Establishing the GWAS Catalog as a resource for large-scale association studies

建立 GWAS 目录作为大规模关联研究的资源

• 批准号: 10218233
• 负责人: Fiona Cunningham
• 金额: $ 81.86万
• 依托单位: EUROPEAN MOLECULAR BIOLOGY LABORATORY
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-09-01 至 2022-09-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10218233
• 关键词: Adopted; Automation; Award; Biomedical Research; Bipolar Disorder; Cardiovascular system; Catalogs; Communication; Communities; Community Developments; Complex; Complex Genetic Trait; Data; Data Reporting; Deposition; Development; Diabetes Mellitus; Disease; Drug Targeting; Eligibility Determination; Emerging Technologies; Ensure; Family member; Feedback; Funding; Future; Generations; Genetic Variation; Genotype; Guidelines; Health; Heart Diseases; Human; Human Genetics; Human Resources; Infrastructure; Journals; Knowledge; Lead; Literature; Malignant Neoplasms; Manuals; Metadata; Methods; Monitor; National Human Genome Research Institute; Paper; Pathway interactions; Procedures; Process; Publications; Publishing; Research; Research Design; Research Personnel; Resources; Route; Schizophrenia; Structure; Surveys; System; Technology; Variant; Visualization; annotation system; data access; data acquisition; data curation; data exchange; data integration; data resource; data submission; data visualization; database of Genotypes and Phenotypes; design; drug development; experimental study; genome wide association study; improved; infrastructure development; prevent; recruit; research and development; response; trait

The GWAS Catalog’s objective is to summarise GWAS data acquired from scientific publications, and to give the results structure, in order to summarize research findings to a broad scientific community. The Catalog is used by a growing user community of biologists and bioinformaticians worldwide. Over the next five years, the Catalog will continue to provide the most thoroughly curated resource for human variation data, by engaging journals in data recruitment, and by allowing co-submission/data transfer from other resources like dbGAP and the EGA. In order to underpin the Catalog’s relevance, a multi-stranded approach combining data generation, infrastructure development and liaison with the Catalog’s user community will be adopted. The first Aim for the next five years is for the Catalog to continue to deliver the Catalog as a community resource with high quality content. The curation system will evolve from manual curation, towards identification of data for automated extraction and review of submitted metadata, supporting author deposition, and the development of supporting QC processes. In Aim 2, the scope of the Catalog will be broadened to include new GWAS study designs, additional associated data, and emerging technologies. The Catalog’s eligibility criteria will ensure alignment with current research and the needs of the user community, but will be monitored and re-evaluated as needed. Building on previous pilots, the focus of Aim 2 will be on the inclusion of targeted array data and other genotyping methods, such as sequencing or imputation from family members. In Aim 3, the Catalog will be delivered as a scalable and sustainable resource for the future, which will allow for an extended scope of data. The development and promotion of standard formats for GWAS study design and results will be critical to ensure an efficient process for incorporating data into the Catalog. Authors will be encouraged to submit all SNP-trait associations, irrespective of p-value: this will vastly expand the depth of data available, and the utility of the Catalog. The manual curation system will be re-developed, with process automation to increase curator efficiency. Curation resources will be allocated in order to prioritise studies with the highest utility, therefore expediting the publication of these data in the Catalog. Finally, the Catalog’s resources, interfaces, and data access will be improved for all researchers by enhancing data representation, the search functionality, data visualization and integration with data from other relevant resources. User needs will be identified through surveys, and combined with feedback from other communication routes; existing data curation processes will then be modified to improve data representation, visualization, access and versatility. The continuation of the Catalog, as the main resource for data published on diseases with complex genetic traits, is of crucial importance for the biomedical research community, as a more efficient and effective way to better understand and to prevent, or cure, diseases like cardiovascular conditions, cancer and diabetes.

GWAS 目录的目标是总结从科学出版物中获得的 GWAS 数据，并给出 结果结构，以便向广泛的科学界总结研究成果。目录是 全世界越来越多的生物学家和生物信息学家用户社区都在使用它。未来五年内， Catalog 将继续为人类变异数据提供最全面的资源，通过参与 数据招募中的期刊，并允许从其他资源（如 dbGAP 和 尾气分析法。为了巩固目录的相关性，采用了结合数据生成、 将采用基础设施开发以及与目录用户社区的联络。第一个目标是 未来五年，目录将继续将目录作为高质量的社区资源提供 内容。管理系统将从手动管理发展到自动识别数据 提取和审查提交的元数据、支持作者沉积以及支持的开发 质量控制流程。在目标 2 中，目录的范围将扩大到包括新的 GWAS 研究设计， 其他相关数据和新兴技术。目录的资格标准将确保一致性 根据当前的研究和用户社区的需求，但将根据需要进行监控和重新评估。 在之前试点的基础上，目标 2 的重点将是纳入目标阵列数据和其他数据 基因分型方法，例如来自家庭成员的测序或插补。在目标 3 中，目录将是 作为未来可扩展且可持续的资源提供，这将允许扩展数据范围。 GWAS 研究设计和结果的标准格式的开发和推广对于 确保将数据纳入目录的高效流程。我们将鼓励作者提交所有 SNP 性状关联，无论 p 值如何：这将极大地扩展可用数据的深度和实用性 目录的。将重新开发手动策展系统，通过流程自动化来增加策展人 效率。将分配策展资源，以便优先考虑具有最高效用的研究，因此 加快在目录中发布这些数据。最后，目录的资源、接口和数据 通过增强数据表示、搜索功能、数据 可视化以及与其他相关资源的数据集成。用户需求将通过以下方式确定 调查，并结合其他沟通渠道的反馈；现有的数据管理流程将 然后进行修改以改进数据表示、可视化、访问和多功能性。的延续 目录作为发布具有复杂遗传特征的疾病数据的主要资源，至关重要 作为一种更高效、更有效的方式来更好地理解生物医学研究界的重要性 预防或治疗心血管疾病、癌症和糖尿病等疾病。

项目成果

Ensembl 2021.

• DOI: 10.1093/nar/gkaa942
• 发表时间: 2021-01-08
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Howe KL;Achuthan P;Allen J;Allen J;Alvarez-Jarreta J;Amode MR;Armean IM;Azov AG;Bennett R;Bhai J;Billis K;Boddu S;Charkhchi M;Cummins C;Da Rin Fioretto L;Davidson C;Dodiya K;El Houdaigui B;Fatima R;Gall A;Garcia Giron C;Grego T;Guijarro-Clarke C;Haggerty L;Hemrom A;Hourlier T;Izuogu OG;Juettemann T;Kaikala V;Kay M;Lavidas I;Le T;Lemos D;Gonzalez Martinez J;Marugán JC;Maurel T;McMahon AC;Mohanan S;Moore B;Muffato M;Oheh DN;Paraschas D;Parker A;Parton A;Prosovetskaia I;Sakthivel MP;Salam AIA;Schmitt BM;Schuilenburg H;Sheppard D;Steed E;Szpak M;Szuba M;Taylor K;Thormann A;Threadgold G;Walts B;Winterbottom A;Chakiachvili M;Chaubal A;De Silva N;Flint B;Frankish A;Hunt SE;IIsley GR;Langridge N;Loveland JE;Martin FJ;Mudge JM;Morales J;Perry E;Ruffier M;Tate J;Thybert D;Trevanion SJ;Cunningham F;Yates AD;Zerbino DR;Flicek P
• 通讯作者: Flicek P

SNPs associated with colorectal cancer at 15q13.3 affect risk enhancers that modulate GREM1 gene expression.

• DOI: 10.1002/humu.24166
• 发表时间: 2021-03
• 期刊: Human mutation
• 影响因子: 3.9
• 作者: Fortini BK;Tring S;Devall MA;Ali MW;Plummer SJ;Casey G
• 通讯作者: Casey G

Improving reporting standards for polygenic scores in risk prediction studies.

• DOI: 10.1038/s41586-021-03243-6
• 发表时间: 2021-03
• 期刊: Nature
• 影响因子: 64.8
• 作者: Wand H;Lambert SA;Tamburro C;Iacocca MA;O'Sullivan JW;Sillari C;Kullo IJ;Rowley R;Dron JS;Brockman D;Venner E;McCarthy MI;Antoniou AC;Easton DF;Hegele RA;Khera AV;Chatterjee N;Kooperberg C;Edwards K;Vlessis K;Kinnear K;Danesh JN;Parkinson H;Ramos EM;Roberts MC;Ormond KE;Khoury MJ;Janssens ACJW;Goddard KAB;Kraft P;MacArthur JAL;Inouye M;Wojcik GL
• 通讯作者: Wojcik GL

Ensembl 2022.

• DOI: 10.1093/nar/gkab1049
• 发表时间: 2022-01-07
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Cunningham F;Allen JE;Allen J;Alvarez-Jarreta J;Amode MR;Armean IM;Austine-Orimoloye O;Azov AG;Barnes I;Bennett R;Berry A;Bhai J;Bignell A;Billis K;Boddu S;Brooks L;Charkhchi M;Cummins C;Da Rin Fioretto L;Davidson C;Dodiya K;Donaldson S;El Houdaigui B;El Naboulsi T;Fatima R;Giron CG;Genez T;Martinez JG;Guijarro-Clarke C;Gymer A;Hardy M;Hollis Z;Hourlier T;Hunt T;Juettemann T;Kaikala V;Kay M;Lavidas I;Le T;Lemos D;Marugán JC;Mohanan S;Mushtaq A;Naven M;Ogeh DN;Parker A;Parton A;Perry M;Piližota I;Prosovetskaia I;Sakthivel MP;Salam AIA;Schmitt BM;Schuilenburg H;Sheppard D;Pérez-Silva JG;Stark W;Steed E;Sutinen K;Sukumaran R;Sumathipala D;Suner MM;Szpak M;Thormann A;Tricomi FF;Urbina-Gómez D;Veidenberg A;Walsh TA;Walts B;Willhoft N;Winterbottom A;Wass E;Chakiachvili M;Flint B;Frankish A;Giorgetti S;Haggerty L;Hunt SE;IIsley GR;Loveland JE;Martin FJ;Moore B;Mudge JM;Muffato M;Perry E;Ruffier M;Tate J;Thybert D;Trevanion SJ;Dyer S;Harrison PW;Howe KL;Yates AD;Zerbino DR;Flicek P
• 通讯作者: Flicek P

The European Bioinformatics Institute: empowering cooperation in response to a global health crisis.

• DOI: 10.1093/nar/gkaa1077
• 发表时间: 2021-01-08
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Cantelli G;Cochrane G;Brooksbank C;McDonagh E;Flicek P;McEntyre J;Birney E;Apweiler R
• 通讯作者: Apweiler R