Suzanne de Bruijn

175 Structural variants cause ectopic enhancer-gene contact in retinitis pigmentosa For the 12 UK RP17 founder haplotype families, WGS revealed a duplicated inversion: chr17:57,456,098-57,468,960delins57,275,839_57,559,114inv (UK-SV2) ( Figure 2B ). The SV was characterized and breakpoint junctions were validated ( Figure S1 , Supplementary Results ). This SV involved four coding genes ( PRR11 , SMG8 , GDPD1 and YPEL2 ) and two non-coding RNA genes ( MIR4729 and LINC01476 ) ( Figure 2B ). UK- SV2 segregated with adRP in all families where DNA was available for analysis. UK-SV2 was absent inWGS control genome data generated for 58,000 UK individuals (Genomics England). Different structural variants within the RP17-locus in multiple adRP families These data prompted us to investigate whether SVs were present in the two original SouthAfrican families (SA1andSA2) thatwere linked to theRP17-locus ( FigureS2A ). 8,10 In addition, a Canadian adRP family (CA1) was alsomapped to the RP17-locus (unpublished data, Figure S2B ). WGS was performed for affected individuals from these families, and inversion duplication events were identified in all samples analyzed ( Figure 2C ). In SA1 and SA2, an identical SV, SA-SV3, was revealed suggesting this is a founder variant in this population. SA-SV3 was also found by breakpoint PCR in two additional families of South African origin (SA3 and SA4), confirming the founder effect ( Figure S2A ). In the Canadian family, a different inversion duplication event was identified, CA-SV4. SA-SV3 and CA-SV4 breakpoints were characterized and validated ( Figure S1 ), and segregation of the SVs with the adRP phenotype was confirmed. Our data suggested that SVs at the RP17-locus are an important cause of adRP. Therefore, WGS and WES data for genetically unexplained adRP-affected families were analyzed for SVs within this locus. In four unrelated families of Dutch or UK origin, four additional unique complex SVs were discovered ( Figure 2D , S2C ). For individuals that had only undergone WES, WGS was performed to determine the breakpoint junctions and identify potential inversions or other SVs. In all families, breakpoints were validated and segregation analysis was performed where possible. Triplication for UK-SV6 was confirmed by qPCR in family UK13 ( Figure S3 , Supplementary Results ). Details of all SVs identified in this study are shown in Table S6 , Figure 2 and Figure S4 , and an overview of SV-specific breakpoint junctions is shown in Figure S1 . All RP17-SVs share a common duplicated (or triplicated) region of 11.5 kb and harbor unique breakpoints disrupting the genomic region spanning YPEL2 to LINC01476 (chr17:57,499,214-57,510,765) ( Figure S4 ). We analyzed all breakpoint junction sequences to investigate the potential mechanism(s) that created RP17-SVs. No single