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MAGMA GTEx analysis

I applied MAGMA to the PGC 2022 GWAS of Schizophrenia1 using the GTEx bulk RNAseq dataset 2 as a reference. The results are plotted below:

GTEX_RNA_MAGMA_SCH.

Similar to the results when S-LDSC is applied to this GWAS using the GTEx/Franke lab reference, GTEx MAGMA analysis identifies the brain as a key site of disease activity, but is unable to pinpoint a specific region.

  1. Vassily Trubetskoy, Antonio F Pardiñas, Ting Qi, Georgia Panagiotaropoulou, Swapnil Awasthi, Tim B Bigdeli, Julien Bryois, Chia-Yen Chen, Charlotte A Dennison, Lynsey S Hall, and others. Mapping genomic loci implicates genes and synaptic biology in schizophrenia. Nature, 604(7906):502–508, 2022. URL: https://pmc.ncbi.nlm.nih.gov/articles/PMC9392466/. ↩

  2. GTEx Consortium. The GTEx consortium atlas of genetic regulatory effects across human tissues. Science, 369(6509):1318–1330, 2020. URL: https://www.science.org/doi/full/10.1126/science.aaz1776. ↩