Omics Analyses in Two Genetic Disorders: Multi-Omics Approach in Neurofibromatosis Type I and Long Read DNA Sequencing in Facioscapulohumeral Muscular Dystrophy Type I

Abstract

In our quest to understand how omics approaches can aid in disease research, we applied comprehensive analyses to two distinct genetic disorders: neurofibromatosis type 1 (NF1) and facioscapulohumeral muscular dystrophy type 1 (FSHD1). The first part of our study focuses on neurofibromatosis type 1 (NF1), a rare disease characterized by the development of multiple benign tumors along nerves due to mutations in the NF1 gene. We conducted extensive multi-omics analyses, including long and short-read whole genome sequencing (WGS), long-read transcriptome, and methylome on samples from an affected child and unaffected family members. Our analysis identified a pathogenic de novo mutation in the splicing site of the NF1 gene in the affected child, absent in both parents and the healthy sibling. This mutation led to a transcript with a 16-nucleotide deletion in exon 2, suggesting cryptic splicing as a driving force of the disease. Additionally, a mutation-induced CpG site with associated methylation changes was found, providing new insights into the pathogenic mechanisms of NF1. The second study addresses facioscapulohumeral muscular dystrophy type 1 (FSHD1), a common adult myopathy linked to the reduction of D4Z4 repeats below ten in the 4qA allele. Traditional diagnosis via Southern blot is laborious, taking up to seven days. We introduced a new diagnostic technique using long-read DNA sequencing to directly measure D4Z4 repeats without further manipulation. Nanopore sequencing was performed on seven FSHD1-confirmed patients, successfully capturing and filtering reads containing D4Z4 repeats. The results from nanopore sequencing matched those from Southern blot analysis, accurately identifying the repeat numbers in five patients, demonstrating the efficacy of this new diagnostic approach. Together, these findings underscore the significance of omics approaches in uncovering the complex genetic underpinnings of diseases like NF1 and FSHD1. The integration of comprehensive genomic, transcriptomic, and methylomic data for NF1 and the application of advanced genomic techniques for FSHD1 offers powerful strategies for identifying pathogenic mutations, understanding their molecular consequences, and developing improved diagnostic techniques, ultimately paving the way for targeted therapeutic interventions.