Heterozygous and Homozygous RFC1 AAGGG Repeat Expansions are Common in Idiopathic Peripheral Neuropathy

ObjectiveBiallelic intronic AAGGG repeat expansions in RFC1 cause Cerebellar Ataxia with Neuropathy and Vestibular Areflexia Syndrome and may also contribute to isolated sensory neuropathy. The clinical significance of both heterozygous and biallelic RFC1 expansions in more diverse patient populations remains unclear--partly due to the absence of accurate, user-friendly computational pipelines specifically tailored for tandem repeat analysis. MethodsTo discern the relationship between RFC1 expansions and idiopathic peripheral neuropathy (iPN), we performed whole-genome sequencing (WGS) followed by PCR-based confirmation in a large, well-characterized U.S. cohort consisting of 788 iPN patients (369 pure small fiber neuropathy (SFN), 266 sensorimotor, 144 pure sensory, and 9 pure motor). We developed an integrative pipeline combining ExpansionHunter Denovo and ExpansionHunter coupled with unsupervised clustering to reliably detect and genotype RFC1 expansions from short-read WGS data, achieving 98.2% concordance with repeat-primed PCR based validation. ResultsBiallelic RFC1 expansions were present in only one out of 854 controls but present in 2.3% of iPN patients (Fishers exact p = 2x10-5), including 6.9% of pure sensory, 1.1% of SFN, and 1.5% of sensorimotor neuropathy, indicating that motor nerve involvement should not exclude patients from RFC1 repeat screening. We also observed an increased frequency of monoallelic expansions in iPN compared to controls (9.4% versus 6.3%; Fishers exact p = 0.02), without evidence of secondary mutations or expansions on the other allele. InterpretationOur approach provides a robust, cost-effective method for detecting RFC1 expansions from WGS data. Our findings indicate that both heterozygous and homozygous AAGGG repeat expansions in RFC1 contribute to development of iPN.