Suzanne de Bruijn

59 The impact of modern technologies on molecular diagnostics Although LRS techniques are rapidly developing and show a great ability to identify SVs, their routine application in clinical diagnostics still requires several improvements in terms of sequencing, and variant interpretation; it also requires a cost reduction. In addition, despite the fact that these technologies can provide substantial read length, the reads can only be assembled to the scaffold-level and not to the chromosome- level. 192 Complementary approaches to identify SVs can be offered by cytogenetics. 190 One of these recent technologies is optical genome mapping (Bionano Genomics), which is a de novo assembly-based method that allows the visualization of the genomic structure in high resolution. 193 The approach is based on ultra-long dsDNA molecules that are fluorescently labeled at CTTAAG hexanucleotide motifs, which are found on average 15 times per 100 kb across the human genome. The distances and patterns of these labels can be compared to those in a reference genome. Therefore, copy number aberrations and other SVs, including insertions, inversions and translocations, can be detected ( Figure 5 ). Optical genome mapping has a much higher resolution compared to standard karyotyping and microarray technologies, and therefore enables much more precise data analysis. As it is an imaging method and not a sequencing method, SNVs cannot be detected. However, for the analysis of SVs, optical genome mapping can be used in a complementary manner to sequencing techniques. 190 With the ability to map ultra-long dsDNA molecules at a low cost, optical genome mapping has facilitated SV detection, haplotype phasing, and genome assembly. 192 In a recent study, researchers utilized optical genome mapping to identify a 48-kb duplication at the LAMA1 locus, that causes Poretti-Boltshauser syndrome. Affected individuals present with ataxia, cognitive impairment, and language delay as well as ocular phenotypes such as ocular motor apraxia, abnormal eye movement, and RD. TheWES and chromosome microarray pre-screening methods failed to reveal the large SV in the studied family. 194 The authors reasoned that LRS technologies offer promising applications in comprehensive SV analysis, however the costs and accuracy may represent a burden. Therefore, they suggested that a combinationof different technologies suchas optical genomemapping and SRS provides a more comprehensive understanding of SVs when considering cost, time, and throughput. 194 Multi-omic approaches Besides genome sequencing, other omic-technologies, such as transcriptomics, proteomics, metabolomics or epigenomics, hold the promise to further close the diagnostic gap for RD and HL. It is evident that for each identified disease-associated gene, the isoform landscape and levels of involved gene regulation are more