I want to do a GWAS analysis using the differentially expressed genes that I got from a differential analysis. The purpose is the identification of biomarkers.

It's my first time using GWAS, can you please suggest to me a pipeline to use?

  • $\begingroup$ If you are looking for biomarkers, why not look at all genes? There will be a lot more information there. $\endgroup$ Sep 27, 2021 at 16:54
  • $\begingroup$ ok thank u, so we have to use all genes as phenotypes. it's my first time using GWAS, can you suggest me a pipeline to use. $\endgroup$
    – Zahrae
    Sep 28, 2021 at 12:34
  • $\begingroup$ @MaximilianPress $\endgroup$
    – Zahrae
    Sep 29, 2021 at 15:50

1 Answer 1


I am not an expert on recent packages but I would suggest using Matrix eQTL for purposes of the statistical analysis.

As mentioned in the comments I think that it is worth testing all transcripts for eQTL associations. This will additionally give some idea of the false discovery rate. It is possible that testing "candidate gene" differentially expressed genes will lead to a lot of false positives relative to the background level of associations.


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