Unraveling the complex genetic landscape of OTOF-related hearing loss: a deep dive into cryptic variants and haplotype phasing.

IF 6 2区医学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Medicine Pub Date : 2025-05-09 DOI:10.1186/s10020-025-01225-2

Pei-Hsuan Lin, Cheng-Yu Tsai, Yu-Ting Chiang, Chang-Han Ho, Yue-Sheng Lu, Jacob Shu-Jui Hsu, Yen-Fu Cheng, Shih-Feng Tsai, Chuan-Jen Hsu, Pei-Lung Chen, Chen-Chi Wu

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引用次数: 0

Abstract

Background: Pathogenic variants in OTOF are a major cause of auditory synaptopathy. However, challenges remain in interpreting OTOF variants, including difficulties in confirming haplotype phasing using traditional short-read sequencing (SRS) due to the large gene size, the potential incomplete penetrance of certain variants, and difficulties in assessing variants at non-canonical splice sites. This study aims to revisit the genetic landscape of OTOF variants in a Taiwanese non-syndromic auditory neuropathy spectrum disorder (ANSD) cohort using a combination of sequencing technologies, predictive tools, and experimental validations.

Methods: We performed SRS to analyze OTOF variants in 65 unrelated Taiwanese patients diagnosed with non-syndromic ANSD, complemented by long-read sequencing (LRS) for haplotype phasing. A prediction-to-validation pipeline was implemented to assess the pathogenicity of cryptic variants using SpliceAI software and minigene assays.

Results: Biallelic pathogenic OTOF variants were identified in 33 patients (50.8%), while monoallelic variants were found in five patients. Three novel variants, c.3864G > A (p.Ala1288 =), c.4501G > A (p.Ala1501Thr), and c.5813 + 2T > C, were detected. The pathogenicity of two non-canonical mis-splicing variants, c.3894 + 5G > C and c.3864G > A (p.Ala1288 =), was confirmed by minigene assays. LRS-based haplotype phasing revealed that the common missense variant c.5098G > C (p.Glu1700Gln) and the novel variant c.5975A > G (p.Lys1992Arg) are in cis and form a founder pathogenic allele in the Taiwanese population.

Conclusions: Our study highlights the genetic heterogeneity of DFNB9 and emphasizes the importance of population-specific variant interpretation. The integration of advanced sequencing technologies, predictive algorithms, and functional validation assays will improve the accuracy of molecular diagnosis and inform personalized treatment strategies for individuals with DFNB9.

查看原文本刊更多论文

揭示与耳部失聪相关的听力损失的复杂遗传景观：深入研究隐性变异和单倍型相位。

背景：OTOF的致病变异是听觉突触病的主要原因。然而，在解释OTOF变异方面仍然存在挑战，包括由于基因大小较大，使用传统的短读测序（SRS）确认单倍型相位存在困难，某些变异的潜在不完全外显率，以及在非规范剪接位点评估变异的困难。本研究旨在结合测序技术、预测工具和实验验证，重新审视台湾非综合征型听觉神经病变谱系障碍（ANSD）队列中OTOF变异的遗传格局。方法：我们对65名台湾非综合征性ANSD患者的OTOF变异进行SRS分析，并辅以单倍型分期的长读测序（LRS）。使用SpliceAI软件和minigene检测，实施了从预测到验证的流程来评估隐变的致病性。结果：33例（50.8%）患者检出双等位基因致病性OTOF变异，5例检出单等位基因变异。检测到三种新的变异，C . 3864g > A (p.a ala1288 =), C . 4501g > A （p.a ala151thr）和C .5813 + 2T > C。两个非典型错剪接变异体C .3894 + 5G > C和C . 3864g > A （p.Ala1288 =）的致病性通过微基因分析得到证实。基于lrs的单倍型分期结果显示，台湾人群中常见的错义变异C . 5098g > C （p.Glu1700Gln）和新变异C . 5975a > G （p.Lys1992Arg）是顺式的，形成了一个创始致病等位基因。结论：我们的研究强调了DFNB9的遗传异质性，并强调了群体特异性变异解释的重要性。先进的测序技术、预测算法和功能验证分析的整合将提高分子诊断的准确性，并为DFNB9患者提供个性化的治疗策略。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Molecular Medicine 医学-生化与分子生物学

CiteScore

8.60

自引率

0.00%

发文量

137

审稿时长

1 months

期刊介绍： Molecular Medicine is an open access journal that focuses on publishing recent findings related to disease pathogenesis at the molecular or physiological level. These insights can potentially contribute to the development of specific tools for disease diagnosis, treatment, or prevention. The journal considers manuscripts that present material pertinent to the genetic, molecular, or cellular underpinnings of critical physiological or disease processes. Submissions to Molecular Medicine are expected to elucidate the broader implications of the research findings for human disease and medicine in a manner that is accessible to a wide audience.