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

2. Schedule

3. Genetic Association Results Databases
Outline
Genetic Association Results Databases

4. NHGRI-EBI GWAS Catalog
Link:

5. NHGRI-EBI GWAS Catalog
Link:
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
Link:

7. GRASP Download
GRASP eQTL datasets download:
Full GWAS dataset download:
Link:

8. PhenoScanner
Link:

9. PhenoScanner Displays top 10 results
Link:
Includes results of proxies and with GRASP eQTL associations as well.
Only shows top 10 results. All results are downloadable as a single file.
Reference:
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.
Link:

11. GWASdb
Link:
GWASdb does not contain information on SNPs that have not yet shown a GWAS association.
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
Link:
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
Link:

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

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 …..

17. Course material: http://www.dorak.info/genbiol/course.html