Poster Presentation 47th Lorne Genome Conference 2026

Characterising the distribution and sequence composition of ZFHX3 GGC repeat expansions in ALS  (133333)

Zoe Zussa 1 , Andrew N Smith 1 , Daniel O'Shaughnessy 1 , Natalie Grima 1 , Dominic B Rowe 1 2 , Susan D'Silva 1 2 , Roger Pamphlett 3 4 5 , Matthew C Kiernan 6 , Srestha Mazumder 6 , Ian P Blair 1 , Kelly L Williams 1 , Lyndal Henden 1
  1. Macquarie University MND Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, NSW, Australia
  2. Macquarie Health Neurology, Macquarie University, Sydney, NSW, Australia
  3. Brain and Mind Centre, The University of Sydney, Sydney, NSW, Australia
  4. Discipline of Pathology, The University of Sydney, Sydney, NSW, Australia
  5. Department of Neuropathology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
  6. Neuroscience Research Australia, University of NSW, South Eastern Sydney Local Health District, NSW, Australia

Short tandem repeats (STRs) expansions are increasingly recognised as key contributors to neurodegenerative diseases, where both repeat size and sequence composition influence pathogenicity. Over 70 pathogenic STR expansions have been implicated in neurological and neurodegenerative disorders. In amyotrophic lateral sclerosis (ALS), a repeat expansion in C9orf72 accounts for ~40% of familial and ~10% of sporadic cases. Similarly, pathogenic expansions in ATXN1 and ATXN2 cause spinocerebellar ataxia (SCA) types 1 and 2, respectively, while intermediate expansions in these loci have been associated with ALS risk [1]. 

Recently, a GGC repeat expansion in ZFHX3, encoding a polyglycine tract, was identified as the cause of SCA4 [2]. Expansions exceeding 41 GGC units result in motor neuron degeneration, a hallmark of both SCA4 and ALS. Importantly, the composition of polyglycine-coding STRs can modify disease phenotypes. As seen in NOTCH2NLC, increased interruptions within the repeat sequence are associated with a muscle-weakness-dominant subtype of NOTCH2NLC-realted GGC expansion disorders [3]. 

Given the genetic overlap between ALS and SCAs, we investigated the size distribution and sequence composition of ZFHX3 GGC expansions in Australian ALS patients. Using ExpansionHunter v5 [4], we genotyped the repeat in whole-genome sequencing data from 802 ALS patients and 6,215 population-matched controls (gnomAD). Alleles ≥24 repeat units were visually validated using REViewer [5]. Case-control associations were assessed using Fisher’s exact test, and TRMotifAnnotator [6] was used to analyse sequence composition. 

ZFHX3 GGC repeat sizes ranged from 13–27 units in ALS cases and 5–29 in controls. There were no expansions exceeding the SCA4 pathogenic threshold. Sequence analysis revealed interruptions within the polyglycinetract, including serine, aspartic acid, and glycine conformations. 

While ZFHX3 repeat lengths were not linked to the genetic continuum between ALS and SCA in Australian cases, repeat sequence composition may be important for understanding the role of STRs in neurodegenerative diseases. 

  1. 1. Henden L, et al. (2023) Short tandem repeat expansions in sporadic amyotrophic lateral sclerosis and frontotemporal dementia. Sci Adv. 9(18):eade2044
  2. 2. Figueroa K P, et al. (2024) A GGC-repeat expansion in ZFHX3 encoding polyglycine causes spinocerebellar ataxia type 4 and impairs autophagy. Nature Genetics. 56(6): 1080-1089
  3. 3. Huang X.R, et al. (2021) The phenotypes and mechanisms of NOTCH2NLC-related GGC repeat expansion disorders: a comprehensive review. Molecular Neurobiology 59(1) 523-534
  4. 4. Dolzhenko E, et al. (2019) ExpansionHunter: a sequence-graph-based tool to analyze variation in short tandem repeat regions. Bioinformatics. 35 (22): 4754-4756
  5. 5. Dolzhenko E, et al. (2022) REViewer: haplotype-resolved visualization of read alignments in and around tandem repeats. Genome medicine 14(1): 84
  6. 6. Rajan Babu I.S, et al. (2025) Population-scale disease-associated tandem repeat analysis reveals locus and ancestry-specific insights. medRxiv