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MAGMA

Definition
AI-generated

MAGMA is a software package for gene-level and gene-set analysis using GWAS summary statistics together with an LD reference panel.

Topics
GWAS
Synonyms
Multi-marker Analysis of GenoMic Annotation
URL
https://ctg.cncr.nl/software/magma
Related
Gene-Based Test GWAS Summary Statistics Linkage Disequilibrium (LD)

Why it matters in GWAS

Single-variant hits often do not clearly reveal the relevant biology. MAGMA is a widely used bridge from association statistics to genes, pathways, and tissue-level interpretation, especially in post-GWAS follow-up studies.

Example usage

"MAGMA gene-set analysis highlighted immune pathways enriched for association signal in the autoimmune disease GWAS."

Gene-Based Test GWAS Summary Statistics Linkage Disequilibrium (LD) Pathway Analysis Variant Annotation
Related-term network

Click any node to open that term page.

Node order. The current term is first. Next come every page linked from Related terms, in the same top-to-bottom order as that list. Then new terms appear in two-hop layers: for each of those direct neighbors (in that same order), their related terms are appended if not already listed. A third pass does the same for two-hop nodes. The walk stops when a fixed maximum number of nodes is reached.

References

  • de Leeuw CA, Mooij JM, Heskes T, Posthuma D. (2015). MAGMA: generalized gene-set analysis of GWAS data. PLoS Comput Biol. https://doi.org/10.1371/journal.pcbi.1004219
  • GWASTutorial: Gene / Gene-set tests by MAGMA.
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