Is there a way to find the GWAS traits to a gene programmatically?

Question

[cmcouto.silva]

Hello folks,

I would like to use a gene name (e.g. DOCK2) or its ENSEMBL ID as input, and get as output the reported GWAS traits to the respective gene. I did give a look into the GWAS Catalog API webpage, but I didn't find a way to use gene as input. Also, I looked for R and Python libraries for doing that, and I couldn't find either (maybe I didn't search well).

I know it's possible to do that for associations, studies, SNPs, and efoTraits. For instance, I could just use https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs4918943 url, where it returns info for the SNP "rs4918943". I would like something similar for a gene ID, or a library that does it.

It would be great to input a gene and receives any output where I could retrieve the GWAS trais related to such gene. Thanks in advance!

[eyb]

I have the same problem. Did you manage to solve it?

[cmcouto.silva]

Hi! Yes, I did! I just posted the solution I came across.

Answer 1

[cmcouto.silva]

I didn't find the usage for it, but I figured out how to query it by using the following URL:

https://www.ebi.ac.uk/gwas/api/search/downloads?q=ensemblMappedGenes:{gene}&pvalfilter=&orfilter=&betafilter=&datefilter=&genomicfilter=&genotypingfilter[]=&traitfilter[]=&dateaddedfilter=&facet=association&efo=true

where we should replace {gene} with the gene symbol (e.g. TP53).

Example using R:

# Required library # could be readr::read_delim() as well
library(data.table)

# Set the function 
genesymbol2gwas <- function(gene){
  url <- paste0(
    "https://www.ebi.ac.uk/gwas/api/search/downloads?q=ensemblMappedGenes:", gene,
    "&pvalfilter=&orfilter=&betafilter=&datefilter=&genomicfilter=&genotypingfilter[]=&traitfilter[]=&dateaddedfilter=&facet=association&efo=true"
  )
  return(fread(url))
}

# Use the function for gene "TP53"
genesymbol2gwas("TP53")

Example using Python:

# Load library to read the result table as a dataframe
import pandas as pd

# Define the function
def genesymbol2gwas(gene):
    url = "https://www.ebi.ac.uk/gwas/api/search/downloads?q=ensemblMappedGenes:{}&pvalfilter=&orfilter=&betafilter=&datefilter=&genomicfilter=&genotypingfilter[]=&traitfilter[]=&dateaddedfilter=&facet=association&efo=true"
    return pd.read_csv(url.format(gene), sep='\t')

# Use the function for gene "TP53"
genesymbol2gwas("TP53")

Hope it helps someone in a similar situation =)

[eyb]

Thanks for taking the time to share this!

[eyb]

I wonder how you came up with the link though since this type of query seems to be not documented.

[eyb]

I've tested your code. It works, but it returns associations, not traits. Do you know how to make it to return traits?