Genetic and epigenetic profiling of FSHD by nanopore sequencing

Abstract

The genetic diagnosis of facioscapulohumeral muscular dystrophy (FSHD) poses a significant clinical challenge, eluding detection through standard sequencing methods despite its status as the third most prevalent muscular dystrophy. Conventional diagnostic strategies address the known genetic parameters of FSHD: the required presence of a permissive haplotype, a size reduction of the D4Z4 repeat of chromosome 4q35 (FSHD1), or a pathogenic variant in an epigenetic suppressor gene (FSHD2). However, we and others have recently shown that methylation not only acts as a marker of disease severity but may also function as a potential prognostic marker, suggesting the feasibility of predictive testing for FSHD disease severity. To circumvent the known limitations of conventional diagnostics and to complement genetic parameters with epigenetic ones, we leverage targeted nanopore sequencing to simultaneously analyse permissive haplotypes, the number of repeat units, methylation profiles, single nucleotide variations, structural variants and hybrid alleles, somatic mosaicism, and the orientation of the contracted repeat array in FSHD patients — all within a single sequencing run. Additionally, we present initial findings on the potential clinical utility of our nanopore sequencing method for FSHD diagnosis, using a patient cohort that we have validated through conventional methods such as KASP genotyping, Sanger sequencing, Southern blot, optical genome mapping, and Illumina-based bisulfite sequencing.

Biography

Morghan Lucas is the co-lead of R&D at the Medical Genetics Centre (MGZ) Munich and a research scientist at the Ludwig Maximilian University of Munich (LMU). Her primary research focuses on developing molecular diagnostic tests for various diseases, including hereditary cancers and muscular dystrophy, with an emphasis on sequencing technologies. Prior to this, Morghan obtained her PhD at the Centre for Genomic Regulation (CRG) under the guidance of Dr. Eva Maria Novoa, where she developed various direct RNA nanopore sequencing-based methods for RNA modification detection, short RNA sequencing, and multiplexing.