NCM 2023 Houston: Unraveling complex Mendelian diseases with nanopore sequencing

A precise genetic diagnosis is vital for clinical management and informed care decisions. While clinical genetic testing has advanced with sequencing, it has also revealed many rare genetic disorders. However, over half of the individuals with suspected disorders remain undiagnosed after thorough evaluation. Therefore, there is a pressing need for new tools and techniques to improve the diagnostic rate. In the GREGoR consortium, our objective is to unravel the genetic causes of complex Mendelian diseases that have eluded traditional methods (approximately 100 unsolved cases per year). We leveraged nanopore sequencing, enabling accurate haplotyping and variant calling, including SNVs, indels, SVs, and methylation events. By utilizing PRINCESS pipelines, we identified variants in 40 samples from affected individuals with various disorders, such as Aicardi-Goutières syndrome, craniofacial microsomia, Charge syndrome, and Multifocal lymphanioendotheliomatosis (12 trios and 3 single samples). Parental genomes aided in detecting de novo mutations and distinguishing inherited variants from disease-associated mutations. Our framework for variant calling and interpretation incorporated diverse functional genomics and population annotations as well as in silico prediction tools. Through the investigation of multiple trios, we will obtain a better understanding of these disorders and explore the potential of nanopore sequencing in uncovering the variants linked to the diseases. Preliminary analysis has yielded promising results, revealing several candidate genes and variants that warrant further investigation to discern their functional consequences. This research paves the way for improved diagnostics, prognostics, and interventions in the realm of genetic medicine.