Gene Set Identification

In the following software tutorials, you will get an introduction to gene and gene-set analysis in MAGMA, Hi-C informed or H-MAGMA, eQTL-informed MAGMA or E-MAGMA, and pathway-specific polygenic risk scores with PRSet. Multi-marker Analysis of GenoMic Annotation (MAGMA) is a software tool for performing gene and gene-set analysis of GWAS data. H-MAGMA integrates Hi-C data to better inform gene positioning through a tissue and cell-type specific regulatory landscape. E-MAGMA similarly informs gene analysis with eQTL data. PRSet allows for more functionally-informed polygenic risk scores by integrating gene pathway information into generation of risk scores and testing for enrichment of various genetic pathways.

MAGMA

Title: Gene- and gene-set analysis in MAGMA

Presenter(s): Christiaan de Leeuw, PhD (Department of Complex Trait Genetics, Vrije Universiteit Amsterdam)

Level: Intermediate

Length: 12:09

Link to video transcript here.

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H-MAGMA

Title: Annotating Genetic Variants to Target Genes Using H-MAGMA

Presenter(s): Nancy Y.A. Sey, PhD (National Human Genome Research Institute)

Level: Intermediate

Length: 10:09

Link to video transcript here.

Link to GitHub tutorial and datasets.

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E-MAGMA

Title: E-MAGMA: an eQTL-informed method to identify risk genes using genome-wide association study summary statistics

Presenter(s): Zac Gerring, PhD (Translational Neurogenomics, QIMR Berghofer Medical Research Institute)

Coauthor(s): Eske Derks, PhD (Translational Neurogenomics, QIMR Berghofer Medical Research Institute)

Level: Intermediate

Length: 7:16

Link to video transcript here.

Link to GitHub tutorial and datasets.

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PRSet

Title: How to run pathway specific Polygenic Risk Scores

Presenter(s): Judit García-González, PhD (Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai)

Level: Intermediate

Length: 15:28

Link to video transcript here.

Link to PRSet website (part of the PRSice-2 website).