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Gene expression


Genetic regulatory effects modified by immune activation contribute to autoimmune disease associations

Sarah Kim-Hellmuth, Matthias Bechheim, Benno Pütz, Pejman Mohammadi, Yohann Nédélec, Luis B Barreiro, Jessica Becker, Vera Kaiser, Nadine Fricker, Esther Beier, Peter Boor, Markus M. Nöthen, Bertram Müller-Myhsok, Tuuli Lappalainen, Johannes Schumacher, Veit Hornung



What do you mean by expression QTL and response eQTL ?

We studied the impact of a genetic variant (SNP in our case) on different gene regulatory traits:

  • Expression levels (expression QTL or eQTL): These refer to genetic variants that affect the expression levels of a gene.
  • Response to infection (response QTL or reQTL): These refer to eQTLs where the regression slope is significantly different between baseline and stimulated cells.

Which tool and parameters were used for QTL analyses ?

All linear regressions were performed using the R package Matrix eQTL.

We tested SNPs with a minor allele frequency above 5% and falling in a +/- 100 Kb region around each gene (in our data, it represents ~ 3M SNPs).

Why is my gene or SNP of interest missing from the results?

A SNP can be missing because:

  • it had a MAF < 5% in our sample (all individuals combined);
  • if that SNP did not pass our quality control checks post-imputation.

A gene can be missing because :

  • it was very lowly or not expressed in any of the experimental conditions tested;
  • because no SNPs were available to test in the cis window around the gene.