Detailed information for the included phenotypes.

BackgroundFibromyalgia, insomnia, depression, and anxiety share common clinical comorbidities, but their underlying genetic architecture and mechanism remain unclear.MethodsWe conducted phenotype-specific Genome-wide association study (GWAS) meta-analyses for fibromyalgia, insomnia, depression, and anxiety, respectively. Genomic structural equation modeling was employed to identify a shared genetic factor (mvFibroPsych). Lead SNPs and associated genes were annotated using Functional Mapping and Annotation (FUMA), followed by gene-set and tissue enrichment analyses. The Latent Causal Variable (LCV) method was utilized to identify modifiable risk factors and phenotypes influenced by mvFibroPsych. Additionally, brain-wide and proteome-wide Mendelian randomization (MR) analyses were applied to explore brain regions and biomarkers associated with mvFibroPsych. Multi-layer molecular quantitative trait locus (QTL) analyses were conducted for mechanistic insights into mvFibroPsych.ResultsStrong genetic correlations were observed among the four phenotypes (rg = 0.55–0.84), with excellent model fit for the common factor [comparative fit index (CFI) = 0.999, standardized root mean square residual (SRMR) = 0.015]. The mvFibroPsych GWAS identified 49 lead SNPs across 43 loci, including 32 novel loci. Gene prioritization revealed 342 protein-coding genes, and pathway analysis indicated enrichment in synaptic function pathway. LCV identified 133 phenotypes causally linked to mvFibroPsych. Brain-wide MR found fractional anisotropy in the splenium of the corpus callosum to be inversely associated with mvFibroPsych. Proteome-wide MR identified five proteins significantly associated with mvFibroPsych, while multi-layer brain QTL analysis prioritized CD40 as a potential target.ConclusionsThis study provides strong evidence for a shared genetic factor underlying fibromyalgia, insomnia, depression, and anxiety, linked to synaptic function, brain structure integrity, and neuroinflammatory pathways.