Genotype-Phenotype Correlations in Autoinflammatory Diseases: Insights from a targeted NGS Panel

Autoinflammatory diseases (AIDs) are characterized by dysregulation of the innate immune system, often driven by genetic variants affecting key inflammatory pathways. The study aims to correlate specific genetic variants of interest, particularly variants of unknown significance (VUS) with clinical data, including symptoms and response to therapy. The study encompasses approximately one hundred AIDs patients with the majority of them belonging to the North-Eastern Italy subgroup population. An NGS analysis was performed by Illumina MISeq sequencing platform using a personalized kit provided by Sophia Genetics: Fever and Autoinflammatory Disease (FAID_GenEra_v1) which includes the following genes: ADA2, CARD14, ELANE, IL10RA, IL10RB, IL1RN, LPIN2, MEFV, MVK, NLRP12, NLRP3, NLRP7, NOD2, PSMB8, PSTPIP1, TNFRSF11A, TNFRSF1A. Variants were classified following the ACMG criteria. A total of 96 non-synonymous variants were identified, 7 of which were classified as pathogenic, and 36 classified as VUS. These variants were distributed unevenly across the different genes, with an increase in occurrence in the genes CARD14, MEFV and NOD2. The most frequently observed overall were variants p.(Arg702Trp) and p.(Leu1007Profs*2) in the NOD2 gene, and the p.(Arg820Trp) in CARD14. Correlation analysis between genetic mutations and clinical manifestations revealed several significant (p-value < 0.05) and borderline associations, suggesting that specific haplotypes, including variants classified as VUS or benign, may contribute to phenotypic variability and influence therapeutic response. Notably, potential interactions emerged between mutations in genes such as CARD14, MEFV, ELANE, NLRP3 and NOD2 and systemic inflammatory symptoms, warranting further functional and clinical investigation. These findings highlight the diagnostic and clinical utility of NGS in complex inflammatory phenotypes and support further investigation of the biological impact of rare and low-penetrance variants in AIDs.