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Chunk #57 — Online Methods — Gene and gene-set analyses

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Genome-wide meta-analysis of depression identifies 102 independent variants and highlights the importance of the prefrontal brain regions.
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A gene-based analysis was applied to the results from our meta-analysis using Multi-marker Analysis of GenoMic Annotation (MAGMA) 14 to assess the simultaneous effect of multiple genetic variants on 17,842 genes. To account for LD the European panel of the 1,000 Genomes data (phase 3) 80 was used as a reference panel. Genetic variants were assigned to genes based on their position according to the NCBI 37.3 build. To identify those genes that were genome-wide significant a P-value threshold was calculated by applying a Bonferroni correction (α = 0.05 / 17,842; P < 2.80 × 10-6). Regional visualisation plots were produced using the online LocusZoom platform81.