Suzanne de Bruijn

321 Summary patient-derived cells, disruption of the chromosome organization could be observed. Rewiring of enhancer-promoter contacts were shown to cause the ectopic expression of GDPD1 , a gene that is normally not expressed in the retina. Ectopic expression of this gene was confirmed by RNA analyses in both patient-derived photoreceptor progenitor cells and retinal organoids. From these results it was concluded that the reorganization of the chromosome landscape and consequently ectopic expression of GDPD1 most likely was the true cause of disease. This work did not only explain the genetic defect involved in RP17, but it also highlighted a novel mechanism of disease that involves ectopic gene expression. Not all affected individuals can be genetically explained by the implementation of WES orWGS. A significant number of patients withmonoallelic SLC26A4 variants, and affected with HL and a uni- or bilateral enlarged vestibular aqueduct, remain unsolved after screening of all coding regions of the gene . In chapter 5 , 28 individuals with one or no pathogenic SLC26A4 variants were subjected to extensive genetic analyses that included short- and long read WGS and optical genome mapping. Important insights that could (partially) explain the missing heritability were obtained: a significant enrichment of a 0.89-Mb haplotype (previously coined as the CEVA-haplotype) in monoallelic cases, potential digenic inheritance for SLC26A4 and FOXI1 variants, and two novel splice variants. Unfortunately, the true genetic defect present on the CEVA-haplotype could not be pinpointed despite the fact that it is highly unlikely that a genomic variant was missed by the combination of the applied tools. This underlines that our understanding of the human genome and genomic variation is still incomplete as we currently fail to recognize the causative variant. In line with the conclusions drawn from chapters 2 to 5 , chapter 6 elaborated on the developments that canbeexpected in thenext years and thatwill help togaina complete understanding of all genomic variation. Strategies andmethods that should be explored include multi-omics approaches, single-cell RNA and epigenetic technologies. Also the potential non-Mendelian inheritance patterns should be addressed. With the advent of genetic therapies, complete knowledge of the genomic landscape of sensory disorders is even more pressing. The work described in this thesis indicated that by implementing and combining novel and existing technologies, and integrating information from the (epi)genome, RNA and protein level, a significant portion of the missing heritability can potentially be resolved. Hopefully, by applying all the knowledge that was collected during decades of research, every individual affected with inherited RD or HL can obtain a genetic diagnosis in the near future.