Identifying and discovering genetic variants for monogenic lupus , Sergey Naumenko 224 , Jingjing Cao 107 , Declan Webber 195 , Daniela Dominguez 195 , Bhooma Thiruvahindrapuram 223 , Deborah Levy 195 , Andrew Paterson 107 , Earl Silverman 195 Linda Hiraki 195

224 The Centre for Computational Medicine, Research Institute, SickKids

107 Genetics & Genome Biology, Research Institute, SickKids

195 Rheumatology, SickKids

223 The Centre for Applied Genomics , SickKids

Background : There is strong evidence that genetics plays an important role in the pathogenesis of systemic lupus erythematosus (SLE). Within the broad category of SLE, there are genetically distinct Mendelian diseases presenting with lupus features, also known as monogenic lupus. This theory has been proven by the discovery of variants in single causing monogenic SLE in small numbers of individuals with young- onset disease and/or families with multiple members diagnosed with SLE. Specific Aims: To assemble a North American cohort and bio-repository comprised of families with monogenic lupus. Next generation sequencing (NGS) including whole exome sequencing (WES) and whole genome sequencing (WGS) of this population will identify variants and genes associated with disease risk.

Methods : 1. WES (Illumina HiSeq 2500 platform) n=17 patients with both cSLE and macrophage activation syndrome (MAS). 2. WGS (Illumina HiSeq X platform) n=8 cSLE patients diagnosed < 10 years and/or evidence of consanguinity. Variant calling completed with GATK and HAS, and functional annotation with ANNOVAR at The Centre for Applied Genomics, SickKids (annotation pipeline, v26.2, v.26.5). Small variants recalled and reannonated with gatk4/bcbio/VEP/vcfanno gemini. We prioritized variants based on population frequency in GNOMAD, functional impact (HIGH or MED: coding stop gain or lost, missense, frameshift, splice site and splice region) and panels of MAS-specific genes (AP3B1, BLOC1S6, CD27, GATA2, ITK, LYST, NLRC4, PRF1, RAB27A, SH2D1A, SIRPA, SLC7A7, STX11, STXBP2, UNC13D, XIAP) and lupus genes (ACP5, ADAR, C1QA, C1QB, C1QC, C1R, C1S, C2, C3, C4A, C4B, CYBB, DNASE1, DNASE1L3, FASLG, IFIH1, KRAS, MAN2B1, NEIL3, PEPD, PRKCD, PSMA3, PSMB4, PSMB8, PTEN, PTPN11, RAG2, RNASEH2A, RNASEH2B, RNASEH2C, SAMHD1, SHOC2, SLC7A7, TMEM173, TNFRSF6B, TREX1).

Results : We discovered 5 rare (MAF < 1%) variants in 3/17 MAS samples in 5 genes (SLC7A7; ITK, LYST, SIRPA - 3 variants in 1 sample; BLOCK1S6 ). When relaxing MAF threshold to MAF < 5% we discovered additional 8 variants in 7/17 MAS samples in 6 genes (SLC7A7, AP3B1, PRF1, UNC13D, LYST, STXBP2). In total, we discovered 13 rare (MAF < 5%) variants in 8/17 MAS samples. 4/13 variants were in splice regions and 9/13 were missense variants. Among SLE WGS samples we discovered rare (MAF < 1%) variants in 5/8 samples in genes (PKRCD, ADAR, DNASE1, SLC7A7, C4A, C2). One samples carried variants in two genes (stop gain in DNASE1 and missense in SLC7A7) In addition, we filtered many rare non-coding variants in target genes, however, their functional interpretation is not yet established.

Conclusions : NGS has identified candidate variants leading to MAS in SLE, as well as monogenic lupus. These findings provide insights into the pathogenesis of SLE as well as being potential prognostic factors and therapeutic targets. Local IRB obtained.