Securing and developing the IPD-MHC database to enhance research into livestock diseases

保护和开发 IPD-MHC 数据库以加强对牲畜疾病的研究

• 批准号: BB/M011488/1
• 负责人: John Hammond
• 金额: $ 67.45万
• 依托单位: The Pirbright Institute
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2015
• 资助国家: 英国
• 起止时间: 2015 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FM011488%2F1
• 关键词: Securing; developing; IPD; MHC; database

The Immuno Polymorphism Database (IPD) (https://www.ebi.ac.uk/ipd/) is a set of specialist databases that contain curated sequence datasets of polymorphic immune genes. Developed and maintained by the Anthony Nolan, these databases help save the lives of people with blood cancer by matching donors major histocompatibility complex (MHC; (also known as HLA in humans) to prevent rejection. One of these databases is IPD-MHC, a repository of non-human MHC genes that includes the major farmed animals species; cattle, sheep, pigs, trout and salmon. All these species exhibit high degrees of variation within their MHC genes. This diversity differentially influences how the adaptive and innate immune systems respond to pathogens and vaccines. Therefore a greater understanding of this diversity and the tools to analyse it offer a significant advance to our broad capability to examine immune function in these fundamental food producing species.Since the first release in 2003, IPD-MHC has become the central source of curated and annotated comparative MHC data and nomenclature globally. The website now receives nearly 250 visitors every day and over 500 sequences were submitted in 2013 from all over the world. However, this success has created problems. The database and website have never been specifically funded. IPD-MHC has existed as an 'in kind' project that the research community and bioinformaticians at Antony Nolan have considered important enough to create and continue. The demands that the level of traffic has created mean that this model is no longer sustainable. Indeed, there is already a chronic lack of development and this data repository is in danger of becoming redundant. This proposal will support a dedicated IPD-MHC bioinformatician located at Anthony Nolan to work alongside the other IPD bioinformaticians. Their role will be to unify the individual species websites, incorporate the extensive chicken MHC data as a key farmed animal and create one streamlined data submission processes. Once this is in place, the capability of IPD-MHC will be significantly enhanced to accept a greater range of data and an expanded suite of analysis tools will be imbedded to allow advanced analysis for non-bioinformaticians. IPD-MHC still has overwhelming support from the research community, Anthony Nolan and the offer of free infrastructure from the European Bioinformatics Institute. This project is aimed at securing this central resource and expertise in the UK, to benefit this important UK research community and reach out to the rest of the world as part of the global food security agenda.

免疫多态数据库(https://www.ebi.ac.uk/ipd/))是一组专家数据库，包含多态免疫基因的精选序列数据集。这些数据库由Anthony Nolan开发和维护，通过匹配捐赠者的主要组织相容性复合体(MHC；在人类中也称为HLA)来防止排斥反应，从而帮助挽救血癌患者的生命。其中一个数据库是IPD-MHC，这是一个非人类MHC基因库，其中包括主要的养殖动物物种；牛、羊、猪、鲑鱼和鲑鱼。所有这些物种的MHC基因都表现出高度的变异。这种多样性以不同的方式影响适应性免疫系统和先天免疫系统对病原体和疫苗的反应。因此，更好地了解这种多样性和分析它的工具为我们检查这些基本食品生产物种的免疫功能提供了显著的进步。自2003年第一次发布以来，IPD-MHC已经成为全球经过精选和注释的比较MHC数据和命名的中心来源。该网站现在每天接待近250名访问者，2013年来自世界各地的500多个序列被提交。然而，这种成功也带来了问题。该数据库和网站从未得到过专门的资金支持。IPD-MHC已经作为一个“实物”项目存在，安东尼·诺兰的研究界和生物信息学家认为这个项目足够重要，应该创建并继续下去。流量水平带来的需求意味着这种模式不再可持续。事实上，已经存在长期缺乏开发的问题，这个数据存储库正面临变得多余的危险。这项提议将支持设在Anthony Nolan的一名专门的IPD-MHC生物信息学家与其他IPD生物信息学家一起工作。他们的角色将是统一各个物种的网站，将大量的鸡肉MHC数据整合为关键的养殖动物，并创建一个简化的数据提交流程。一旦这一点到位，IPD-MHC的能力将大大增强，以接受更大范围的数据，并将嵌入一套扩展的分析工具，以便为非生物信息学家进行高级分析。IPD-MHC仍然得到了研究界Anthony Nolan的压倒性支持，以及欧洲生物信息学研究所提供的免费基础设施。该项目旨在确保英国的这一核心资源和专业知识，使这一重要的英国研究社区受益，并作为全球粮食安全议程的一部分，接触世界其他地区。

项目成果

Allelic nomenclature for the duplicated MHC class II DQ genes in sheep.

绵羊中重复的 MHC II 类 DQ 基因的等位基因命名法。

• DOI: 10.1007/s00251-018-1096-9
• 发表时间: 2019
• 期刊: Immunogenetics
• 影响因子: 3.2
• 作者: Ballingall KT

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

• DOI: 10.1093/nar/gkw1050
• 发表时间: 2017-01-04
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Maccari G;Robinson J;Ballingall K;Guethlein LA;Grimholt U;Kaufman J;Ho CS;de Groot NG;Flicek P;Bontrop RE;Hammond JA;Marsh SG
• 通讯作者: Marsh SG

P013 Development of the IPD-MHC database

P013 IPD-MHC数据库的开发

• DOI: 10.1016/j.humimm.2016.07.078
• 发表时间: 2016
• 期刊: Human Immunology
• 影响因子: 2.7
• 作者: Robinson J

IgMAT: immunoglobulin sequence multi-species annotation tool for any species including those with incomplete antibody annotation or unusual characteristics.

• DOI: 10.1186/s12859-023-05624-2
• 发表时间: 2023-12-21
• 期刊: BMC bioinformatics
• 影响因子: 3