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BACKGROUND: Whereas genetic variants influencing total amygdala volume have been identified, the genetic architecture of its distinct nuclei have yet to be explored. We aimed to investigate whether increased phenotypic specificity through nuclei segmentation aids genetic discoverability and elucidates the extent of shared genetic architecture and biological pathways with related disorders.METHODS: T1-weighted brain MRI scans (n=36,352, 52% female) from the UK Biobank were segmented into nine amygdala nuclei with FreeSurfer v6.1. Genome-wide association analyses were performed on the entire sample, a European-only subset (n=31,690) and a generalization (trans-ancestry) subset (n=4,662). We estimated SNP-based heritability, derived polygenicity, discoverability and power estimates, and investigated genetic correlations and shared loci with psychiatric disorders.RESULTS: The heritability of the nuclei ranged between 0.17-0.33. Across the whole amygdala and the nuclei volumes, we identified 28 novel genome-wide significant (p < 5x10) loci in the European analysis, with significant en masse replication for the whole amygdala and central nucleus volumes in the generalization analysis, and identified ten additional candidate loci in the combined analysis. The central nucleus had the highest statistical power for discovery. The significantly associated genes and pathways show unique and shared effects across the nuclei, including immune-related pathways. Shared variants were identified between specific nuclei and autism spectrum disorder, Alzheimer's disease, Parkinson's disease, bipolar disorder, and schizophrenia.CONCLUSIONS: Through investigation of amygdala nuclei volumes, we have identified novel candidate loci in the neurobiology of amygdala volume. These nuclei volumes have unique associations with biological pathways and genetic overlap with psychiatric disorders.