Mendelian Randomisation with GTEx data

Question

[ciarancampbell]

Hi there,

I have a set of GWAS results that found significant associations in a gene I'm interested in.

I'm looking to perform mendelian randomisation using gene expression data from the GTEx dataset. The GTEx website shows me that eQTLs in this gene affect expression levels in a particular tissue.

Is there a way to download the complete expression data for these eQTLs in this tissue from GTEx so that the data can be incorporated into mendelian randomisation analysis using GCTA-GREML? I believe the exact data I need are: BETA, Standard error, and p-value.

Thanks for the help

Answer 1

[Aamiralizai]

Hi there You can use your SNPs to extract the eQTL association data from GTEx via API (https://gtexportal.org/home/api-docs/index.htm#!/association/post_association_dyneqtl), for this you need to convert your data to JSON format, you can use online websites such as (http://convertcsv.com/csv-to-json.htm) to convert your data to JSON format.

Answer 2

[Michael Love]

One concern here would be the correlation of the candidate instruments (eSNPs) for MR analysis. For example, in the MRLocus paper we performed a sensitivity analysis on correlation across clumped eQTL as instruments for gene expression. Note that as the r2 increases across the instruments the false positive rate increases, and the trend is present for various number of instruments (n).

Supp Fig F: