Cattle MHC nomenclature: is it possible to assign sequences to discrete class I genes?

Hammond, John A.; Marsh, Steven G.E.; Robinson, James T.; Davies, Christopher J.; Stear, M. J.; Ellis, Shirley A.

doi:10.1007/s00251-012-0611-7

Cited by 23 publications

(25 citation statements)

References 21 publications

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“…The HLA Nomenclature and its publication through the IMGT/HLA Database has been taken as a model by other groups working on curating MHC sequence variation. The MHC sequences of many different species have been reported ( 22 – 33 ), often in different formats and with different nomenclature systems used in the naming and identification of new genes and alleles in each species ( 34 ). This disparate approach has led to many individual studies, often unrelated, with the potential for conflicting nomenclature.…”

Section: Imgt/hla As a Model For Other Highly Polymorphic Gene Systemmentioning

confidence: 99%

“…The first version of the IPD-MHC database involved the work of groups specializing in non-human primates (NHP) ( 32 ), canines (DLA) ( 28 ) and felines (FLA) ( 41 ) and incorporated all data previously available in the IMGT/MHC Database ( 40 ). Further developments have been able to add sequences from cattle (BoLA) ( 33 ), teleost fish ( 42 ), rats (RT1) ( 43 ), sheep (OLA) ( 31 ) and swine (SLA) ( 30 ). In 2012 the nomenclature used to describe the alleles of non-human primates was extensively revised and updated ( 32 ).…”

Section: Imgt/hla As a Model For Other Highly Polymorphic Gene Systemmentioning

confidence: 99%

“…The number of sequences deposited in IPD-MHC has increased by at least 10% each year. This has resulted in regular publications reporting updates or changes to the nomenclature ( 31 – 33 , 44 ).…”

Section: Imgt/hla As a Model For Other Highly Polymorphic Gene Systemmentioning

confidence: 99%

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The IPD and IMGT/HLA database: allele variant databases

Robinson

Halliwell

Hayhurst

et al. 2014

Nucleic Acids Research

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1,649

1,793

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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.

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Section: Imgt/hla As a Model For Other Highly Polymorphic Gene Systemmentioning

confidence: 99%

Section: Imgt/hla As a Model For Other Highly Polymorphic Gene Systemmentioning

confidence: 99%

See 1 more Smart Citation

The IPD and IMGT/HLA database: allele variant databases

Robinson

Halliwell

Hayhurst

et al. 2014

Nucleic Acids Research

Self Cite

1,649

1,793

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show abstract

“…Since the first version, we have been able to add sequences from cattle (BoLA) (17), teleost fish (28), rats (RT1) (29), sheep (OLA) (15) and swine (SLA) (14). In 2012, the nomenclature used to describe the alleles of NHP was extensively revised and updated (16).…”

Section: Introductionmentioning

confidence: 99%

IPD—the Immuno Polymorphism Database

Robinson

Halliwell

McWilliam

et al. 2012

Nucleic Acids Research

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225

130

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The Immuno Polymorphism Database (IPD), http://www.ebi.ac.uk/ipd/ is a set of specialist databases related to the study of polymorphic genes in the immune system. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The IPD project stores all the data in a set of related databases. IPD currently consists of four databases: IPD-KIR, contains the allelic sequences of killer-cell immunoglobulin-like receptors, IPD-MHC, a database of sequences of the major histocompatibility complex of different species; IPD-HPA, alloantigens expressed only on platelets; and IPD-ESTDAB, which provides access to the European Searchable Tumour Cell-Line Database, a cell bank of immunologically characterized melanoma cell lines. The data is currently available online from the website and FTP directory. This article describes the latest updates and additional tools added to the IPD project.

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“…The initial version in 2003 was modelled on the IPD-IMGT/HLA Database, and involved the work of groups specializing in non-human primates (NHP) (5), canids (DLA) (6) and felids (7). Since then the database underwent various updates and expanded to include bovins (BoLA) (8), equids (ELA) (9), salmonids (10), murids (RT1) (11), ovids (12) and suids (13). …”

Section: Introductionmentioning

confidence: 99%

IPD-MHC 2.0: an improved inter-species database for the study of the major histocompatibility complex

et al. 2016

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The IPD-MHC Database project (http://www.ebi.ac.uk/ipd/mhc/) collects and expertly curates sequences of the major histocompatibility complex from non-human species and provides the infrastructure and tools to enable accurate analysis. Since the first release of the database in 2003, IPD-MHC has grown and currently hosts a number of specific sections, with more than 7000 alleles from 70 species, including non-human primates, canines, felines, equids, ovids, suids, bovins, salmonids and murids. These sequences are expertly curated and made publicly available through an open access website. The IPD-MHC Database is a key resource in its field, and this has led to an average of 1500 unique visitors and more than 5000 viewed pages per month. As the database has grown in size and complexity, it has created a number of challenges in maintaining and organizing information, particularly the need to standardize nomenclature and taxonomic classification, while incorporating new allele submissions. Here, we describe the latest database release, the IPD-MHC 2.0 and discuss planned developments. This release incorporates sequence updates and new tools that enhance database queries and improve the submission procedure by utilizing common tools that are able to handle the varied requirements of each MHC-group.

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Cattle MHC nomenclature: is it possible to assign sequences to discrete class I genes?

Cited by 23 publications

References 21 publications

The IPD and IMGT/HLA database: allele variant databases

The IPD and IMGT/HLA database: allele variant databases

IPD—the Immuno Polymorphism Database

IPD-MHC 2.0: an improved inter-species database for the study of the major histocompatibility complex

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