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Genome Biology & Applied Bioinformatics Virtual Association Studies

Genome Biology & Applied Bioinformatics Virtual Association Studies Mehmet Tevfik DORAK, MD PhD. Schedule. Outline. Genetic Association Results Databases. NHGRI-EBI GWAS Catalog. NHGRI-EBI GWAS Catalog.

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Genome Biology & Applied Bioinformatics Virtual Association Studies

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  1. Genome Biology & Applied Bioinformatics Virtual Association Studies Mehmet Tevfik DORAK, MD PhD

  2. Schedule

  3. Outline Genetic Association Results Databases

  4. NHGRI-EBI GWAS Catalog

  5. NHGRI-EBI GWAS Catalog Other databases always give a larger number of results for the same phenotype or variant. GWAS catalog may have a missing results issue.

  6. GRASP

  7. GRASP Download GRASP eQTL datasets download: https://grasp.nhlbi.nih.gov/Updates.aspx Full GWAS dataset download: https://grasp.nhlbi.nih.gov/FullResults.aspx

  8. PhenoScanner

  9. PhenoScanner Displays top 10 results Complete results are downloadable as a spread sheet Includes results for proxy SNPs

  10. PheGenI Besides those from GWAS Catalog, results include dbGAP results with P ≤ 5x10-4. Also shows eQTL results from lymphoblastoid cell lines.

  11. GWASdb One of the most integrative databases on SNPs with existing GWAS associations. See the coverage on the right side of this slide (which is from the bottom of this opening page).

  12. GWAS Central Includes results with any P value in any trait (but only if the original GWAS dataset was accessible, or has been made accessible). Has a browser and a BioMart facility.

  13. GWAS Central

  14. PheWAS PheWAS dataset download: https://phewas.mc.vanderbilt.edu/datatable

  15. Key Points - There are many databases that provide results of genetic associations. - Each database has some advantages and disadvantages. MR catalog is unique in providing results also on proxy SNPs. - It is best to know the features of each database by reading the publication introduces it and the online guide or manual. - The best practice is to use multiple databases.

  16. … Looking forward …..

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