Virtual Association Studies

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Presentation transcript:

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

Schedule

Genetic Association Results Databases Outline Genetic Association Results Databases

NHGRI-EBI GWAS Catalog Link: http://www.ebi.ac.uk/gwas

NHGRI-EBI GWAS Catalog Link: http://www.ebi.ac.uk/gwas/docs/about Other databases always give a larger number of results for the same phenotype or variant. GWAS catalog may have a missing results issue.

GRASP Link: https://grasp.nhlbi.nih.gov/Search.aspx

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

PhenoScanner Link: http://www.phenoscanner.medschl.cam.ac.uk/phenoscanner

PhenoScanner Displays top 10 results Link: http://www.phenoscanner.medschl.cam.ac.uk/phenoscanner 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: http://www.ncbi.nlm.nih.gov/pubmed/27318201 Displays top 10 results Complete results are downloadable as a spread sheet Includes results for proxy SNPs

PheGenI Besides those from GWAS Catalog, results include dbGAP results with P ≤ 5x10-4. Also shows eQTL results from lymphoblastoid cell lines. Link: http://www.ncbi.nlm.nih.gov/gap/phegeni

GWASdb Link: http://jjwanglab.org:8080/gwasdb 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).

GWAS Central Link: http://www.gwascentral.org 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.

GWAS Central Link: http://help.gwascentral.org/info/data/database-content

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

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.

… Looking forward ….. http://www.dorak.info

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

http://www.hope.ac.uk