Objective: To evaluate whether there is an enrichment of rare variants in familial hemophagocytic lymphohistiocytosis (HLH) genes and systemic juvenile idiopathic arthritis (sJIA) with or without macrophage activation syndrome (MAS). Methods: Targeted sequencing of HLH genes (LYST, PRF1, RAB27A, STX11, STXBP2, UNC13D) was performed in sJIA subjects from an established cohort. Sequence data from control subjects were obtained in silico (dbGaP:phs000280.v8.p2). Rare variant association testing (RVT) was performed with sequence kernel association test (SKAT) package. Significance was defined as p<0.05 after 100,000 permutations. Results: Sequencing data from 524 sJIA cases were jointly called and harmonized with exome-derived target data from 3000 controls. Quality control operations produced a set of 481 cases and 2924 ancestrally-matched control subjects. RVT of sJIA cases and controls revealed a significant association with rare protein-altering variants (minor allele frequency [MAF]<0.01) of STXBP2 (p=0.020), and ultra-rare variants (MAF<0.001) of STXBP2 (p=0.007) and UNC13D (p=0.045). A subanalysis of 32 cases with known MAS and 90 without revealed significant association of rare UNC13D variants (p=0.0047). Additionally, sJIA patients more often carried ≥2 HLH variants than did controls (p=0.007), driven largely by digenic combinations involving LYST. Conclusion: We identified an enrichment of rare HLH variants in sJIA patients compared with healthy controls, driven by STXBP2 and UNC13D. Biallelic variation in HLH genes was associated with sJIA, driven by LYST. Only UNC13D displayed enrichment in patients with MAS. This suggests that HLH variants may contribute to the pathophysiology of sJIA, even without MAS.

M. Correia Marques: NIAMS Intramural Research Program, American College of Rheumatology, Childhood Arthritis and Rheumatology Research Alliance, Paediatric Rheumatology European Society (PReS); D. Rubin: None; E. Shuldiner: Supported by NIH Postbaccalaureate IRTA Program, Tobacco-Related Disease Research Program (TRDRP) predoctoral fellowship (T33DT6556); M. Datta: None; E. Schmitz: None; G. Gutierrez-Cruz: none, A. Patt: None, E. Bennett: None, A. Grom: Up-to-date, Novartis, Sobi, D. Foell: Boehringer, Novartis, Sobi; M. Gattorno: Novartis, Sobi; J. Bohnsack: Abbvie, Janssen, Pfizer, Sobi, Genentech, BMS, 5; R. S. M. Yeung: Canadian Institutes for Health Research, Genome Canada, The Arthritis Society (Canada); S. Prahalad: None; E. Mellins: Codexis, Genentech, GlaxoSmithKlein(GSK); J. Anton Lopez: None; C. A. Len: None; S. Oliveira: None; P. Woo: None; S. Ozen: Novartis, SOBI, Bayer, President-elect of Pediatric Rheumatology European Society; Z. Deng: None; M. Ombrello: None.

This study was funded by the Intramural Research Program of the National Institute of Arthritis and Musculoskeletal and Skin Diseases (Z01-AR041198). The work utilized the computational resources of the NIH high-performance computing cluster Biowulf (http://hpc.nih.gov) Dr. Prahalad is supported in part by The Marcus Foundation Inc., Atlanta.

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