 .

[45]  G. Pawelec,et al.  The European searchable tumour line database , 2009, Cancer Immunology and Immunotherapy.

[46]  S. E. Marsh,et al.  Cattle MHC nomenclature: is it possible to assign sequences to discrete class I genes? , 2012, Immunogenetics.

[47]  P. Cresswell,et al.  A nomenclature solution to mouse MHC confusion. , 1999, Journal of immunology.

[48]  Jürgen Sauter,et al.  Cost-efficient high-throughput HLA typing by MiSeq amplicon sequencing , 2014, BMC Genomics.

[49]  G. Hong,et al.  Nucleic Acids Research , 2015, Nucleic Acids Research.

[50]  B. Koop,et al.  Comprehensive analysis of MHC class I genes from the U-, S-, and Z-lineages in Atlantic salmon , 2010, BMC Genomics.

[51]  C-S Ho,et al.  Nomenclature for factors of the SLA system, update 2008. , 2009, Tissue antigens.

[52]  Marcia M. Miller,et al.  2004 Nomenclature for the chicken major histocompatibility (B and Y ) complex , 2004, Immunogenetics.