Novel, complex configurations of the MARCHF6 repeat expansion associated with progressive myoclonic epilepsy and familial adult myoclonic epilepsy.

Repeat expansions are a known cause of progressive myoclonic epilepsy (PME) and familial adult myoclonic epilepsy (FAME). We hypothesized that PME and FAME may have an overlapping phenotypic spectrum and searched for pathogenic repeat expansions in 18 individuals from 15 families with later-onset PME or FAME. We generated whole genome sequencing data by short-read sequencing and searched for known and novel repeat expansions. No known, pathogenic repeat expansions were identified. Instead, we discovered a novel TTGTA expansion in the gene MARCHF6 at the same location as the known, pathogenic FAME3 expansion in a PME family. Targeted long-read sequencing of this locus revealed a large, complex repeat structure harbouring an expansion of the pathogenic TTTCA repeat that causes FAME, surrounded by TTTTA and TTGTA expansions. Motivated by this discovery, we developed a new bioinformatic approach, mixSTR, to search for evidence of such complex expansions and discovered an additional novel configuration of the FAME3 expansion containing hidden pathogenic TTTCA expansions embedded within a TTTTA expansion in a second family clinically diagnosed with FAME. Both families had initially tested negative for the FAME3 expansion with standard RP-PCR and short-read genome sequencing analysis. We searched large epilepsy and population cohorts but did not identify any additional new individuals with complex FAME3 expansions. These findings have two important implications. Firstly, known repeat expansion loci with unusual repeat expansions, even if not known to be pathogenic, warrant further investigation as they may contain hidden pathogenic repeat expansions. Secondly, they provide molecular support for the clinical idea that PME and FAME have an overlapping phenotypic spectrum, and that the known FAME repeat expansions should be part of the diagnostic assessment of unsolved PMEs.