Show GWAS Catalog info on [LZ, PheWAS]

[pjvandehaar]

The GWAS Catalog

The GWAS Catalog has 25k entries. Each entry has:

• a study name (eg, "Newly identified genetic risk variants for celiac disease related to the immune response.")
• one of 1400 "Disease/Trait" labels (eg, "Type 2 diabetes", "Systemic lupus erythematosus")
• a link to an abstract (eg http://www.ncbi.nlm.nih.gov/pubmed/18204446).

  Approaches to selecting GWAS Catalog entries for each phewas code:

  1. For each phewas code, manually search for matching GWAS Catalog label.
     • I would need help with this, because I need to understand the diseases.
  2. Then search for matching study names that were missed.

Is it worth automating? Let's do some by hand and then decide.

Goncalo's Approach for BDSI

1. Filter to rs#s that match nicely between MGI and GWAS Catalog (MAF, etc).
2. For each phewas_code, find the GWAS Catalog trait that makes our data most likely:

product_{each row}(P(OR_{obs} | OR_{GWAS}, SE)) / the null

[abecasis]

I think there might be too many to highlight in Manhattans... might get better mileage highlighting them on LocusZoom plots.

G

Sent from my iPhone

On Nov 3, 2017, at 7:24 PM, Peter VandeHaar notifications@github.com wrote:

Simple solution:

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[pjvandehaar]

Without any attempt to connect the 1400 GWAS Catalog traits to pheweb traits:

• on LZ: highlight all GWAS Catalog variants (toggleable?)
• on a variant (PheWAS) page: mention if a variant is in the GWAS Catalog
  • and also if it's within 10kb of one? or perhaps LD > 0.2?
• on Manhattan plots: allow the user to search for GWAS Catalog traits to show.
  • we could try to remember & suggest the traits people search for, but that's likely as much work as simple statistics comparing GWASCatalog traits to PheWeb traits.

[pjvandehaar]

The EBI API doesn't appear to support GRCh37 (only GRCh38). Let's build this into PheWeb before looking into adding it to the portal API and mainline LZ.

Two options:

• merge field .gwascatalog into /api/region/<phenocode>/lz-results (just a string?)
• serve /api/gwas-catalog/region/<chr>-<start>-<end> and append it to the LZ chain (gonna be slow...)

Since PheWeb tooltips aren't interact-able, we'll need to show GWASCat info on the PheWAS page.

[sgagliano]

GWAS Catalog has been incorporated into LZ plots.