Sulaiman M Al-Mayouf1*, Asma Sunker2*, Reem Abdwani3*, Safiya Al Abrawi5, Fathiya

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1 Loss of function variant in DNASE1L3 causes a familial form of systemic lupus erythematosus Sulaiman M Al-Mayouf1, Asma Sunker2, Reem Abdwani3, Safiya Al Abrawi5, Fathiya Almurshedi4, Nadia Alhashmi5, Abdullah Al-Sunbul1, Wafaa Sewairi6, Aliya Qari7, Eiman Abdallah3, Mohammed Al-Owain7,8, SalehAl-Motewea6, Hanan Al-Rayes9, Mais Hashem2, Latifa Al-Jebali2, Fowzan S Alkuraya2,8,10 These authors contributed equally to this work and should be considered co-first authors 1Rheumatology Section, Department of Pediatrics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia 2Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia 3Department of Child Health, Sultan Qaboos University Hospital, Muscat, Oman 4Department of Genetics, Sultan Qaboos University Hospital, Muscat, Oman 5Department of Child Health, Royal Hospital, Muscat, Oman 6Division of Rheumatology, Department of Medicine, National Guard Hospital, Riyadh, Saudi Arabia 7Department of Medical Genetics, King Faisal Specialist Hospital, Riyadh, Saudi Arabia 8Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia 9Department of Medicine, Riyadh Military Hospital, Riyadh, Saudi Arabia 10Department of Pediatrics, King Khalid University Hospital and College of Medicine, King Saud University, Riyadh, Saudi Arabia 1

2 Supplementary Methods Human Subjects and Phenotyping Familial cases of SLE were chosen such that parents were healthy and consanguineous and there are several affected siblings. All patients were enrolled using written informed consent that was approved by the IRB of the respective institution. Definition of SLE was based on the revised criteria by the American College of Rheumatology 1. There is no individual laboratory test or clinical finding that measures the disease severity. However; the disease severity flares can be measured by Systemic Lupus Erythematosus Disease Activity Index (SLEDAI) 2. The SLEDAI is a disease-specific scale of disease activity; it measures potentially reversible manifestations of SLE. The scale consists of 24 weighted attributes grouped into 9 domains (organ systems) as follows: weighting of 8 for central nervous system and vascular, 4 for renal and musculoskeletal, 2 for serosal, dermal, and immunologic, and 1 for constitutional and hematologic. If, during a 10-day period prior to the assessment, a patient manifests a clinical variable, then the corresponding weighted score is assigned. The final score comprises the sum of all weighted attribute scores. The SLEDAI has a theoretically possible range of 0-105, with 0 indicative of no disease activity. Autozygome Analysis For familial cases, we assumed an autosomal recessive pattern of inheritance due to homoallelic mutation but we kept open the possibility that different families may harbor different causative alleles or even different causative genes. Genomewide SNP genotyping using Affymetrix Axiom platform and homozygosity scan using autosnpa were performed essentially as described before

3 Linkage analysis was performed using easylinkage package assuming a fully penetrant autosomal recessive model. For sporadic cases (n=85) we also ran genomewide SNP genotyping and determined their pattern of homozygosity as described above in order to prioritize cases for sequencing of the gene to be identified in the familial cases. Exome Sequencing Full exome capture was performed using TruSeq Exome Enrichment kit (Illumina) following the manufacturer s protocol. Samples were prepared as an Illumina sequencing library, and in the second step, the sequencing libraries were enriched for the desired target using the Illumina Exome Enrichment protocol. The captured libraries were sequenced using Illumina HiSeq 2000 Sequencer. The reads are mapped against UCSC hg19 ( by BWA ( The SNPs and Indels are detected by SAMTOOLS ( DNase Activity Assay Wt-DNase1L3 template was purchased (TrueORF Gold pcmv6 EntryMyc-DDK-tagged ORF clone of Homo sapiens deoxyribonuclease I-like 3 (DNASE1L3) astransfection-ready DNA (NM_ ) (Origene Cat# RC205611)). Before mutation, the nucleotide of Wt-DNase1L3 template was sequenced in the coding sequence of the enzyme and Myc-DDK tags at C-terminal. Single nucleotide deletion mutation (c.643delt) was then performed and validated by sequencing the coding sequence. The plasmids were maxi-prepared and purified for DNA transient transfection in mammalian cells (HEK-293). Human embryonic kidney 293 cells were grown in serum containing Dulbecco modified Eagle s medium (DMEM) to 70% confluence and transiently transfected with 30 μg DNA(wt-DNASE1L3 and mut-dnase1l3 separately) using calcium phosphate. At 24 h posttransfection, cells were washed with phosphate-buffered saline and transferred to serum-free 3

4 medium containing recombinant human insulin (2 μg/ml). The conditioned medium was harvested after h and concentrated 10-fold using Centriplus-10 concentrators (Amicon, Beverly, MA). Western blot was performed using Anti-DDK tag monoclonal antibody. DNase activity was monitored with a plasmid nicking assay using supercoiled pbr322 (final concentration: 25 μg/ml) in 25 mm HEPES, 1 mm MgCl2, 1 mm CaCl2 100 μg/ml BSA (total reaction volume: 30 μl ). DNase samples were incubated with the pbr322 plasmid and reaction buffer for 30 min at room temperature. Digestion with EcoRI restriction enzyme was used as a control of linearized pbr322. Reactions were stopped by the addition of EDTA to a final concentration of 10 mm followed by DNA analysis by gel electrophoresis and visualization by Ethidium Bromide staining of the gel and photography under UV light. Comparisons were made between wt and mut proteins as well as with the positive control. REFERENCES 1. Hochberg, M.C. Updating the American College of Rheumatology revised criteria for the classification of systemic lupus erythematosus. Arthritis and rheumatism 40, 1725 (1997). 2. Brunner, H.I., Silverman, E.D., To, T., Bombardier, C. & Feldman, B.M. Risk factors for damage in childhood-onset systemic lupus erythematosus: cumulative disease activity and medication use predict disease damage. Arthritis and rheumatism 46, (2002). 3. Shaheen, R. et al. A TCTN2 mutation defines a novel Meckel Gruber syndrome locus. Human mutation 32, (2011). 4. Alkuraya, F.S. Autozygome decoded. Genetics in medicine : official journal of the American College of Medical Genetics 12, (2010). 5. Carr, I.M., Flintoff, K.J., Taylor, G.R., Markham, A.F. & Bonthron, D.T. Interactive visual analysis of SNP data for rapid autozygosity mapping in consanguineous families. Human mutation 27, (2006). 4

5 Figure Legends Supplementary Figure 1. A) Linkage analysis confirmed the 3p14.3 locus with a LOD score close to 7. B) Cartoon of DNASE1L3 showing the signal peptide (green), nuclear localization signals (blue) and the site of the disulfide bridge (red). Red triangle indicates the site of the truncating mutation on the protein as well as on sequence chromatogram below. Supplementary Figure 2. Pedigrees of the six families with DNASE1L3 mutation. Red asterisks denote individuals whose DNA was available. Supplementary Figure 3. RT-PCR revealed no detectible DNASE1L3 in the two patients from whom RNA was available. Three different primer sets were used to test DNASE1L3 expression per individual. 5

6 Supplementary Figure 1 A B DNASE1L3 Wt Het Homo

7 Supplementary Figure 2 F1 F2 F3 F4 F5 F6

8 Supplementary Figure 3 RT PCR Patient 1 Patient 2 Control DNASE1L3 β actin DNASE1L3 β actin DNASE1L3 β actin

9 Supplementary Table 1. Shared founder haplotype in the six families is highlighted in orange and the location of DNASE1L3 is indicated in red. 6

10 db SNP RS ID chr chromosomal position Patient ID F1 A F1 B F1 C F2 A F2 B F2 C F3 A F3 B F4 A F4 B F5 A F5 B F5 C F6 A F6 B rs AA AA AA AA AA AA AA AA AA NoCall AA AA AA AB AA rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB NoCall BB rs AA AA AA AA AA AA AA AA AA NoCall AA AA AA AA AA rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs BB BB BB BB BB BB NoCall BB BB BB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB NoCall BB BB BB BB BB rs BB BB BB BB BB BB BB BB NoCall BB BB BB NoCall NoCall BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs AA AA AA AA AA AA AA AA AA AA AA AA AB AA AA rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB NoCall BB BB BB AB BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB AB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs AA AA AA AA AA AA AA AA AA NoCall AA AA AA AA AA rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs BB BB BB BB BB BB BB BB BB NoCall BB BB BB BB BB rs AA AA AA AA AA AA AA AA AA AB AA AA AA AA AA rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB NoCall BB BB BB BB BB rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB NoCall BB BB BB BB BB rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB NoCall BB

11 rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA DNASE1L3 rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs BB BB BB NoCall BB BB BB BB BB BB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs NoCall AA AA AA AA AA AB AA AA AA AA AA AA AA AA rs AB AA AA AA AA AA AB AA AA AA AA AA AA AA AA rs BB BB BB BB BB BB BB BB BB AB BB BB BB BB BB rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs AB BB BB BB BB BB AB BB NoCall AB BB BB BB BB BB rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB AB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB AB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB AB BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB NoCall BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs BB BB BB BB BB BB NoCall BB NoCall BB BB BB BB BB BB rs AB BB BB BB BB BB BB BB NoCall NoCall BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB AB BB BB BB BB BB rs AB AA AA AA AA AA AA AA NoCall AB AA AA AA NoCall AA rs BB BB BB BB BB BB BB BB BB NoCall BB BB BB BB BB rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs BB BB BB BB BB BB BB BB BB NoCall BB BB BB BB BB rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB NoCall BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs BB BB BB BB BB BB BB BB BB AB BB BB BB BB BB rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs AA AA AA AA AA AA AA AA AA NoCall AA AA AA AA AA rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA

12 rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs AA AA AA AA AA AA NoCall AA AA AB AA AA AA AA AA rs BB BB BB BB BB BB BB BB BB AB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs AA AA AA AA AA AA AA AA AA NoCall AA AA AA AA AA rs AA AA AA AA AA AA AA AA NoCall NoCall AA AA AA NoCall AA rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs AA AA AA AA AA AA AA AA AA AB AA AA AA AB AA rs BB BB BB BB NoCall BB BB BB AB BB BB BB BB AB NoCall rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs NoCall AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs NoCall BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs BB BB BB BB BB BB BB BB NoCall BB BB BB BB BB BB rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs AA AA AA AA AA AA AA AA AA AB AA AA AA AA AA rs BB BB BB BB BB BB BB BB BB NoCall BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs AA AA AA AA AA AA AA AA AA NoCall AA AA AA AA AA rs AA AA AA AA AA AA AA AA AA AB AA AA AA AA AA rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs NoCall AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA NoCall rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs AA AA AA AA AA AA AB AA AA AA AA AA AA AA AA rs BB BB BB BB BB BB BB BB BB AB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs AA AA AA AA AA AA AA AA AA AA NoCall AA AA AA AA rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB NoCall BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs AA AA AA AA AA AA AA AA AA AB AA AA AA AA AA

13 rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs AA AA AA AA AA AA AA AA NoCall AA AA AA AA AA AA rs BB BB NoCall BB BB BB BB BB BB BB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB NoCall BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs AA AA AA AA AA AA AA AA AA AA AA AA AA BB BB rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs AA AA AA AA AA AA AA AA AA AA AA AA AA BB BB rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs AA AA AA AA AA AA AA AA AA AA AA AA AA BB BB rs AA AA AA AA AA AA AA AA AA AB AA AA AA AA AA rs BB BB BB BB BB BB BB BB BB BB BB BB BB NoCall AA rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs AA AA AA AA AA AA AA AA AA AA AA AA AA BB BB rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs AA AA AA AA AA AA AA AA AA AA AA AA AA BB BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs AA AA AA AA AA AA AA AA AA AA AA AA AA NoCall AA rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs AA AA AA AA AA AA AA AA AA AB AA AA AA NoCall AA rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs BB BB BB BB BB BB BB BB BB BB BB BB BB BB BB rs AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA rs BB BB BB BB BB BB BB BB BB BB BB BB BB AA AA rs BB BB BB BB BB BB BB BB BB BB BB BB BB NoCall BB

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