Advanced genomic diagnostics for discovering the mechanisms of congenital anomalies

Congenital anomalies present important public health and epidemiologic challenge. Despite our success in improving the yield of genetic testing by implementing routine use of molecular karyotyping and exome sequencing with our past project (J3-8205), etiology of a significant proportion of congenital anomalies still remains unexplained. Mutations not detectable by previous diagnostic approaches include intronic, regulatory and intergenic regions, and may be due to structural genetic variants of different sizes. Recently, new genomic technologies have been developed which can improve our understanding of the genomic etiology: whole genome sequencing (WGS), optical genome mapping (OGM), and bioinformatics tools that can aid the interpretation of structural changes of non-coding functional genomic regions. All three state-of-the-art genomic approaches can contribute toward resolving genomic etiology and detecting novel mechanisms in congenital anomalies, and their performance should now be systematically evaluated on larger population cohorts. WGS includes both all coding regions as well as intronic, regulatory, and intergenic genomic regions and enables a higher diagnostic yield than the currently routine exon sequencing. We already used this approach to identify causes of many different genetic diseases and discover new genes for human disorders (1-5). Furthermore, we developed new innovative analytical approaches which we use also in the ongoing Slovenian genome project (V3-1911) where we coordinate (6). In addition, OGM enables next-generation cytogenomics and represents the current state-of-the art in this field (7). The method is based on the laser image acquisition of single, labelled, high-molecular weight DNA molecules for the unprecedentedly sensitive and specific detection of structural genomic variants (insertions/deletions/complex structural rearrangements). OGM is the only method currently enabling us to detect structural genomic variants that are either too big or too small to detect using any other methods. At CIGM we have recently implemented the OGM for research and routine diagnostic purposes. Finally, novel bioinformatics tools offer new possibilities in improving interpretation of non-coding functional regions of the genome (8–12). The WGS and OGM methods can be combined, so that the OGM data serves as a structural genomic scaffold on which WGS data can be assembled (13), providing novel insight, while the mentioned bioinformatics approaches facilitate improved clinical interpretation of variants detected by all existing technologies. Our aim is to collect at least 100 undiagnosed samples of CA (both isolated and complex) from the SLOCAT registry of CA at CIGM. In this registry we systematically collected cases with CA using EUROCAT methodology and already contains more than 300 cases. Additionally, we will collect prospective cases of CA which test negative with conventional approaches. We will analyze the selected cases by the three genomic approaches: WGS, OGM, and novel bioinformatics tools for assessing non-coding variants, representing the current global state-of-the-art approach in genomics. Through this approach we aim to contribute to discovery of new genetic and pathophysiologic mechanisms of CA and improve clinical diagnostics. References 1. Maver & Peterlin. Bioinformatics 2011 2. Zaman et al. Ann Neurol 2018 3. Renou et al. J Med Gen 2008 4. Graham et al. Am J Respir and Crit Care Med 2005 5. Writzl et al. Am J Hum Gen 2017 6. Bergant et al. Life 2021 7. Mantere et al. Am J Hum Gen 2021 8. Requena et al. Nucl Acid Res 2021 9. Nieboer et al. Bioinformatics 2020 10. Zhou et. al Nat Genet 2019 11. Wells A et al. Nat Commun 2019 12. Jaganathan et. al. Cell 2019 13. Pan et. al. J Comput Biol 2020