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MAGMA EDU Analysis

As another follow-up to the application of MAGMA to the DecodeME summary statistics, I applied MAGMA to the educational attainment study of Lee et al. (2018)1, to see if the results recapitulated known biology.

Data

I used summary statistics from Lee et al.'s GWAS of Educational attainment.

Results

As before, I ran the gene analysis set, followed by the gene property analysis step. In the gene property analysis step, I used tissue-specific RNAseq data from GTEx2 to try to link genes associated with educational attainment to specific tissues. The results are shown in the bar plot below:

bar_plot_edu

The significant tissues identified by MAGMA lie exclusively in the brain, consistent with leading theories of the biology of the genetic component of educational attainment.

How to Reproduce this

To reproduce this analysis run the Educational Attainment GWAS Analysis Script.

  1. James J Lee, Robbee Wedow, Aysu Okbay, Edward Kong, Omeed Maghzian, Meghan Zacher, Tuan Anh Nguyen-Viet, Peter Bowers, Julia Sidorenko, Richard Karlsson Linnér, and others. Gene discovery and polygenic prediction from a genome-wide association study of educational attainment in 1.1 million individuals. Nature Genetics, 50(8):1112–1121, 2018. URL: https://www.nature.com/articles/s41588-018-0147-3. ↩

  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. ↩