RARE VARIANT AND COPY NUMBER VARIANT ANALYSIS TO IDENTIFY SHARED AND SPECIFIC GENE SETS ACROSS ANXIETY DISORDERS AND PTSD

Background Although the evidence for genetic influence on ANX (panic disorder, generalized anxiety disorder, phobias) and posttraumatic stress disorder (PTSD) is well established, the corresponding molecular pathophysiology remains poorly understood. Methods We leveraged whole genome and exome sequencing (WGS/WES) data and electronic health record (EHR)-defined ANX and PTSD from the All of Us (AoU) study in EUR ancestry to examine the associated gene and gene-set burden of rare single nucleotide and copy number variants (rSNV/rCNVs,minor allele frequency [MAF] < 1%). SAIGE-GENE+ was used to perform single variant and gene based tests using WES for ANX (N cases=54,074, N controls=114,322) and PTSD (N cases=6,361, N controls=145,776). Genome-wide burden analyses of rCNVs were completed using PLINK for neurodevelopmental (NDD) gene sets (N=53) using WGS data. These analyses were conducted across ANX (11,161 cases, 24,359 controls) and PTSD (1,179 cases, 34,868 controls) cohorts and included rCNVs of all lengths. We used three distinct burden metrics: gene-set deletion count, gene-set duplication count, and total CNV count (deletions + duplications). We employed a generalized linear model (GLM) adjusting for covariates, including age, sex, and the first five within-ancestry principal components (PCs). To properly assess the association of rCNVs and gene-sets independent of overall genomic burden or rCNV size, the models further adjusted for total genome-wide burden (Mb) and average rCNV length. Results Gene-based rSNV analyses identified two ANX-associated genes enriched for damaging variants—KCNA1 and MRPS34—and one PTSD-associated gene, the MHCII regulator RFX5 (all SKAT-O p FDR=0.02). While KCNA1 expression is largely brain-specific, MRPS34 is ubiquitously expressed across various tissues, including the brain. MRPS34 enriched for rare damaging variants associated with ANX have been implicated in differential gene expression in trauma-exposed male mice. No significant single rSNVs were identified in ANX or PTSD analyses. rCNV analyses of genome-wide burden across NDD gene sets identified 12 significant results for PTSD (FDR < 0.05). While no gene sets reached FDR significance for ANX, 20 were nominally significant (P < 0.05). Notably, eight of the 12 FDR-significant PTSD gene sets overlapped with the nominally significant ANX sets. We performed a functional enrichment analysis of the top 10 most significant genes from the ANX and PTSD SAIGE-GENE+ analyses with MSigDB collections, and identified a convergence of rare-variant enrichment across four primary functional domains. These top-tier genes implicated shared risk across: inflammatory response, ion regulation, developmental processes, and transcriptional stress regulation. Conclusions Analysis of NDD gene-sets for rCNVs in ANX/PTSD showed signals converging on pathways related to neurodevelopment and spatiotemporal brain expression. Future gene-set analyses with rSNVs will be conducted to examine whether enrichment of rCNVs is mirrored by rSNV burden in the same biological pathways. We will also perform analysis for other ancestry groups to better understand rare variant signals. This study utilized only the subset of All of Us participants with high-quality CNV data available and rCNVs of all lengths; future WGS studies with larger sample sizes and testing for different lengths may further elucidate the shared and distinct genetic etiologies of both disorders.