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1.
Nucleic Acids Res ; 51(D1): D977-D985, 2023 01 06.
Artigo em Inglês | MEDLINE | ID: mdl-36350656

RESUMO

The NHGRI-EBI GWAS Catalog (www.ebi.ac.uk/gwas) is a FAIR knowledgebase providing detailed, structured, standardised and interoperable genome-wide association study (GWAS) data to >200 000 users per year from academic research, healthcare and industry. The Catalog contains variant-trait associations and supporting metadata for >45 000 published GWAS across >5000 human traits, and >40 000 full P-value summary statistics datasets. Content is curated from publications or acquired via author submission of prepublication summary statistics through a new submission portal and validation tool. GWAS data volume has vastly increased in recent years. We have updated our software to meet this scaling challenge and to enable rapid release of submitted summary statistics. The scope of the repository has expanded to include additional data types of high interest to the community, including sequencing-based GWAS, gene-based analyses and copy number variation analyses. Community outreach has increased the number of shared datasets from under-represented traits, e.g. cancer, and we continue to contribute to awareness of the lack of population diversity in GWAS. Interoperability of the Catalog has been enhanced through links to other resources including the Polygenic Score Catalog and the International Mouse Phenotyping Consortium, refinements to GWAS trait annotation, and the development of a standard format for GWAS data.


Assuntos
Estudo de Associação Genômica Ampla , Bases de Conhecimento , Animais , Humanos , Camundongos , Variações do Número de Cópias de DNA , National Human Genome Research Institute (U.S.) , Fenótipo , Polimorfismo de Nucleotídeo Único , Software , Estados Unidos
2.
Cell Genom ; 1(1)2021 Oct 13.
Artigo em Inglês | MEDLINE | ID: mdl-34870259

RESUMO

Genome sequencing has recently become a viable genotyping technology for use in genome-wide association studies (GWASs), offering the potential to analyze a broader range of genome-wide variation, including rare variants. To survey current standards, we assessed the content and quality of reporting of statistical methods, analyses, results, and datasets in 167 exome- or genome-wide-sequencing-based GWAS publications published from 2014 to 2020; 81% of publications included tests of aggregate association across multiple variants, with multiple test models frequently used. We observed a lack of standardized terms and incomplete reporting of datasets, particularly for variants analyzed in aggregate tests. We also find a lower frequency of sharing of summary statistics compared with array-based GWASs. Reporting standards and increased data sharing are required to ensure sequencing-based association study data are findable, interoperable, accessible, and reusable (FAIR). To support that, we recommend adopting the standard terminology of sequencing-based GWAS (seqGWAS). Further, we recommend that single-variant analyses be reported following the same standards and conventions as standard array-based GWASs and be shared in the GWAS Catalog. We also provide initial recommended standards for aggregate analyses metadata and summary statistics.

3.
Cell Genom ; 1(1)2021 Oct 13.
Artigo em Inglês | MEDLINE | ID: mdl-36082306

RESUMO

Genome-wide association studies (GWASs) have enabled robust mapping of complex traits in humans. The open sharing of GWAS summary statistics (SumStats) is essential in facilitating the larger meta-analyses needed for increased power in resolving the genetic basis of disease. However, most GWAS SumStats are not readily accessible because of limited sharing and a lack of defined standards. With the aim of increasing the availability, quality, and utility of GWAS SumStats, the National Human Genome Research Institute-European Bioinformatics Institute (NHGRI-EBI) GWAS Catalog organized a community workshop to address the standards, infrastructure, and incentives required to promote and enable sharing. We evaluated the barriers to SumStats sharing, both technological and sociological, and developed an action plan to address those challenges and ensure that SumStats and study metadata are findable, accessible, interoperable, and reusable (FAIR). We encourage early deposition of datasets in the GWAS Catalog as the recognized central repository. We recommend standard requirements for reporting elements and formats for SumStats and accompanying metadata as guidelines for community standards and a basis for submission to the GWAS Catalog. Finally, we provide recommendations to enable, promote, and incentivize broader data sharing, standards and FAIRness in order to advance genomic medicine.

4.
Nucleic Acids Res ; 47(D1): D1005-D1012, 2019 01 08.
Artigo em Inglês | MEDLINE | ID: mdl-30445434

RESUMO

The GWAS Catalog delivers a high-quality curated collection of all published genome-wide association studies enabling investigations to identify causal variants, understand disease mechanisms, and establish targets for novel therapies. The scope of the Catalog has also expanded to targeted and exome arrays with 1000 new associations added for these technologies. As of September 2018, the Catalog contains 5687 GWAS comprising 71673 variant-trait associations from 3567 publications. New content includes 284 full P-value summary statistics datasets for genome-wide and new targeted array studies, representing 6 × 109 individual variant-trait statistics. In the last 12 months, the Catalog's user interface was accessed by ∼90000 unique users who viewed >1 million pages. We have improved data access with the release of a new RESTful API to support high-throughput programmatic access, an improved web interface and a new summary statistics database. Summary statistics provision is supported by a new format proposed as a community standard for summary statistics data representation. This format was derived from our experience in standardizing heterogeneous submissions, mapping formats and in harmonizing content. Availability: https://www.ebi.ac.uk/gwas/.


Assuntos
Bases de Dados Genéticas , Estudo de Associação Genômica Ampla , Doença/genética , Variação Genética , Humanos , Análise em Microsséries , Publicações , Software , Interface Usuário-Computador
5.
Genome Biol ; 19(1): 21, 2018 02 15.
Artigo em Inglês | MEDLINE | ID: mdl-29448949

RESUMO

The accurate description of ancestry is essential to interpret, access, and integrate human genomics data, and to ensure that these benefit individuals from all ancestral backgrounds. However, there are no established guidelines for the representation of ancestry information. Here we describe a framework for the accurate and standardized description of sample ancestry, and validate it by application to the NHGRI-EBI GWAS Catalog. We confirm known biases and gaps in diversity, and find that African and Hispanic or Latin American ancestry populations contribute a disproportionately high number of associations. It is our hope that widespread adoption of this framework will lead to improved analysis, interpretation, and integration of human genomics data.


Assuntos
Estudo de Associação Genômica Ampla/normas , Genômica/normas , Variação Genética , Humanos , Grupos Raciais
6.
Nucleic Acids Res ; 45(D1): D896-D901, 2017 01 04.
Artigo em Inglês | MEDLINE | ID: mdl-27899670

RESUMO

The NHGRI-EBI GWAS Catalog has provided data from published genome-wide association studies since 2008. In 2015, the database was redesigned and relocated to EMBL-EBI. The new infrastructure includes a new graphical user interface (www.ebi.ac.uk/gwas/), ontology supported search functionality and an improved curation interface. These developments have improved the data release frequency by increasing automation of curation and providing scaling improvements. The range of available Catalog data has also been extended with structured ancestry and recruitment information added for all studies. The infrastructure improvements also support scaling for larger arrays, exome and sequencing studies, allowing the Catalog to adapt to the needs of evolving study design, genotyping technologies and user needs in the future.


Assuntos
Bases de Dados de Ácidos Nucleicos , Estudo de Associação Genômica Ampla/métodos , Software , Mineração de Dados , Genômica/métodos , Humanos , Anotação de Sequência Molecular , National Human Genome Research Institute (U.S.) , Estados Unidos , Interface Usuário-Computador , Navegador
7.
Nucleic Acids Res ; 42(Database issue): D1001-6, 2014 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-24316577

RESUMO

The National Human Genome Research Institute (NHGRI) Catalog of Published Genome-Wide Association Studies (GWAS) Catalog provides a publicly available manually curated collection of published GWAS assaying at least 100,000 single-nucleotide polymorphisms (SNPs) and all SNP-trait associations with P <1 × 10(-5). The Catalog includes 1751 curated publications of 11 912 SNPs. In addition to the SNP-trait association data, the Catalog also publishes a quarterly diagram of all SNP-trait associations mapped to the SNPs' chromosomal locations. The Catalog can be accessed via a tabular web interface, via a dynamic visualization on the human karyotype, as a downloadable tab-delimited file and as an OWL knowledge base. This article presents a number of recent improvements to the Catalog, including novel ways for users to interact with the Catalog and changes to the curation infrastructure.


Assuntos
Bases de Dados de Ácidos Nucleicos , Estudo de Associação Genômica Ampla , Polimorfismo de Nucleotídeo Único , Ontologia Genética , Genoma Humano , Humanos , Internet , Cariótipo
8.
Am J Med Sci ; 343(6): 510-1, 2012 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-22314106

RESUMO

The authors present a case of severe meningoencephalitis with cryptococcomas and hydrocephalus due to Cryptococcus gattii of the molecular type VGI in an otherwise healthy man native to Southwest Georgia without any history of travel. Clinicians need to be aware of this fungal emerging pathogen in the Southern United States.


Assuntos
Doenças Transmissíveis Emergentes/diagnóstico , Criptococose/diagnóstico , Cryptococcus gattii , Idoso , Doenças Transmissíveis Emergentes/genética , Doenças Transmissíveis Emergentes/microbiologia , Criptococose/microbiologia , Cryptococcus gattii/isolamento & purificação , Cryptococcus gattii/patogenicidade , Humanos , Masculino , Sudeste dos Estados Unidos
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