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Juvenile Idiopathic Arthritis (JIA) is the most common type of arthritis among children, encompassing a highly heterogeneous group of immune-mediated joint disorders, being classified into seven subtypes based on clinical presentation. To systematically understand the distinct and shared genetic underpinnings of JIA subtypes, we conducted a heterogeneity-sensitive GWAS encompassing a total of 1245 JIA cases classified into 7 subtypes and 9250 controls. In addition to the MHC locus, we uncovered 16 genome-wide significant loci, among which 15 were shared between at least two JIA subtypes, including 11 novel loci. Functional annotation indicates that candidate genes at these loci are expressed in diverse immune cell types. Further, based on the association results, the 7 JIA subtypes were classified into two groups, reflecting their autoimmune vs autoinflammatory nature. Our results suggest a common genetic mechanism underlying these subtypes in spite of their different clinical disease phenotypes, and that there may be drug repositioning opportunities for rare JIA subtypes.

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