Question

How to find any GWAS associations my genes have

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5.7 years ago

arissaoulidis • 0

Hello,

I have a list of 1000 genes and I want to produce a file summarising the known GWAS associations of each one of those genes. Is there a way to do this programmatically please?

Many thanks

GWAS gene associations • 853 views

ADD COMMENT • link updated 5.7 years ago by Kevin Blighe 89k • written 5.7 years ago by arissaoulidis • 0

score 1 · Answer 1 · 2020-01-19

There are likely many ways. One way is to download the NHGRI's GWAS Catalog as TSV and then programmatically overlap your data with these: https://www.ebi.ac.uk/gwas/downloads

Be wary of gene synonyms and general gene naming conventions, which may affect the overlap. May be better to convert all symbols to Entrez IDs or Ensembl gene IDs just for the purpose of the overlap.

Kevin