# First clinical diagnosis of FAME3 via commercial Long-Read sequencing reveals mosaic repeat expansion in MARCHF6 gene

## TL;DR

A rare epilepsy disorder, FAME3, was diagnosed using long-read sequencing, revealing complex genetic repeats in the MARCHF6 gene.

## Contribution

First clinical diagnosis of FAME3 using commercial long-read sequencing, uncovering repeat mosaicism in MARCHF6.

## Key findings

- PacBio HiFi sequencing identified a pathogenic MARCHF6 intronic expansion with 661 TTTTA and 12 TTTCA repeats.
- TRGT-instability analysis revealed somatic mosaicism in affected individuals, explaining variable disease expression.
- Long-read sequencing proved diagnostic for FAME3, resolving limitations of conventional genetic testing.

## Abstract

Familial Adult Myoclonic Epilepsy type 3 (FAME3) is a rare autosomal dominant disorder characterized by cortical tremor and epilepsy, caused by a noncoding pentanucleotide repeat expansion (TTTTA/TTTCA)n in the MARCHF6 gene. Conventional genetic testing often fails to detect this expansion due to its repetitive structure and intronic location. We evaluated a 61-year-old woman with refractory myoclonic and generalized tonic-clonic seizures, whose prior genetic testing—including exome and genome sequencing—was non-diagnostic. Using PacBio HiFi long-read whole-genome sequencing and the tandem repeat genotyping tool TRGT, we identified a pathogenic MARCHF6 intronic expansion. The proband harbored one allele with 15 TTTTA repeats and a second allele with a compound expansion of 661 TTTTA and 12 TTTCA repeats. Three affected relatives shared similarly expanded alleles, but with increasing repeat size in the latter generations. Importantly, analysis using TRGT-instability revealed repeat mosaicism in all affected individuals, reflected by variability in motif counts across individual sequencing reads. This somatic heterogeneity may contribute to the phenotypic penetrance, variable expressivity and pleiotropism seen in FAME3 disease expression. To our knowledge, this is the first clinical diagnosis of FAME3 using a commercially available long-read sequencing platform, underscoring its diagnostic utility in resolving complex repeat expansion disorders and uncovering biologically relevant mosaicism.

The online version contains supplementary material available at 10.1007/s10048-025-00835-6.