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MAGMA Analysis of LDL

MAGMA Results

I applied the MAGMA1 pipeline to summary statistics from a GWAS of LDL from the Million Veterans Program2. In the gene set analysis step, I incorporated tissue-specific RNAseq data from GTEx3 to try to link genes associated with LDL to specific tissues.

The results are shown below:

bar_plot

indicating that genes that increase LDL tend to be expressed in the liver. This is consistent with known biology: the liver plays a major role in clearing excess LDL from the bloodstream.

Reproducing Analysis

To reproduce this analysis, run the LDL GWAS Analysis Script.

  1. Christiaan A De Leeuw, Joris M Mooij, Tom Heskes, and Danielle Posthuma. MAGMA: generalized gene-set analysis of GWAS data. PLoS Computational Biology, 11(4):e1004219, 2015. URL: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004219. ↩

  2. Anurag Verma, Jennifer E Huffman, Alex Rodriguez, Mitchell Conery, Molei Liu, Yuk-Lam Ho, Youngdae Kim, David A Heise, Lindsay Guare, Vidul Ayakulangara Panickan, and others. Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program. Science, 385(6706):eadj1182, 2024. URL: https://www.science.org/doi/10.1126/science.adj1182. ↩

  3. 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. ↩