Suzanne de Bruijn

172 Chapter 4 RESULTS Refinement of the RP17-locus in two unrelated adRP families The affected haplotype for a Dutch adRP family (NL1) ( Figure 1A ) was previously mapped to a 7.18 Mb region spanning the RP17-locus on chromosome 17. 9 The RP17- locus was refined to a 5.16 Mb interval by SNP haplotyping in an extended pedigree ( Figure 1D , Supplementary Results ). No rare coding or splice site heterozygous variants (MAF ≤0.0001) shared between affected individuals were found through whole exome sequencing (WES). Subsequently WGS was performed, and similarly no rare candidate coding, splice site, intronic or intergenic heterozygous single nucleotide variants were identified ( Table S4 , Supplementary Results ). In parallel, WES and WGS was performed for affected individuals from a genetically unexplained UK adRP family (UK1) ( Figure 1B ). This also failed to identify a rare causative variant, however, a disease-associated haplotype on chromosome 17 was identified ( Figure 1E , Table S5 , Supplementary Results ). Interrogation of unsolved IRD sequence data generated through the UK IRDC, UCL-Ex, NIHR-Bioresource, and Genomics England identified other adRP probands that shared the same haplotype of Chr17 SNVs, and established this as a founder haplotype in eleven additional UK adRP families ( Figure 1C ). The adRP locus was refined to a 4.4 Mb interval on Chr17q22 ( Figure 1E ). This genomic interval overlaps the previously described RP17-locus in families of Dutch and South African origin ( Figure 1F ). Amissense variant in CA4 (c.40C>T; p.Arg14Trp; NM_000717.4) was previously described as the cause of adRP at the RP17-locus in families of South African origin. 10 No rare coding, intronic or upstreamvariants in CA4 were identified in the Dutch and UK families. Identification of structural variants within the RP17-locus Next, we analyzed genome and exome data for copy number variants and SVs ( Supplementary Results ). In family NL1, WGS revealed a 226-kb duplication within the RP17-locus: chr17:57,291,905_57,518,137dup (NL-SV1). This SV involves two duplicated genes ( GDPD1 and YPEL2 ), an intragenic microRNA ( MIR4729 ), and partial duplication of SMG8 and the long non-coding RNA LINC01476 . The duplication creates a breakpoint junction (chr17:g.57,518,137-57,291,905) specific for the mutated allele in NL1 ( Figure 2A-B , Figure S1 ), which was used to confirm segregation of the SV with the adRP phenotype in this family. No overlapping SVs in the RP17-locus were observed in WES of ~7,500 individuals without retinal disease generated in-house at the Department of Human Genetics, Radboudumc.