Tang Zitian, Ovunc Sinem S, Mehinovic Elle, Thomas Simone, Ulibarri Jenna, Li Zefan, Baldridge Dustin, Cruchaga Carlos, Johnson Matt, Milbrandt Jeffrey, Callaghan Brian, Höke Ahmet, Todd Peter K, Jin Sheng Chih
medRxiv. 2025 Apr 23:2025.04.18.25325809. doi: 10.1101/2025.04.18.25325809.
Biallelic intronic AAGGG repeat expansions in 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 expansions in more diverse patient populations remains unclear-partly due to the absence of accurate, user-friendly computational tools specifically tailored for tandem repeat analysis.
To discern the relationship between 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 Expansion Hunter coupled with unsupervised clustering to reliably detect and genotype expansions from short-read WGS data, achieving 98.2% concordance with repeat-primed PCR based validation.
Biallelic expansions were absent in 879 controls but present in 2.8% of iPN patients (Fisher's exact = 5.9×10 ), including 6.2% of pure sensory, 2.2% of SFN, and 1.5% of sensorimotor neuropathy, indicating that motor nerve involvement should not exclude patients from repeat screening. We also observed a markedly increased frequency of monoallelic expansions in iPN compared to controls (13.2% versus 2.5%; Fisher's exact = 3.4×10 ), without evidence of secondary mutations or expansions on the other allele.
Our approach provides a robust, cost-effective method for detecting expansions from WGS data. Our findings indicate that both heterozygous and homozygous AAGGG repeat expansions in can contribute to development of iPN.
双等位基因内含子AAGGG重复序列扩增可导致伴有神经病变和前庭无反射综合征的小脑共济失调，也可能导致孤立性感觉神经病变。在更多样化的患者群体中，杂合子和双等位基因扩增的临床意义仍不明确，部分原因是缺乏专门为串联重复分析量身定制的准确、用户友好的计算工具。
为了明确AAGGG扩增与特发性周围神经病变（iPN）之间的关系，我们对一个由788例iPN患者（369例单纯小纤维神经病变（SFN）、266例感觉运动型、144例纯感觉型和9例纯运动型）组成的特征明确的大型美国队列进行了全基因组测序（WGS），随后进行基于PCR的验证。我们开发了一种整合流程，将ExpansionHunter Denovo和Expansion Hunter与无监督聚类相结合，以从短读长WGS数据中可靠地检测AAGGG扩增并进行基因分型，与基于重复引物PCR的验证达成了98.2%的一致性。
879名对照者中不存在双等位基因AAGGG扩增，但在2.8%的iPN患者中存在（Fisher精确检验P = 5.9×10⁻⁵），包括6.2%的纯感觉型、2.2%的SFN和1.5%的感觉运动型神经病变，这表明运动神经受累不应排除患者进行AAGGG重复序列筛查。我们还观察到，与对照者相比，iPN中单个等位基因扩增的频率显著增加（13.2%对2.5%；Fisher精确检验P = 3.4×10⁻¹²），且没有证据表明另一个等位基因存在二次突变或扩增。
我们的方法为从WGS数据中检测AAGGG扩增提供了一种强大且经济高效的方法。我们的研究结果表明，AAGGG中的杂合子和纯合子重复序列扩增均可导致iPN的发生。
