Optical Genome mapping: a new look over genomic structural variants in neurodevelopmental diseases with or without congenital abnormalities

• Grant number: 24/07932-0
• Support Opportunities: Regular Research Grants
• Start date: November 01, 2024
• End date: October 31, 2026
• Field of knowledge: Biological Sciences - Genetics - Human and Medical Genetics
• Principal Investigator: Carla Rosenberg
• Grantee: Carla Rosenberg
• Host Institution: Instituto de Biociências (IB). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• Associated researchers: Ana Cristina Victorino Krepischi ; Débora Romeo Bertola

Abstract

Over 7000 rare diseases have been described, approximately 80% of which have genetic etiology. Despite individually rare, such diseases are collectively responsible for 35% of first year deaths. Nevertheless, the molecular-genetic diagnosis is achieved in less than 50% of the cases. Structural variants (SV) are frequent in the human genome, resulting in phenotypic diversity and representing one of the main causes of genetic disorders. The detection of SVs is challenging and, in Brasil, mostly depends on conventional cytogenetic techniques, such as karyotype and chromosome microarray analyses (CMA). Although sequencing the genome allows the detection of all variant types, the detection of SVs based on DNA short reads is unsuitable and the sequencing of long reads (~20-25kb) is too expensive, in addition to implicate in computational challenges. Optical genome mapping (OGM) is an innovative and efficient biotechnology for high-throughput identification of balanced and unbalanced SVs. The technique uses ultra-high molecular weight DNA fragments (>150kb) and is based on digitalization of captured images, which represent optical bar codes that are used to generate genomic maps. Publications on the use of OGM to investigate constitutive alterations are still scarce. The main objective of this project is to elucidate the genomic structure and corresponding phenotypic impact of SVs, for research and diagnosis of post-natal neurodevelopmental disorders, with or without congenital abnormalities. The OGM biotechnology (Bionano Saphyr® System) will be used in combination with sequencing and cytogenetic methods in two main axles: (a) de novo balanced or complex SVs: characterization of previously identified SVs, with potential clinical resolution and investigation of the mechanism of origin from the breakpoints identification; (b) investigation of idiopathic cases: as a complementary tool in cases with non-elucidated genetic basis. As a result, the work will lead to the identification of new pathogenic variants in known genes, or in novel candidate genes for the several phenotypes investigated, as well as to the understanding of the SVs formation mechanisms. Selected cases will be further investigated by genome sequencing and transcriptome analysis. These results will increase the knowledge regarding the contribution of SVs in the etiology of neurodevelopmental disorders and congenital abnormalities, allowing the resolution by OGM of the structure of genetic variants and evaluation of their phenotypic impact. We have recently illustrated the utility of the combined use of methodologies, including OGM, in the investigation of a complex rearrangement which segregates in 5 generation of a family exhibiting heart defect. (AU)