Characterising the motif composition and allele length distribution of ZFHX3 GGC repeat expansions in amyotrophic lateral sclerosis

Abstract Background and objectives A pathogenic GGC repeat expansion in the zinc finger homeobox 3 ( ZFHX3 ) gene, encoding a pure polyglycine tract, is the cause of spinocerebellar ataxia type 4 (SCA4). Intermediate expansions of other SCA loci contribute to the risk of amyotrophic lateral sclerosis (ALS), a fatal neurodegenerative disease involving the progressive loss of motor neurons. There is increasing awareness of the role of short tandem repeat (STR) motif composition and configuration in disease pathogenicity. Given the genetic pleiotropy between ALS and SCA, this study aimed to evaluate whether ZFHX3 GGC expansions were associated with ALS and to characterise repeat motif composition. Methods ExpansionHunter v5 was used to genotype ZFHX3 GGC repeat sizes in short-read whole genome sequencing data from people with ALS and healthy controls of European ancestry. Repeat sizes were visually inspected using REViewer v2. Repeat motif configurations of Australian ALS cases and healthy controls were manually derived from REViewer images. Receiver operating characteristic (ROC) curve analysis and Youden’s J statistic were performed to find a candidate repeat size threshold for association testing. Fisher’s exact tests were performed to evaluate the associations of repeat size and motif composition with disease status. Results Analysis of 5,785 people with ALS and 7,982 healthy controls found no association between ZFHX3 GGC repeat expansions and disease risk. Fifty unique repeat motif compositions were identified across 802 people with ALS and 800 healthy controls. Of these, eleven distinct configurations coded a pure polyglycine tract which, when expanded, is canonical to SCA4, though no association with ALS was found. Discussion Although no association was observed between ZFHX3 GGC repeat expansions and ALS, this study established the dynamic nature of ZFHX3 repeat motif composition and configuration. Unique motif compositions were identified both within and between repeat sizes, including the presence of pure polyglycine repeats. Consideration of repeat motif composition and configuration, in addition to repeat allele length, may be important for assessing neurodegenerative disease risk.